Novelty	HGNC gene symbol	Chr	CDS start	CDS end	Strand	Top rank	List	Model status	GENCODEv22 biotype	Human GENCODEv28 gene ID	Human GENCODEv28 transcript ID	CDS size (aa)	No. coding exons	Conservation	Mouse GENCODE M18 annotation	Non-murine representative model or genome coordinates (START-STOP)	Human short-read data expression	Mouse short read-data expression	Contemporary RefSeq annotation	Bicistronic?	Peptide support	sorfs.org support	Comments	Edge case?	CDS sequence
New discovery	C1orf232	1	26168499	26164161	-1	118	1000	gene added	absent	ENSG00000282872	ENST00000634842	186	4	avians; potential ortholog in fish without synteny, e.g. carp XP_018954235.1	previously undescribed coding gene ENSMUSG00000108398	chicken LOC419602	no CAGE; no HPA; Intropolis finds expression in brain and eye experiments (e.g. SRR548613).	CAGE supports inner ear cell expression; no ENCODE RNAseq	absent				Uncharacterised protein. Previously absent due to complete lack of cDNA or EST transcript evidence in human or mouse.	no	MNQAFWKTYKSKVLQTLSGESEEDLAEERENPALVGSETAEPTEETFNPMSQLARRVQGVGVKGWLTMSSLFNKEDEDKLLPSEPCADHPLAARPPSQAAAAAEARGPGFWDAFASRWQQQQAAAASMLRGTEPTPEPDPEPADEAAEEAAERPESQEAEPVAGFKWGFLTHKLAEMRVKAAPKGD
New discovery	AC119676.1	1	41628816	41585306	-1	419	1000	existing transcript	5' UTR of HIVEP3	ENSG00000284895	ENST00000646142	26	2	mammals	previously undescribed coding gene ENSMUSG00000028634	/	all sources support general expression	all sources support general expression	absent	cotranscribed with HIVEP3		gawron_2016:38097	Uncharacterised protein within the 5' UTR of HIVEP3. Current evidence indicates it is co-transcriptional with HIVEP3, based on a single shared TSS for both loci.	no	MNAGFQREQRFSFGHRKWCLQHRRRA
New discovery	CTXND2	1	150912315	150912482	1	937	1000	gene added	absent	ENSG00000283324	ENST00000636087	55	1	mammals	previously undescribed coding gene ENSMUSG00000105734	/	all sources support testis / placenta expression	all sources support testis / placenta expression	ncRNA XR_158744.3			no	Cortexin family member.	no	MEDSSLSSGVDVDKGFAIAFVVLLFLFLIVMIFRCAKLVKNPYKASSTTTEPSLS
New discovery	SPRR5	1	152948555	152948881	1	233	1000	gene added	absent	ENSG00000283227	ENST00000636302	108	1	mammals	known coding gene ENSMUSG00000102308	/	CAGE supports salivary acinar, skin and tongue expression; HPA supports high skin expression; Intropolis is dominated by psoriasis experiments (e.g. SRR1146240)	CAGE supports tongue, vagina and skin expression; ENCODE RNAseq supports low expression in various tissues	absent				Small proline-rich protein family member. Located within a cluster of previously known paralogs.	no	MSQQKQKQCAPPQQCCPPPQQRCPPPQQCCPPPQQCCPPPQQCCPPPQQCCPPPQQCCPPPQQCCPPPQQYCPPPQQTKQPCQPPPKCQEPCAPKCPPPQQCQTSKQK
New discovery	MYOCOS	1	171623884	171626601	1	2157	unannotated	gene added	absent	ENSG00000283683	ENST00000637642	80	2	mammals	known coding gene ENSMUSG00000091060	/	all sources support testis expression; HPA also finds female reproductive tissue expression	all sources support testis expression	ncRNA XR_922279.1			no	Uncharacterised protein. In rodents the CDS is longer, lacking the human initiation and termination codons. However, the human CDS is seen to be ancestral based on comparison with other mammals, e.g. dog PLAR model  linc|3P|XLOC_054809|TCONS_00133026:6.09827|109AA|76AA.	no	MAQKSLANNSINLPYKDLTSEVTRRRVTMITRKEIITQKSDEAKEMLSHLDLEQAPPPHRTYLTVPPAPPPSPAEDPTVS
New discovery	CCDC195	2	224716365	224703764	-1	583	1000	gene added	absent	ENSG00000283428	ENST00000638102	201	3	avians	previously undescribed coding gene ENSMUSG00000110100	lizard XP_008104485.1	no CAGE; no HPA; Intropolis is dominated by cancer experiments, the top ranked normal tissue is B-cells (SRR315115); BLUEPRINT finds expression in blood cancers especially	No CAGE; no ENCODE RNAseq	absent				Member of the coiled-coil domain protein family.	no	MEADIQLMRLIQEMRAEIHKLEKENQALRMKLTASSQRASGSGRESGDEREEEAPGQSPATLQGAVSTDAAPAVQEHQGNVMIVRRYSISSSVCSSAVNDPWKSGKSHPKSGILEGQRTLKSLACSPIKKQDMEEKVFATDSLTSNRTSQRASPEHVCGCRDKTKAVSFLLPMDMSSYSKNSSSLKHSPNQATNQLSIIAE
New discovery	SCYGR1	2	227387949	227387683	-1	8412	paralog	gene added	absent	ENSG00000284629	ENST00000641359	88	1	there is a cluster in mammals with conserved synteny, though 1:1 orthologs cannot be deduced with confidence	12 novel protein-coding genes have been added to mouse in a location with overall synteny:ENSMUSG00000114299; ENSMUSG00000113880; ENSMUSG00000113973; ENSMUSG00000113846; ENSMUSG00000113084; chr1:82946339-82946764 (a late addition, not yet in GENCODE); ENSMUSG00000113925; ENSMUSG00000114011; ENSMUSG00000113097; ENSMUSG00000100190; ENSMUSG00000113267; ENSMUSG00000104423. This cluster also contains a single known gene, Krtap28-13.	/	no data	/	absent			no	Small cysteine and glycine repeat containing family member, with prospective similarity to keratin associated proteins. The accuracy of the underlying genomic alignments may be suspect, leading to spurious PhyloCSF signals  (see main text). 	no	MGCCGCGGCGGCGGCGGGCGGGCGRCTTCRCYRVGCCSSCCPCCRGCCGGCCSTPVICCCRRTCSSCGYSCGKGCCQQKCCCQKQCCC
New discovery	SCYGR2	2	227598893	227599255	1	853	1000	gene added	absent	ENSG00000284643	ENST00000641394	120	1	there is a cluster in mammals with conserved synteny, though 1:1 orthologs cannot be deduced with confidence	see above	/	no data	/	absent				Small cysteine and glycine repeat containing family member, with prospective similarity to keratin associated proteins. The accuracy of the underlying genomic alignments may be suspect, leading to spurious PhyloCSF signals  (see main text). 	no	MGCCGCGGCGGCGGRCGGCGGGCGGGCGGGCGGGCGGGCGGGCGGGCGGGCGGSCGSCTTCRCYRVGCCSSCCPCCRGCCGGCCSTPVICCCRRTCHSCGCGCGKGCCQQKCCCQKQCCC
New discovery	SCYGR10	2	227608784	227609101	1	853	1000	gene added	absent	ENSG00000284622	ENST00000641246	105	1	there is a cluster in mammals with conserved synteny, though 1:1 orthologs cannot be deduced with confidence	see above	/	no data	/	absent			no	Small cysteine and glycine repeat containing family member, with prospective similarity to keratin associated proteins. This member is annotated as a polymorphic pseudogene on the reference genome due to nonsense SNP rs563988735, although based on frequency data the gene may be coding in over 10% of the population. Frequency data for adjacent SNP rs575523495 within the same codon indicates that [TGC] is the more common codon in individuals lacking the nonsense mutation, so this translation is provided here. 	no	MGCCGCGGCGGRCSGGCGGGCGGGCGGGCGGGCGGCGGGCGSYTTCRCYRVGCCSSCCPCCRGCCGGCCSTPVICCCRRTCRSCGCGCGKSCCQQKCCCQKQCCC
New discovery	SCYGR3	2	227614840	227614538	-1	853	1000	gene added	absent	ENSG00000284704	ENST00000642029	100	1	there is a cluster in mammals with conserved synteny, though 1:1 orthologs cannot be deduced with confidence	see above	/	no data	/	absent				Small cysteine and glycine repeat containing family member, with prospective similarity to keratin associated proteins. The accuracy of the underlying genomic alignments may be suspect, leading to spurious PhyloCSF signals  (see main text). 	no	MGCCGCGSCGGCGGGCGGCGGGCGGGCGGGCGGVCGSCTTCRCYRVGCCSSCCPCCRGCCGGCCSTPVICCCRRTCRSCGCGCRKGCCQQKCCCQKQCCC
New discovery	SCYGR4	2	227617498	227617815	1	853	1000	gene added	absent	ENSG00000284631	ENST00000641801	105	1	there is a cluster in mammals with conserved synteny, though 1:1 orthologs cannot be deduced with confidence	see above	/	no data	/	absent				Small cysteine and glycine repeat containing family member, with prospective similarity to keratin associated proteins. The accuracy of the underlying genomic alignments may be suspect, leading to spurious PhyloCSF signals  (see main text). 	no	MGCCGCGSCGGCGGRCGGGCGGGCSGGCGGGCGGGCGGGCGSCTTCRCYRVGCCSSCCPCCRGCCGGCCSTPVICCCRRTCGSCGCGYGKGCCQQKCCCQKQCCC
New discovery	SCYGR5	2	227666804	227667061	1	19673	paralog	gene added	absent	ENSG00000284667	ENST00000641976	85	1	there is a cluster in mammals with conserved synteny, though 1:1 orthologs cannot be deduced with confidence	see above	/	no data	/	absent			no	Small cysteine and glycine repeat containing family member, with prospective similarity to keratin associated proteins. The accuracy of the underlying genomic alignments may be suspect, leading to spurious PhyloCSF signals  (see main text). 	no	MGCCGCGGCGGCGGGCGGGCGSCTTCRCYRVGCCSSCCPCCRGCCGGCCSTPVICCCRRTCCSCGCGCGKGCCQQKGCCQKQCCC
New discovery	SCYGR6	2	227724757	227724440	-1	1636	unannotated	gene added	absent	ENSG00000284725	ENST00000641918	105	1	there is a cluster in mammals with conserved synteny, though 1:1 orthologs cannot be deduced with confidence	see above	/	no data	/	absent		neXtProt		Small cysteine and glycine repeat containing family member, with prospective similarity to keratin associated proteins. The accuracy of the underlying genomic alignments may be suspect, leading to spurious PhyloCSF signals  (see main text). 	no	MGCCGCGGCGGGCGGCGGGCSGGCGGGCGGGCGSCTTCRCYRVGCCSSCCPCCRGCCGGCCSTPVICCCRRTCHSCGCGCGCGKGCCQQKGCCQQKGCCKKQCCC
New discovery	SCYGR7	2	227728335	227728625	1	2286	paralog	gene added	absent	ENSG00000284718	ENST00000641700	96	1	there is a cluster in mammals with conserved synteny, though 1:1 orthologs cannot be deduced with confidence	see above	/	no data	/	absent			no	Small cysteine and glycine repeat containing family member, with prospective similarity to keratin associated proteins. The accuracy of the underlying genomic alignments may be suspect, leading to spurious PhyloCSF signals  (see main text). 	no	MGCCGCGSCGGCGGGCGGCGGGCGGGCGGGCGSCTTCRCYRVGCCSSCCPCCRGCCGGCCSTPVICCCRRTCGSCGCGCGKGCCQQKGCCQKQCCC
New discovery	SCYGR8	2	227745894	227746220	1	608	1000	gene added	absent	ENSG00000284635	ENST00000641981	108	1	there is a cluster in mammals with conserved synteny, though 1:1 orthologs cannot be deduced with confidence	see above	/	no data	/	absent		neXtProt		Small cysteine and glycine repeat containing family member, with prospective similarity to keratin associated proteins. The accuracy of the underlying genomic alignments may be suspect, leading to spurious PhyloCSF signals  (see main text). 	no	MGCCGCGGCGGGCGGCSGGCGGGCGGGCGGGGCGGGCGSCTTCRCYRVGCCSSCCPCCRGCCGGCCSTPVICCCRRTCSSCGCGYGKGCCQQKGCCQQKCCCQKQCCC
New discovery	FAM240C	2	241897331	241894213	-1	22742	lincRNA	existing transcript	lincRNA; protein-coding in v19	ENSG00000216921	ENST00000401641	90	2	mammals; potential ortholog in coelacanth without synteny, linc|3P|XLOC_096740|TCONS_00126143:5.57183|93AA|92AA|	absent; apparently lost in rodents	tupaia TREES_T100012573	CAGE is highly specific to tongue and diaphragm; HPA and Intropolis suggests more general expression	/	ncRNA NR_135766.1, though previously found as coding LOC285095			no	Protein has homology to FAM240A and FAM240B, both of which are on this sheet. Actually a 'rediscovery', as both GENCODE and RefSeq had the locus annotated as protein-coding in earlier releases. FAM240C is notably more divergent with respect to FAM240A and FAM240B than those two CDS are to each other. 	no	MSKSLTLKNPGRVAYDSGGIKMFWEKKIEHHARHLQNEDIRVRRSALNKLRVGWAEQLEGRNKMLQGPGRCPDRVPEATESLHTKDKKAA
New discovery	MDFIC2	3	70311973	70196926	-1	692	1000	existing transcript	antisense lncRNA	ENSG00000242120	ENST00000567252	189	3	avians; potential ortholog in fish without synteny, e.g. zebrafish OTTDARG00000038399	known coding gene ENSMUSG00000090667	chicken ENSGALT00000012550	no CAGE; no HPA; weak Intropolis support dominated by cell lines and cancer cells	CAGE supports mesenchymal stem cell expression; ENCODE RNAseq supports certain brain experiments and limb	absent				MyoD family inhibitor domain-containing protein. The human model was initially built using mouse cDNA evidence.	no	MSETELEKIKVRTAEHLENDKNNISWLKEDTQLTNAKHADEKPINAIVINSVSDFNITDGPAKENPNEKKLSESSTSLSSLEECQTTFSYLQTDTSVHHRDTDEECASLILACLFCQFWDCLLMLPGTCETVCTKMCCPSRRYHHTSDENHSRNDCSCNCDMDCSLFESCHETSECLELAMEISEICYR
New discovery	C3orf85	3	109136848	109149894	1	2594	lincRNA	transcript extended	lincRNA	ENSG00000241224	ENST00000622536	90	3	avians; potential ortholog in coelacanth without synteny, LOC106704520	previously undescribed coding gene ENSMUSG00000110573	chicken XP_416629.1	CAGE supports specific gastrointestinal expression; HPA and Intropolis are dominated by gastrointestinal expression, the former also finding support for liver and kidney expression	CAGE supports specific gastrointestinal expression; ENCODE RNAseq supports gastrointestinal expression	ncRNA NR_033977.1		neXtProt	no	Uncharacterised protein.	no	MAYKMLQVVLCSTLLIGALGAPFLLEDPANQFLRLKRHVNLQDYWDPDHSSDVWVNTLAKQARETWIALKTTAQYYLDMNTFTFDMSTAQ
New discovery	TMEM271	4	576062	574905	-1	703	1000	transcript extended	lincRNA	ENSG00000273238	ENST00000610212	385	1	vertebrates	previously undescribed coding gene ENSMUSG00000105867	zebrafish OTTDARG00000041905	all sources support brain / CNS expression	all sources support brain / CNS expression	absent				Transmembrane family protein.	no	MKWSVRGACAALSSCLLLACALSAAAVGLKCFSLGSELRGEPFRLGAAAGAFYSGLLLAAGLSLLGAALLCCGPRDAPLAGSEPGPGLGVPAAPAGAPEATPGESGAAAGAPGPVSSQNLLLLGVLVFMLGVLSAFAGAVIDGDTVSLVERKYSHYCLPPRAPGSSPGSAPGSTPGSAPGSAPGSAPGSAPGAPRARSTLDSATSAKCRQLKDYQRGLVLSTVFNSLECLLGLLSLLLVKNYKSSQARRGRRGRRRGGRALARPRGGSGLRAQPPASRARRGRRGRRGRRLQQRPSEASILSPEESDLAAPGDCAGFAAHHAVSYINVGVLHALDEAGAEVRCGGHPSVELPGYAPSDPDLNASYPYCCRPPCETPRPWETHRAC
New discovery	AC092442.1	4	6070162	6064977	-1	426	1000	gene added	absent	ENSG00000284684	ENST00000636216	45	2	vertebrates	previously undescribed coding gene ENSMUSG00000113373	zebrafish OTTDARG00000044229	no CAGE; no HPA; minimal Intropolis support, not indicative of a particular expression pattern	CAGE supports weak olfactory brain expression; no ENCODE RNAseq; conventional support limited to cDNA clone I220006B15 from olfactory sensory neurons	absent	cotranscribed with JAKMIP1		no	Uncharacterised protein.The CDS is co-transcribed with JAKMIP1, being translated on an alternative first exon within a JAKMIP1 intron and sharing an out of frame CDS overlap in coding exon 2. Transcriptional support in zebrafish is limited to ESTs from olfactory tissues, i.e. matching the mouse RNA. JAKMIP1 has a well established role in brain development, and has a clear brain expression profile in all species examined. Of further interest, this work established that C4orf50 immediately 3' of JAKMIP1 is also co-transcribed in brain as part of the locus, and this pattern of transcription is conserved across to avians at least. Although co-transcribed, the C4orf50 and JAMKIP1 CDS are separated by a large non-coding exon that is conserved across this evolutionary distance (human chr4:6022704-6025013). Thus, this locus apparently produces three distinct, non-overlapping translations. 	no	MEYVLFVLYFSFFLCLCALVCLYFSGCQEMTYKHEEACCGDIFWI
New discovery	AC093323.1	4	6674213	6674572	1	17969	re-ranking	existing transcript	lincRNA	ENSG00000170846	ENST00000635031	119	1	human	absent	/	CAGE is dominated by blood / immune cell experiments; HPA supports general expression; Intropolis finds extremely high expression in primary foot fibroblasts (SRR201164)	/	pseudogene NR_015433		neXtProt		Presumably a duplicant of Morf4 family associated protein 1 (MRFAP1), found 5' adjacent. Additional duplicants were found in the vicinity not based on PhyloCSF; these are clearly pseudogenic due to CDS disruptions. The novel protein duplication is primate specific, and the PhyloCSF signal is potentially based on improper genome alignments.	no	MRPVDADEAREPREEPGSPLSPAPRAGRENLASLERERARAHWRARRKLLEIQSLLDAIKSEVEAEERGARAPAPRPRAEAEERVARLCAEAERKAAEAARMGRRIVELHQRIAGCECC
