General information for g1205.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Transcription initiation factor TFIID subunit 5.
Parent gene
- The parent gene g1205 is located on chr_3: 8736774..8737637 (+ strand)
Gene structure
- The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.
| Chromosome | Gene | Transcript | Category | ID | Start | End |
|---|---|---|---|---|---|---|
| chr_3 | g1205 | g1205.t1 | TSS | g1205.t1 | 8734543 | 8734543 |
| chr_3 | g1205 | g1205.t1 | isoform | g1205.t1 | 8734641 | 8736774 |
| chr_3 | g1205 | g1205.t1 | exon | g1205.t1.exon1 | 8734641 | 8734700 |
| chr_3 | g1205 | g1205.t1 | cds | g1205.t1.CDS1 | 8734641 | 8734700 |
| chr_3 | g1205 | g1205.t1 | exon | g1205.t1.exon2 | 8734765 | 8734941 |
| chr_3 | g1205 | g1205.t1 | cds | g1205.t1.CDS2 | 8734765 | 8734941 |
| chr_3 | g1205 | g1205.t1 | exon | g1205.t1.exon3 | 8735000 | 8735960 |
| chr_3 | g1205 | g1205.t1 | cds | g1205.t1.CDS3 | 8735000 | 8735960 |
| chr_3 | g1205 | g1205.t1 | exon | g1205.t1.exon4 | 8736020 | 8736774 |
| chr_3 | g1205 | g1205.t1 | cds | g1205.t1.CDS4 | 8736020 | 8736774 |
| chr_3 | g1205 | g1205.t1 | TTS | g1205.t1 | 8736839 | 8736839 |
Sequences
>g1205.t1 Gene=g1205 Length=1953
ATGGCAAATAAAAATGACATCCTAGCAGTATTGCAGGTGTTGAAAAAGTACAATTTAAAG
GGAACTGAAAATCTCTTAAGACAAGAAGCTAATCTTACAGATATTCCTGAAAATTTCACA
CATGATGCATCTGACAGCGTTCTGCAAGCATATCAAAGTGAAGGCGATCCAAATTCCTAT
GAATCTTGCTATATTGAGTTGAGAAAATTTGTTGATTCGGCACTGGATATTTATAAATAT
GAACTCAGTATGATCCTTTATCCAGTTTTTGTGCATATGTATATTGAGCTCGTTTATAAT
AATCATGAAGAACAAGCGAAAGCATTGATGGAAAAATTTGGTGAAGAGCAGGAATATTAT
TATCAAGATGATTTAAAAAGACTCGCAATGATAACTAAAAGAGACCAAATGAGTGGCAAT
GATTTGACTGATACTTTTAAATCTAATGAATTTATTATAAGAATATCTCGCGACACCCTT
TCACTTCTAAAACGTCACTTACAAGAAAAGAAAGCAAGTGTTGTTATGAACATTATAAAT
GAGCATTTGTATTTTGATTTATATGAAGGAATGGCTAGAAATAAGAAGCAATGCGATGCA
ACTGCTGGTGCTTTGCTTGGTGAAGCAAGAAGACAAGACAACAAAGTTAAAGTATATTAT
GGATTATTGAAGGAACCAGATTATCAACAAATGACTACAACACAAGCACCACCGCCTGAA
GAGGATGACGATGAAGTTCAAGATGGTGATAAACCAAAGAAAAAAAAACAAAAGAAGGAT
CCACTATTTTCAAAAAAATCCAAAACTGACCCAAATGCACCTGCTTCTGATAGAATTCCT
CTACCTCAACTAAGAGATAATGATAAAAGTGAAAAAATTAAAGCATTGCGTGAAGCACAA
AAAAGAGTTAATCTTGGTCCAGATAGTTTACCATCAGTTTGTTACTACACTCTATTGAAC
TCACTTTATTCTGTAACTTGTGCTGAAATAAGTGAAGACTCAAGTCTCGTTGCTATTGGA
TTTTCGGATGCTACAATAAAAATTTGGCCGCTCACACCTGCAAAACTTCGAGAGCTCAAA
TCAGCTGAACAATTAAAAGATATTGATCGCGATGTTGATGATGTTCTTGTGAGAATGATG
GATGATAGGAAAGCAGAAACATCAAGAATTTTTACTGGACATAGTGGACCTGTATATCGT
TGCTCATTTACTTTTGATCGATCATTATTGCTGTCTTGTTCAGAAGATAGTACAATTAGA
TTATGGTCACTTCAAACATGGACTTGCTTAGTGGTTTATAAAGGTCATTTAAATCCAGTT
TGGGATGTTCGTTTTTCACCACACGGACATTATTTTGTGAGTTGTTCACATGATAAAACA
GCAAGAGTATGGGCAACAGATTCCCATCAACCTCTCCGCATATTCACTGGACATTTATCT
GACGTTGATTGTTGTGTATTTCATCCAAATTCAAATTATGTAGCAACAGGATCGTCAGAT
CGTACTGTAAGATTGTGGGATGTTTTATCAGGAAATCATGTAAGATTGATGACAGGTCAT
AAAGCATCAATTTTCTCTCTTGCATTTTCAATGTGTGGACGATATTTGGCATCAGGTGGA
AGTGATAAAGTAATAAATCTATGGGATTTAGCTCATGGTCATTTAGTTGCAACTCTTGAA
GGCCATACGTCTACAATTCATACCTTATGCTTCAGTCGTGATGGAACAATTTTAGCAACA
GGTGCACTTGACTGTAATCTAAAATTATGGGATTTTTCAAAGTTATGTGAAGACTTGAGT
GGTGAAAATGTAAACGTTTCTCATAATCCAGATGTTAGAAGTGGAGAAAATTATTTACTC
CGAACTTTTCCAACAAAACAATCACCCTTTATTGCTCTACATTTCACTCGTCGTAACTTG
CTGTATGGTGTAGGAATGTTTGAAAGCTCTTAA
>g1205.t1 Gene=g1205 Length=650
MANKNDILAVLQVLKKYNLKGTENLLRQEANLTDIPENFTHDASDSVLQAYQSEGDPNSY
ESCYIELRKFVDSALDIYKYELSMILYPVFVHMYIELVYNNHEEQAKALMEKFGEEQEYY
YQDDLKRLAMITKRDQMSGNDLTDTFKSNEFIIRISRDTLSLLKRHLQEKKASVVMNIIN
EHLYFDLYEGMARNKKQCDATAGALLGEARRQDNKVKVYYGLLKEPDYQQMTTTQAPPPE
EDDDEVQDGDKPKKKKQKKDPLFSKKSKTDPNAPASDRIPLPQLRDNDKSEKIKALREAQ
