pombase-admin
commented
13 years ago note, pho1 is curated differently because the transcript does not cover the CDS. This seems arbitrary to me...
| systematic ID | name(s) | PMID | notes |
|---|---|---|---|
| ?? | apn1 | https://www.pombase.org/reference/PMID:21193357 | |
| ?? | suc22 | PMID:8479429 | is this the earliest report of a regulatory RNA? |
| SPBP4H10.15 | aco2 | PMID:25724335 | fusion protein |
| SPAC17G6.02c ~SPNCRNA.600~ | tco1 | PMID:18276645 | DONE |
| SPAC1556.06.1 | meu1 &2 | PMID:11376151 | -- |
| SPAC140.02 | gar2 | PMID:8493104 | -- |
| SPCC622.17 | apn1 | -- | major transcript is pseudo |
| SPAC29B12.03 | spd1 | -- | -- |
| SPAC31G5.09c | spk1 | -- | alternative UTRs for this feature are represented by different polyA sites |
| SPAC1A6.03c | n/a | PMID:24929437 | genome organisation alternative splicing Annotated intron retained in most reads (but a few trans-reads detected); when retained truncated protein is produced we have annotated the smaller version (more examples in figure 4 d) |
| SPAC1142.03c | swi2 | PMID:22209903 | JQ308183 Swi2S, JQ308182 JQ308182 Swi2L |
| SPAC1486.05 | nup98 | - | DDJB:LC043101 Makes a N-terminally truncated version of the protein |
| SPAC1486.05 | nup189 | PMID:26137436 | ..detected two isoforms ... the shorter tran-script, a stretch of 65 nucleotides flanked by typical 50 and 30 splicing sites was removed from the longer transcript (Fig 1A), suggesting putative splicing. To confirm splicing of the nup189+ transcript, mutations were introduced into the putative intron sequences as indicated in Fig. 1B. |
| SPAC22A12.15c | bip1 | PMID:23066505 | bip1 mRNA is cleaved by ire1 during ER stress, this stabilises bip1 (this is unusual - normally ire1 cleavage has to do with catabolism so bip1 is a special case) |
| SPBC1718.02 | hop1 | - | LT963776 |
| SPBC649.04 | uvi15 | PMID:7898433 PMID:10954610 | pombase has 791 bp primary transcript annotated, but that's probably not right from PMID:7898433 - txn start mainly -50, some -53; polyA at 980, 1175 from PMID:10954610 - 54 bp 1186-1239 (inclusive) important for reg, so initial transcript must extend at least that far (but note this is beyond polyA, so not part of mature mRNA) also, primary transcript goes at least to 1287 (fig 7) |
| SPBC16E9.17c | rem1 | PMID:16024772 |
mah11
Need to curate some alternative transcript examples for Chado loading
can do some from the gene expression list:
gene expression, alternative splicing (3) gene expression, alternative transcript, alternative start (1) gene expression, alternative transcripts (7) gene expression, alternative transcripts detected (1) gene expression, alternative transcripts, alternative initiation site (1) gene expression, alternative transcripts, alternative polyadenylation (2) genome organization, alternative transcripts, alternative mRNA processing (1)
Original comment by: ValWood