New discovery	EXOC1L	4	55820027	55837351	1	126	1000	existing transcript	lincRNA	ENSG00000250821	ENST00000636125	172	3	avians	previously undescribed coding gene ENSMUSG00000091204	chicken ENSGALT00000042649	weak pineal gland support in CAGE; testis expression in HPA; Intropolis top rank expression is in embryo (SRR490995)	no CAGE; ENCODE RNAseq supports weak brain / CNS expression; cDNA is from testes	pseudogene NR_003935.2				Partial duplication of the EXOC1 locus located 3' adjacent. Human annotation was originally based on cDNA BC171876 from pooled tissues, while we also find PacBio capture-seq support in brain and K562 experiments.	no	MSSLVKEDLEKKLFKPLSQNLYEFIEIEFSVQDRYYLCVSVTKKEEVKIVMVKHYRIGLDEKYEVTKKWSLNDLQMIDGKEADTDNPFFDLHFKKVYSLEAYSCASKYAFARTVNKLNHAYLKKDLQIVNFDSTYINDDSIWSSNNKDCLVLMRICFYAFNLVCLSLCPLPL
New discovery	AC079341.3	4	121765105	121764914	-1	472	1000	existing transcript	5' UTR of TMEM155	ENSG00000164112	ENST00000643802	63	1	mammals; potential ortholog in avians without synteny or transcript evidence, e.g. allMis1/American alligator JH733013:223,996-224,181	previously undescribed coding gene ENSMUSG00000085007	/	CAGE supports brain expression; HPA is dominated by brain expression, alongside evidence of weaker more general expression; the highest ranked Intropolis introns are in brain	CAGE supports brain expression; ENCODE RNAseq is dominated by brain	absent	cotranscribed with TMEM155		gonzalez_2014:723790	Uncharacterised protein. Initially found within the 5' UTR of TMEM155 (ENSG00000284849). However, the 130aa TMEM155 CDS was found to be dubious, lacking conservation beyond higher primates and being partially composed of transposable element sequence. Its supposed transmembrane domain prediction could not be recapitulated. The 130aa TMEM155 CDS will thus be removed from GENCODE, and Ensembl ID of this locus has changed from ENSG00000284849 to ENSG00000164112. 	no	MEWELNLLLYLALFFFLLFLLFLLLFVVIKQLKNSVANTAGALQPGRLSVHREPWGFSREQAV
New discovery	REELD1	4	146216953	146230513	1	309	1000	transcript extended	lincRNA	ENSG00000250673	ENST00000636502	526	6	vertebrates	previously undescribed coding gene ENSMUSG00000112190	coelacanth ENSLACT00000006652, 3' truncated by assembly gap; fugu AUGUSTUS g21894.t3 has a conserved N-t region	no CAGE; HPA finds weak general expression; Intropolis finds weak expression without an obvious pattern	/	'unknown' XR_939298.1				Reeler domain-containing protein. The original human lincRNA annotation was based on EST AV698927 only, which is cancer derived and does not cover the entire CDS.	no	MRMQAALVGWACTTLCLASCSSAFSHGASTVACDDMQPKHIQAQPQHQDSHHITIHTHRTSYAPGDKIPVTVRSSRDFMGFLLQARRVSDHQIAGTFVLIPPHSKLMTCFQEADAVTHSDKSLKRNLSFVWKAPAQPVGDIKFLLSVVQSYFVYWARIESSVVSQQTHSSAHSDDRMEPRLLMPNLHQRLGDVEGAAPAPRTPITLPQQHTHVFAVALPGAAEEDNLDPVPASIWVTKFPGDAETLSQPSSHTATEGSINQQPSGDSNPTLEPSLEVHRLERLVALKRVSSESFASSLSTHHRTQDDPSFDSLETCLSSDGGEQDKTKASNRTVTQPPLSTVQLTYPQCLWSSETFTGNGVRASNPIPVLQTSGTSGLPAAGDQSEASRASASFLPQSKHKELRAGKGNGEGGVGYPRQTNPRPDIGLEGAQAPLGIQLRTPQLGILLCLSATLGMALAAGLRYLHTQYCHQQTEVSFSEPASDAVARSNSGETVHVRKIGENSFVLVQAEYNWITPSVGSKKTVL
New discovery	SMIM31	4	164770444	164801194	1	285	1000	existing transcript	lincRNA	ENSG00000248771	ENST00000507311	71	2	coelacanth	previously undescribed coding gene ENSMUSG00000074300	coelacanth PLAR model EnsShortNonCoding|3P|XLOC_155298|TCONS_00200728|0:0.366284|93AA|72AA| (72aa CDS)	CAGE supports gastrointestinal expression; HPA and Intropolis support gastrointestinal expression alongside weaker expression in certain other organs	CAGE supports gastrointestinal expression; ENCODE RNAseq supports gastrointestinal expression	ncRNA NR_038834.1 (LINC01207)			no	Member of the small integral membrane protein family.	no	MELPYTNLEMAFILLAFVIFSLFTLASIYTTPDDSNEEEEHEKKGREKKRKKSEKKKNCSEEEHRIEAVEL
New discovery	SMIM32	5	136192524	136192213	-1	256	1000	existing transcript	lincRNA	ENSG00000271824	ENST00000607574	103	1	vertebrates	previously undescribed coding gene ENSMUSG00000110086	zebrafish OTTDARG00000044227	CAGE supports expression in kindey and gastrointestinal tissues, and also brain; HPA finds highest expression in gastrointestinal tissues but also expression in brain, kidney, prostate; no introns for Intropolis	CAGE finds highest expression in pancreas, though is otherwise dominated by brain experiments; ENCODE RNAseq is dominated by brain expression, alongside certain gastrointestinal tissues and limb	ncRNA NR_024418.1 (LOC389332)				Member of the small integral membrane protein family.	no	MYGDIFNATGGPEAAVGSALAPGATVKAEGALPLELATARGMRDGAATKPDLPTYLLLFFLLLLSVALVVLFIGCQLRHSAFAALPHDRSLRDARAPWKTRPV
New discovery	SMIM33	5	139471122	139472921	1	56	1000	gene added	absent	ENSG00000283288	ENST00000637503	132	2	avians	known coding gene ENSMUSG00000073598	chicken XP_004944821	no CAGE; HPA and Intropolis are dominated by gastrointestinal tissues, with evidence of weaker expression in other organs	CAGE and ENCODE RNAseq are dominated by gastrointestinal expression	absent				Member of the small integral membrane protein family.	no	MHQAGHYSWPSPAVNSSSEQEPQRQLPEVLSGTWEQPRVDGLPVVTVIVAVFVLLAVCIIVAVHFGPRLHQGHATLPTEPPTPKPDGGIYLIHWRVLGPQDSPEEAPPGPLVPGSCPAPDGPRPSIDEVTCL
New discovery	SMIM40	6	33329265	33329026	-1	635	1000	existing transcript	5' UTR of DAXX	ENSG00000285064	ENST00000494082	79	1	mammals	previously undescribed coding gene ENSMUSG00000092349	/	eye specific in CAGE; no HPA; Intropolis is dominated by cancer-derived experiments	no CAGE; general ENCODE RNAseq expression	absent			no	Uncharacterised protein. Identified within the 5' UTR of DAXX. However, the novel CDS locus has polyA features in human and mouse, while DAXX has a distinct promoter downstream. Also, transcriptional overlap betweem the novel CDS locus and DAXX is limited to human, and is weakly supported. It thus apparent that these two loci are separate genes. 	no	MAEEGDVDEADVFLAFAQGPSPPRGPVRRALDKAFFIFLALFLTLLMLEAAYKLLWLLLWAKLGDWLLGTPQKEEELEL
New discovery	SMIM29	6	34247791	34246803	-1	204	1000	existing transcript	protein-coding gene with a CDS in wrong frame	ENSG00000186577	ENST00000476320	102	4	avians	known coding gene ENSMUSG00000062753	alligator XP_006025159	all sources support general expression	all sources support general expression	spurious NM_001008703.2 (C6orf1)		neXtProt		Member of the small integral membrane protein family. Previously known as C6orf1, which had a spurous CDS annotated in the wrong frame in RefSeq and GENCODE. The spurious CDS is actually longer than the novel CDS described here at 159aa. 	no	MSNTTVPNAPQANSDSMVGYVLGPFFLITLVGVVVAVVMYVQKKKRVDRLRHHLLPMYSYDPAEELHEAEQELLSDMGDPKVVHGWQSGYQHKRMPLLDVKT
New discovery	SMIM28	6	138378073	138382847	1	212	1000	existing transcript	lincRNA; protein-coding in v19	ENSG00000262543	ENST00000573100	152	2	coelacanth; potential ortholog in fish without synteny, e.g. tetraodon CAF95351	absent	coelacanth AUGUSTUS g11564.t1	no CAGE; HPA and Intropolis are dominated by gastrointestinal tissues	/	absent				Member of the small integral membrane protein family. The CDS was annotated in GENCODEv19 and subsequently removed.	no	MRGLLGSSWKKFGHAGRGTYEWLTSEPGLPLLETQLQGTQGVSSTQEDVEPFLCILLPATILLFLAFLLLFLYRRCKSPPPQGQVFSIDLPEHPPAGEVTDLLPGLAWSSEDFPYSPLPPEATLPSQCLPPSYEEATRNPPGEEAQGCSPSV
New discovery	AC187653.1	7	290170	291488	1	506	1000	transcript extended	lincRNA and adjacent pseudogene	ENSG00000248767	ENST00000506382	233	3	vertebrates	known coding gene ENSMUSG00000094504	zebrafish OTTDARG00000040484	no CAGE; no HPA; Intropolis finds weak expression in developmental cells and cancer experiments	no CAGE; ENCODE RNAseq supports testis and brain / CNS expression	ncRNA WI2-2373I1.2				Forkhead box L1-like protein. Previously absent due to a complete lack of cDNA or EST transcriptional support in human or mouse.	no	MFDSSQYPYNCFNYDADDYPAGSSDEDKRLTRPAYSYIALIAMAIQQSPAGRVTLSGIYDFIMRKFPYYRANQRAWQNSIRHNLSLNSCFVKVPRSEGHEKGKGNYWTFAGGCESLLDLFENGNYRRRRRRRGPKREGPRGPRAGGAQGPSGPSEPPAAQGRLAPDSAGEGAPGREPPASPAPPGKEHPRDLKFSIDYILSSPDPFPGLKPPCLAQEGRYPRLENVGLHFWTM
New discovery	CCDC201	7	45873007	45863085	-1	944	1000	gene added	absent	ENSG00000283247	ENST00000636578	187	3	avians	previously undescribed coding gene ENSMUSG00000087512	chicken ENSGALT00000020330	no CAGE; HPA supports placenta and testis expression; the top ranked introns in Intropolis are from a series of early embryo experiments (e.g. SRR490970)	weak ovary CAGE support; ENCODE RNAseq supports placenta and ovary expression	absent				Uncharacterised protein. Previously absent due to a complete lack of cDNA or EST evidence in human or mouse. Genomes in the rodent / squirrel clade have lost the ancestral STOP (found in other mammals and birds), giving an C-t extended CDS.	no	MEPGVQDLGLSSSEDESPSLAIRSPTLRKPLKHSTPEEAALGWSPRPSGGASYLSGSPMPAHFSQDLASHPAGVSPPATVRKRRLSTLWASKESSLDLSAPGEEPPTSASLTQRQRQRQQQQQQQESLRAKSWAQNPGLPGILNTTGRKRRDPKKRAAAMERVRQWEIYVLQNIEEATQHELTIEDD
New discovery	FAM237B	7	90319748	90319329	-1	428	1000	gene added	absent	ENSG00000283267	ENST00000637645	139	1	avians	previously undescribed coding gene ENSMUSG00000073234	ground tit XP_005518842.1	no CAGE; HPA supports testis expression; Intropolis shows strong expression in a series of experiments on preovulatory cumulus and mural granulosa cells, which are associated with developing oocytes (e.g. SRR836179)	weak CAGE; ENCODE RNAseq show high brain / CNS expression, and also placenta	absent				Uncharacterised protein. It has clear homology to human FAM237A (LOC200726) on chr2, which is also on this list. 	no	MCFATRRWFYLHLGCMMLINLVNADFEFQKGVLASISPGITKDIDLQCWKACSLTLIDLKELKIEHNVDAFWNFMLFLQKSQRPGHYNVFLNIAQDFWDMYVDCLLSRSHGMGRRQVMPPKYNFPQKITGGNLNVYLRE
New discovery	TCAF2C	7	143647646	143639670	-1	81	1000	gene added	absent	ENSG00000283528	ENST00000636941	711	6	potential primate specific duplication	mouse has a cluster of three TCAF loci in a syntenic location, though 1:1 relationships are not discernible	/	no expression data	/	absent				TRPM8 channel-associated factor protein, adjacent to known protein-coding family member TCAF2. It is a gene fragment leading into a 5' sequence gap, which is likely why it was not annotated already.	no	YGEDVRQDQQQLLEGISELDIRTGGVPSQLLVHGALAFPLGLDASLNCFLAAAHYGRGRVVLAAHECLLCAPKMGPFLLNAVRWLARGQTGKVGVNTNLKDLCPLLSEHGLQCSLEPHLNSDLCVYCCKAYSDKEAKQLQEFVAEGGGLLIGGQAWWWASQNPGHCPLAGFPGNIILNCFGLSILPQTLKAGCFPVPTPEMRSYHFRKALSQFQAILNHENGNLEKSCLAKLRVDGAAFLQIPAEGVPAYISLHRLLRKMLRGSGLPAVSRENPVASDSYEAAVLSLATGLAHSGTDCSQLAQGLGTWTCSSSLYPSKHPITVEINGINPGNNDCWVSTGLYLLEGQNAEVSLSEAAASAGLRVQIGCHTDDLTKARKLSRAPVVTHQCWMDRTERSVSCLWGGLLYVIVPKGSQLGPVPVTIRGAVPAPYYKLGKTSLEEWKRQMQENLAPWGELATDNIILTVPTTNLQALKDPEPVLRLWDEMMQAVARLAAEPFPFRRPERIVADVQISAGWMHSGYPIMCHLESVKEIINEMDMRSRGVWGPIHELGHNQQWHGWEFPPHTTEATCNLWSVYVHETVLGIPRAQAHEALSPPERERRIKAHLGKGAPLCDWNVWTALETYLQLQQAFGWEPFTQLFAEYQTLSHLPKDNTGRMNLWVKKFSEKVKKNLVPFFEAWGWPIQKEVADSLASLPEWQENPMQVYLRARK
New discovery	H2BE	7	151210318	151207871	-1	60	1000	spliceform added	alternative CDS of ABCF2 in different reading frame	ENSG00000285480	ENST00000644661	122	2	avians	absent; apparently lost in rodents	chicken ENSGALG00000013346	no CAGE; no HPA; Intropolis finds expression specific to embryonic cells (e.g. SRR499827)	/	absent				Histone protein, member of the H2B family. The second exon was previously incorporated in ABCF2 upstream, and this cDNA can now been seen as a misleading 'read-through' transcript event; these are clearly separate genes.	no	MSAEYGQRQQPGGRGGRSSGNKKSKKRCRRKESYSMYIYKVLKQVHPDIGISAKAMSIMNSFVNDVFEQLACEAARLAQYSGRTTLTSREVQTAVRLLLPGELAKHAVSEGTKAVTKYTSSK
New discovery	PRSS51	8	10517954	10496385	-1	31	1000	spliceform added	antisense lncRNA	ENSG00000253649	ENST00000636217	220	6	mammals	known coding gene ENSMUSG00000052099	/	very weak CAGE; HPA supports testis expression; the topped ranked Intropolis introns are from cell lines, but there is also early embryo expression (e.g. SRR893067).	all sources support testis expression	absent				Protease, serine family member. Human has a premature termination codon in the final exon, giving a shorter protein compared to other mammals including apes (the truncation is 23aa versus the mouse CDS). However, this termination is found downstream of the trypsin domain, and additional confidence in the coding potential of the human locus comes from mass spectromtery support.	no	MFQLLIPLLLALKGHAQDNPENVQCGHRPAFPNSSWLPFHERLQVQNGECPWQVSIQMSRKHLCGGSILHWWWVLTAAHCFRRTLLDMAVVNVTVVMGTRTFSNIHSERKQVQKEEERTWDWCWMAQWVTTNGYDQYDDLNMHLEKLRVVQISRKECAKRINQLSRNMICAWNEPGTNGIFKVLTPAQPPPPSRETVGHLWFVLFMEPRDSSKWVSSVGA
New discovery	AC138647.1	8	141514697	141518715	1	102	1000	existing transcript	lincRNA; protein-coding in v19	ENSG00000226490	ENST00000427937	188	2	mammals	known coding gene ENSMUSG00000086361	/	all sources support testis expression	all sources support testis expression	absent				Uncharacterised protein. This was a protein-coding gene in GENCODEv19 before being switched to lncRNA. While the first coding exon, the splice junction, and the bulk of the second exon CDS are conserved in mammals, the STOP region is highly divergent. It has not been possible to establish an ancestral state for the STOP: human, mouse, dog, opossum use different C-ts. However, these translations are similar in size. Avian genomes have a region of prospective homology to the CDS of exon 2. However, this is not syntenically conserved and the first exon of the mammalian gene is not seen. The provenance of this locus is clearly as protein-coding sequence, although it the possibility that it is pseudogenic in human and / or mouse cannot be ruled out.	yes, potential unitary pseudogene in human and / or mouse.	MASSCPGTPSPAGLPPPSVATPGPAAPPEPAFPDIYGGDAQLWEAHFRGIGRAYRALGKQDDFAIRVLTENFTLPFPFAWPPGSDPACGPLFYDPRDRADFDFLLRGPGASPPALLRPLHATAQAAMRKRRLERLALSCARARGPGPASSCCCPAPPPPSRSPRPALPATAPPGWPRPRRCPESEQNK
New discovery	SMIM27	9	32552435	32552923	1	324	1000	existing transcript	antisense lncRNA	ENSG00000235453	ENST00000453396	55	2	coelacanth	previously undescribed coding gene ENSMUSG00000028407	coelacanth linc|3P|XLOC_149553|TCONS_00193392:1.03778|96AA|53AA|	all sources support general expression	all sources support general expression	ncRNA NR_033991.1			no	Small integral membrane protein, previously known as TOPORS-AS1.	no	MKPVSRRTLDWIYSVLLLAIVLISWGCIIYASMVSARRQLRKKYPDKIFGTNENL
New discovery	FAM240B	9	38703999	38694776	-1	214	1000	gene added	absent	ENSG00000283329	ENST00000637493	78	2	mammals; potential ortholog in avians without synteny, e.g. lizard XP_016846473	known coding gene ENSMUSG00000096537	/	CAGE supports eye expression; no HPA; Intropolis supports eye expression (e.g. SRR548613), but also skeletal muscle (ERR030899)	no expression data	ncRNA XR_242549.3			no	Protein with homology to FAM240A and FAM240C, both of which are on this sheet. 	no	MNNQYIRREVFCCGTCHELKSFWEKEISKQTFYRELEEDRQERSALKKLREEWRQRLERRLRMLDNPVEKEKPAHTAD
New discovery	AL353572.3	9	87956267	87956500	1	67	1000	gene added	absent	ENSG00000283205	ENST00000636536	77	1	mammals, although with a primate-specific genomic rearrangement; synteny is maintained between the dog, cow and mouse loci	previously undescribed coding gene ENSMUSG00000114559	/	all sources support testis expression	all sources support testis expression	absent			no	Uncharacterised protein.	no	MGFVTNKSAFKAGDSLYLRRAFVNNLGEERRTRIQIQSIQKALDIQIREIDREKAALKRFLVKLHKTTGYFPQKPLW
