Table 1.

Features of Alu-Containing Alternatively Spliced Internal Exons

EST/RNA confirming exon skip (1) EST/RNA confirming exon insertion (2) Exon len.(3) No.sequences confirming exon skip (4) No.sequences confirming exon insertion (5) Place (6) Effect on CDS (7) Alu subfamily (8) GenBank annotation (9)
1 AB046854 AF257238 7511CDS+AluScMembrane-associated guanylate kinase
2 D86198 BF223241 811456CDS+AluJbDolichol-phosphate-mannose synthase
3 HSU76420 HSU76421 12039CDS+AluJbdsRNA edenosine deaminase
4 AF161516 AF152097 4261CDS+AluSpSimilar to Rattus novergicus CDS5  activator binding
5 AB000459 AB000460 123101CDS+AluSqUnknown protein product
6Al791889HS426106210213CDS+AluSpUnknown protein product
7 AF013970 AF069747 7631CDSalt nAluJoMTG8-like protein
8 AF042345 H41675 9827CDS3′tAluJbEctopic viral integration site 5
9HSGPLP BF207526 210692CDS3′tAluJbGlutathione peroxidase-like
10 HSU64564 HSU64570 138152CDS3′tAluJbMyelin/oligodendrocyte glycoprotein
11 AF177862 AA157902 951391CDS3′tAluJbNuclear protein of unknown function
12 AF086904 AF217975 114141CDS3′tAluSqProtein kinase Chk2
13HSM802141 AK002113 13882CDS3′tFLAM_CStrong similarity to rat exocyst complex  protein Sec15
14 AB032995 BF087651 123123CDS3′tAluJoUnknown protein product
15HSM800948 AA195214 12611CDS3′tAluJoUnknown protein product
16HSARSE AA160312 28621CDSf/sFLAM_CArylsulfatase E
17 HSU43746 BE869603 12621CDSf/sAluSxBreast cancer susceptibility (BRCA2)
18 HSU15782 BF247748 96182CDSf/sAluJoCleavage stimulation factor 77kDa  subunit
19 AF280109 AF280111 12141CDSf/sAluSgCytochrome P450 subfamily IIIA  polypeptide 43
20 AF121908 AF065216 9821CDSf/sAluSxCytosolic phospholipase A2 β
21 HSU06654 AA071342 106361CDSf/sAluJbDifferentiation antigen melan-A protein
22 HSU07707 BE842355 10141CDSf/sAluJbEpidermal growth factor receptor  substrate (eps15)
23 AF244135 A194938261173CDSf/sAluSgHepatocellular carcinoma-associated  antigen 66
24HUMHRLFB BE513181 151233CDSf/sAluJohRlf β subunit (p102 protein)
25HSICAM2 BE261894 116291CDSf/sAluJbICAM-2, cell adhesion ligand for LFA-1
26 AB018010 AW381165 132534CDSf/sAluJbMembrane glycoprotein 4F2 heavy  chain
27 AF072247 AA285195 128252CDSf/sAluSg/xMethyl-CpG binding domain-containing  protein MBD3
28HUMMEVKIN AF217536 118122CDSf/sAluJbMevalonate kinase
29 AK001322 AK022939 8911CDSf/sAluJomRNA from NT2 neuronal precursor  cells
30 D83735 BE836938 122543CDSf/sAluSxNeutral calponin
31 AF010316 AF217965 12271CDSf/sAluJbMicrosomal glutathione transferase  homolog
32HSAJ4875 AA225691 753610CDSf/sAluSpPutative glucosyltransferase
33 AF021819 BE567765 931981CDSf/sFLAM_CRNA-binding protein regulatory subunit
34 AF095742 BF038501 95201CDSf/sAluSxSerine protease ovasin
35 AF151858 AA397587 71344CDSf/sAluScSimilar to putative t1/st2 receptor  binding protein precursor
36 AF072810 AW835499 8261CDSf/sAluJoTranscription factor WSTF
37 AK026835 AA460397 77131CDSf/sAluJbUnknown protein product
38HUMRSC765 AU151565 91331CDSf/sFLAM_AUnknown protein product
39 BF513753 AK000502 9751CDSf/sAluSxUnknown protein product
40 AK024815 AL046389 10111CDSf/sAluJoUnknown protein product
41 AK001755 AK023461 13471CDSf/sAluScUnknown protein product
42 AB002315 AL043085 15131CDSf/sAluJbUnknown protein product
43 AK022568 BE898836 76165CDSf/sAluJbWeakly similar to Acyl-CoA  dehydrogenase
44 AK022147 AV714478 12761CDSf/sAluSxWeakly similar to the yeast GTPase-activating protein GYP7
45 AF003924 AW954573 12263CDSf/sAluSgZinc finger protein ANC_2H01
46 AF039918 BE867770 117215UTRFRAMCD39-like protein CD39L4
47 AF070674 BF216095 130725UTRAluSxInhibitor of apoptosis protein-1 (MIHC)
48 AF071107 AF071108 84825UTRFLAM_ASMAD5
49 AF130312 BF184073 1033715UTRAluSxTATA box binding protein-related  factor 2
50AFO78864 BE747669 1312115UTRAluSxTS58
51 BF086933 AK002100 71725UTRAluSxUnknown protein product
52 AK001235 BE788268 1191825UTRFLAM_CUnknown protein product
53 AK001715 BE740371 2482015UTRAluJbUnknown protein product
54HUMZFXHSZFX3128215UTRAluSxZinc finger protein X-linked
55 BF306258 AK024074 7422N/AAluSxModerately similar to zinc finger  protein 91
56 AA435797 HSU9299212281N/AAluSgmRNA from brain tissue, CAG  repeat region
57HSM801006HSM80087710622N/AAluJbSimilar to zinc finger helicase
58 AK023856 AA344993 98162N/AAluYUnknown protein product
59 AA210960 AK021447 11463N/AAluSgUnknown protein product
60 T99367 AB007962 11821N/AAluJbUnknown protein product
61 AK026653 BF037972 14781N/AAluYUnknown protein product

[i] (1) One of the GenBank sequences (RNA or EST) showing the exon-skipping pattern. The name presented is the GenBank locus.

[ii] (2) One of the GenBank sequences (RNA or EST) confirming the existence of the Alu-containing exon. The name presented is the GenBank locus.

[iii] (3) The length of the Alu-containing exon.

[iv] (4) Number of expressed sequences (RNAs and ESTs) showing the exon-skipping pattern.

[v] (5) Number of expressed sequences (RNAs and ESTs) confirming the existence of the Alu-containing exon.

[vi] (6) The location of the Alu-containing exon along the mRNA is denoted as follows: (CDS) the exon is inserted within the protein-coding region; (5UTR) the exon is inserted within the 5′UTR; (N/A) missing or contradictory GenBank annotation.

[vii] (7) The effects of the insertion of the Alu-containing exon in the protein-coding region is denoted as follows: (+) the exon adds a domain, namely inserted in frame and do not contain an in-frame stop codon; (alt n) exon insertion causes the alteration of the amino terminus of the protein; (3′t) exon insertion contains an in-frame premature stop codon; (f/s) exon insertion causes a frame-shift.

[viii] (8) The subfamily of the Alu element, see Table 2. RepeatMasker (http://repeatmasker.genome.washington.edu/cgi-bin/RepeatMasker) was run on the DNA around each Alu-containing exon to determine the subfamily type.

[ix] (9) GenBank annotation of the locus.