KRVNLGPDSLPSVCYYTLLNSLYSVTCAEISEDSSLVAIGFSDATIKIWPLTPAKLRELK
SAEQLKDIDRDVDDVLVRMMDDRKAETSRIFTGHSGPVYRCSFTFDRSLLLSCSEDSTIR
LWSLQTWTCLVVYKGHLNPVWDVRFSPHGHYFVSCSHDKTARVWATDSHQPLRIFTGHLS
DVDCCVFHPNSNYVATGSSDRTVRLWDVLSGNHVRLMTGHKASIFSLAFSMCGRYLASGG
SDKVINLWDLAHGHLVATLEGHTSTIHTLCFSRDGTILATGALDCNLKLWDFSKLCEDLS
GENVNVSHNPDVRSGENYLLRTFPTKQSPFIALHFTRRNLLYGVGMFESS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g1205.t1 | CDD | cd08044 | TAF5_NTD2 | 57 | 189 | 8.31628E-52 |
| 17 | g1205.t1 | CDD | cd00200 | WD40 | 324 | 591 | 4.26114E-79 |
| 16 | g1205.t1 | Gene3D | G3DSA:1.25.40.500 | - | 37 | 189 | 2.3E-51 |
| 15 | g1205.t1 | Gene3D | G3DSA:2.130.10.10 | - | 224 | 469 | 3.2E-38 |
| 14 | g1205.t1 | Gene3D | G3DSA:2.130.10.10 | - | 470 | 629 | 3.6E-45 |
| 28 | g1205.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 228 | 288 | - |
| 8 | g1205.t1 | PANTHER | PTHR19879 | TRANSCRIPTION INITIATION FACTOR TFIID | 7 | 647 | 5.3E-186 |
| 9 | g1205.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 410 | 424 | 7.3E-9 |
| 10 | g1205.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 494 | 508 | 7.3E-9 |
| 11 | g1205.t1 | PRINTS | PR00320 | G protein beta WD-40 repeat signature | 536 | 550 | 7.3E-9 |
| 1 | g1205.t1 | Pfam | PF04494 | WD40 associated region in TFIID subunit, NTD2 domain | 54 | 183 | 1.0E-42 |
| 4 | g1205.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 324 | 349 | 0.14 |
| 5 | g1205.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 387 | 423 | 9.1E-7 |
| 3 | g1205.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 427 | 464 | 1.6E-8 |
| 7 | g1205.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 470 | 507 | 2.4E-11 |
| 6 | g1205.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 512 | 549 | 4.2E-6 |
| 2 | g1205.t1 | Pfam | PF00400 | WD domain, G-beta repeat | 555 | 591 | 1.7E-7 |
| 26 | g1205.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 494 | 508 | - |
| 27 | g1205.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 536 | 550 | - |
| 25 | g1205.t1 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 578 | 592 | - |
| 29 | g1205.t1 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 391 | 600 | 56.447 |
| 31 | g1205.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 391 | 432 | 13.55 |
| 34 | g1205.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 433 | 474 | 13.783 |
| 33 | g1205.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 475 | 516 | 16.657 |
| 32 | g1205.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 517 | 558 | 15.688 |
| 30 | g1205.t1 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 559 | 593 | 14.352 |
| 24 | g1205.t1 | SMART | SM00320 | WD40_4 | 311 | 350 | 0.066 |
| 20 | g1205.t1 | SMART | SM00320 | WD40_4 | 384 | 423 | 3.5E-8 |
| 19 | g1205.t1 | SMART | SM00320 | WD40_4 | 426 | 465 | 7.3E-11 |
| 23 | g1205.t1 | SMART | SM00320 | WD40_4 | 468 | 507 | 6.3E-12 |
| 22 | g1205.t1 | SMART | SM00320 | WD40_4 | 510 | 549 | 6.9E-9 |
| 21 | g1205.t1 | SMART | SM00320 | WD40_4 | 552 | 591 | 2.9E-10 |
| 13 | g1205.t1 | SUPERFAMILY | SSF160897 | Taf5 N-terminal domain-like | 44 | 188 | 5.1E-46 |
| 12 | g1205.t1 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 310 | 625 | 8.7E-79 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K03130 (transcription initiation factor TFIID subunit 5)
Pathway
- This transcript belongs to the following pathways
Expression
Transcript expression in Pv11 cells
TPM values are indicated as average +/- STDEV. 
Differential expression
Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.