New discovery	B3GNT10	9	120796604	120799678	1	1441	re-ranking	transcript extended	pseudogene	ENSG00000214654	ENST00000464488	369	2	mammals; potential ortholog seen in avians: e.g. chicken B3GNTL2, with partial syntenty (PSDM5 flank)	previously undescribed coding gene ENSMUSG00000107167	/	CAGE supports weak expression in cell lines and cancer experiments; however, alternative transcript ENST00000437707 skips coding exon 1 with high general expression in HPA; Intropolis finds weak support for coding intron 1, limited to cell lines and cancer experiments	No CAGE; ENCODE RNAseq is limited to liver (support was also found in liver PacBio capture-seq experiments)	NR_027442.1 (LOC100288842)				Galactosyltransferase superfamily member. The human cDNA and EST evidence - and the vast bulk of RNAseq evidence - supports an alternative first exon that does not contain the initiation codon. This may be why the locus was previously annotated as a pseudogene fragment. Just two codons are present on this first coding exon; there is no PhyloCSF signal here, although the [ATG] is found in all therian mammals. This locus could be pseudogenised in human, or potentially it could be translated with a truncated N-terminus, i.e. using an [ATG] in coding exon 2. Nonetheless, it was annotated as a protein-coding locus in human because there is evidence for the transcription of coding exon 1, albeit  limited.	yes, potential unitary pseudogene in human	MQVTFCRLRTHQWCFILFNVILFHALLFGTDFVEEYFLHSLPYIDVKVLEIKNKARKLNIEPLRSNLSKYYVLSQSEICKGKNIFLLSLIFSSPGNGTRRDLIRKTWGNVTSVQGHPILTLFALGMPVSVTTQKEINKESCKNNDIIEGIFLDSSENQTLKIIAMIQWAVAFCPNALFILKVDEETFVNLPSLVDYLLNLKEHLEDIYVGRVLHQVTPNRDPQNRDFVPLSEYPEKYYPDYCSGEAFIMSQDVARMMYVVFKEVPMMVPADVFVGICAKFIGLIPIHSSRFSGKRHIRYNRCCYKFIFTSSEIADPEMPLAWKEINDGKECTLFETSYELISCKLLTYLDSFKRFHMGTIKNNLMYFAD
New discovery	BX255925.3	9	137217997	137218602	1	549	1000	gene added	absent	ENSG00000284976	ENST00000645271	201	1	avians	previously undescribed coding gene ENSMUSG00000115018	chicken AUGUSTUS g10876.t1	CAGE supports esophagus, tonsil, tongue, testis expression; HPA shows general expression, though likely includes readthrough transcription from NDOR1 upstream so hard to interpret; no introns for Intropolis	CAGE supports stomach, skin, ileum, vesicular gland, gastrointestinal tissues expression; ENCODE RNAseq likely includes readthrough transcription from Ndor1, although transcription in stomach notable increases at the CAGE region	absent				RING finger protein. The initiation codon has not been defined with confidence, i.e. based on conservation. This could suggest the PhyloCSF signal actually finds an alternative final exon of NDOR1, found a short distance upstream. However, several lines of evidence argue against this: (1) there is no support for splicing between the two loci in human, and while mouse does contain connections these are weakly supported, only incorporate part of the PhyloCSF signal and are poorly conserved; (2) the CAGE region of the novel locus is conserved between human and mouse, and in human it colocalises with rich TF-binding data; (3) there is no expectation that NDOR1 – an oxireductase metabolic enzyme – would utilise a RING finger domain; (4) there are multiple RING finger loci in the region, which presumably represent a series of ancient duplications. The possibility that this locus is a pseudogene cannot be ruled out, although its age argues against this. The 5' of the PhloCSF signal corresponds to the edge of a sharp signal in multiz, which corresponds to an in-frame [GAG]. The human model could was constructed with an [ATG] a short distance upstream, which is listed here. Nonetheless, it is possible the locus uses a non-ATG initiation codon. 	no	MEGAWALPTWKEEGREQAAGQGEEEECPICTEPYGPRERRLALLNCSHGLCVGCLHRLLGSASSADLGRVRCPLCRQKTPVLEWEICRLQEELLQADGPSRQPRREAPASYHRNPGPWGSLEHRYQLRFLAGPVGGRGCLPFLPCPPCLGARLWTLRERGPCARRLALLSLLALELLGLLLVFTPLLLLGLLFVLLDRSGR
New discovery	HSPA14	10	14842285	14843894	1	43	1000 / ms	transcript extended	non-coding transcript within HSPA14	ENSG00000284024	ENST00000640019	361	2	mammals	previously undescribed coding gene ENSMUSG00000051396	/	all sources support general expression	all sources support general expression	absent	cotranscribed with HSPA14	Kim et al		Myb/SANT-like DNA-binding domain containing protein. Found within UTR exons of HSPA14. All evidence indicates that transcription occurs from the shared HSPA14 promoter in human and mouse, with no evidence of differential expression between the two loci. It is thus not obvious how translation of the two CDS is distinguished. This CDS was initially suggested by a GENCODE reanalysis of the Kim et al and Wilhelm et al mass spectrometry datasets, although the supporting evidence was not considered strong enough to support annotation at that time. HSPA14 is found in all vertebrates, which suggests the novel CDS arose at a later time. 	no	MASANSSAGIRWSRQETRTLLSILGEAEYIQRLQTVHHNADVYQAVSKRMQQEGFRRTERQCRSKFKVLKALYLKAYVAHATSMGEPPHCPFYDTLDQLLRNQIVTDPDNLMEDAAWAKHCDQNLVASDAPGEEGTGILKSKRTQAADHQPILKTVKASDEDCQLRISDRIRETSDLEDSWDESSGAGCSQGTPSYSSSHSLFRGAVAPCQSSPMARLGVSGEPSPCTSTNRSTPGVASTPQTPVSSSRAGFVSGGDRPLTSEPPPRWARRRRRSVARTIAAELAENRRLARELSKREEEKLDRLIAIGEEASAQQDTANELRRDAVIAVRRLATAVEEATGAFQLGLEKLLQRLISNTKS
New discovery	C10orf143	10	130110772	130064354	-1	1601	lincRNA	spliceform added	lincRNA	ENSG00000237489	ENST00000637128	108	4	xenopus; potential ortholog in fish without synteny, e.g. salmon XP_020333744	known coding gene ENSMUSG00000040139	xenopus OCT69938	all sources support general expression	all sources support general expression	ncRNA NR_034125.1 (LINC00959)				Uncharacterised protein. Previous not annotated in human as the cDNA evidence supports non-coding transcripts within the locus.	no	MDSLALGRWRQRRAEDLQVPGDVKRVCRRLEASGHERGCHQVNACALASWGPEDRELPSRGCLPAPRPESGQGRLSTGISQNGGRSSAQPCPRCIAGESGHFSHTKNH
New discovery	C10orf95	10	102451093	102450452	-1	493	1000	existing transcript	lincRNA	ENSG00000120055	ENST00000625129	213	1	xenopus	previously undescribed coding gene ENSMUSG00000099655; CDS previously annotated in the wrong frame	xenopus LOC105948016	CAGE supports expression in various epithelial cells; HPA supports expression in lung and colon; top ranking Intropolis introns are from trophoblasts (e.g. SRR486238)	CAGE supports expression in tracheal epithelial cells; ENCODE RNAseq supports expression in lung and gastrointestinal tissues	spurious NM_024886.2 (C10orf95)				Uncharacterised protein. While RefSeq and UniProt have long recognised this locus as protein-coding, they represent a spurious 257aa ORF in the wrong frame. GENCODE represented this false translation up to v19, after which the gene became a lincRNA.	no	MYVYSWPPPKQGVWPPPPQLLTCTYLAAPLLLPPVQAHSFRSRPGSLHAGEWAAPREYHRFYGPAAPPEAAPPWWACPPAYATTLRRPCAAAGISGLSLQAPAAVAESWAPWPEGGSLQTELRWGRVERARGPPLQLPDFVRRELRRAYGTYPRADVRVTQRRGQFLLQATPRVLEPDHRVEWRVRRRPDSGDSSPAREAAERGRPRKSKGLS
New discovery	TEX54	11	62832750	62832376	-1	402	1000 / ms	gene added	absent	ENSG00000283268	ENST00000636508	124	1	mammals	known coding gene ENSMUSG00000090840	/	CAGE supports macrophage expression in a small number of experiments; HPA supports testis and bone marrow expression, although BLUEPRINT finds only weak expression in blood cells; no introns for Intropolis	all sources support testis expression	absent		neXtProt		Uncharacterised CDS. The locus apparently lost its single intron in primates. It is found within a small genomic region between WDR74 and STX5 on the same strand, and although it is clearly distinct from the latter it does have limited readthrough transcription evidence from the former. Nonetheless it seems most likely to be a separate coding gene in human and mouse due to CAGE support and its high specificity to testis, which is not seen for WDR74. Evidence for translation in testis has been observed in the HPP mass spectromery datasets, which included PhyloCSF in the search space. This data had not been previously considered strong enough to support CDS annotation in isolation.  	no	MGCCQDKDFEMSDEQSKEEESEDGREDETTDTQRGPRECERGLPEGRGELRGLVVPSGAEDIDLNSPDHPNHKSNESLLITVLWRRLSTFGRRGSSRPSKRQPDQIRKQESPIREGNQEEPEKG
New discovery	SMIM38	11	69157847	69158002	1	219	1000	gene added	absent	ENSG00000284713	ENST00000641568	51	1	mammals	previously undescribed coding gene ENSMUSG00000109305	/	no CAGE; HPA supports stomach expression; Intropolis has highest support in stomach (e.g. SRR980483)	all sources support stomach expression	absent			no	This CDS was reported by Saghatelian based on mass spec peptide [LILWSCLGTYIDYR] and conservation [PMID:27010111]. It is orthologous to rat protein-coding gene Rmt1, previously reported to be highly expressed in rat mammary tumours [PMID:11675151].	no	MTSWPGGSFGPDPLLALLVVILLARLILWSCLGTYIDYRLAQRRPQKPKQD
New discovery	SMIM35	11	118086757	118013781	-1	391	1000	transcript extended	antisense lncRNA	ENSG00000255274	ENST00000636151	85	4	mammals	known coding gene ENSMUSG00000091996	/	no CAGE in normal tissues; HPA shows weak expression in kidney, lung, placenta; Intropolis support is weak in non-cancer experiments, although expression is apparent in most BLUEPRINT experiments	no CAGE;  ENCODE RNAseq supports testis and thymus expression, alongside more general, weaker transcription	ncRNA NR_038318.1			no	Uncharacterised protein.	no	MTGEDSISTLGLILGVGLLLLLVSILGYSLAKWYQRGYCWEGPNFVFNLYQIRNLKDLEMGPPFTISGHISSTDGGYMKFSNGLV
New discovery	TEX49	12	48727481	48765655	1	184	1000	existing transcript	lincRNA	ENSG00000257987	ENST00000548380	131	4	vertebrates	known coding gene ENSMUSG00000022993	zebrafish OTTDARG00000041067	all sources support testis expression	all sources support testis expression	ncRNA NR_029448.1 (LINC00935)				Uncharacterised protein.	no	MAFFNLYLLGYQNSFQNKKRNTTEETNQKEPEPTRLPPIISKDGNYSVHQNSHTRYHEAVRKVLLKTFPNQVFRIPLTDAQNFSFWWSHDPGVRPEETMPWIRSPRHCLIKSAMTRFMDHSILNDRTFSLY
New discovery	DIABLO	12	122226564	122226430	-1	279	1000	existing transcript	5' UTR of DIABLO	ENSG00000284934	ENST00000475784	44	1	avians, within the DIABLO 5' UTR; a syntenic ORF exists in fish without transcript evidence, e.g. fr3/Fugu HE591722:58,952-59,158.	previously undescribed coding gene ENSMUSG00000114278	chicken mRNA CR353660, ICGSC Gallus_gallus-4.0/galGal4 [chr15:5,798,711-5,798,845]	CAGE expression is limited to neuroblastoma, except a weak signal in fetal rectum; no HPA; minimal Intropolis, almost entirely from neuroblastoma experiments	CAGE supports embryo and neonate expression, especially in neurons and adrenal gland; ENCODE RNAseq finds transcription in most experiments	absent	cotranscribed with DIABLO		no	Uncharacterised protein. Found within a 5' UTR exon of DIABLO. Current evidence suggests this novel CDS is co-transcriptional with DIABLO in human and mouse, i.e. it is found on a transcript that also contains the DIABLO CDS. This also appears to be the case at least across to avians, i.e. chicken. However, DIABLO also has a strong, conserved TSS downstream of the novel CDS with general expression; while the novel CDS may always be transcribed in conjunction with DIABLO, it seems DIABLO is typically transcribed independently of the novel CDS. Although the human novel CDS has weak expression data, annotation was originally supported by cDNA BC046209 and 7 ESTs. All but one of these is from neuroblastoma. 	no	MPASSTVHVLQLLRELLAFVLLSYTVLIGALLLAGWTTYFLVLK
New discovery	C12orf81	12	51814893	51813940	-1	173	1000	gene added	absent	ENSG00000284730	ENST00000642069	317	1	avians	previously undescribed coding gene ENSMUSG00000113558	lizard: Broad AnoCar2.0/anoCar2 [chr2:92,335,927-92,335,957 (-)]	no CAGE; HPA coverage is weak, and cannot be deconvoluted from a prospective long-form of the SCN8A 3' UTR on the opposite strand; no introns for Intropolis	all sources support testis expression	absent				Uncharacterised protein. This single exon locus appears to be homologous to a multiexon locus found in multiple fish species and amphibians, e.g. zebrafish OTTDARG00000002022, although without preserved synteny.  An equivalent multi-exon locus cannot be found in mammals or avians. The most parsimonious explanation would seem to be that the single exon locus represents an ancient retroinsertion near the base of the mammalian / avian clade, accompanied by the loss of the parent.	no	MAARTLASALVLTLWVWALAPAGAVDAMGPHAAVRLAELLTPEECGHFRSLLEAPEPDVEAELSRLSEDRLARPEPLNTTSGSPSRRRRREAAEDPAGRVAGPGEVSDGCREALAAWLAPQAASLSWDRLARALRRSGRPDVARELGKNLHQQATLQLRKFGQRFLPRPGAAARVPFAPAPRPRRAAVPAPDWDALQLIVERLPQPLYERSPMGWAGPLALGLLTGFVGALGTGALVVLLTLWITGGDGDRASPGSPGPLATVQGWWETKLLLPKERRAPPGAWAADGPDSPSPHSALALSCKMGAQSWGSGALDGL
New discovery	SMIM41	12	52079780	52080061	1	562	1000	existing transcript	non-coding transcript within OR7E47P	ENSG00000284791	ENST00000546390	93	1	avians	previously undescribed coding gene ENSMUSG00000075408	alligator AUGUSTUS g4669.t1	CAGE supports expression in smooth muscle cells in colon and trachea, and also lung, urethra, testis, prostrate; HPA supports expression in lung and colon and prostate, and weaker expression in spleen, stomach and adrenal gland; Intropolis is dominated by prostate tumours	CAGE supports strong expression in cardiac myocytes, and also fetal testis and fetal lung; ENCODE RNAseq supports high expression in lung and testis, alongside weak general expression	ncRNA NR_120437			no	Uncharacterised protein.	no	MNGSQAGAAAQAAWLSSCCNQSASPPEPPEGPRAVQAVVLGVLSLLVLCGVLFLGGGLLLRAQGLTALLTREQRASREPEPGSASGEDGDDDS
New discovery	C13orf42	13	51111209	51084151	-1	136	1000	transcript extended	lincRNA	ENSG00000226792	ENST00000563710	325	4	coelacanth; potential ortholog in fish without synteny, e.g. tetraodon CAG05779	previously undescribed coding gene ENSMUSG00000100486	coelacanth ENSLACT00000010662	No CAGE; no HPA; Intropolis supports expression in a variety of developmental tissues or cell lines (e.g. SRR488136)	CAGE has a weak inner ear signal; no ENCODE RNAseq support	ncRNA NR_102432 (LINC00371)				Uncharacterised protein.	no	MFRKIHSIFNSSPQRKTAAESPFYEGASPAVKLIRSSSMYVVGDHGEKFSESLKKYKSTSSMDTSLYYLRQEEDRAWMYSRTQDCLQYLQELLALRKKYLSSFSDLKPHRTQGISSTSSKSSKGGKKTPVRSTPKEIKKATPKKYSQFSADVAEAIAFFDSIIAELDTERRPRAAEASLPNEDVDFDVATSSREHSLHSNWILRAPRRHSEDIAAHTVHTVDGQFRRSTEHRTVGTQRRLERHPIYLPKAVEGAFNTWKFKPKACKKDLGSSRQILFNFSGEDMEWDAELFALEPQLSPGEDYYETENPKGQWLLRERLWERTVP
New discovery	TMEM272	13	51838530	51816751	-1	10679	lincRNA	existing transcript	lincRNA	ENSG00000281106	ENST00000629372	187	4	avians; potential ortholog in fish without synteny, e.g zebrafish OTTDARG00000042329	absent; apparently lost in rodents	chicken LongAUGORFlinc|3PO|XLOC_009333|TCONS_00025932:1.79557|220AA|187AA||Pfam_1_doms|RNACode|HSS_689_1.0E-16	CAGE supports expression in brain, although almost entirely limited to caudate nucleus and putamen; HPA supports expression in most tissues, especially duodenom, small intestine and appendix; Intropolis is dominated by blood expression (e.g. SRR976769), and Blueprint supports expression in innate immune cells especially	/	ncRNA NR_027047 (LINC00282)				Transmembrane domain-containing protein.	no	MPGGLEKTCHQCISKIASNACFVVVLCAFLALPLSMTFIGMKFLEDCPIQPLIPLYLLVGGIVGTLKVSLLLYDSTRMRRLLSKAVVIDDDDDDEYPWRQNAHRYYIHLLLSLFLFLWFILGNYWVFSVYLPDFLPPFQQPQDYCDKTLYLFAVGVLALSHTVLVLLLLCSGCVYLCSRWRLAADED
