General information for g8139.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Transcription initiation factor TFIID subunit 4.
Parent gene
- The parent gene g8139 is located on chr_2: 28761683..28762748 (+ 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_2 | g8139 | g8139.t1 | TSS | g8139.t1 | 28755717 | 28755717 |
| chr_2 | g8139 | g8139.t1 | isoform | g8139.t1 | 28755747 | 28761683 |
| chr_2 | g8139 | g8139.t1 | exon | g8139.t1.exon1 | 28755747 | 28755945 |
| chr_2 | g8139 | g8139.t1 | cds | g8139.t1.CDS1 | 28755747 | 28755945 |
| chr_2 | g8139 | g8139.t1 | TTS | g8139.t1 | 28756226 | 28756226 |
| chr_2 | g8139 | g8139.t1 | exon | g8139.t1.exon2 | 28756366 | 28756907 |
| chr_2 | g8139 | g8139.t1 | cds | g8139.t1.CDS2 | 28756366 | 28756907 |
| chr_2 | g8139 | g8139.t1 | exon | g8139.t1.exon3 | 28757141 | 28757293 |
| chr_2 | g8139 | g8139.t1 | cds | g8139.t1.CDS3 | 28757141 | 28757293 |
| chr_2 | g8139 | g8139.t1 | exon | g8139.t1.exon4 | 28757356 | 28757526 |
| chr_2 | g8139 | g8139.t1 | cds | g8139.t1.CDS4 | 28757356 | 28757526 |
| chr_2 | g8139 | g8139.t1 | exon | g8139.t1.exon5 | 28758206 | 28758688 |
| chr_2 | g8139 | g8139.t1 | cds | g8139.t1.CDS5 | 28758206 | 28758688 |
| chr_2 | g8139 | g8139.t1 | exon | g8139.t1.exon6 | 28758747 | 28758857 |
| chr_2 | g8139 | g8139.t1 | cds | g8139.t1.CDS6 | 28758747 | 28758857 |
| chr_2 | g8139 | g8139.t1 | exon | g8139.t1.exon7 | 28758913 | 28759167 |
| chr_2 | g8139 | g8139.t1 | cds | g8139.t1.CDS7 | 28758913 | 28759167 |
| chr_2 | g8139 | g8139.t1 | exon | g8139.t1.exon8 | 28760176 | 28761054 |
| chr_2 | g8139 | g8139.t1 | cds | g8139.t1.CDS8 | 28760176 | 28761054 |
| chr_2 | g8139 | g8139.t1 | exon | g8139.t1.exon9 | 28761114 | 28761287 |
| chr_2 | g8139 | g8139.t1 | cds | g8139.t1.CDS9 | 28761114 | 28761287 |
| chr_2 | g8139 | g8139.t1 | exon | g8139.t1.exon10 | 28761346 | 28761465 |
| chr_2 | g8139 | g8139.t1 | cds | g8139.t1.CDS10 | 28761346 | 28761465 |
| chr_2 | g8139 | g8139.t1 | exon | g8139.t1.exon11 | 28761522 | 28761683 |
| chr_2 | g8139 | g8139.t1 | cds | g8139.t1.CDS11 | 28761522 | 28761683 |
Sequences
>g8139.t1 Gene=g8139 Length=3249
ATGTCTGACTTTCCTCTTAATGAGGCATTAAGAAAAATAAAAAATGAGATTGCCGTGAAC
GTGAACCAACAAGTAGATTCGTTAGAAAAGTTATTAGAACAGGAATCGGGTACGGTGCAA
TATAAAAATGGCAGTAATGATTCGAAAGAATCCATCATGATTGAATTGACGACTACATCA
GTAAATTCGCAGAATAATGTTTCTTCTACGTTAAAAGATAGCGCAAATCTCACAAGGTCT
ATCGATACTAATTTTAACTTTAATCAATCCTATCAATCAACTTTAAACAATAATAATCAT
TTAGTTCTTCACAATCATCATCAACATATTGATAATCAACAACAACAACAGAGTCATCAG
CAGATATTTTCAAATTTTATTGCTGGTCAACAGCAAAACAACATAAATAATAATAATCGC
AGTGTATCAAATATGCCAAAGAATGAGCCTGTCAAACTAGTATATCCTTCGTCACAGGCA
ACGTCTTCGACTATCGTGACTATGAACAATAATCGTGTCACATTCACAAGTGCACCCGTT
CAAAATGGTACAATAAGTTTATCACCAATGACCGCGAATCAATTAACACAGCCAAATCAA
