General information for g179.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative General transcription factor IIH subunit 4.
Parent gene
- The parent gene g179 is located on chr_3: 1505371..1507138 (- 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 | g179 | g179.t2 | TTS | g179.t2 | 1505332 | 1505332 |
| chr_3 | g179 | g179.t2 | isoform | g179.t2 | 1505371 | 1507138 |
| chr_3 | g179 | g179.t2 | exon | g179.t2.exon1 | 1505371 | 1505655 |
| chr_3 | g179 | g179.t2 | exon | g179.t2.exon2 | 1505717 | 1506076 |
| chr_3 | g179 | g179.t2 | exon | g179.t2.exon3 | 1506145 | 1506247 |
| chr_3 | g179 | g179.t2 | cds | g179.t2.CDS1 | 1506227 | 1506247 |
| chr_3 | g179 | g179.t2 | exon | g179.t2.exon4 | 1506337 | 1506613 |
| chr_3 | g179 | g179.t2 | cds | g179.t2.CDS2 | 1506337 | 1506613 |
| chr_3 | g179 | g179.t2 | exon | g179.t2.exon5 | 1506697 | 1506828 |
| chr_3 | g179 | g179.t2 | cds | g179.t2.CDS3 | 1506697 | 1506828 |
| chr_3 | g179 | g179.t2 | exon | g179.t2.exon6 | 1506894 | 1507138 |
| chr_3 | g179 | g179.t2 | cds | g179.t2.CDS4 | 1506894 | 1507138 |
| chr_3 | g179 | g179.t2 | TSS | g179.t2 | 1507236 | 1507236 |
Sequences
>g179.t2 Gene=g179 Length=1402
ATGTCAAGTAAAAAAGGTTCATCAGCTGCCAGTCAAGTAGTGCATTTAGAATGTAAAAAT
CTGCATAGCTATCTTAAGTCACAAACACAAATAATTTCGAAACTCTATGAAGAACCATCA
ATTTGTTTAGCGGCATATCGTGATTTACCAGAAATTGCAAAACAATTTGTAATTAGAATG
TTGTGTGTTGAACAGCCAGTACCTCAAGCTGTAGTTCAATCTTGGGGATCACAAGTCTAT
GCTAAAGAAAATTTGGCAGCTTGTGAAGCTTTAACAGAACTTAGAATATGGACTGAAGCC
TCAATAAGTGGTGGATTAACAGCATGGGATTTGACTCCTTCATTTAAACGAAACTTGAAA
ATAGCTTGGCTTGGCGGAGGACGATCTTGGTCAATGTTCAACTCTGTAGAACAAAATGAT
GCAAAAAGTCGTGATATAAGTTTTCTAGACAACTATGCAATGTCTCGATGGAATTGCTTA
CTTCATTATATGGTGGACTCAAATGCATCCAAAGGCTCAGAAATGGAAGGAATTTCTGTT
GATGCTGTTCGAATTATTTTACACGCCAACTTAATGAATCGTAACGAACAAGATGGCTCA
TATATGCTGACAAGTCAAGGATTTCAATTTCTTTTGATGGACACACAATCGCAATTTCTC
TACATTGGGACGTGATTATAGCTCAGAGGGTTTGAGTGAGAACATGCAAACATTCTTACA
ACATTTGCGAGAATTTGGTCTCGTTTATCAACGAACTCGAAAAGAAAGAAGGTTTTTTCC
AACTCGTTTAGCTTTGAATTTTACAACAAAAAATGCAATTGTGCCAGAAAATATCATTGA
GAATGGAAATATCAATAATAATATTAACAAATTACAACAAAGTGATGACACTAATTATGA
AAAGGGTTATATTATAGTAGAGACAAATTATCGCGTTTATGCATACACAGACTCAAAATT
ACAAATTTCATTACTAGCATTGTTTACGGAACTTCTTTATCGTTTTCCTAATGTGACTGT
TGGAGTAATTACACGAGATTCTATACGACAAGCACTACGGGGTGGAATCACATCGAGACA
AATTATCAGCTATTTAGAGCAGCATGCGCACCCAAAGATGATTGCAAATGCGTCCACATC
ATCATTCAAAACAACATCCTTTCTTCCTCCAACAGTGATTGATCAAATAAAGCTATGGGA
AAATGAACGCAATAGATTCTCTTTTATCGATGGAGTGGTTTACAATCAATTTCTCTCAGA
AGCCGATTTCATGACGCTAAGAGATTATGCACAATCAATTGATGTACTTCTTTGGCAGAA
TGAACGCACAAGAACGATGGTTGTTAAAAAAACGGGTCATGAAGATGTAAAAAAATTTTG
GAAACGCTATTCAAAGGGTTAA
>g179.t2 Gene=g179 Length=224
MSSKKGSSAASQVVHLECKNLHSYLKSQTQIISKLYEEPSICLAAYRDLPEIAKQFVIRM
LCVEQPVPQAVVQSWGSQVYAKENLAACEALTELRIWTEASISGGLTAWDLTPSFKRNLK
IAWLGGGRSWSMFNSVEQNDAKSRDISFLDNYAMSRWNCLLHYMVDSNASKGSEMEGISV
DAVRIILHANLMNRNEQDGSYMLTSQGFQFLLMDTQSQFLYIGT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g179.t2 | PANTHER | PTHR13152 | TFIIH, POLYPEPTIDE 4 | 15 | 222 | 0 |
| 1 | g179.t2 | Pfam | PF03849 | Transcription factor Tfb2 | 24 | 219 | 0 |
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:0001671 | ATPase activator activity | MF |
| GO:0006289 | nucleotide-excision repair | BP |
| GO:0000439 | transcription factor TFIIH core complex | CC |
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.