New discovery	LMLN2	14	23104920	23099282	-1	156	1000	gene added	absent	ENSG00000283654	ENST00000644000	730	14	vertebrates	previously undescribed coding gene ENSMUSG00000114865	zebrafish OTTDARG00000043717	CAGE support limited to tetracarcinoma; no HPA; Intropolis has low scores, with the highest score in retina (SRR548611) alongside evidence of embyro and brain expression	no CAGE; ENCODE RNAseq has weak support in brain / CNS, liver and testis	'unknown' XR_944274.1				Peptidase family member. The RefSeq non-coding model is based on a cDNA with a retained intron (BC153822).	no	MLLLLLLLLLLPPLVLRVAASRCLHDETQKSVSLLRPPFSQLPSKSRSSSLTLPSSRDPQPLRIQSCYLGDHISDGAWDPEGEGMRGGSRALAAVREATQRIQAVLAVQGPLLLSRDPAQYCHAVWGDPDSPNYHRCSLLNPGYKGESCLGAKIPDTHLRGYALWPEQGPPQLVQPDGPGVQNTDFLLYVRVAHTSKCHQEPSVIAYAACCQLDSEDRPLAGTIVYCAQHLTSPSLSHSDIVMATLHELLHALGFSGQLFKKWRDCPSGFSVRENCSTRQLVTRQDEWGQLLLTTPAVSLSLAKHLGVSGASLGVPLEEEEGLLSSHWEARLLQGSLMTATFDGAQRTRLDPITLAAFKDSGWYQVNHSAAEELLWGQGSGPEFGLVTTCGTGSSDFFCTGSGLGCHYLHLDKGSCSSDPMLEGCRMYKPLANGSECWKKENGFPAGVDNPHGEIYHPQSRCFFANLTSQLLPGDKPRHPSLTPHLKEAELMGRCYLHQCTGRGAYKVQVEGSPWVPCLPGKVIQIPGYYGLLFCPRGRLCQTNEDINAVTSPPVSLSTPDPLFQLSLELAGPPGHSLGKEQQEGLAEAVLEALASKGGTGRCYFHGPSITTSLVFTVHMWKSPGCQGPSVATLHKALTLTLQKKPLEVYHGGANFTTQPSKLLVTSDHNPSMTHLRLSMGLCLMLLILVGVMGTTAYQKRATLPVRPSASYHSPELHSTRVPVRGIREV
New discovery	ALDOA	16	30053494	30063842	1	226	1000	existing transcript	5' UTR of ALDOA	ENSG00000285043	ENST00000338110	139	4	vertebrates	previously undescribed coding gene ENSMUSG00000114515	zebrafish OTTDARG00000037560	CAGE supports weak expression in cell lines; HPA supports cerebral cortex expression, alongside weaker transcription in other organs; Intropolis scores are low, dominated by brain	CAGE supports weak expression in testis; ENCODE RNAseq supports brain / CNS expression, alongside weaker general transcription	absent	cotranscribed with ALDOA			Uncharacterised protein. Identified within 5' UTR exons of ALDOA. While ALDOA has its own downstream promoter in human and mouse, there is no evidence that the novel CDS is transcribed without also reading into ALDOA exons. In zebrafish the novel CDS is clearly a separate transcription unit from aldoaa. 	no	MDASSSPWNPTPAPVSSPPLLLPIPAIVFIAVGIYLLLLGLVLLTRNCLLAQGCCADGSSPCRKQGSSGPPDCCWTCAEACNFPLPSPAHFLDACCPQPTRADWAPRCPRCCPLCDCACTCQLPDCQSLNCLCFEIKLR
New discovery	AC233723.1	17	4802319	4801289	-1	651	1000	spliceform added	lincRNA	ENSG00000262165	ENST00000635921	79	2	coelacanth	previously undescribed coding gene ENSMUSG00000109833	coelacanth AUGUSTUS g10900.t1	all sources support only weak expression in cancer experiments and cell lines	no CAGE: ENCODE RNAseq supports very low expression in brain and limb	absent			no	Uncharacterised protein. While there is very little evidence for the expression of the first coding exon in human, there is an alternative first exon that is divergently transcribed from the PLD2 promoter region at appreciable levels. This alternative transcript is likely not protein-coding. The paucity of transcript evidence in human and mouse may call the functionality of the gene into question. However, given the depth of conservation across vertebrates, and the fact that there at least some support for the splice junction in both species, it was decided to annotate the gene in both species as protein-coding.	yes, potential unitary pseudogene in human and / or mouse.	MGLKGAWCFPWCGCRRQRGTERGAGLSPAAPPDPSPAIAPTMAEGGVPSPGPGAYFSRKARLSFRHQLHDIASANDSTI
New discovery	LINC00854	17	43228554	43221571	-1	228	1000	existing transcript	antisense lncRNA	ENSG00000236383	ENST00000636331	168	4	zebrafish	previously undescribed coding gene ENSMUSG00000085486	zebrafish OTTDARG00000040503	all sources support testis expression	all sources support testis expression	ncRNA NR_047479.2 (LINC00854)				Uncharacterised protein. PMID:22196729 had previously reported this locus as a deeply conserved lncRNA, first identified in zebrafish.	no	MGSAYHWEARRRQMALDRRRWLMAQQQQELQQKEQELKNHQEEEQQSEEKLQPHKKLNVPQPPVAKLWTSQEQPQPSQQQPSVQPPSQPPPQPSTLPQAQVWPGPQPPQPQPPPQPTQPSAQARCTQHTSKCNLQDSQRPGLMNPCQSSPIRNTGYSQLKSTNYIQQW
New discovery	ANKRD40CL	17	50766913	50761363	-1	17729	re-ranking	spliceform added	lincRNA	ENSG00000167117	ENST00000643007	142	4	avians	previously undescribed coding gene ENSMUSG00000094091	chicken ENSGALT00000045234 (5' truncated, though ESTs can extend it to full length)	all sources support expression in gastrointestinal tissues	all sources support expression in gastrointestinal tissues	ncRNA NR_073199.1 (LINC00483)				Member of the ankyrin repeat domain-containing protein family.	no	MAEPEQDIGEKPAGEYKQEGTNPHLPTTDPSDNKKPSDTCLVRIQNPKENDFIEIELKRQELSYQNLLNVSCCELGIKPERVEKIRKLPNTLLRKDKDIRRLRDFQEVELILMKNGSSRLTEYVPSLTERPCYDSKAAKMTY
New discovery	AC015802.6	17	76569648	76568797	-1	14	1000	existing transcript	retained intron transcript of ST6GALNAC2	ENSG00000284526	ENST00000640006	283	1	mammals	previously undescribed coding gene ENSMUSG00000110170	/	all sources support testis expression	all sources support testis expression	absent	contranscribed with ST6GALNAC2	Kim et al		Uncharacterised protein. Identified within a non-coding transcript of the ST6GALNAC2 locus. The termination codon of the novel CDS overlaps with a conserved splice acceptor site of ST6GALNAC2. A 'conceptual translation' of the novel mouse locus was supplied to GenBank as ACL12360 as part of a 2009 investigation into sperm proteins [PMID: 19186949]. The human CDS was initially noted by GENCODE as part of the analysis into the Kuster et al and Wilhelm et al proteomics datasets, although without enough statistical confidence to support annotation in isolation.	no	MSSPSHTPNPSPTQSPSQSRSNNIVTPPGQQPAPSPSPTRGSSSRPPSHPPTPNASQPSSRTSSLNPSPQVQHVPRGAAQTPTPPTSKSPSQSGFKSLSRNPSLTPAVPPKSSFYSPATSSSYIGPIQNIPSYITPYVPRFLKEPPFFQPPTAPLPQNPCFACPSPCPARKPPPPPDSLYLPLLPPPPHHPQFNCPFPTPPGLFMPPSSLSYTPPVEVLVSGKPHVVPNVLPATFYTPFSRYYSQPRSYRSGYRGYSGALTLPSISPLQYDGSGRSVHFYHGS
New discovery	MBD3L2B	19	7021397	7019161	-1	7145	lincRNA	existing transcript	lincRNA	ENSG00000196589	ENST00000636986	204	2	potential human-specific duplication	absent; the cluster is apparently lost in rodents	cow XP_015327519.1	no CAGE; no HPA; Intropolis supports expression in early embryo (e.g. SRR490988) and other developmental cells	/	absent				Methyl-CpG binding domain protein 3-like family member. One of 5 members of a series of local duplications. It is not possible to say which locus is ancestral – other apes and monkeys have just two copies with conserved synteny - and the PhyloCSF signal may be based on improper genome alignments.	no	MGEPAFTSFPSLPVLGKLKRNMMPWALQKKREIHMAKAHRRRAARSALPMRLTSCIFRRPVTRIRSHPDNQVRRRKGDEHLEKPQQLCAYRRLQALQPCSSQGEGSSPLHLESVLSILAPGTAGESLDRAGAERVRSPLEPTPGRFPAVAGGPTPGMGCQLPPPLSGQLVTPADIRRQARRVKKARERLAKALQADRLARRAEM
New discovery	AC008397.1	19	18255307	18250130	-1	1071	re-ranking	spliceform added	5' UTR of PDE4C	ENSG00000284797	ENST00000643046	234	4	vertebrates	known coding gene ENSMUSG00000095026	zebrafish OTTDARG00000012535	CAGE supports expression in lung and gastrointestinal tissues; HPA supports expression in gastrointestinal tissues alongside weaker expression in other organs; aside from cancer experiments, Intropolis is dominated by gastrointestinal experiments (e.g. SRR364829)	all sources support expression in gastrointestinal tissues	ncRNA NR_036575.1 (LOC729966)				Uncharacterised CDS. Initially found within the 5' UTR of PDE4C. A reappraisal of the transcript evidence indicates that the two are separate loci, and that the existing model unifying the two (ENST00000355502) is a read-through event based on cDNA AK095384. Also, these genes do not appear to be co-transcribed in mouse or other species. The novel CDS was previously recognised in cow as 'cattle intestine-specific transcript 1' (CIST1) based on an in silico genome survey [PMID:16554549], i.e. with an expression profile that matches the human and mouse inferences provided here.	no	MACPQLPPLLLLVLVVLLKAGVNYNTPFTDIVTSENSMETSPVSSLISSPFAHSTHSSGEPPKSYSSTMSLETDSITHLSPSSSGATPTIQPSPSSTDSRMIPSSPQPETITHPSSGSPSAELTPSSHSTLPSSESLTPHWSPTSHSPGTEPLTSTDQTLEPPGPAPGDTGPRELHRNPSVVVVVCLLVSLLLIGSVVMAVRFCHRNESKFENLDEVSMGSVNDRLSFAHHLQE
New discovery	PNMA8C	19	46428359	46427745	-1	191	1000	gene added	absent	ENSG00000277531	ENST00000617053	204	1	mammals	previously undescribed coding gene ENSMUSG00000108348	/	all sources support brain expression	all sources support brain expression	absent				Paraneoplastic antigen-like protein family member, derived from an LTR / Gypsy element in common with other family members.	no	MLFGVKDIALLEHGCKALEVDSYKSLMILGIPEDCNHEEFEEIIRLPLKPLGKFEVAGKAYLEEDKSKAAIIQLTEDINYAVVPREIKGKGGVWRVVYMPRKQDIEFLTKLNLFLQSEGRTVEDMARVLRQELCPPATGPRELPARKCSVPGLGEKPEAGATVQMDVVPPLDSSEKESKAGVGKRGKRKNKKNRRRHHASDKKL
New discovery	AC008687.4	19	49020515	49017968	-1	34	1000	spliceform added	lincRNA	ENSG00000268655	ENST00000637680	334	5	coelacanth	previously undescribed coding gene, first appeared in GENCODE M19	coelacanth XP_005991057	no CAGE; HPA supports testis expression; Intropolis supports testis expression	CAGE supports testis expression, with weaker though consistent expression in tracheal epithelial cells; ENCODE RNAseq supports expression in testis, lung and ovary	ncRNA NR_073552.1 (LOC101059948); partial match				Uncharacterised protein-coding gene. Located within the LHB region, which contains numerous genes for pregnancy-related hormones. However, this novel CDS does not share obvious homology with these loci. A human unprocessed pseudogene was also added 40kb downstream not based on PhyloCSF (ENSG00000283251), an event that apparently occurred in the primate lineage.	no	MASGTLAPGCRISATEVPGSRPNCHLTSSYFSHRIIPPIPFTPPTVQSTVADPLPQVAKQDSHNWAFDEVLSRWETTSGSAYVPKTHGGPCAQPRAPEPADPTRTVGIKDLGEKLRHRGWRLPLTTKYQSSETRAQYTGSPSGDPRAPEYFGPQPPQLADHHRGGPSQALIAWTKNPELSGRPFTVSDRGVLDRRQLYLTTSARDFRFYPKTELSGYPRKDSLTYWSFEETPQVWSHGPQRPPCPRSSRPPRPPRVRVPRVSPVTSAMPHRGALSLAQESYSPLLHPLRRLDRFCPLEAPWGGPHWKPLRGIYSVPKAYSTENSSYGSLKPALV
New discovery	C19orf85	19	55464554	55463472	-1	337	1000	gene added	absent	ENSG00000283567	ENST00000635964	222	2	mammals; potential ortholog in fish without synteny, e.g. tetraodon CAF97887	previously undescribed coding gene ENSMUSG00000110221	/	CAGE supports testicular germ cell embryonal cancer and embryonic stem cell expression; no HPA; Intropolis supports stem cell expression, especially embryonic (e.g. SRR488685)	no CAGE; weak ENCODE RNAseq support for brain expression	absent				Uncharacterised protein.	no	MHPGVPEGPGVSEPGPRELCAFVSGAAAHMLRALQPRRTRPPKRRPNHRRFLHNQICRQFTKIEAATQRLALSILSQEAPPQRPSLQKPPPPPPSPFLGVACAVAPTEAPHASASLSLAALDTSTLDLFDNIALTPECASMPWDPSSGSDAPLPAPGLSHRDLGQLDLRQVPHFCGPLPLPQHALGEEADLVAPDWGWVDCWEVPRAWDSQGIPEGWGTSSP
New discovery	EDDM13	19	56272835	56310148	1	609	1000	spliceform added	antisense lncRNA	ENSG00000267710	ENST00000637802	161	15	mammals	known coding gene ENSMUSG00000053367	/	CAGE supports epididymis expression; no HPA; Intropolis supports expression in early embryogenesis (e.g. SRR893051)	CAGE supports epididymis expression; no ENCODE RNAseq	XR_001754018.1 (LOC100506374); partial match				Uncharacterised protein. Eleven of the coding exons are micro-exons, i.e. under 30bp in size; PhyloCSF produced a signal across 4 of them. This transcript was included in GENCODEv27, mistakenly removed in v28 and reinstated in v29 with the new ID ENST00000649256. 	no	MHRSEPFLKMSLLILLFLGLAEACTPREVATKEKINLLKGIIGLMSRLSPDGLRHNITSLKMPPLVSPQDRTEEEIKKILGLLSLQVLHEETSGCKEEVKPFSGTTPSRKPLPKRKNTWNFLKCAYMVMTYLFVSYNKGDWCYCHYCNLELDIRDDPCCSF
New discovery	PMIS2	19	35586260	35587146	1	1763	unannotated	gene added	absent	ENSG00000283758	ENST00000646476	135	2	mammals	known coding gene ENSMUSG00000049761	/	all sources support testis expression	all sources support testis expression	absent				Already recognised as 'Pmis2, sperm specific protein' in mouse, although it could potentially be classed as a member of the CD255 protein superfamily due to the presence of an interferon-induced transmembrane protein domain.	no	MALKPPSATQPAPNAPATPDAPPTTGDPGASAAPGSPTTTGGPGAPAEVPQEPQEPTQTPEELAFYAPNYLCLTIFAILLFPPFGLAALYFSYETMKANQNSEWEEAYINSGRTGWFGAFVVMIGLGIIYGLVLY
New discovery	AC005551.1	19	3483403	3482804	-1	30	1000	gene added	absent	ENSG00000284638	ENST00000641816	149	2	avians; potential ortholog in vertebrates without synteny, e.g. zebrafish OTTDARG00000037948	previously undescribed coding gene ENSMUSG00000078440	/	CAGE supports retina expression; weak HPA; Intropolis also supports retina epxression (SRR548613), although the highest scores are in fetal intestine (SRR643742)	CAGE supports eyeball; while ENCODE RNAseq suggests general expression, this is likely confounded by readthrough transcription from Dohh found 5' adjacent as these read coverages highlight a splice donor site only utilised in the readthrough model	absent				Uncharacterised protein. While the CDS is incorporated into transcripts that are shared with Dohh in mouse, the novel CDS also has its own TSS. A series of mouse ESTs begin at this TSS, all of which are from eye experiments e.g. CK628151. 	no	MPGLAAEGEAEGWSPSPPLYEEYRPPPLDSIRLPRYVLYLLLAALVVVAVAYAIVGHLIKDLAHDLADWAFGPKPDQEAAPRELRPSLTGEDLEGLDLQLALAWQGEEDAGGGGEGAPSEPPPPPEPRRPSIAFKDPPSRSSFWKLMAT
New discovery	C20orf204	20	64036324	64038759	1	199	1000	spliceform added	lincRNA	ENSG00000196421	ENST00000636176	189	4	avians	previously undescribed coding gene ENSMUSG00000108976	chicken AUGUSTUS g5189.t1	CAGE supports cancer expression only; HPA supports colon expression; Intropolis is dominated by cancer expression and cell lines	no CAGE; weak general expression in ENCODE RNAseq	ncRNA NR_027686.1 (LINC00176)		neXtProt		Uncharacterised protein. The mouse gene was initially annotated based on EST DV645834 from oocyte.	no	MVPPKPALWALLLALLGTAPSRAYSPACSVPDVLRHYRAIIFEDLQAAVKWGGAGAEKTRPGSRHFHFIQKNLTRPGSSGRRGRPRASCGAQKEHSILLSISSLGRTLRGAVAGGRRGALERAAWTVAVRTEAVMRRHCRTLRQRSRRPKMRPARRRGGRRQLLLRALDAVATCWEKLFALRAPASRDS
New discovery	ETDC	X	135309480	135309659	1	no signal	paralog	gene added	absent	ENSG00000283644	ENST00000635820	59	1	potential primate-specific duplication	absent	/	no evidence for expression	/	absent			no	ETDA, ETDB and ETDC are a cluster of three 59aa single exon CDS on chrX listed here, 2 of which are identical. ENSG00000229015 is an additional  pseudogene, identified as part of this work based on regional analysis. The loci have clear homology to mouse Etd on mouse chrX, although gene synteny has been lost. The duplication events occurred in the primate lineage. In contrast to the other two, ETDC does not have transcriptional support at the present time and on that basis is potentially pseudogenic.	yes, potential human pseudogene	MDKELPKASPSEPALNIKKSGKSFKCKKPTKNVQVFLINRQLGRNRSDTDLSKWLWMLP
XP/XM match	CSNKA2IP	3	88465358	88467562	1	585	1000	gene added	absent	ENSG00000283434	ENST00000637986	734	1	mammals	known coding gene ENSMUSG00000068167, previously incomplete CDS	/	all sources support testis expression	all sources support testis expression	coding XP_011532645		neXtProt		Ortholog of mouse casein kinase 2, alpha prime interacting protein (Csnka2ip), which has itself now been extended from 276 to 720aa by a 5' extension based on comparative annotation.	no	MVPLAYYGQHFVPLDYFYQLSSANTLTHQHTGEKLNQFNNQPMAKVQSHSNHFAVPPLGSNKKVQRCSVLPSPKSQDKISQSFCDRFLNSPLFHAKHQNTPSIGLHWRSSLWPAQRALNSHLLHSKAQTTSSSDLNMTSSLELNQAALSLQLPFCKPQTTSSSLDVCWRSLSLKSHQRVSSSSLFRLQNQEIPSINIIWTSSSLGPKRKALSSTLLQSKPQKTSSLDYLWTSSLQRNQRSLSSPSLNTKLQTSDLFWTSPSFKPNQIALTSPLLDSRLQKTPILNSNPTIGGLPVSHSKARQSASSYFVHPSENLPLFQLNSQSMFMLDCNFQTTNSPVCHSKFQNTTSPNGKHRVTHLPSPHPKTNISGQLLSSSKHCTRNTAASTLGFRLQSKSSFQFSPKTESNKEIPWTLKYSQPCIVKGGTVPDDVVNKIVNSISNTRIQRDLCRQILFRRMRGRPNPHPGPRLSSNYVVCLACASCLKSPCNHLRGKKNPHCATLSVIPTPEANSEGKIEVKLVLILSLPETFSSCLPFPMKENQPNEVPEDNLEGVEKIQQFFPTSERDIQGLNMKQIWWAVAPENKVIGQQPQAIDWLFYVKKNNSQPQSLLPSTSSSTSSSSTTSSSSSVASASSDSSSSSSSSSSFSISSSSSPSKEFMTLTLSRPVFRKVLSYHRLPAGVSWLEFIYSKDYQLHPRKPNRSQSSSLKTKPVRNNNTVKWRKGANTLFKFFRTK