CAACAACAGACCACTGTCATGCAGCAGCGTGCAACTGGCGGTCAGCAACAAGCACCGACA
CTTATATTCAAAAATACAAGTAATTCTGGACCAGGAACGCTCATTTCAGCACCGGTTTCA
GTGTCAAAAGCAAACAGTCAGGCACCAGCCTCGAATATTGTTTTGCCTGGTAATTTAGTG
GTAAATATTCGACCACAAACAACATCTGGAGCTCAAAATGCTCAAAAAACAGTTGGACCA
CAGCGAATGGTGAATGTAATTAATCAACAAGTAGTTAGGCCTCAAAATAATACAATTACA
CTTTCAAGCCTTCCACAAAATATGCAAGGCAATACAATTCTATTAAAGCAAGATAATGGA
TCGTATCAACTATTACGTATTAGTACGCAACCAGGAACAAACGTCACTCCAGGTTTAACA
CCAACGGCAGGCTCTACAATTCGTTTACAAACGGTACCCGCTGCTTCTATTGCACCGACT
AATACAATACTAGTAAATACATCGTCTGCATCAAATCAACATCAGCAGCAACAAATTCTC
ACGTCACAATCGACGCCTATTGTATCTGTAACCCAACAAGTGCCCGCTCTCACAACGACA
CAACAAGTACAATCACAAAGTCAAAGTAATTCTGCTCCTGGGAGTGCTGTAGTTGTTCAA
CAACAAAGTGGAACTAATGCCACAGTTACAAATTCAACTACGGCAACTGGTGGCGTTGTT
GTAACTCAATCTCCTGCTCAACGTAATGATAATGCCAAAGAAAAATGTCGCAAGTTTTTG
ACAAATTTAATTGATTTGTCAAAAAGAGAACCTGCACAAGTTGAGCTTAATGTAAAAACT
TTAATTCAAGAGCTGGTGGATGCAAATGTAGGGCCAGAAGATTTCTGTAAGAAATTAGAA
AATTTACTCAATGCAGCACCTCAACCATGTCTTGTAGGATTTCTCAAAAGAAGCCTTCCA
CTTTTGAGACAATCACTAGTGACGAAAGAAACTGTAATAGAAGGAATAAACCCTCCAAGT
CCAAGCGTTGCTTTCTCGGGTGCAATTACTCAAATTCCTGCACAAATTCGACCAATCGGT
CAGACTGTAGTGTCAGGTCAAACTCAAATTAGAATGGTACAACCGGCACCAAGGATAGGA
CAGACAACAATCAGACCAACAGCAGCACCTCACATTGTTCGAACAACAGCACCTACTATG
CGACCTTTAACGACCATAAGAGGACAAACGACGATTGTGCAAACACAAGCAAATAATCAA
GTGCCCGCATTACATCCTGTTGGATCAACTCTTATTTCAACAGGAACTGCTCAGATACGA
TCCCAAACTGCGTCTAACGTTGTCACTCGCCCTCAAACATCAGTGGCACAAATTCGACCC
ACACAAACTTCCACAACCCCGAATCGTACACAAAAAGCCCAAACCTTGTCATCGCCACTT
TCAAATTCAGTTCAAGTGACAAAAACGCAAGCATCTAGCGGTGCGCAATTAAAACAAATT
GTAACTAATAATGTAAATATCAATAATAATAATAATAATAACAACAATAATTCAAAAAGT
AATAACAACAAGAATGAAGTTTCCATCGCTGTGGTTTCAACAGTTAATAATAGCACACAT
GTGACGAACAGTAAAACGAGCACTACTAGTCCCAATAGTAAATCACCCACAAAATCTAAT
GCTCTTTCTAATTCCCATTCCTCTATAACCACATCGAACACTACACCTACCAAATCACCT
ACATTCAATAATAAAATGCATCACGAAAAAAAATCTCAGGGTTCAGCTGTGAAAGCTGCA
AAAGAAAAGAAAACTTCTCTTGCATCCGTGGTGGCGGCTTCTGTGTCCAGTGGAAGTGTG
AACTCTATGTCAAATAGTTTCTATCCTTCAACATTTGGTGATGATGATATCAATGATGTT
GCCGCAATGGGCGGTGTGAATTTGGCTGAGGAAAGTCAAAGAATTTTAGGTTCGACTGAG
TTTGTTGGTACACAAATTCGCTCATGTAAAGACGAAGTACTACTAAATCTTCCTATTCTG
CAACAACGTATTCGACAACAAATGGCACGTCACGGTTTAGATGAACCATCGTCCGATATT
GCTGTTCTCATATCTCATGCTGCGCAAGAGCATCTTAAAAATATTGTCGAAAAACTTGCA
GTGATAGCTGAACACAGGATAGATATTTTAAAAATGGATCCACGTTATGAAATGACAAGT
GATGTTCGAGGACAAATTAAATTTTTAGAGGAACTTGATAAAGCAGAGCAAAAGCGACAC
GAAGAAGTTGAGCGTGAGATTCTTTTACGAGCGGCAAAGTCACGATCAAAAACTGAAGAT
CCCGAACAAGCAAAGCTGAAAGCGAAAGCAAAAGAAATGCAAAGAGCAGAATTAGAAGAA
CTGCGGCATCGTGAAGCAAATAACACTGCACTGCAAGCTATTGGTCCAAGAAAAAGGAAA
CTTGAATCAGACACAACAACGACTGCGATTGGAAATGGAACAAATGTTGGTTCAACACCA
ATGATGAAGACGTCATCGGTTGCGCGACCACGTATTAAGAGAGTTAACATGAGAGATATG
ATCTTTTATATGGAACAGGAGAAAGAAACTTGTCGCAGCGTTATGCTGTATAAAACTTAT
CTCAAGTGA
>g8139.t1 Gene=g8139 Length=1082
MSDFPLNEALRKIKNEIAVNVNQQVDSLEKLLEQESGTVQYKNGSNDSKESIMIELTTTS
