Identification of Chromosome 22 Genes with Unambiguous Transcripts of Exon-Skipped Isoforms
| Locus name | Skipped exon(s) | Effect of exon skip | No. ESTs confirming exon skip | Average no. ESTs confirming reference isoform | Database annotation |
| J_explorer identified an experimentally confirmed isoform | |||||
| CLTCL1 ‡ | 29 | C+ | 6 | 4.0 | Clathrin heavy polypeptide-like 1 |
| ADSL ‡ * | 12 | 3′ | 11 | 63.0 | Adenylosuccinate lyase |
| NF2 ‡ | 2–3 | C f/s | 1 | 5.7 | Neurofibromatosis 2 (bilateral acoustic neuroma) |
| J_exploreridentified an experimentally confirmed isoform and a novel isoform | |||||
| GGT1 ‡ | 7 | C f/s | 2 | — | Gamma-glutamyltransferase 1 |
| 3 | 5′ | 4 | — | ||
| J_exploreridentified a novel isoform and not the experimentally confirmed isoform | |||||
| PLA2G6 ‡ | 3 + 5 | C f/s | 2 | 1.5 | Phospholipase A2 groups VI |
| EWS ‡ * | 6 | C+ | 1 | 48.0 | Ewing sarcoma breakpoint region 1 |
| Novel exon skipping events identified byJ_explorer | |||||
| ATP6E * | 2 | C+ | 1 | 73.5 | ATPase H+ transporting lysosomal (vacuolar proton pump) |
| 5–7 | C+ 3′t | 1 | 38.0 | 31kD | |
| MIL1 | 3 | C+ | 2 | 13.0 | Homo sapiens MIL1 protein |
| UFD1L * | 2–3 | C+ 3′t | 1 | 21.7 | Ubiquitin fusion-degradation 1-like |
| TR | 13 | C+ | 1 | 6.0 | Thioredoxin reductase beta |
| ARVCF | 19 | C+ | 1 | 1.5 | Armadillo repeat gene deletes in velocardiofacial syndrome |
| AC005500.4 | 2–3 | C+ | 1 | 5.4 | Zinc finger protein |
| PIK4CA | 36–42 | C f/s | 1 | 5.6 | Phosphatidylinositol 4-kinase catalytic alpha polypeptide |
| BCR | 20 | C f/s | 1 | 5.5 | Active BCR-related gene |
| AP000350.2 | 5 | C+ | 2 | 1.0 | Similar to glucose transporters SW:P22732 |
| GSTT1 | 2 | C f/s | 4 | 7.5 | Glutathione S-transferase theta 1 |
| 2–3 | C f/s | 1 | 8.0 | ||
| 3–4 | C+ | 1 | 9.3 | ||
| AC004997.1† | 5 | C N/A | 1 | 4.0 | GATS protein |
| 5–6 | C+ | 1 | 4.0 | ||
| SEC14L2 | 10 | C f/s | 2 | 4.5 | SEC14 (S. cerevisiae)-like 2 |
| SMTN † | 14–15 | C N/A | 1 | 5.7 | Smoothelin |
| dJ858B16.1 | 27 | C+ 3′t | 1 | 2.3 | Homo sapiens mRNA for KIAA0542 protein complete cds. |
| AC005004.1 | 22–23 | C+ | 2 | 1.7 | Homo sapiens mRNA for KIAA0645 protein complete cds |
| HMG2L1 | 2 | 5′ | 4 | 1.5 | High-mobility group protein 2-like 1 |
| 5 | 5′ | 1 | 4.0 | ||
| 2 + 5 | 5′ | 1 | 4.6 | ||
| CE132D12.1 | 6 | C f/s | 1 | 21.5 | Similar to RAS-related protein |
| 7 | C f/s | 5 | 46.0 | RAB-5A (HS) | |
| MFNG † | 2 | C+ | 1 | 16.0 | Manic fringe (Drosophila) homolog |
| LGALS1 * | 3 | C f/s | 5 | >100.0 | Lectin galactoside-binding soluble 1 (galectin 1) |
| GCAT | 2–3 + 5 | C N/A | 1 | 2.8 | Glycine C-acetyltransferase (2-amino-3-ketobutyrate-CoA ligase) |
| dJ1014D13.1* | 12 | C+ | 1 | >100.0 | Weakly similar to casein kinase 1 homolog HRR25 |
| GTPBP1 | 2 | C+ 5′t | 8 | 17.0 | GTP binding protein 1 |
| dJ508I15.1 | 2 | C+ 5′t | 1 | 8.0 | Novel human gene mapping to chromosome 22 |
| dJ508I15.4 | 3 | C N/A | 1 | 1.5 | Homo sapiens mRNA for KIAA0668 protein |
| RPL3 † * | 8 | C+ | 7 | >100.0 | Ribosomal protein L3 |
| dJ1042K10.2 | 2 | C+ 5′t | 1 | 10.5 | Similar to C. elegans predicted protein with probable rabGAP domains and src homology |
| SLC25A17 | 2–4 | C f/s | 1 | 9.0 | Solute carrier family 25 |
| 3–4 | C+ | 2 | 9.0 | (mitochondrial carrier-peroxisomal membrane protein 34kD) member 17 | |