XP/XM match	MARCOL	5	148238598	148243254	1	1343	unannotated	transcript extended	lincRNA	ENSG00000248109	ENST00000638089	285	2	mammals	previously undescribed coding gene ENSMUSG00000110628	/	CAGE supports fingernail expression alongside cancer cells and cell lines; no HPA; Intropolis is dominated by cell line and cancer experiments	CAGE supports forelimb embryo expression; no ENCODE RNAseq	coding XP_011536019.1		neXtProt		A paralog of macrophage receptor with collagenous structure (MARCO). 	no	MRAFIFFLFMLLAMFSASSTQISNTSVFKLEENPKPALILEEKNEANHLGGQRDSNKQGGSYTQGNPGTFRLQGQPGYFNKLEKPRHFKQGRAGVLNQPGILKNSGKSNQKGNPESSNKQENSGSSSQLGRPGISTQQGNPGSSDQQEKPGSFSQKVMVGSSSQQGKPGSSSQHGNLGSSTQKGNLGSSSLQGHLGLSSHQGKPESSGQQGKPGSSSQQGNLGTSGQQEKPGSSSQQGKPGLSSHQGKPGSSSQQGNLHLSSQQGNQGPSSKQRKPGSSSRQGNL
XP/XM match	AL354761.1	9	135614240	135618952	1	1311	lincRNA	transcript extended	antisense lncRNA	ENSG00000236543	ENST00000430816	181	6	mammals	known coding gene ENSMUSG00000085484	/	no CAGE support; HPA supports skin expression; Intropolis supports skin expression (e.g. SRR836000)	No CAGE; no ENCODE RNAseq	coding XP_011517581.1 (LOC102723971)				Lipocalin family member, found within a cluster of these loci.	no	MALEKGPLLLLALGLGLAGAQKALEEVPVQPGFNAQKVEGRWLTLQLAANHADLVSPADPLRLALHSIRTRDGGDVDFVLFWKGEGVCKETNITVHPTQLQGQYQGSFEGGSMHVCFVSTDYSNLILYVRFEDDEITNLWVLLARRMLEDPKWLGRYLEYVEKFHLQKAPVFNIDGPCPPP
XP/XM match	C13orf46	13	113973997	113956773	-1	257	1000	gene added	absent	ENSG00000283199	ENST00000636427	212	7	mammals	known coding gene ENSMUSG00000031452	/	all sources support testis expression	all sources support testis expression	coding XP_011533161 (LOC100507747)		neXtProt		Uncharacterised protein. Rodent genes splice out before the STOP conserved in other mammals, adding another 2 putative coding exons.  All but one exon was missing in a sequence gap in GRC37.	no	MEKDTGTTHRRHRPGLRALPSGVALGHLKAASEASELQRSRSLGGLQPEGDPPSRPRKPHKELESEDQGKDPSSNAEDASCQKNLAQDKKESFSTLGKLGHESGKQDPEREKSDLEASMQEVQEGEHADGGLQEAKEQEAESIKLNDLQEEEKASVFVEIDLGDHAEEVVTDAKKEEKPSQMDVEDLSEDEMQTSWVCCIPYSTRKRAKEST
XP/XM match	CFAP97D2	13	114179331	114222507	1	673	1000	gene added	absent	ENSG00000283361	ENST00000635901	99	4	xenopus	known coding gene ENSMUSG00000090336	xenopus AUGUSTUS g3716.t1	CAGE supports brain expression; HPA supports lung and brain expression; Intropolis finds cancer expression with lung as the top scoring normal tissue (ERR030879)	CAGE supports tracheal epithelial cells, microlia and lung expression; ENCODE RNAseq finds lung and brain expression	coding XP_006720062.1 (C17orf105-like)			no	KIAA1430-domain containing CDS, which is a domain of unknown function. The avian and amphibian loci have a 5 exon CDS structure in common, although this final exon has apparently been lost in mammals. Furthermore, exon 4 has a frameshift in all primates, which could suggest pseudogenisation. However, there is substantial transcriptional support for the skipping of this exon, potentially making a CDS with a different C-terminus as listed here.	yes, potential human pseudogene	MHGAPRLTFPCASEYLWHAREKAYQDHRRKVQSAQPLVDTRAPLTFRHLHLKLKRLKLEEERLSVIERDNRLLLEKVASVMRTRGQTDSKNNSKHRSRK
XP/XM match	PERCC1	16	1432594	1433397	1	320	1000	gene added	absent	ENSG00000284395	ENST00000640283	267	1	coelacanth; potential ortholog in fish without synteny, e.g. zebrafish OTTDARG00000044228	previously undescribed coding gene ENSMUSG00000114245	coelancanth ENSLACT00000014522 (3' truncated)	weak CAGE support for cancer expression; HPA supports stomach, small intestine and prostate expression; Intropolis supports cancer expression	CAGE supports weak tracheal epithelial cell  expression; ENCODE RNAseq supports weak lung and stomach expression	coding XP_011521082 (LOC105371045)				Recently experimentally characterised as a protein-coding gene critical for intestinal function in mice (PMID:31217582).	no	MAAGVIRPLCDFQLPLLRHHPFLPSDPEPPETSEEEEEEEEEEEEEEGEGEGLGGCGRILPSSGRAEATEEAAPEGPGSPETPLQLLRFSELISDDIRRYFGRKDKGQDPDACDVYADSRPPRSTARELYYADLVRLARGGSLEDEDTPEPRVPQGQVCRPGLSGDRAQPLGPLAELFDYGLQQYWGSRAAAGWSLTLERKYGHITPMAQRKLPPSFWKEPTPSPLGLLHPGTPDFSDLLASWSTEACPELPGRGTPALEGARPAEA
XP/XM match	C17orf113	17	42043376	42039705	-1	246	1000	existing transcript	sense intronic lncRNA	ENSG00000267221	ENST00000587304	675	2	coelacanth	novel unitary pseudogene ENSMUSG00000109112	coelacanth XP_006006434.1	CAGE supports weak expression, especially in brain, cancer cells and cell lines; HPA supports weak general expression; Intropolis top scoring experiments are leukaemia (SRR948491) and CD34+ cells (SRR534325), and an examination of BluePrint RNAseq read coverage indicates general expression in blood cells	no evidence for expression	coding XP_011522778.1				Uncharacterised protein. Found within an intron of a ZNF gene, although no evidence that the two loci are contranscribed.	no	MVPPGKKPAGEASNSNKKCKRYFNEHWKEEFTWLDFDYERKLMFCLECRQALVRNKHGKAENAFTVGTDNFQRHALLRHVTSGAHRQALAVNQGQPPFEGQAEGGGACPGLATTPASRGVKVELDPAKVAVLTTVYCMAKEDVPNDRCSALLELQRFNLCQALLGTEHGDYYSPRRVRDMQVAIASVLHTEACQRLKASPYVGLVLDETRDWPESHSLALFATSVSPCDGQPATTFLGSVELQEGEATAGQLLDILQAFGVSAPKLAWLSSSLPSERLGSVGPQLRATCPLLAELHCLPGRTDPEPPAYLGQYESILDALFRLHGGPSSHLVPELRAALDLAAIDLAGPRPVPWASLLPVVEAVAEAWPGLVPTLEAAALASPVAGSLALALRQFTFVAFTHLLLDALPSVQKLSLVLQAEEPDLALLQPLVMAAAASLQAQRGSGGARLQGFLQELASMDPDASSGRCTYRGVELLGYSEAAVRGLEWLRGSFLDSMRKGLQDSYPGPSLDAVAAFAAIFDPRRYPQAPEELGTHGEGALRVLLRGFAPAVVRQRALGDFALFKRVVFGLGRLGPRALCTQLACAHSELHELFPDFAALAALALALPAGAGLLDKVGRSRELRWWGQSGAGEGRGGHMVKIAVDGPPLHEFDFGLAVEFLESGWGEGFLGSQLT
XP/XM match	HSFX4	X	149929645	149931105	1	1263	lincRNA	transcript extended	antisense lncRNA	ENSG00000283463	ENST00000457775	333	2	Mammals have a single copy of this gene pair	novel pseudogene ENSMUSG00000114356 is a presumptive ortholog to either ENSG00000283463 or ENSG00000283697	Rat XP_017443635.1 is a presumptive ortholog to one duplicant, based on sequence homology as opposed to synteny	all sources support testis expression	no evidence for expression	coding XP_005274830.1 (LOC101927685)		neXtProt		Heat-shock factor family member. A duplicant of ENSG00000283697 elsewhere on this spreadsheet, ~380kb distant. The translations differ in a single amino acid, and both have PhyloCSF signals despite the fact that the duplication apparently occurred in the human lineage.	no	MASQNTEQEYEAKLAPSVGGEPTSGGPSGSSPDPNPDSSEVLDRHEDQAMSQDPGSQDNSPPEDRNQRVVNVEDNHNLFRLSFPRKLWTIVEEDTFKSVSWNDDGDAVIIDKDLFQREVLQRKGAERIFKTDNLTSFIRQLNLYGFCKTRPSNSPGNKKMMIYCNSNFQRDKPRLLENIQRKDALRNTAQQATRVPTPKRKNLVATRRSLRIYHINARKEAIKMCQQGAPSVQGPSGTQSFRRSGMWSKKSATRHPLGNGPPQEPNGPSWEGTSGNVTFTSSATTWMEGTGILSSLVYSDNGSVMSLYNICYYALLASLSVMSPNEPSDDEEE
XP/XM match	HSFX3	X	149549852	149548392	-1	44	1000	existing transcript	antisense lncRNA	ENSG00000283697	ENST00000431993	333	2	Mammals have a single copy of this gene pair	novel pseudogene ENSMUSG00000114356 is a presumptive ortholog to either ENSG00000283463 or ENSG00000283698	Rat XP_017443635.1 is a presumptive ortholog to one duplicant, based on sequence homology as opposed to synteny	all sources support testis expression	no evidence for expression	coding XP_005262408.1		neXtProt		Heat-shock factor family member. A recent duplicant of ENSG00000283463 elsewhere on this spreadsheet.	no	MASQNTEQEYEAKLAPSVGGEPTSGGPSGSSPDPNPDSSEVLDRHEDQAMSQDPGSQDNSPPEDRNQRVVNVEDNHNLFRLSFPRKLWTIVEEDTFKSVSWNDDGDAVIIDKDLFQREVLQRKGAERIFKTDSLTSFIRQLNLYGFCKTRPSNSPGNKKMMIYCNSNFQRDKPRLLENIQRKDALRNTAQQATRVPTPKRKNLVATRRSLRIYHINARKEAIKMCQQGAPSVQGPSGTQSFRRSGMWSKKSATRHPLGNGPPQEPNGPSWEGTSGNVTFTSSATTWMEGTGILSSLVYSDNGSVMSLYNICYYALLASLSVMSPNEPSDDEEE
XP/XM match	UPK3BL2	7	102543636	102538417	-1	no signal	re-ranking	existing transcript	3' UTR of POLR2J3	ENSG00000284981	ENST00000644544	263	6	potential human-specific duplication	absent	/	all sources support general expression, although perhaps confounded by paralogy issues	/	coding XP_016868385.1				Uncharacterised protein. Identified within the 3' end of POLR2J3 after additional coding exons were found by PhyloCSF. It can now be seem that these are separate loci, previously merged into one due to the misinterpretation of readthrough cDNA evidence. This is a tandem duplicant of the adjacent POLR2J2 / UPK3BL locus, i.e. the novel CDS is a paralog of UPK3BL which is itself a paralog of UPK3B elsewhere on chromosome 7. In non-primate mammals, UPK3B and UPK3BL are adjacent to one another. This rearrangement thus seems to have occurred in the primate lineage, towards the base of the gibbon / ape clade. However, the local duplication between this novel CDS and UPK3BL is human-specific, and the PhyloCSF signal is likely based on genomic misalignments. 	no	MDNSWRLGPAIGLSAGQSQLLVSLLLLLTRVQPGTDVAAPEHISYVPQLSNDTLAGRLTLSTFTLEQPLGQFSSHNISDLDTIWLVVALSNATQSFTAPRTNQDIPAPANFSQRGYYLTLRANRVLYQTRGQLHVLRVGNDTHCQPTKIGCNHPLPGPGPYRVKFLVMNDEGPVAETKWSSDTRLQQAQALRAVPGPQSPGTVVIIAILSILLAVLLTVLLAVLIYTCFNSCRSTSLSGPEEAGSVRRYTTHLAFSTPAEGAS
NP/NM match	TEX50	1	173635522	173637036	1	1550	lincRNA	transcript extended	antisense lncRNA	ENSG00000232113	ENST00000417563	177	2	mammals	previously undescribed coding gene ENSMUSG00000049160	/	all sources support testis expression	all sources support testis expression	coding NM_001195190.1		Kim et al; neXtProt		Uncharacterised protein.	no	MSNQRLPLIFSLLFICFFGESFCICDGTVWTKVGWEILPEEVHYWKVKGSPSHCLPYLLDKLCCDFANMDIFQGCLYLIYNLLQAVFFVLFVLSVHYLWKKWKKHQKKLKKQASLEKPGNDLESPLINNIDQTLHRVATTASVIYKIWEHRSHHPSSKKIKHCKLKKKSKEEGARRY
NP/NM match	FAM237A	2	206644237	206648794	1	527	1000	existing transcript	lincRNA	ENSG00000235118	ENST00000441223	181	2	avians	previously undescribed coding gene ENSMUSG00000115378	chicken ENSGALT00000033404	CAGE supports weak brain expression; HPA supports weak brain and heart expression; Intropolis supports weak cancer expression	no CAGE; ENCODE RNAseq supports weak brain expression	coding NM_001102659.1 (LOC200726)				Uncharacterised protein. It has clear homology to FAM237B, also on this list. The chicken ortholog was recently found to encode 'a novel small secretory protein, neurosecretory protein GL, in the chicken hypothalamic infundibulum' [PMID:24582750]).	no	MADPGNRGGIHRPLSFTCSLLIVGMCCVSPFFCHSQTDLLALSQADPQCWESSSVLLLEMWKPRVSNTVSGFWDFMIYLKSSENLKHGALFWDLAQLFWDIYVDCVLSRNHGLGRRQLVGEEEKISAAQPQHTRSKQGTYSQLLRTSFLKKKELIEDLISMHVRRSGSSVIGKVNLEIKRK
NP/NM match	GIMD1	4	106367435	106358183	-1	338	1000	transcript extended	lincRNA	ENSG00000250298	ENST00000507153	217	2	coelacanth	known coding gene ENSMUSG00000091721	coelacanth ENSLACT00000012949	all sources support gastrointestinal expression, including gall bladder	all sources support gastrointestinal expression, with ENCODE RNAseq also supporting lung and liver expression	coding NM_001195138.1		neXtProt		Already known as GIMAP family P-loop NTPase domain containing 1 (GIMD1)	no	MTDPNKMIINLALFGMTQSGKSSAGNILLGSTDFHSSFAPCSVTTCCSLGRSCHLHSFMRRGGLEVALQVQVLDTPGYPHSRLSKKYVKQEVKEALAHHFGQGGLHLALLVQRADVPFCGQEVTDPVQMIQELLGHAWMNYTAILFTHAEKIEEAGLTEDKYLHEASDTLKTLLNSIQHKYVFQYKKGKSLNEQRMKILERIMEFIKENCYQVLTFK
NP/NM match	UMAD1	7	7673372	7877538	1	1087	lincRNA	existing transcript	antisense lncRNA	ENSG00000219545	ENST00000636849	137	3	mammals	known coding gene ENSMUSG00000089862	/	all sources support general expression	all sources support general expression	coding NM_001302350.1		neXtProt		Already known as UBAP1-MVB12-associated (UMA) domain containing 1 (UMAD1)	no	MFHFFRKPPESKKPSVPETEADGFVLLGDTTDEQRMTARGKTSDIEANQPLETNKENSSSVTVSDPEMENKAGQTLENSSLMAELLSDVPFTLAPHVLAVQGTITDLPDHLLSYDGSENLSRFWYDFTLENSVLCDS
NP/NM match	AC025594.2	7	128866410	128868775	1	206	1000	transcript extended	lincRNA	ENSG00000272899	ENST00000609480	176	2	coelacanth	known coding gene ENSMUSG00000090685	coelacanth ENSLACT00000003968	all sources support testis expression	all sources support testis expression	coding NM_001195150.1		neXtProt		Uncharacterised protein	no	MSRQLNIDALRQNFWKEEYLREKMLRCEWYRKYGSMVKAKQKAKAAARLPLKLPTLHPKAPLSPPPAPKSAPSKVPSPVPEAPFQSEMYPVPPITRALLYEGISHDFQGRYRYLNTRKLDMPETRYLFPITTSFTYGWQLGPPVKQELVSCKMCRIESFFRKNGAFALLDPRDLAL
NP/NM match	NPY4R2	10	47921988	47923115	1	121	1000	existing transcript	lincRNA	ENSG00000264717	ENST00000576178	375	1	potential ape-specific duplication	absent	/	weak CAGE; HPA supports gastrointestinal expression, as well as lung, skin, salivary gland; Intropolis provides no support	/	coding NM_001278795.1				An identical duplicant of NPY4R, found several Mb downstream. The duplication is ape-specific, so the PhyloCSF signal may be based on incorrect genome alignments. 	no	MNTSHLLALLLPKSPQGENRSKPLGTPYNFSEHCQDSVDVMVFIVTSYSIETVVGVLGNLCLMCVTVRQKEKANVTNLLIANLAFSDFLMCLLCQPLTAVYTIMDYWIFGETLCKMSAFIQCMSVTVSILSLVLVALERHQLIINPTGWKPSISQAYLGIVLIWVIACVLSLPFLANSILENVFHKNHSKALEFLADKVVCTESWPLAHHRTIYTTFLLLFQYCLPLGFILVCYARIYRRLQRQGRVFHKGTYSLRAGHMKQVNVVLVVMVVAFAVLWLPLHVFNSLEDWHHEAIPICHGNLIFLVCHLLAMASTCVNPFIYGFLNTNFKKEIKALVLTCQQSAPLEESEHLPLSTVHTEVSKGSLRLSGRSNPI
NP/NM match	C11orf97	11	94512529	94531900	1	158	1000	existing transcript	lincRNA	ENSG00000257057	ENST00000542198	126	4	mammals	known coding gene ENSMUSG00000031927	/	CAGE finds lung, trachea, testis and brain tissues; HPA finds testis, kidney and endometrium; Intropolis finds lung as top non-cancer experiment (e.g. SRR192333)	CAGE supports testis expression; ENCODE RNAseq supports testis expression alongside weaker general expression	coding NM_001190462.1		neXtProt		Already known as chromosome 11 open reading frame 97 (C11orf97). This CDS had been previously been removed from GENCODE. 	no	MTGEEAVVVTAVVAPKAGREEEQPPPPAGLGCGARGEPGRGPLEHGQQWKKFLYCEPHKRIKEVLEEERHIKRDECHIKNPAAVALEGIWSIKRNLPVGGLKPGLPSRNSLLPQAKYYSRHGGLRR
NP/NM match	ZNF888	19	52917873	52906165	-1	12307	lincRNA	spliceform added	lincRNA	ENSG00000213793	ENST00000638862	718	3	potential ape-specific duplication	absent	/	all sources support general expression	/	coding NM_001310127.1		neXtProt		Already known as zinc finger protein 888 (ZNF888). 	no	MALPQGLLTFRDVAIEFSQEEWKCLDPAQRTLYRDVMLENYRNLVSLDISSKCMMEFSSIGKGNTEVIHTGTLQRLASHHIGECCFQEIEKDIHDFVFQWQEDETNGHEAPMTEIKELTGSTDQYDQRHAGNKPIKYQLGSSFHSHLPELHIFQPEGKIGNQLEKSINNASSVSTSQRISCRPKTHISNNYGNNFFHSSLLTQKQDVHRKEKSFQFNESGKSFNCSSLFKKHQIIHLGEKQYKCDVCGKDFNQKRYLAHHRRCHTGEKPYMCNKCGKVFNKKAYLARHYRRHTGEKPYKCNECGKTFSDKSALLVHKTIHTGEKPYKCNECGKVFNQQSNLARHHRVHTGEKPYQCKECDKVFSRKSYLERHRRIHTGEKPYKCKVCDKAFRHDSHLAQHIVIHTREKPYKCNECGKTFGENSALLVHKTIHTGEKPYKCNECGKVFNQQSNLARHHRLHTGEKPYKCKECDKVFSRKSHLERHRRIHTGEKPYKCKVCDKAFRRDSHLAQHTVIHTGEKPYKCNECGKTFVQNSSLVMHKVIHTGEKRYKCNECGKSFNHKSSLAYHHRLHTGEKPYKCNECGKVFRTQSQLACHHRLHTGEKPYKCEECDKVFNIKSHLEIHRRVHTGEKPYKCRVCDKAFGRDSYLAQHQRVHTGEKPYKCKVCDKAFKCYSHLAQHTRIHTGEKPFKCSECGKAFRAQSTLIHHQAIHGVGKLD
NP/NM match	TMEM191C	22	21467319	21469651	1	1328	lincRNA	existing transcript	lincRNA	ENSG00000206140	ENST00000432134	284	10	mammals	known coding gene ENSMUSG00000055692	/	no CAGE; HPA supports testis expression alongside weaker general expression; Intropolis finds weak expression; BluePrint and CAGE suggest a 5' truncated model is transcribed in blood cells generally	all sources support testis expression; ENCODE RNAseq also finds weaker general expression	coding NM_001207052.1 (TMEM191C)		neXtProt		Already known as ransmembrane protein 191C (TMEM191C)	no	MCRATLGLPLPPIVIQPARRSLPPIVTPASRRLGPRGGRHLGSVSTAMAATQELLLQLQKDNRDGRQRKQELEKLMRGLEAESESLNQRLQDLSERERSLLRRRSQAAQPLQGEAREAARERAERVRRRLEEAERHKEYLEQHSRQLQEQWEELSSQLFYYGGELQSQKSTEQQLAAQLVTLQNELELAETKCALQEEKLQQDALQTAEAWAIFQEQTVVLQEVQVKVMEAAEELDAWQSGRELCDGQLRGVQYSTESLMEEMARADRETRLFGGPRALAIRCC