VNSQNNVSSTLKDSANLTRSIDTNFNFNQSYQSTLNNNNHLVLHNHHQHIDNQQQQQSHQ
QIFSNFIAGQQQNNINNNNRSVSNMPKNEPVKLVYPSSQATSSTIVTMNNNRVTFTSAPV
QNGTISLSPMTANQLTQPNQQQQTTVMQQRATGGQQQAPTLIFKNTSNSGPGTLISAPVS
VSKANSQAPASNIVLPGNLVVNIRPQTTSGAQNAQKTVGPQRMVNVINQQVVRPQNNTIT
LSSLPQNMQGNTILLKQDNGSYQLLRISTQPGTNVTPGLTPTAGSTIRLQTVPAASIAPT
NTILVNTSSASNQHQQQQILTSQSTPIVSVTQQVPALTTTQQVQSQSQSNSAPGSAVVVQ
QQSGTNATVTNSTTATGGVVVTQSPAQRNDNAKEKCRKFLTNLIDLSKREPAQVELNVKT
LIQELVDANVGPEDFCKKLENLLNAAPQPCLVGFLKRSLPLLRQSLVTKETVIEGINPPS
PSVAFSGAITQIPAQIRPIGQTVVSGQTQIRMVQPAPRIGQTTIRPTAAPHIVRTTAPTM
RPLTTIRGQTTIVQTQANNQVPALHPVGSTLISTGTAQIRSQTASNVVTRPQTSVAQIRP
TQTSTTPNRTQKAQTLSSPLSNSVQVTKTQASSGAQLKQIVTNNVNINNNNNNNNNNSKS
NNNKNEVSIAVVSTVNNSTHVTNSKTSTTSPNSKSPTKSNALSNSHSSITTSNTTPTKSP
TFNNKMHHEKKSQGSAVKAAKEKKTSLASVVAASVSSGSVNSMSNSFYPSTFGDDDINDV
AAMGGVNLAEESQRILGSTEFVGTQIRSCKDEVLLNLPILQQRIRQQMARHGLDEPSSDI
AVLISHAAQEHLKNIVEKLAVIAEHRIDILKMDPRYEMTSDVRGQIKFLEELDKAEQKRH
EEVEREILLRAAKSRSKTEDPEQAKLKAKAKEMQRAELEELRHREANNTALQAIGPRKRK
LESDTTTTAIGNGTNVGSTPMMKTSSVARPRIKRVNMRDMIFYMEQEKETCRSVMLYKTY
LK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g8139.t1 | CDD | cd08045 | TAF4 | 834 | 1078 | 3.21929E-74 |
| 8 | g8139.t1 | Coils | Coil | Coil | 946 | 966 | - |
| 9 | g8139.t1 | Coils | Coil | Coil | 988 | 1008 | - |
| 6 | g8139.t1 | Gene3D | G3DSA:1.20.120.1110 | - | 435 | 544 | 7.6E-33 |
| 7 | g8139.t1 | Gene3D | G3DSA:1.10.20.10 | Histone | 874 | 921 | 5.5E-15 |
| 12 | g8139.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 641 | 696 | - |
| 13 | g8139.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 736 | 782 | - |
| 14 | g8139.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 736 | 796 | - |
| 3 | g8139.t1 | PANTHER | PTHR15138 | TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 4 | 262 | 1082 | 6.0E-134 |
| 2 | g8139.t1 | Pfam | PF07531 | NHR1 homology to TAF | 453 | 539 | 3.9E-30 |
| 1 | g8139.t1 | Pfam | PF05236 | Transcription initiation factor TFIID component TAF4 family | 837 | 1078 | 3.3E-68 |
| 15 | g8139.t1 | ProSiteProfiles | PS51119 | TAFH/NHR1 domain profile. | 449 | 545 | 26.538 |
| 11 | g8139.t1 | SMART | SM00549 | nervy_1 | 452 | 542 | 1.7E-40 |
| 5 | g8139.t1 | SUPERFAMILY | SSF158553 | TAFH domain-like | 451 | 543 | 2.49E-29 |
| 4 | g8139.t1 | SUPERFAMILY | SSF47113 | Histone-fold | 874 | 922 | 2.09E-11 |
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:0046982 | protein heterodimerization activity | MF |
| GO:0006351 | transcription, DNA-templated | BP |
| GO:0005669 | transcription factor TFIID complex | CC |
| GO:0006352 | DNA-templated transcription, initiation | BP |
KEGG
Orthology
- This transcript has been annotated with K03129 (transcription initiation factor TFIID subunit 4)
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.
