Table 2.
Summary of bfsp2/Bfsp2 sequences resulting from database mining to illustrate the extent of the conservation of the helix IB extension and the presence of C-terminal tail domains.
| Species (splice variant) | Exon No | C-terminal Sequence (3′ end Exon 6 – Exon7 –Exon 8). Residues on the exon boundaries indicated in contrasting colours. | Exon 6/7 end phase | cDNA/EST evidence (GenBank ref. no) | ENSEMBL reference (UniGENE) |
|---|---|---|---|---|---|
| Danio rerio (Bfsp2α) | 7 | KVEMEIGTYHGILDGEESRFYTSTFPAGSSVPEGPTDPTPSTSGQQSC AQTDGTLLTEYYNTE* | 2 | YES (NM_001008633.1 and BC165202.1) | ENSDART00000004712 (UGID:112945; zgc:103750) |
| Danio rerio (Bfsp2β) | 8 | KVEMEIGTYHGILDGEESRFYTSTFPAGSSVPEGPTDPTPSTSGQQSC AQTDGSSAPEAPEEKNKF* | 2 and 1 | YES (EH478706.1, EH477771.1, EH477419.1, EH469985.1, EH469616.1, EH463619.1, EH463390.1) | ENSDART00000125889 |
| Gasterosteus aculeatus | 7a | HLEQEIGIYHGILDGEESRFHPAYLACPGQHSEPEGATGGSAPPGPQ* | 2 | YES (DW608316.1, DW604438.1, DW600648.1, DW593699.1, DN691906.1, DN692062.1, DW597869.1, DW597286.1, DN723004.1, DW600502.1, DN690742.1, DN685169.1, DW603481.1, DW600649, DN705778.1, DN723005.1) | ENSGACT00000003202 (UGID:1671045) |
| Oryzias latipes | 7 | KLEQEIGLYHGILDGEESRFQPTTTTQCTAPNAECEGATPAPPEQ* | 2 | YES (AM373876.1, AM354986.1, AM372182.1, BJ739079.1, FS537903.1, FS513580.1, FS538891.1, FS514567.1, FS540557.1, FS516248.1) | ENSORLT00000009608b |
| Tetraodon nigroviridisc | 7 | RLEQEIGLYHGILDGEESRFQVVQPQCPGLPPELEGAAAVPDPGA DPAGPGGGPAP* | 2 | YES (CR693727.1, CR688948.2, CR691352.2, CR704350.2, CR702307.2, CR689298.2, CR703338.1, CR694039.2, CR693777.2, CR682294.2, CR702596.2, CR682354.2, CR697322.2, CR703892.1, CR685998.2, CR693576.2, CR701067.2, CR699002.2) | ENSTNIT00000005791 |
| Oncorhynchus mykissd | NAe | RLELEIGTYHGILDGEESRYHPSMCTGASEPEGKQTPLPPHSEPSG NPALQGSNTSSP* | NA | YES (CU071847.1, FP319084.1) | NA |
| Ophthalmotilapia ventralis | NAe | f RLEQEIDLYHGILDGEENRFETLCSDLHSEPEGAAAPDSRSNPPG SPGPAAQ | NA | YES (JL564127.1) | NA |
| Xenopus tropicalisa | 7 | HLEKDIAAYHAILDGEENR* | 2 | YES (ES687881.1, ES680166.1) | ENSXETT00000060324 |
| Taeniopygia guttataa | 7 | QQLEKDIAAYHCLLDGEQSR* | 2 | YES (DV953306.1, FE712239.1) | ENSTGUT00000004669 |
| Gallas gallusa | 8h | QLEKDIAAYHCLLDGEQSS* | 2 | YES (NM_205218, X84807) | ENSGALG00000011712 andh ENSGALT00000019140. (UGID:117124) |
| Meleagris gallopavog | 8h | QLEKDIAAYHCLLDGEQSS* | 2 | NO | ENSMGAG00000011532 |
| Mus musculus | 7 | QLQKDVASYHALLDREENN* | 2 | YES (NM_001002896) | ENSMUSG00000032556 (UGID:1134439) |
| Home sapiens | 7 | QLQKDVASYHALLDREESG* | 2 | YES (NM_003571) | ENSG00000170819 (UGID:2729180) |
| Predicted sequence for a reptilian Bfsp2 | |||||
| Anolis carolinensisi | 7 | QLEKDIATYHCLLDKEESRYFSG* | 2 | NO | ENSACAG00000004403 |
Incomplete information in the ENSEMBL database, but Exon 7 containing an inframe STOP codon was deduced from available EST data.
Two transcripts given in the ENSEMBL database, but exon prediction for ENSORLT00000009605 is defies convention.
Two transcripts in the database, but there is no cDNA or EST evidence for ENSTNIT00000002586.
cDNA and predicted protein sequence published by Binkley et al.
Exon structure can not be confirmed.
The published cDNA sequence does not include an STOP codon.
In birds there is an extra exon that is alternatively spliced, which lengthens helix 1 by 49 residues. This exon was first identified in chicken. There is high sequence identity between G.gallus and M. gaaopavo and a similar sequence (VSYLSQEPRGSHRRRKTTLWELRRARRRQEQQVFHGSLRRTTLKRTANM) is present in intron 1 of T. guttata Bfsp2. There are issues affecting the predicted protein sequences for the all three ENSEMBL database entries. The insert sequences need to be formally proven for both turkey and zebra finch.
The predicted exon pattern for this splice variant claims 9 exons by splitting Exon 1 which accounts for this discrepancy.
This is predicted from an analysis of the genome sequence. As found for all other Bfsp2, the end phase of the penultimate exon is 2, and occurs just before an in frame STOP codon.