NP/NM match	DPEP2NB	16	68015770	68014108	-1	1080	lincRNA	existing transcript	antisense lncRNA	ENSG00000263201	ENST00000574912	123	2	mammals	previously undescribed coding gene ENSMUSG00000084782	/	weak CAGE supports testis and placenta expression; HPA supports testis and placenta expression, with weaker expression in bone marrow; Intropolis finds additional placetal experiments (e.g. SRR638937)	all sources support testis expression	coding NM_001282442.1 (LOC100131303)		neXtProt		Uncharacterised protein.	no	MTDRILYIVSNMSSVPWEGSAAAAVPATSPPTPGHYHVLYRGCGETQVGWHGETYCLVGGYRVHGDAPLATPTKAEAEKPAPRRAPKRRQATIESDKDLGCSSPKIRRLEHRGRRLTPQKLAG
NP/NM match	SPACA6	19	51693527	51705123	1	36	1000	existing transcript	lincRNA	ENSG00000182310	ENST00000637797	324	9	mammals	known coding gene ENSMUSG00000080316	/	all sources support general expression	all sources support general expression	coding NM_001316972.1		neXtProt		Already known as sperm acrosome associated 6 (SPACA6)	no	MALLALASAVPSALLALAVFRVPAWACLLCFTTYSERLRICQMFVGMRSPKLEECEEAFTAAFQGLSDTEINYDERSHLHDTFTQMTHALQELAAAQGSFEVAFPDAAEKMKKVITQLKEAQACIPPCGLQEFARRFLCSGCYSRVCDLPLDCPVQDVTVTRGDQAMFSCIVNFQLPKEEITYSWKFAGGGLRTQDLSYFRDMPRAEGYLARIRPAQLTHRGTFSCVIKQDQRPLARLYFFLNVTGPPPRAETELQASFREVLRWAPRDAELIEPWRPSLGELLARPEALTPSNLFLLAVLGALASASATVLAWMFFRWYCSGN
NP/NM match	C14orf132	14	96039501	96086735	1	787	1000	existing transcript	lincRNA	ENSG00000227051	ENST00000555004	83	2	vertebrates	known coding gene ENSMUSG00000094910	zebrafish OTTDARG00000044232	all sources support general expression	CAGE is dominated by brain experiments though also supports weak general expression; ENCODE RNAseq supports general expression, highest in brain / CNS	coding NM_001252507.2			no	Already known as chromosome 14 open reading frame 132 (C14orf132). The locus was previously annotated as protein-coding in GENCODEv19 with a spurious CDS. 	no	MDLSFMAAQLPMMGGAFMDSPNEDFSTEYSLFNSSANVHAAANGQGQPEDPPRSSNDAVLLWIAIIATLGNIVVVGVVYAFTF
NP/NM match	RAB34	17	28717708	28716053	-1	248	1000	existing transcript	5' UTR of RAB34	ENSG00000109113	ENST00000636154	198	3	mammals	known coding gene ENSMUSG00000002059	/	all sources support general expression	all sources support general expression	coding NM_001256281	contranscribed with RAB34	neXtProt		Transcribed from an alternative TSS within the RAB34 locus, having a substantial overlap with the RAB34 CDS though in an alternative frame. Identified and confirmed as functionally distinct in 2011, where the protein was unofficially named NARR (PMID:21586586). 	no	MVGQPQPRDDVGSPRPRVIVGTIRPRVIVGTIRPRVIVGSARARPPPDGTPRPQLAAEESPRPRVIFGTPRARVILGSPRPRVIVSSPWPAVVVASPRPRTPVGSPWPRVVVGTPRPRVIVGSPRARVADADPASAPSQGALQGRRQDEHSGTRAEGSRPGGAAPVPEEGGRFARAQRLPPPRHLRLPGAPDRHRGQI
NP/NM match	TMEM225B	7	99604389	99610565	1	1102	lincRNA	existing transcript	readthrough transcript from GS1-259H13.1 with NMD annotated in alternative reading frame	ENSG00000244219	ENST00000431679	221	4	mammals	absent	dog ENSCAFT00000050123.2	all sources support testis expression	/	coding NM_001195541		neXtProt		Already known as transmembrane protein 225B (TMEM225B).	no	MLTLEDKDMKGFSWAIVPALTSLGYLIILVVSIFPFWVRLTNEESHEVFFSGLFENCFNAKCWKPRPLSIYIILGRVFLLSAVFLAFVTTFIMMPFASEFFPRTWKQNFVLACISFFTGACAFLALVLHALEIKALRMKLGPLQFSVLWPYYVLGFGIFLFIVAGTICLIQEMVCPCWHLLSTSQSMEEDHGSLYLDNLESLGGEPSSVQKETQVTAETVI
UniProt match	SMIM30	7	113117578	113117399	-1	726	1000	existing transcript	lincRNA	ENSG00000214194	ENST00000397764	59	1	xenopus	known coding gene ENSMUSG00000052419	xenopus OCT87389	all sources support general expression	all sources support general expression	ncRNA NR_024412.1 (LINC00998)			no	Putative transmembrane protein according to UniProt. The CDS was present in GENCODEv19 although subsequently removed. There are at least 8 duplications of this sequence in human; each of the others are likely pseudogenes.	no	MTSVSTQLSLVLMSLLLVLPVVEAVEAGDAIALLLGVVLSITGICACLGVYARKRNGQM
UniProt match	TEX52	12	2857026	2849231	-1	6	1000	gene added	absent; protein-coding in v19	ENSG00000283297	ENST00000637658	305	3	mammals	known coding gene ENSMUSG00000079304	/	all sources support testis expression	all sources support testis expression	coding XP_005253874.2				Uncharacterised protein. Had been made coding in v19 but subsequently removed.	no	MASNRQRSLRGPSHPSHMEEPFLQMVQASESLPPSQTWAQREFFLPSESWEFPGFTRQAYHQLALKLPPCTDMKSKVRQRLIHPWKGGAQHTWGFHTWLDVCRLPATFPTQPDRPYDSNVWRWLTDSNAHRCPPTEHPIPPPSWMGQNSFLTFIHCYPTFVDMKRKKQVIFRTVKELKEVEKLKLRSEARAPPLDAQGNIQPPASFKKYRHISAGGRFEPQGLQLMPNPFPNNFARSWPCPNPLPHYQEKVLKLALLPSAPLSQDLIRDFQTLIKDRTALPLHHLSKAQASKSPARKRKRRPGHF
UniProt match	SMIM34B	21	7793827	7789206	-1	526	1000	existing transcript	lincRNA	ENSG00000278961	ENST00000624951	139	2	potential human specific duplication	absent	/	no expression data; locus was absent on GRC37	/	absent				Uncharacterised protein. It is a non-local duplicant of SMIM34A on chr21, within the large duplication on the p-arm of the chromosome. The duplication event is human specific, so the PhyloCSF signal is presumably based on paralogous alignments. SMIM34A has highly specific kidney expression. 	no	MEWAKWTPHEASNQTQASTLLGLLLGDHTEGRNDTNSTRALKVPDGTSAAWYILTIIGIYAVIFVFRLASNILRKNDKSLEDVYYSNLTSELKMTGLQGKVAKCSTLSISNRAVLQPCQAHLGAKGGSSGPQTATPETP
UniProt match	ETDA	X	135253277	135253456	1	41242	lincRNA	existing transcript	lincRNA	ENSG00000238210	ENST00000427686	59	1	potential primate-specific duplication	absent	/	all sources support testis expression	/	ncRNA XR_938601.1 (LOC101928677)			no	ETDA, ETDB and ETDC are a cluster of three 59aa single exon CDS on chrX listed here, 2 of which are identical. ENSG00000229015 is an additional pseudogene, identified as part of this work based on regional analysis. The loci have clear homology to mouse Etd on mouse chrX, although gene synteny has been lost. The duplication events occurred in the primate lineage. 	no	MDKEVPKGSPREPALNIKKSDKSFKRKKPTENVLIFLINRQLGRHRSDIDLSRWVWMLS
UniProt match	ETDB	X	135119261	135119082	-1	27432	lincRNA	existing transcript	lincRNA	ENSG00000224107	ENST00000423661	59	1	potential primate-specific duplication	absent	/	all sources support testis expression	/	ncRNA NR_033941.1 (LINC00633)			no	ETDA, ETDB and ETDC are a cluster of three 59aa single exon CDS on chrX listed here, 2 of which are identical. ENSG00000229015 is an additional pseudogene, identified as part of this work based on regional analysis. The loci have clear homology to mouse Etd on mouse chrX, although gene synteny has been lost. The duplication events occurred in the primate lineage. 	no	MDKEVPKGSPREPALNIKKSDKSFKRKKPTENVLIFLINRQLGRHRSDIDLSRWVWMLS
Mackowiak match	CTXND1	15	80201949	80201770	-1	617	1000	existing transcript	lincRNA	ENSG00000259417	ENST00000560778	59	1	vertebrates	previously undescribed coding gene ENSMUSG00000097789	zebrafish OTTDARG00000044230	CAGE is dominated by brain experiments; HPA supports expression in liver, kidney, brain, spleen heart; Intropolis shows no obvious expression pattern, with the highest top ranking normal experiment from fetal intestine (SRR643742)	CAGE is dominated by various developmental cells, especially mesenchymal; ENCODE RNAseq supports general expression, highest in adrenal gland	ncRNA NR_120317.1 (LINC01314)			no	Homology to cortexin family members.	no	MEEPTPEPVYVDVDKGLTLACFVFLCLFLVVMIIRCAKVIMDPYSAIPTSTWEEQHLDD
Mackowiak match	BRD3OS	9	134026748	134027002	1	592	1000	existing transcript	antisense lncRNA	ENSG00000235106	ENST00000603928	84	1	vertebrates	previously undescribed coding gene ENSMUSG00000109946	zebrafish OTTDARG00000043595	all sources support general expression	all sources support general expression	ncRNA NR_015427.2 (LINC00094)		neXtProt	no	Uncharacterised protein. Previously reported as an ultraconserved lncRNA by Ulitsky et al [PMID:22196729], identified in human, mouse and zebrafish.	no	MSGRVPLAEKALSEGYARLRYRDTSLLIWQQQQQKLESVPPGTYLSRSRSMWYSQYGNEAILVRDKNKLEVSRDTGQSKFCTIM
Mackowiak match	TUNAR	14	95922820	95922966	1	392	1000	existing transcript	lincRNA	ENSG00000250366	ENST00000503525	48	2	vertebrates	previously undescribed coding gene ENSMUSG00000097929	zebrafish OTTDARG00000044226	all sources support brain expression	all sources support brain expression	ncRNA NR_038861.1 (TUNAR)			no	This gene had previously been published as functional lncRNA Tunar in mouse, and it may play a role in maintaining pluripotency and the neural differentiation of embryonic stem cells [PMID:24530304]. The human ortholog was since named TUNAR. It was originally reported as a conserved lncRNA by the Ulitsky group in zebrafish, mouse and human [PMID:22196729]. In fact, the experimental work of the Ulitsky group focused a paralogous locus OTTDARG00000038681 (Megamind), which is also conserved in human (BIRC6-AS2; within the intron of BIRC6), though apparently lost in rodents / lagomorphs. This locus lacks PhyloCSF support and so was not found in the present analysis. Ulitsky noted the presence of a plausible CDS in Megamind - which we can see is highly similar to that now annotated in zebrafish Tunar - although insertional mutagenesis led them to rule out its functionality. Furthermore, the putative Megamind CDS is disrupted in human, being ~50% truncated at the 5' end compared to TUNAR. Given these observations, we believe the most likely scenario is that Megamind / BIRC6-AS2 is an ancient duplication of TUNAR, and that it evolved from an earlier pseudogenic state into a potentially functional lncRNA in zebrafish. In human, given the absence of functional support for the transcript and the severe CDS truncation, BIRC6-AS2 has been converted into a pseudogene of TUNAR in GENCODE (ENSG00000279897). Nonetheless, the human locus is transcribed, and could thus also turn out to be a functional lncRNA. 	no	MVITSENDEDRGGQEKESKEESVLAMLGIIGTILNLIVIIFVYIYTTL
Mackowiak match	TMEM238L	17	10803963	10803724	-1	593	1000	existing transcript	lincRNA	ENSG00000263429	ENST00000581851	79	1	mammals; potential ortholog in fish without synteny, e.g. zebrafish AUGUSTUS g16563.t1	previously undescribed coding gene ENSMUSG00000085683	/	CAGE supports gastrointestinal expression; HPA supports gastrointestinal expression alongside weaker expression in certain other organs; the highest scoring Intropolis study is on skin (SRR835999), although gastrointestinal expression is also supported (e.g. SRR364829)	CAGE supports gastrointestinal expression; ENCODE RNAseq supports gastrointestinal expression alonside weaker expression in other organs	ncRNA NR_036581.1 (LINC00675)			no	Putative transmembrane protein. The transcript has a second non-coding exon that may suggest it is a nonsense mediated decay target, although this transcriptional scenario is apparently conserved at least across to chicken	no	MLLGSLWGRCHPGRCALFLILALLLDAVGLVLLLLGILAPLSSWDFFIYTGALILALSLLLWIIWYSLNIEVSPEKLDL
Mackowiak match	TINCR	19	5567924	5562208	-1	2076	lincRNA	existing transcript	lincRNA	ENSG00000223573	ENST00000448587	87	2	avians	previously undescribed coding gene ENSMUSG00000110218	alligator KYO42567.1	CAGE supports expression in placenta and amniotic membrane, with lower scores for esophagus, tongue, skin; Intropolis has a top rank in skin (SRR836000), although there is appreciable data from numerous other tissues	CAGE supports expression in skin, tongue, tracheal epithelial cells, vagina, eye; ENCODE RNAseq supports general expression, highest in bladder	ncRNA NR_027064.2 (TINCR)			no	This gene had previously been functionally characterised as lncRNA TINCR in human, having an apparent role in the control of epidermal differentiation [PMID:23201690]. There are other transcripts in the locus without an obvious CDS, and it could theoretically be a dual function protein-coding gene / lncRNA. 	no	MEGLRRGLSRWKRYHIKVHLADEALLLPLTVRPRDTLSDLRAQLVGQGVSSWKRAFYYNARRLDDHQTVRDARLQDGSVLLLVSDPR
Mackowiak match	AC010325.1	19	50786104	50785812	-1	2506	lincRNA	existing transcript	lincRNA	ENSG00000261341	ENST00000562076	28	3	mammals	previously undescribed coding gene ENSMUSG00000087376	/	all sources support testis expression	all sources support testis expression	ncRNA NR_134883.1 (LOC105372440)			no	Uncharacterised protein.	no	MNFQENVTLAMALFTILTSIYFFNKAQQ
Mackowiak match	SERTM2	X	111518861	111519130	1	452	1000	existing transcript	lincRNA	ENSG00000260802	ENST00000569275	89	1	xenopus	previously undescribed coding gene ENSMUSG00000085139	xenopus OCA25043.1	CAGE supports expression in epididymis, with weaker signals in hepatocytes, seminal vesicles, cervix, uterus; HPA supports high endometrium expression, with weaker expression in other tissues e.g. prostate; Intropolis is dominated by prostate cancer experiments, with mesenchymal cells the top ranked normal experiment (SRR486239)	CAGE supports pituitary gland expression; ENCODE RNAseq supports weak general expression	ncRNA NR_033974.1 (LINC00890)			no	Homology to serine-rich transmembrane proteins.	no	MEAHFKYHGNLTGRAHFPTLATEVDTSSDKYSNLYMYVGLFLSLLAILLILLFTMLLRLKHVISPINSDSTESVPQFTDVEMQSRIPTP
Mackowiak match	STRIT1	3	155293632	155290944	-1	553	1000	existing transcript	lincRNA	ENSG00000240045	ENST00000489090	35	2	avians	previously undescribed coding gene ENSMUSG00000103476	chicken PLAR linc|3P|XLOC_114812|TCONS_00227609:186.408|90AA|35AA|	CAGE supports expression in skeletal muscle, artery, spinal fluid, throat, diaphragm, tongue; HPA supports expression in esophagus and heart; Intropolis is dominated by very high expression in muscle (e.g. SRR1398546)	CAGE supports weak heart expression; ENCODE RNAseq supports heart expression	ncRNA NR_037902.1			no	Subsequently reported as a protein-coding based on experimental data, and unofficially named DWORF [PMID:26816378]. It enhances SERCA activity by displacing the SERCA inhibitors phospholamban, sarcolipin, and myoregulin.	no	MAEKAGSTFSHLLVPILLLIGWIVGCIIMIYVVFS
Mackowiak match	LINC00672	17	38925694	38925771	1	699	1000	existing transcript	lincRNA	ENSG00000263874	ENST00000583195	25	1	vertebrates	previously undescribed coding gene ENSMUSG00000050538	tetraodon CAF94638.1	all sources support brain expression	all sources support brain expression	ncRNA NR_038847			gawron_2016:193602 / gonzalez_2014:386349 / werner_2015:621349	Uncharacterised protein. An existing CDS at the mouse locus was found to be completely spurious (CCDS36298).	no	MLDIFILMFFAIIGLVILSYIIYLL
Mackowiak match	SMIM36	17	55511334	55511053	-1	855	1000	gene added	absent	ENSG00000261873	ENST00000636752	93	1	vertebrates	previously undescribed coding gene ENSMUSG00000110344	zebrafish ENSDART00000173549	CAGE supports pineal gland and eye expression; HPA supports testis expression; top ranked Intropolis experiment is retina (SRR060734)	CAGE supports eye expression; ENCODE RNAseq supports weak brain expression	ncRNA XR_243721.3 (LOC101927367); partial match		Kim et al; neXtProt	no	Uncharacterised protein. Originally noted during an analysis of the Kim et al and Kuster et al proteomics datasets, although the experimental support was not considered strong enough to support annotation at that time.	no	MEFYLEIDPVTLNLIILVASYVILLLVFLISCVLYDCRGKDPSKEYAPEATLEAQPSIRLVVMHPSVAGPHWPKGPGLSLGDPAPLGKKSTMV
Mackowiak match	MYMX	6	44217472	44217726	1	864	1000	existing transcript	lincRNA	ENSG00000262179	ENST00000573382	84	1	avian	previously undescribed coding gene ENSMUSG00000079471	alligator KYO43399	CAGE supports expression in a variety of muscle-linked experiments, especially skeletal muscle and myoblasts, but also adipocytes; HPA supports adipose expression alongside weaker general expression; Intropolis supports muscle expression, with the top ranked experiment from skeletal muscle (SRR1398564)	CAGE supports embryonic stem cell and embryo expression; ENCODE RNAseq supports limb expression alongside weaker general expression	uncharacterized XR_242025.3 (LOC101929726)			no	Subsequently reported as functional protein-coding gene MYMX / Mymx based on experimental data [PMID:28386024]. It is involved in the formation of skeletal muscle during embryogenesis.	no	MPTPLLPLLLRLLLSCLLLPAARLARQYLLPLLRRLARRLGSQDMREALLGCLLFILSQRHSPDAGEASRVDRLERRERLGPQK
