General information for g8139.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t4 | isoform | g8139.t4 | 28761114 | 28762104 |
| chr_2 | g8139 | g8139.t4 | exon | g8139.t4.exon1 | 28761114 | 28761287 |
| chr_2 | g8139 | g8139.t4 | cds | g8139.t4.CDS1 | 28761114 | 28761287 |
| chr_2 | g8139 | g8139.t4 | exon | g8139.t4.exon2 | 28761346 | 28761465 |
| chr_2 | g8139 | g8139.t4 | cds | g8139.t4.CDS2 | 28761346 | 28761465 |
| chr_2 | g8139 | g8139.t4 | exon | g8139.t4.exon3 | 28761522 | 28762104 |
| chr_2 | g8139 | g8139.t4 | cds | g8139.t4.CDS3 | 28761522 | 28761683 |
| chr_2 | g8139 | g8139.t4 | TTS | g8139.t4 | 28762833 | 28762833 |
| chr_2 | g8139 | g8139.t4 | TSS | g8139.t4 | NA | NA |
Sequences
>g8139.t4 Gene=g8139 Length=877
ATGGATCCACGTTATGAAATGACAAGTGATGTTCGAGGACAAATTAAATTTTTAGAGGAA
CTTGATAAAGCAGAGCAAAAGCGACACGAAGAAGTTGAGCGTGAGATTCTTTTACGAGCG
GCAAAGTCACGATCAAAAACTGAAGATCCCGAACAAGCAAAGCTGAAAGCGAAAGCAAAA
GAAATGCAAAGAGCAGAATTAGAAGAACTGCGGCATCGTGAAGCAAATAACACTGCACTG
CAAGCTATTGGTCCAAGAAAAAGGAAACTTGAATCAGACACAACAACGACTGCGATTGGA
AATGGAACAAATGTTGGTTCAACACCAATGATGAAGACGTCATCGGTTGCGCGACCACGT
ATTAAGAGAGTTAACATGAGAGATATGATCTTTTATATGGAACAGGAGAAAGAAACTTGT
CGCAGCGTTATGCTGTATAAAACTTATCTCAAGTGATTTTCAGCTGAATTCAACATTGTT
AAATTTTTCTGTTGCTTGTTTAACGATTTAACTGTTTTTTTCATTAATTAATTAGTAAAT
CTGATCAAAATCAATTCATTTGATGAAAACCAAAAGTTGCGCGCGGCAAATTATTATGAA
TTGAAACAGAAATGATAAAAAATGAGATACTAATGACCGTCATTAATGAAAAGTTATAAA
TTTATTTTTTGCAATAGATTCATTGATTTAAACGCATGAGAGAAAACTGATAGTTAATAG
TGAATAATTTAAATAGTTTTTAAGTCAAATCACATCCATCTTTCTTTTATAAATGCAAAA
ACATATTTTATGAATGCTCGAACGCCACTAAAAAGTCAATTTTTTACAGCCCAGCGGCAA
TGTGTCGTCGACGCGCGAGAGGTTTTTCAATACAAAA
>g8139.t4 Gene=g8139 Length=151
MDPRYEMTSDVRGQIKFLEELDKAEQKRHEEVEREILLRAAKSRSKTEDPEQAKLKAKAK
EMQRAELEELRHREANNTALQAIGPRKRKLESDTTTTAIGNGTNVGSTPMMKTSSVARPR
IKRVNMRDMIFYMEQEKETCRSVMLYKTYLK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g8139.t4 | CDD | cd08045 | TAF4 | 2 | 147 | 6.91977E-31 |
| 6 | g8139.t4 | Coils | Coil | Coil | 15 | 35 | - |
| 7 | g8139.t4 | Coils | Coil | Coil | 57 | 77 | - |
| 4 | g8139.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 41 | 60 | - |
| 5 | g8139.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 72 | 102 | - |
| 2 | g8139.t4 | PANTHER | PTHR15138:SF22 | SI:DKEY-219C3.2 | 4 | 151 | 3.3E-55 |
| 3 | g8139.t4 | PANTHER | PTHR15138 | TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 4 | 4 | 151 | 3.3E-55 |
| 1 | g8139.t4 | Pfam | PF05236 | Transcription initiation factor TFIID component TAF4 family | 3 | 147 | 8.7E-35 |
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:0005669 | transcription factor TFIID complex | CC |
| GO:0006352 | DNA-templated transcription, initiation | BP |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