| ST13 * | 8 | C f/s | 1 | 17.5 | Suppression of tumorigenicity 13 (Hsp 70-interacting protein) |
| RBX1 | 2 | C f/s | 3 | 50.5 | Ring-box 1 |
| 3–4 | C+ 3′t | 1 | 92.0 | ||
| PMM1 | 4 | C f/s | 1 | 24.5 | Phosphomannomutase 1 |
| TCF20(AR1)† | 3 | C N/A | 1 | 5.0 | Transcription factor 20 (AR1) |
| dJ222E13.3† | 7 | C f/s | 2 | 12.0 | Weak match to Arabidopsis RNA and export factor binding protein |
| dJ222E13.1 | 8–9 | C f/s | 5 | 2.0 | Novel protein with some similarity to DrosophilaKRAKEN |
| bK1191B2.3† | 3 | C+ | 4 | 2.0 | Weakly similar to dJ1118 COA-ACYL carrier protein transacylase |
| dJ796I17.2* | 3 | C+ | 1 | 27.0 | CGI-51 |
| NPAP60L | 4 | C N/A | 1 | 11.5 | Nuclear pore-associated protein 60L |
| dJ355C18.1 | 9 | C+ | 1 | 1.5 | Matches KIAA0027 gene with weak similarity to GTPase activating protein |
| ECGF1 | 5 | C N/A | 1 | 3.0 | Endothelial cell growth factor 1 (platelet-derived) |
| GTSE1(B99) | 8 | C f/s | 1 | 13.5 | Homo sapiens G-2 and S-phase expressed 1 (GTSE1), |
| dJ1163J1.4† | 3 | C+ | 1 | 1.0 | Novel protein similar to C. elegans B0035.16 and bacterial tRNA (5-Methylaminomethyl-2thiouridylate)-Methyltransferases |
| DGCR2 | 2–3 | C+ | 1 | 2.3 | DiGeorge syndrome critical region gene 2 |
| AC007050.6 | 2 | C N/A | 1 | 11.0 | Homo sapiens mRNA- from clone DKFZp434G1017 |
| UBE2L3 | 2 | C+ 5′t | 1 | 71.0 | Ubiquitin-conjugating enzyme E2L3 |
| DJ756G23.3 | 5 | C+ | 1 | 2.0 | Similar to Tr:Q24191 Drosophila TRANSCRIPTIONAL REPRESSOR PROTEIN |
| bK212A2.1 | 2 | C+ 3′t | 1 | — | TNF-inducible protein CG12-1 mRNA |
| G22P1 * | 3 | C+ | 1 | >100.0 | Thyroid autoantigen 70kD (Ku antigen) |
[i] We tested 347 multiple-exon genes on Chromosome 22 for exon-skipping events using J_explorer and EST sequences from GenBank 119. Genes in which novel exon skipping events have been identified are ordered according to their relative physical organization along chromosome 22. Genes are identified using the HUGO name if one exists. In the absence of a HUGO identifier, the accession number of the sequence or the Sanger Centre clone name is used. Exon numbering is based on the exon structure of the original EMBL entries obtained from the Sanger Centre. ESTs confirming a skip were required to span both the 3′ and 5′ flanks of the skipped exon. To calculate the average number of ESTs confirming the reference isoform, the exon flanking ESTs in the reference isoform were totalled and the sum divided by corresponding averaged number of junctions. In cases where the reference isoform was not represented in the public EST databases, the sequence was confirmed using a corresponding experimentally-determined mRNA. Skip location and context is denoted as follows: (C) skip occurs in protein coding region; (+) ORF remains unchanged; (3′) skip occurs in 3′ UTR; (5′) skip occurs in 5′UTR; (f/s) frameshift is introduced by skip; (5′t) alternative start codon is used; (3′t) alternative stop codon is used; (N/A) not possible to reconstruct a protein; (†) genes (eight entries total) with an already-annotated exon skip in EMBL entries; (‡) (six entries total) with experimentally-confirmed notation: 2–4 indicates that exons 2, 3 and 4 skipped exons; 2–3 +5 indicates that exons 2, 3 and 5 are skipped. Experimentally confirmed skipping events in the genes CACNA1I, BZRP, MTMR3, andSEP3 had no EST matches and are not included.