Mackowiak match	RNF227	17	7916195	7915522	-1	436	1000	transcript extended	antisense lncRNA	ENSG00000179859	ENST00000324348	190	2	avians	previously undescribed coding gene ENSMUSG00000043419	lizard XP_008121180	CAGE supports two separate TSS linked to a long and short form of the CDS, the upstream showing highest expression in macrophages and the downstream in eye, skin and brain tissues; HPA supports general expression from the downstream TSS; the top ranked Intropolis experiment is skin (SRR835999)	CAGE supports two TSS as seen in human, with expression of the upstream in skin, forelimb and tongue and expression of the downstream in neurons and visual cortex; ENCODE RNAseq supports brain expression alongside weak general expression, largely from the downstream TSS	ncRNA NR_024349.1 (LOC284023)				Protein containing RING Ubox and DUF4632 domains. While the CDS from Mackowiak is linked to a strong CAGE tag, PhyloCSF extends upstream in the same first exon to a weaker CAGE to give the CDS listed here. It seems likely both proteins exist, thus both have been annotated in GENCODE human and mouse. The shorter form lacks the RING Ubox domain.	no	MQLLVRVPSLPERGELDCNICYRPFNLGCRAPRRLPGTARARCGHTICTACLRELAARGDGGGAAARVVRLRRVVTCPFCRAPSQLPRGGLTEMALDSDLWSRLEEKARAKCERDEAGNPAKESSDADGEAEEEGESEKGAGPRSAGWRALRRLWDRVLGPARRWRRPLPSNVLYCAEIKDIGHLTRCTL
Mackowiak match	SMIM39	2	131035092	131035262	1	62	1000 / ms	existing transcript	non-coding transcript within ARHGEF4	ENSG00000284479	ENST00000635976	56	1	vertebrates	previously undescribed coding gene, annotated within ENSMUSG00000037509 (Arhgef4) as ENSMUST00000211073 in GENCODE M18; will be separated as an independent gene in a future release	zebrafish OTTDARG00000044231	CAGE supports brain expression; HPA supports brain expression but also adipose, and weaker general expression; Intropolis has top ranking experiments from brain (e.g. SRR1047869)	CAGE supports brain / CNS expression; ENCODE RNAseq supports brain expression alongside weaker general expression	absent	cotranscribed with ARHGEF4	Kim et al	no	Uncharacterised protein. Identified within an alternative first non-coding exon of ARHGEF4. There is no evidence that the locus is transcribed independently of the downstream ARHGEF4 exons in human, mouse or zebrafish. Mass spectrometry support for this CDS was previously observed in our reanalysis of the Kim et al and Kuster et al proteomics datasets, although statistical confidence was not high enough to support annotation at that time. 	no	MARAPQPRRGPAAPGNALRALLRCNLPPGAQRVVVSAVLALLVLINVVLIFLLAFR
Published	AL034430.1	20	10413887	10413735	-1	296	1000	existing transcript	5' UTR of MKKS	ENSG00000285508	ENST00000609375	50	1	coelacanth	previously undescribed coding gene ENSMUSG00000027274	coelacanth EnsCodingFull|3P|XLOC_155214|TCONS_00200630|0:0.347849	all sources support general expression	all sources support general expression	no model, although recognised as a uORF in the MKKS gene description	cotranscribed within MKKS		fritsch_2012:48204 / gawron_2016:282740 / liu_2013:602716 / park_2016:1017024 / rubio_2014:1214914	Found within the 5' UTR of MKKS, previously reported and experimentally confirmed in 2013 [PMID:23671934]. The novel protein is found in the mitochondria, whereas MKKS is a skeletal protein. The loci apparently share a promoter, and current data indicate that MKKS is always translated from transcripts that also contain the novel CDS. 	no	MKNTSWIRKNWLLVAGISFIGVHLGTYFLQRSAKQSVKFQSQSKQKSIEE
Published	AL022312.1	22	39504231	39504443	1	860	1000	existing transcript	5' UTR of MIEF1	ENSG00000285025	ENST00000637854	70	1	vertebrates	previously undescribed coding gene ENSMUSG00000115798	Tetraodon CAG02533.1	all sources support general expression	all sources support general expression	absent	cotranscribed within MIEF1	neXtProt	gonzalez_2014:634134 / loayza_puch_2013:926373 / rutkowski_2015:699643	Found within the 5' UTR of MIEF1, previously reported based on ribosome profiling and phylogenetics [PMID:25621764].	no	MAPWSREAVLSLYRALLRQGRQLRYTDRDFYFASIRREFRKNQKLEDAEARERQLEKGLVFLNGKLGRII
Mackowiak partial match	CCDC196	14	66486503	66498472	1	330	1000	existing transcript	lincRNA	ENSG00000196553	ENST00000636229	297	10	mammals	previously undescribed coding gene ENSMUSG00000099418	/	all sources support testis expression	all sources support testis expression	ncRNA NR_024338.2 (LINC00238); partial match		neXtProt		Uncharacterised protein. The locus was for a time recognised as protein-coding gene C14orf53 by RefSeq, prior to becoming reannotated as non-coding gene LINC00238. 	no	MTSGANSSGSYLPSEIRSSKIDDNYLKELNEDLKLRKQELLEMLKPLEDKNNLLFQKLMSNLEEKQRSLQIMRQIMAGKGCEESSVMELLKEAEEMKQNLERKNKMLRKEMEMLWNKTFEAEELSDQQKAPQTKNKADLQDGKAPKSPSSPRKTESELEKSFAEKVKEIRKEKQQRKMEWVKYQEQNNILQNDFHGKVIELRIEALKNYQKANDLKLSLYLQQNFEPMQAFLNLPGSQGTMGITTMDRVTTGRNEHHVRILGTKIYTEQQGTKGSQLDNTGGRLFFLRSLPDEALKN
Mackowiak partial match	PVALEF	17	81181227	81183011	1	7315	lincRNA	spliceform added	antisense lncRNA	ENSG00000225180	ENST00000637878	134	4	coelacanth; potential ortholog in fish without synteny, e.g. herring XP_012675455.1	novel unitary pseudogene ENSMUSG00000113114	coelacanth XP_005988106.1	no CAGE support; no HPA support; Intropolis finds weak support in a series of adipose experiments (e.g. SRR833729)	/	ncRNA NR_027255.1 (AATK-AS1); partial match				Novel EF-hand domain-containing protein. Apparently pseudogenised in the rodent / lagomorph clade. The CDS reported by Mackowiak is incorrect as it has been extrapolated from RNA evidence that retains an intron.	no	MEEDFSSQMKKMALAMGTSLSDKDIELLPTDMRHHGSFNYLKFFKHIRKLHASGQLDDAIHTAFQSLDKDKSGFIEWNEIKYILSIIPSSGPTTPLTDEEAEAMIQAADTHGDGRINYEEFSELIKKEKIPKKK
Mackowiak partial match	C2orf92	2	97669789	97702801	1	818	1000	existing transcript	antisense lncRNA	ENSG00000228486	ENST00000627399	265	8	mammals	previously undescribed coding gene ENSMUSG00000102416	/	CAGE supports testis expression; HPA finds testis expression alongside weaker general expression; Intropolis supports general expression	all sources support testis expression	ncRNA NR_038386.1 (LINC01125); partial match				Uncharacterised protein. There is strong PhyloCSF across the final two coding exons, and the provenance of the locus is clearly as protein-coding. However, it has not been possible to find a consistent CDS among mammals across the 5' end of the locus, and we cannot deduce an ancestral form. Most exons of the human 265aa translation have appreciable conservation, although the model reported here contains exonic duplications not seen in mouse. It seems that the first half of the locus has evolved independently in different lineages during the mammalian radiation, which may undermine confidence in its coding potential. However, there is good ribosome profiling coverage across the human and mouse translations, and Mackowiak found mass spectrometry support for the human translation with peptide [PCGQLLHFLQR].	yes, potentially a unitary pseuodgene in human and / or mouse	MSRAMALFFVLCWIQDEIVLQVFSKVPYDPSFDETRTAVRSITKRDTQKSYSQQKSLNNAAFASGSNEREEHLAKIFDEILLQVFPKFPYDPSFNEATAVRSITKTDMRKGTSIAWNSPKPEYFLGSVDKIPDKDHLSEEKNFKESCLFDRDLREQLTTIDKETLQGAAKPDAHFRTMPCGQLLHFLQRNTIIAAVSGVAILMAIVLLLLGLASYIRKKQPSSPLANTTYNIFIMDGKTWWHNSEEKNFTKLAKKQKQLKSSSCV
NP/NM partial match	GNG14	19	12688049	12688372	1	306	1000	transcript extended	5' UTR of FBXW9	ENSG00000283980	ENST00000640117	69	2	mammals	known coding gene ENSMUSG00000095845	/	no CAGE; HPA coverage cannot be separated from FBXW9 3' UTR on the opposite strand	CAGE supports weak expression in neurons and diencephalon; ENCODE RNAseq supports very weak general expression	coding NM_001316692.1 (LOC105372280); partial match			no	Paralog of GNG12. The 2 exon structure has been taken by comparison to that locus and to the mouse ortholog (Gm5741). RefSeq have annotated the locus as a single-exon model, and although the CDS can be theoretically translated across the intron without disruption, this intronic portion of CDS is poorly conserved.	yes, potential unitary pseudogene in human	MSSKVAINSDIGQALWAVEQLQMEAGIDQVKMAADLLKFCTEQAKNDPFLVGIPAATNSFKEKKPYAIL
NP/NM partial match	C5orf58	5	170234977	170246113	1	1010	lincRNA	existing transcript	antisense lncRNA; protein-coding in v19	ENSG00000234511	ENST00000593851	81	2	mammals	known coding gene ENSMUSG00000085684	/	all sources support testis expression	all sources support testis expression	coding NM_001102609.1; partial match		neXtProt	no	Already known as chromosome 5 open reading frame 58 (C5orf58). RefSeq have extended the CDS to a poorly conserved ATG. It was protein-coding in an earlier GENCODE release. 	no	MGKKRVTDHKLNVDKVIKNINTISSELKKIKELSQLLLCDLILHFNHPIKTENLAEAERNNPLFEESKISDVSLVSNSFSI
NP/NM partial match	TSTD3	6	99521075	99531720	1	1091	lincRNA	existing transcript	antisense lncRNA	ENSG00000228439	ENST00000636394	111	3	vertebrates	known coding gene ENSMUSG00000028251	/	all sources support general expression	all sources support general expression	coding NM_001195131.1; partial match				Already known as thiosulfate sulfurtransferase (rhodanese)-like domain containing 3 (TSTD3), previously missed by GENCODE because the only human cDNA evidence incorporates a 'poison' exon (i.e. an exon that introduces a frameshift). Recognised by RefSeq as protein-coding for many years, although their model uses a downstream ATG within the poison exon, i.e. misses the conserved ATG.	no	MVLPWLLLETARRAVLGSAEAALCGLTSIKGNCHNFYTAISKDVTYKELKNLLNSKNIMLIDVREIWEILEYQKIPESINVPLDEVGEALQMNPRDFKEKYNEVKPSKSDS
NP/NM partial match	FAM240A	3	46617186	46625218	1	79	1000	existing transcript	non-coding transcript within TDGF1	ENSG00000283473	ENST00000640551	77	2	avians; potential ortholog in coelacanth without synteny, e.g. linc|3P|XLOC_096740|TCONS_00126143:5.57183|93AA|92AA| (94aa ORF)	known coding gene ENSMUSG00000096393	lizard LOC107982372	no CAGE; HPA supports salivary gland, cerebral cortex and thyroid expression; highest Intropolis score is from spermatozoa (SRR650364)	CAGE supports weak T cell expression; ENCODE RNAseq supports thymus expression	coding NM_001195442.1; partial match			no	Homology to FAM240B and FAM240C, both of which are on this sheet. RefSeq use an upstream ATG with poor conservation on the same transcript structure.	no	MNNQYTRREVFCRNTCHDLKHFWEREIGKQTYYRESEERRLGRSALRKLREEWKQRLETKLRLRNNPEDTEKRTNVG
NP/NM partial match	TMEM269	1	42789894	42798225	1	135	1000	existing transcript	lincRNA	ENSG00000274386	ENST00000637012	203	5	avians; potential ortholog in zebrafish without synteny, NM_001195246	known coding gene ENSMUSG00000028642	lizard ENSACAT00000012596	all sources support testis expression	all sources support testis expression	coding NM_001242750; partial match				Already known as transmembrane protein 269 (TMEM269). RefSeq use a first exon with poor conservation and transcriptional support, whereas the correct structure became apparent on integrating capture-seq and CAGE data. 	no	MVLGLFSIIFSFSRKCHYASRMLLVSFLLDMAVRAMTSHINICSKLGAELNDFAVFTTFGLASALLLGVDGLLSGILAIIYVSAASFHLCFYSPGVPSTYKGLPCPYASCILASTSLLTKGNRFILCCMASLMILFMMDQSYYPYDKILESENWKKLVYIGGVIMLFFSPLSLSAFYCLMWSLSYIFFPDALWGKAACLSPQH
XP/NM partial match	CLEC20A	1	178496939	178479535	-1	820	1000	transcript extended	lincRNA and adjacent antisense lncRNA	ENSG00000188585	ENST00000623247	400	8	mammals	novel unitary pseudogene ENSMUSG00000109913	/	no CAGE for full length transcript; HPA supports testis expression of the full-length transcript reported here, with evidence of a short form based on an alternative first exon specific to lymph and bone marrow (ENST00000646925); BluePrint supports the existence of this truncated model, which also has CAGE in B cells; Intropolis is dominated by cancer experiments, but also B cells (e.g. DRR013790)	/	coding XP_016858575.1 (LINC00083); partial match				C-type lectin domain-containing protein. Evidence suggests a shorter isoform exists in B cells. RefSeq uses an upstream ATG with poor conservation.	no	MLPRALLLSFCAAALQLVSSKRDLVLVKEALSWYDAQQHCRLHYTDLADLQPSGLWKLYSLMTSTPAWIGLFFDASTSGLRWSSGSTFTALEWGQKLPEFGVGFCATLYTWLKLPSIGAASCTAQKPFLCYCDPDVGHLISTKPSLSLTTSPKPAVVQISGQTFMRFDQVMTWSSALLYCRSHHTDLADLQMVTDETGKEALRSIMSETEAWIGLYLNANSGSLSWSSDLGASIPSWLQVPMMVRGLCTALGIYMTYSPKVYSVNCSSLLPFFCFYDSSTGHRASAELPPLFHTSPTEMTEETTPRPGRAVASVGSGTDRRDTAAATEAQHLSSESKEKTSAQKSGHPFGILKADFTISTLMDPEEMKDQFLRQIQEVLKLTLGHEQFRLKWVSFEVNKK
XP/NM partial match	TEX51	2	126898919	126901402	1	15	1000	spliceform added	lincRNA	ENSG00000237524	ENST00000450035	166	6	mammals	absent in mouse and rat	cow EST DT838655 contains an intact CDS	all sources support testis expression		coding XP_011510574.1 (LOC101929926); partial match				Uncharacterised protein. Alternative splicing allows the potential usage of 4 distinct STOP codons in human, none of which have strong conservation. The first 6 coding exons are conserved in mammals with an open translation, and it is not obvious if the translation after this point has diverged dramatically in mammals, or if there have been pseudogenisation events in certain lineages.	yes, potential unitary pseudogene in human	MLPLLIICLLPAIEGKNCLRCWPELSALIDYDLQILWVTPGPPTELSQNRDHLEEETAKFFTQVHQAIKTLRDDKTVLLEEIYTHKNLFTERLNKISDGLKEKDIQSTLKVTSCADCRTHFLSCNDPTFCPARNRRTSLWAVSLSSALLLAIAGDVSFTGKGRRRQ
XP/NM partial match	MINDY4B	3	150905439	150871045	-1	469	1000	spliceform added	pseudogene; protein-coding in v19	ENSG00000214237	ENST00000465419	460	12	xenopus; potential ortholog in fish without synteny, e.g. salmon XP_014017429	known coding gene ENSMUSG00000101860 (Fam188b2)	xenopus XP_002937138	no CAGE; no HPA; Intropolis finds weak expression in a variety of fetal tissues, e.g. adrenal gland (SRR980484)	CAGE supports expression in inner cells and organ of corti; no ENCODE RNAseq	coding XP_016863110.1; partial match				MINDY family member, previously known as FAM188B2. It was a protein-coding gene in GENCODEv19, but switched to pseudogene as the only transcript evidence at that time supported a truncated CDS. PMID:20717163 previously demonstrated that certain of these exons are transcribed in retina as part of the CLRN1 locus immediately upstream (their coding potential was not examined). In context, these look like readthrough transcription events; both the canonical STOP of CLRN1 and the ATG used for MINDY4B are deeply conserved, and there is no evidence for Clrn1 readthrough transcription in other species. Although the human locus has minimal RNAseq / CAGE support, the annotation of most introns is supported by ESTs. The RefSeq model remains 5' truncated with an incorrect ATG. 	no	MDMEVLGQEQSSEQLDLEEISRKISFLDKWREIFSYHRLGTNNSTPQNHEGNHTSADENEDGTGLSQPKGQGHLPSSGLCSIPNPSIISSKLGGFPISLAMATKLRQILFGNTVHVFSYNWKKAYFRFHDPSSELAFTLEVGKGGARSIQMAVQGSIIKYLLFTRKGKDCNLGNLCEISKKEQEQALAAALAGILWAAGAAQKATICLVTEDIYVASTPDYSVDNFTERLQLFEFLEKEAAEKFIYDHLLCFRGEGSHGVILFLYSLIFSRTFERLQMDLDVTTTQLLQPNAGGFLCRQAVLNMILTGRASPNVFNGCEEGKSQETLHGVLTRSDVGYLQWGKDASEDDRLSQVGSMLKTPKLPIWLCNINGNYSILFCTNRQLLSDWKMERLFDLYFYSGQPSQKKLVRLTIDTHSHHWERDQQEEKHGPRRRFSPVEMAIRTKWSEATINWNGTVPFF
