General information for g8139.t2
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.t2 | isoform | g8139.t2 | 28758913 | 28762104 |
| chr_2 | g8139 | g8139.t2 | exon | g8139.t2.exon1 | 28758913 | 28759167 |
| chr_2 | g8139 | g8139.t2 | cds | g8139.t2.CDS1 | 28758967 | 28759167 |
| chr_2 | g8139 | g8139.t2 | exon | g8139.t2.exon2 | 28760641 | 28761054 |
| chr_2 | g8139 | g8139.t2 | cds | g8139.t2.CDS2 | 28760641 | 28761054 |
| chr_2 | g8139 | g8139.t2 | exon | g8139.t2.exon3 | 28761114 | 28761287 |
| chr_2 | g8139 | g8139.t2 | cds | g8139.t2.CDS3 | 28761114 | 28761287 |
| chr_2 | g8139 | g8139.t2 | exon | g8139.t2.exon4 | 28761346 | 28761465 |
| chr_2 | g8139 | g8139.t2 | cds | g8139.t2.CDS4 | 28761346 | 28761465 |
| chr_2 | g8139 | g8139.t2 | exon | g8139.t2.exon5 | 28761522 | 28762104 |
| chr_2 | g8139 | g8139.t2 | cds | g8139.t2.CDS5 | 28761522 | 28761683 |
| chr_2 | g8139 | g8139.t2 | TTS | g8139.t2 | 28762833 | 28762833 |
| chr_2 | g8139 | g8139.t2 | TSS | g8139.t2 | NA | NA |
Sequences
>g8139.t2 Gene=g8139 Length=1546
GCACAAATTCGACCAATCGGTCAGACTGTAGTGTCAGGTCAAACTCAAATTAGAATGGTA
CAACCGGCACCAAGGATAGGACAGACAACAATCAGACCAACAGCAGCACCTCACATTGTT
CGAACAACAGCACCTACTATGCGACCTTTAACGACCATAAGAGGACAAACGACGATTGTG
CAAACACAAGCAAATAATCAAGTGCCCGCATTACATCCTGTTGGATCAACTCTTATTTCA
ACAGGAACTGCTCAGGGTTCAGCTGTGAAAGCTGCAAAAGAAAAGAAAACTTCTCTTGCA
TCCGTGGTGGCGGCTTCTGTGTCCAGTGGAAGTGTGAACTCTATGTCAAATAGTTTCTAT
CCTTCAACATTTGGTGATGATGATATCAATGATGTTGCCGCAATGGGCGGTGTGAATTTG
GCTGAGGAAAGTCAAAGAATTTTAGGTTCGACTGAGTTTGTTGGTACACAAATTCGCTCA
TGTAAAGACGAAGTACTACTAAATCTTCCTATTCTGCAACAACGTATTCGACAACAAATG
GCACGTCACGGTTTAGATGAACCATCGTCCGATATTGCTGTTCTCATATCTCATGCTGCG
CAAGAGCATCTTAAAAATATTGTCGAAAAACTTGCAGTGATAGCTGAACACAGGATAGAT
ATTTTAAAAATGGATCCACGTTATGAAATGACAAGTGATGTTCGAGGACAAATTAAATTT
TTAGAGGAACTTGATAAAGCAGAGCAAAAGCGACACGAAGAAGTTGAGCGTGAGATTCTT
TTACGAGCGGCAAAGTCACGATCAAAAACTGAAGATCCCGAACAAGCAAAGCTGAAAGCG
AAAGCAAAAGAAATGCAAAGAGCAGAATTAGAAGAACTGCGGCATCGTGAAGCAAATAAC
ACTGCACTGCAAGCTATTGGTCCAAGAAAAAGGAAACTTGAATCAGACACAACAACGACT
GCGATTGGAAATGGAACAAATGTTGGTTCAACACCAATGATGAAGACGTCATCGGTTGCG
CGACCACGTATTAAGAGAGTTAACATGAGAGATATGATCTTTTATATGGAACAGGAGAAA
GAAACTTGTCGCAGCGTTATGCTGTATAAAACTTATCTCAAGTGATTTTCAGCTGAATTC
AACATTGTTAAATTTTTCTGTTGCTTGTTTAACGATTTAACTGTTTTTTTCATTAATTAA
TTAGTAAATCTGATCAAAATCAATTCATTTGATGAAAACCAAAAGTTGCGCGCGGCAAAT
TATTATGAATTGAAACAGAAATGATAAAAAATGAGATACTAATGACCGTCATTAATGAAA
AGTTATAAATTTATTTTTTGCAATAGATTCATTGATTTAAACGCATGAGAGAAAACTGAT
AGTTAATAGTGAATAATTTAAATAGTTTTTAAGTCAAATCACATCCATCTTTCTTTTATA
AATGCAAAAACATATTTTATGAATGCTCGAACGCCACTAAAAAGTCAATTTTTTACAGCC
CAGCGGCAATGTGTCGTCGACGCGCGAGAGGTTTTTCAATACAAAA
>g8139.t2 Gene=g8139 Length=356
MVQPAPRIGQTTIRPTAAPHIVRTTAPTMRPLTTIRGQTTIVQTQANNQVPALHPVGSTL
ISTGTAQGSAVKAAKEKKTSLASVVAASVSSGSVNSMSNSFYPSTFGDDDINDVAAMGGV
NLAEESQRILGSTEFVGTQIRSCKDEVLLNLPILQQRIRQQMARHGLDEPSSDIAVLISH
AAQEHLKNIVEKLAVIAEHRIDILKMDPRYEMTSDVRGQIKFLEELDKAEQKRHEEVERE
ILLRAAKSRSKTEDPEQAKLKAKAKEMQRAELEELRHREANNTALQAIGPRKRKLESDTT
TTAIGNGTNVGSTPMMKTSSVARPRIKRVNMRDMIFYMEQEKETCRSVMLYKTYLK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g8139.t2 | CDD | cd08045 | TAF4 | 108 | 352 | 2.98301E-71 |
| 6 | g8139.t2 | Coils | Coil | Coil | 220 | 240 | - |
| 5 | g8139.t2 | Coils | Coil | Coil | 262 | 282 | - |
| 4 | g8139.t2 | Gene3D | G3DSA:1.10.20.10 | Histone | 148 | 195 | 1.3E-15 |
| 2 | g8139.t2 | PANTHER | PTHR15138 | TRANSCRIPTION INITIATION FACTOR TFIID SUBUNIT 4 | 17 | 356 | 1.6E-106 |
| 1 | g8139.t2 | Pfam | PF05236 | Transcription initiation factor TFIID component TAF4 family | 111 | 352 | 2.7E-69 |
| 3 | g8139.t2 | SUPERFAMILY | SSF47113 | Histone-fold | 148 | 196 | 4.81E-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.
