General information for g8139.t3
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.t3 | isoform | g8139.t3 | 28760641 | 28762104 |
| chr_2 | g8139 | g8139.t3 | exon | g8139.t3.exon1 | 28760641 | 28761054 |
| chr_2 | g8139 | g8139.t3 | cds | g8139.t3.CDS1 | 28760728 | 28761054 |
| chr_2 | g8139 | g8139.t3 | exon | g8139.t3.exon2 | 28761114 | 28761287 |
| chr_2 | g8139 | g8139.t3 | cds | g8139.t3.CDS2 | 28761114 | 28761287 |
| chr_2 | g8139 | g8139.t3 | exon | g8139.t3.exon3 | 28761346 | 28761465 |
| chr_2 | g8139 | g8139.t3 | cds | g8139.t3.CDS3 | 28761346 | 28761465 |
| chr_2 | g8139 | g8139.t3 | exon | g8139.t3.exon4 | 28761522 | 28762104 |
| chr_2 | g8139 | g8139.t3 | cds | g8139.t3.CDS4 | 28761522 | 28761683 |
| chr_2 | g8139 | g8139.t3 | TTS | g8139.t3 | 28762833 | 28762833 |
| chr_2 | g8139 | g8139.t3 | TSS | g8139.t3 | NA | NA |
Sequences
>g8139.t3 Gene=g8139 Length=1291
GGTTCAGCTGTGAAAGCTGCAAAAGAAAAGAAAACTTCTCTTGCATCCGTGGTGGCGGCT
TCTGTGTCCAGTGGAAGTGTGAACTCTATGTCAAATAGTTTCTATCCTTCAACATTTGGT
GATGATGATATCAATGATGTTGCCGCAATGGGCGGTGTGAATTTGGCTGAGGAAAGTCAA
AGAATTTTAGGTTCGACTGAGTTTGTTGGTACACAAATTCGCTCATGTAAAGACGAAGTA
CTACTAAATCTTCCTATTCTGCAACAACGTATTCGACAACAAATGGCACGTCACGGTTTA
GATGAACCATCGTCCGATATTGCTGTTCTCATATCTCATGCTGCGCAAGAGCATCTTAAA
AATATTGTCGAAAAACTTGCAGTGATAGCTGAACACAGGATAGATATTTTAAAAATGGAT
CCACGTTATGAAATGACAAGTGATGTTCGAGGACAAATTAAATTTTTAGAGGAACTTGAT
AAAGCAGAGCAAAAGCGACACGAAGAAGTTGAGCGTGAGATTCTTTTACGAGCGGCAAAG
TCACGATCAAAAACTGAAGATCCCGAACAAGCAAAGCTGAAAGCGAAAGCAAAAGAAATG
CAAAGAGCAGAATTAGAAGAACTGCGGCATCGTGAAGCAAATAACACTGCACTGCAAGCT
ATTGGTCCAAGAAAAAGGAAACTTGAATCAGACACAACAACGACTGCGATTGGAAATGGA
ACAAATGTTGGTTCAACACCAATGATGAAGACGTCATCGGTTGCGCGACCACGTATTAAG
AGAGTTAACATGAGAGATATGATCTTTTATATGGAACAGGAGAAAGAAACTTGTCGCAGC
GTTATGCTGTATAAAACTTATCTCAAGTGATTTTCAGCTGAATTCAACATTGTTAAATTT
TTCTGTTGCTTGTTTAACGATTTAACTGTTTTTTTCATTAATTAATTAGTAAATCTGATC
AAAATCAATTCATTTGATGAAAACCAAAAGTTGCGCGCGGCAAATTATTATGAATTGAAA
CAGAAATGATAAAAAATGAGATACTAATGACCGTCATTAATGAAAAGTTATAAATTTATT
TTTTGCAATAGATTCATTGATTTAAACGCATGAGAGAAAACTGATAGTTAATAGTGAATA
ATTTAAATAGTTTTTAAGTCAAATCACATCCATCTTTCTTTTATAAATGCAAAAACATAT
TTTATGAATGCTCGAACGCCACTAAAAAGTCAATTTTTTACAGCCCAGCGGCAATGTGTC
GTCGACGCGCGAGAGGTTTTTCAATACAAAA
>g8139.t3 Gene=g8139 Length=260
MSNSFYPSTFGDDDINDVAAMGGVNLAEESQRILGSTEFVGTQIRSCKDEVLLNLPILQQ
RIRQQMARHGLDEPSSDIAVLISHAAQEHLKNIVEKLAVIAEHRIDILKMDPRYEMTSDV
RGQIKFLEELDKAEQKRHEEVEREILLRAAKSRSKTEDPEQAKLKAKAKEMQRAELEELR
HREANNTALQAIGPRKRKLESDTTTTAIGNGTNVGSTPMMKTSSVARPRIKRVNMRDMIF
YMEQEKETCRSVMLYKTYLK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g8139.t3 | CDD | cd08045 | TAF4 | 12 | 256 | 6.32078E-68 |
| 6 | g8139.t3 | Coils | Coil | Coil | 124 | 144 | - |
| 5 | g8139.t3 | Coils | Coil | Coil | 166 | 186 | - |
| 4 | g8139.t3 | Gene3D | G3DSA:1.10.20.10 | Histone | 52 | 99 | 8.3E-16 |
| 2 | g8139.t3 | PANTHER | PTHR15138 | TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 4 | 11 | 260 | 1.8E-103 |
| 1 | g8139.t3 | Pfam | PF05236 | Transcription initiation factor TFIID component TAF4 family | 15 | 256 | 9.1E-70 |
| 3 | g8139.t3 | SUPERFAMILY | SSF47113 | Histone-fold | 52 | 100 | 1.95E-12 |
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: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.