XP/NM partial match	IQCM	4	149742691	149351951	-1	169	1000	transcript extended	lincRNA	ENSG00000234828	ENST00000636793	501	12	mammals	known coding gene ENSMUSG00000031620	/	no CAGE; HPA support testis expression with weaker colon expression; Intropolis finds additional support for colon expression (SRR1213821)	all sources support testis expression	14 XPs have partial matches				IQ motif-containing protein.	no	MTTEEAMPEKAKCPTLEITKQDFFQEAKTLIAQHYEKINENKVQGTSINVFRKKHQKPKSGKYIPLEIDKKVTRDVVQEHRAALRRICFPKELSKSEHLQEPPQRISFKEPHIFSRRERCRPIDLITKGQVKLDKIMTIIEPVSKKMETAKQQHFEESRNRMLELLYPFPVHLYLQPGTSNLELLKEPDKAFYDWRGFVLTRSFRLACDSRRVSFSQSSSIFRDYYSKTFKTLIKKERQPIKPEPKSQPRIKGTPNKTDKLDSKVKRIGPHIEIFQVFRERKKFMITPKLIRMVTVMQAHVRGWLERKRLQRVMTKALDHGPDMKAVINMYGRLIHRVRYRRGLWRTRQILNLAELEEWMDRKKFYEIMFAKREDWPKIERNELPNFFSDCGHFPTQKQVDDTWDLVHQDGKEKYSELIKKSKAIEMLFTLYPPEGAHVPDSTLLKSTWLRPIVNGEEGYRYIVNGHPALKRANIRVVGKLVARSIRERKMRQHYKSCKVE
XP/NM partial match	PRRT1B	9	131545616	131558202	1	95	1000	gene added	absent	ENSG00000283526	ENST00000636672	263	4	coelacanth; potential ortholog in fish without synteny, e.g. zebrafish OTTDARG00000036869	previously undescribed coding gene ENSMUSG00000079497	coelacanth XP_014340850	CAGE supports cancer expression only; HPA supports expression in internal organs, lung especially; Intropolis is dominated by cancer and cell lines experiments	CAGE supports pancreas, stomach, kidney and liver expression; ENCODE RNAseq supports expression in these and other organs	coding XP_011517576.1; partial match		neXtProt		Proline-rich transmembrane protein.	no	MEAGAGGAGSDTKGGGSPATPEDPRSPAKPAAPEDPQMPAQPALPQLPRRPRTLDEDGAPSEDGAAGGSEPAPEDAPAQAAGEAGPVSKAAAGGAPHIGFVGEPPPYAPPDPKAAPLLYPPFPQVPVVLQPAPSALFPPPAQLYPAAPTPPALFSPPAGAAFPFPVYNGPMAGVPGPATVEHRPLPKDYMMESVLVTLFCCLLTGLIAIVYSHEARAALGRGDLAQAEEASRKARSLVLFSLLFGVFVSTSWVIYVVVALYLP
XP/NM partial match	VSIG10L2	11	125946056	125955914	1	249	1000	transcript extended	antisense lncRNA	ENSG00000283703	ENST00000638636	767	10	xenopus	previously undescribed coding gene ENSMUSG00000098590	xenopus OCT70428	no CAGE; no HPA; Intropolis finds expression in skin (e.g. SRR836000)	no expression data	coding XP_006719013.2; partial match				V-set and immunoglobulin domain containing protein. Mouse annotation is partly supported by ESTs from inner ear, e.g. BB850581	no	MVGQRAQHSPVSLLLLIHLCLLHLRASGQPHPTPEAPVEEVVSVQGVRGGSVELACGSGPAPLLVLWSFTPLGSLVPRPVAVTDGAMSKVEAIASALGVVSLRNSSLVLGELHEGARGHFLCQVLHVAGGQLHAAYSHLTLAVLVPVSKPQVRLSNPSPVEGASVVATCAVREGTEPVTFAWQHRAPRGLGEALVGVTEPLFQLDPVNRTHLGWYMCSASNSVNRLSSDGAFLDVIYGPDKPVITMEPLGLTEEGFWASEREEVTLSCLAASNPPSHYVWLRDHTQVHTGPTYVIARAGRVHTGLYTCLARNSYLDTRTQTTVQLTIYYPPEGQPSCAVHPSPEAVTLLCAWPGGLPPAQLQWEGPQGPGPTAPSNVTWSHAAAQLPSGSVFTCTGQHPALAPPALCTVMLWEPLGRPTCWSTATMGDQFIMLSCEWPGGEPPATLGWLDEQQQPLGGSSSSMAVHLLQAQEDLAGREFTCRGTHLLRTPDPHCHLQLEAPQLDVAEPRVSVLEGGEAWLECSLRGGTPPAQLLWLGPQQQKVDPGTSGFMLHPEGAQLRLGIYDADPAHHRGTYQCVARNAVGNSSQSVLLEVLRYPAPPNVTISRLTYGRHRREVQLQWAILGPGNLTGFLVQRKASALGPGAGAWETAASDIEPESRGRRLGGLDPGVLYAFRILALNHHTAGHPSEVKIPADPPFSAYPAVLGAAGTGMVVATVASLLVFQYAARHPETFPRLETPTTTPGLDPAQETTDSPVNVTITVTATP
XP/NM partial match	AC022167.5	16	8884356	8885295	1	1466	unannotated	gene added	absent	ENSG00000283516	ENST00000636296	72	2	avians	previously undescribed coding gene ENSMUSG00000107252	lizard chrUn_GL343263:1,930,831-1,931,738 [Broad AnoCar2.0/anoCar2]; partial alignment to AUGUSTUS g12243, which is 5' extended	all sources support testis expression	all sources support testis expression	XP_011521085.1; XP_011521084.1; XP_011521086.1 (LOC101929989); all partial matches			no	A truncated homolog of lipopolysaccharide-induced tumor necrosis factor-alpha factor (LITAF). The first coding exon of LITAF has been lost, with the novel CDS beginning instead within coding exon 2 of LITAF using an alternative ATG. This prospective human initiation codon is not stongly conserved in mammals, although the mouse translation uses a species-specific ATG 6 codons downsteam. Nonethless, this locus is potentially pseudogenic in any mammalian lineage.	yes, potentially a unitary pseudogene in human and / or mouse	MPVQAVCPYCGNRIITVTTFVPGALTWLLCTTLFLFGYVLGCCFLAFCIRSLMDVKHSCPVCQRELFYYHRL
XP/NM partial match	CCDC194	19	17394158	17390509	-1	112	1000	spliceform added	lincRNA	ENSG00000269720	ENST00000636079	234	4	mammals	previously undescribed coding gene ENSMUSG00000108900	/	CAGE supports cancer expression only; no HPA support; Intropolis is dominated by cancer experiments	CAGE supports weak expression in multiple neonate cell types including bone and epididymis	XP_011507149.1 (LOC105372343); partial match				Uncharacterised protein. The RefSeq model uses an additional exon that is poorly conserved.	no	MAEPGPEPGRAWRVLALCGVAVFLAAAAAGGALVAWNLAASAARGPRCPEPGANATAPPGDPPPGVDDLRRRLAEAAEREEALARQLDQAESIRHELEKALKACEGRQSRLQTQLTTLKIEMDEAKAQGTQMGAENGALTEALARWEAAATESTRRLDEALRRAGVAEAEGEACAAREAALRERLNVLEAEMSPQRRVPRPRPRSGSRPRPSPRSRSRSGPSGGCRRPARRARG
XP/NM partial match	TLE7	16	71433324	71430262	-1	1	1000	transcript extended	pseudogene	ENSG00000260734	ENST00000561754	441	9	mammals	previously undescribed coding gene ENSMUSG00000095941	/	weak CAGE support for testis and testicular cancer expression; HPA supports testis expression; Intropolis supports embryo expression in multiple experiments (e.g. SRR499827)	weak CAGE support for embryonic stem cells and testis expression; ENCODE RNAseq supports testis expression	XP_016879408.1; partial match		neXtProt		Member of the transducin like enhancer proteins family. However, the first 3 coding exons are apparently unique to this locus and only seen in mammals. The RefSeq model uses a spurious intronic ATG.	no	MSGEKEEASLRMFGAYGEPEERRDVLESSGVSSQPEPQVQQQLGSLLGVPWQPPGPPIQHSPADQETSTVTQQQWHLQGLGRSELQAAGLPDAQPGEAAESSPSFLLGSEVGQPYSSSSPSEEVLSLLRAIPPIPDEVVVRQKRAPQGSWKVGTLFHGKRVYAVAISGSTHHVYTCGSGYIRVWDESALHAGEKAPRAQLDLQHPQDRVVTCKLFPDERSLITGGASQAVTLWDLAPTPQVRAQLTSTGPTCYSLAVSSDAHICLACFHGFVEIWDLQNQILIRKHEVPVYGSRCVDITGNIFWTGGEDTILYSWDLRSYQRLHQHNLQNEILSITHDPGEEWVLAGLRTSDIVFLHTRRNEQFKALMKKYTRHHSLKFASCGSYFVTAIDTRLSGLEAPSLQKLFQIEESSGILCCDVSSDNQYLVMGSSSSATIYQLLY
UniProt partial match	IQANK1	8	143735854	143790608	1	85	1000	spliceform added	three adjacent lincRNAs	ENSG00000203499	ENST00000527139	560	13	coelacanth	previously undescribed coding gene ENSMUSG00000102018	coelacanth ENSLACT00000013317 (5' truncated)	all sources support testis expression	CAGE supports testis expression; ENCODE RNAseq supports general expression	ncRNA NR_033849.1 (FAM83H-AS1)				IQ motif and ankyrin repeat domain-containing protein. Incorporates exonic GWAS SNP rs4875053 linked to menarche, which can now be reinterpreted as mis-sense [ACG]-[AGG]. UniProt A8MXQ7 uses a spurious first coding exon and misses the first two coding exons presented here.	no	MDSKKGRPKAAAGKWQTLHPGPKTRAAAGKPGENRPPQRKAGWQAREPASAESPQAPTGPAEDRAARAIQGAFRQLRARRELARRREERREYLEQMETPQKEAYLAPVRREQEAARRLREQEEAAQRERREELQRRRRLLDAAFDGDVGEIRAVLKEVEQLLTREGVGHDEAGEARRLQRRVALAECEDSYGNTPLSEAAAGGQPLAIQLRAELGASPNSKGAFGPTPLYRAAFGGHLAAVEVLLKLGADPRVYAEDGSTPERVASLDTVVSVLRSWDLSLTEAMLQNMEAEQQRRAQEAQRHKEAEAERCGSMTLKVQQLTREQQQCHKELQQAYCELSRRISEHDQCEWRCMDKTKLTLQAIKDTEAQVDRLRQEAQKAEEALAMARLELREQTQEGEEEAPGLKCQVTELHDVLMKDVGNRIRADGRWPLVIDPLGQAATFLRYQDTNYVDTVNPEPLRPETMWLALLGALRYGKPLVFDLREEDLFPVVQRQLEAVQERYLSLLRPTDGPEYSPTQFQEQRLEHFRLFFVTKVQWPPAEQLQVLLPVRVQLPGTGL
UniProt partial match	CCDC197	14	93998132	94008812	1	8715	lincRNA	existing transcript	lincRNA	ENSG00000175699	ENST00000636493	272	6	mammals	novel unitary pseudogene ENSMUSG00000110677	/	CAGE supports testis expression; HPA finds testis expression alongside heart expression for a specific model with an alternative multi-exon 5' UTR; Intropolis is dominated by testis experiments	/	ncRNA NR_024183 (LINC00521)		neXtProt		Coiled-coil domain-containing protein. UniProt Q8NCU1.1 and Q8NCU1-2.1 are 3' truncated.	no	MAAMDTGQRADPSNPGDKEGDLQGLWQELYQLQAKQKKLKREVEKHKLFEDYLIKVLEKIPEGCTGWEEPEEVLVEATVKHYGKLFTASQDTQKRLEAFCQMIQAVHRSLESLEEDHRALMLSLKIRLCQLQKKCYRKQEQWWQLKHSITYQKDIDFDTHTSSSYNDQLLGYMQMTITNMARQCCPSAHGVPKSMDLFSKLDLIKEFMLDKMETVRLIALLTEPKVCWSWDSFGDQWLRRHPKPFRKCPRRRVSTPRTPFPSPHASECSGLY
C-HPP match	SPEM3	17	7428903	7432762	1	1096	unannotated	gene added	absent	ENSG00000283439	ENST00000636696	1196	3	mammals	previously undescribed coding gene ENSMUSG00000109737	/	all sources support testis expression	all sources support testis expression	coding XP_011522098.1		Weisser et al; neXtProt		Putative transmembrane protein, potentially an ancient duplication of adjacent C17orf74.	no	MGERAYHGAQVCSGTNPRKCQDLGDSILLLLGSFILLNVWINVVTLLWKHLKSSLRILFRHFFPKDKQPSGSHPICICSSVDPKNLCSKVSSRVHPRPGFLLRRVNHLDSWIPDTNDEKVSACCCVPPKCGHAGVPRESARGLYKAGMMGGGEAPQVTASKAQASLLSRPETSSQFPKMSKLDTGPCHLPQESKTKTPDCAPAEAPAQAQVHSPTHTPVCTPTHPWTRSTDHTAVHTPAHSWTHSKARTPEGTHSQAQDTSAQAQAHTSAPTPAQTPAHIQAHTPAPTPAKASAHTKAHTSAQAQTHSPPHTPEYTHSQAHSPEHTSAHSPAQAPMPVPAHPQAHAPEYTSAHAPAYIPDHSHLVRSSVPVPTSAPAPPGTLAPATTPVLAPTPAPVPASAPSPAPALVMALTTTPVPDPVPATTPAPIITPIPSTPPAFSHDLSTGHVVYDARREKQNFFHMSSPQNPEYSRKDLATLFRPQEGQDLVSSGISEQTKQCSGDSAKLPAGSILGYLELRNMEWKNSDDAKDKFPQTKTSPYCSFHPCSSEKNTDSQAPFYPKFLAYSRDTACAKTCFHSATTAQSSVCTLPPPFTLSLPLVPPRSFVPPQPTNHQRPSTLIQTPTVLPTSKSPQSILTSQFPIPSLFATISQPLIQPQCPECHESLGLTQDSGLQRTPGPSKDSRVPRNLDLAQNPDLYKNPGLTQDPGLHENPGLAPNQGLHEFPGLPQDSYLCQNPSPSQDFGLHKNSGITQDSHPQKNTGLTQEAGILRSPCLTQSPGLHKKTPFTQTSDLQRSSGFTQDSGIYRNLEPNQETVIYKNQDLSQATDHQKNLGSSKDSGGHKNTGNVQDPGVCSTAGLTEDSGSQKGPYVPQDSEVNKSSGVIQESFLHKSPGLVQTSGLPKCSGLTQNSGDYKNPGLIQDCGGHKVKGLTQDSNLPSLTQATKVERRFSLPQDVGVYRSSEHSQDSNLHKCPGINQDPGPHKDPALVQDSGLPKISGLTQESGPYKSSCLIPDPSLYKNPSPALGSDFVQLLSLLQTPKSTLSLMKSSVPEKAAQKEDAQRHVLWARVQLNENSCPSKAQVVSNDLQTFSEVPVLIELQSSSWRAGSQHGAYRPVDTVPSGYQNYRQMSMPTHINWKSHCPGPGTQAGHVVFDARQRRLAVGKDKCEALSPRRLHQEAPSNSGKPSRSGDIRM
C-HPP match	AC007906.2	16	53044158	53044000	-1	2335	lincRNA	existing transcript	antisense lncRNA	ENSG00000277639	ENST00000619363	52	1	xenopus	previously undescribed coding gene ENSMUSG00000110332	xenopus EST cluster gives a CDS at [KB021653:23,707,665-23,707,817](-) JGI 7.0/xenTro7	all sources support general expression	all sources support general expression	ncRNA NR_136518.1 (LOC105371267; p53-regulated lncRNA 1)		Weisser et al	no	Uncharacterised protein. Previously described as a lncRNA p53 target [PMID:25524025].	no	MGCHSSKSTTVAAESQKLEEEREGREPGLETGTQAADCKDAPLKDGTPEPKS
C-HPP match	TEX53	9	114657774	114656529	-1	2004	lincRNA	existing transcript	lincRNA	ENSG00000230054	ENST00000423632	70	2	mammals	previously undescribed coding gene ENSMUSG00000084782	/	all sources support testis expression	all sources support testis expression	ncRNA XR_930261.1		Weisser et al	no	Uncharacterised CDS. Apparently a partial duplicant of TEX48 immediately upstream.	no	MGSKIFCCCRKTSEGSSTTVGFHNPRMFEQHHPRSFNLNTNSLHSAVPKRHPRLPYDNRMMLKACILRRP
C-HPP match	AL451007.3	1	244730923	244730375	-1	1827	unannotated	gene added	absent	ENSG00000284188	ENST00000640271	182	1	mammals	previously undescribed coding gene ENSMUSG00000070489; currently annotated as non-coding due to a known error in the genome assembly		all sources support testis expression	all sources support testis expression	absent		Weisser et al		Uncharacterised protein. The ATG region is well conserved in mammals although the CDS diverges notably towards its middle portion. The STOP has limited conservation. Peptide evidence was therefore necessary to support confident protein-coding annotation.	no	MAAPRFGGPRRGGAQHELLEKAARLERGPPPRGDPEAVGRRAVAGDGGSCSGCWCWRRLFRGPRRKKLRQAHARAGKEAPERGLWGPSSLQRLLQRLATWRRRYLRRKERPDRLEEIPLLVLDRAQGGHEAAAGPQSSVPGRPAQAAPARQPRRRSATRSRSPVAPPVHAQDCFFLFGQQKQ
C-HPP match	SPAAR	9	35910464	35910691	1	389	1000	existing transcript	lincRNA	ENSG00000235387	ENST00000443779	75	1	mammals	known coding gene ENSMUSG00000028475	/	all sources support general expression	all sources support general expression	ncRNA NR_024283 (LINC00961)		Weisser et al; neXtProt	no	Subsequently identified and confirmed experimentally by PMID:28024296. The protein negatively regulates mTORC1 activation. However, the CDS reported here is is 15aa shorter due to the usage of an alternative initiation codon with stronger conservation.	no	METAVIGVVVVLFVVTVAITCVLCCFSCDSRAQDPQGGPGRSFTVATFRQEASLFTGPVRHAQPVPSAQDFWTFM
C-HPP match	CCDC192	5	127703389	127941468	1	127	1000	existing transcript	lincRNA	ENSG00000230561	ENST00000514853	292	7	mammals	known coding gene ENSMUSG00000058925	/	all sources support testis expression	all sources support testis expression	ncRNA XR_159059.3 (LINC01183)		Weisser et al; neXtProt		Coiled-coil domain-containing protein.	no	MMPVDVCPRDRGSQWVWLEMGQCYSKKSVVPESDTSERSSMTSGSSESDIPQENKVSKASLDTGQMAFTLAQLESLEICLKEAEEKAKALSEQLSVSEGTKSKLLEQVSRLEEKLEAVDHKEASGGPYEKMVLVKDQCIQKLQAEVKASQEQLIAQKLKHEKKVKKLQTDLATANAITVLELNEKIKTLYEGKPAPREDSLLEGFCGGLPPVEEGDRKISLIMELSTQVSLQTERITQLKEVLEEKERKIQQLEAERSPHPPQEVKDPPGCLPEAPVFSTHDIPPVVSDENL
Wright et al match	LBHD2	14	103086013	103089797	1	307	1000 / ms	gene added	absent	ENSG00000283071	ENST00000634353	108	3	xenopus	known coding gene ENSMUSG00000087075	xenopus XP_018086063	weak though consistent CAGE support for adipocytes; HPA supports adipose and testis expression; Intropolis finds highest expresion in cancer cells, though there is consistent support in adipose (e.g. SRR833729)	weak CAGE support for ovary and brain expression; ENCODE RNAseq supports weak general expression	absent		Wright et al; neXtProt		Homology to limb bud and heart development (LBH).	no	MSTPRPAPPQPGAAEGAGGPEGKAVAGAWEKGPRLGQRLPSIVVEPSEADPVESGELRWPLESAQRGPSQSRAAAAPSPSLPGEPGKAADNAGSECACSEDPAAPARG
Wright et al match	AC073111.5	7	150407612	150408223	1	488	1000 / ms	existing transcript	ZNF775 3' UTR	ENSG00000284691	ENST00000642087	203	1	mammals	known coding gene ENSMUSG00000053297	/	all sources support general expression	all sources support general expression	pseudogene NR_027237.1		Wright et al		Zinc finger protein.	no	MTELASSGGGSPAGDGEEGLGDERGLVIHHPAEEQPYRCPLCGQTFSQQPSLVRHQKAHAGAGRAAAFVCPECGKAFSVKHNLEVHQRTHTGERPFPCPECGRCFSLKQNLLTHQRIHSGEKPHQCAQCGRCFREPRFLLNHQRTHARMPAPHPRRPGVFGERRPYFCPRCGKSFAREGSLKTHQRSHGHGPEGQAAHLGRVL
Wright et al match	MMP24OS	20	35277929	35277714	-1	1109	lincRNA	existing transcript	antisense lncRNA	ENSG00000126005	ENST00000424358	71	1	avians	known coding gene ENSMUSG00000074649	chicken PLAR EnsASCoding|3P|XLOC_103732|TCONS_00201937|MTG1:2.69588	all sources support general expression	all sources support general expression	ncRNA NR_102705.1 (MMP24-AS1)		Wright et al; neXtProt	fritsch_2012:46839 / gonzalez_2014:598039 / loayza_puch_2013:872810 / rubio_2014:1237497 / rutkowski_2015:659335 / stern_ginossar_2012:22799	Uncharacterised protein.	no	MGAQLSGGRGAPEPAQTQPQPQPQPAAPEGPEQPRHPPQPQPQPQPQPQPEPSPWGPLDDVRFLIACTSWY
Wright et al match	SPTY2D1OS	11	18599929	18603179	1	1296	lincRNA	existing transcript	antisense lncRNA	ENSG00000247595	ENST00000635674	59	3	mammals	known coding gene ENSMUSG00000056509	/	all sources support testis expression	all sources support testis expression	ncRNA NR_038360.1 (SPTY2D1-AS1)		Wright et al; neXtProt	no	Uncharacterised protein. This locus remains difficult to resolve, as the peptide data provided support for a CDS that represents a different isoform in a different frame. Thus, PhyloCSF provides support for coding potential outside of the peptide-supported CDS.	no	MIVLGWMFFVGLVCYMGTFPELMPPTLKWQERWPVQESKTQLRRRALGEDLLQNHVEGI
Wright et al match	TMEM275	1	46533527	46532994	-1	991	1000 / ms	gene added	absent	ENSG00000282881	ENST00000634804	177	1	vertebrates	known coding gene ENSMUSG00000034185	zebrafish NM_001128377	no CAGE; HPA supports testis and brain expression; Intropolis supports brain expression (e.g. SRR921936) alongside cancer expression	no CAGE; ENCODE RNAseq supports brain / CNS expression	absent		Wright et al		Uncharacterised protein.	no	MPPAEKSEGPPVPAPAERARGRVPGLPSPALCCACGLCALLAGVNVTLAGAFASFLPEHNALLVVGLALLVLALGFFAACCVCSRRGLAPRGRSAAAAGPGQGGGRAGPVALEMESSEPTAQDTTAVQLSPAVSAASSGCSSPGPSPLALEAPAPAAVCALRSEGVQLNPPRARAAP