General information for g5035.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been not been annotated.
Parent gene
- The parent gene g5035 is located on chr_2: 6543565..6543845 (+ 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 | g5035 | g5035.t1 | TSS | g5035.t1 | 6543439 | 6543439 |
| chr_2 | g5035 | g5035.t1 | isoform | g5035.t1 | 6543565 | 6543845 |
| chr_2 | g5035 | g5035.t1 | exon | g5035.t1.exon1 | 6543565 | 6543599 |
| chr_2 | g5035 | g5035.t1 | cds | g5035.t1.CDS1 | 6543565 | 6543599 |
| chr_2 | g5035 | g5035.t1 | exon | g5035.t1.exon2 | 6543659 | 6543845 |
| chr_2 | g5035 | g5035.t1 | cds | g5035.t1.CDS2 | 6543659 | 6543845 |
| chr_2 | g5035 | g5035.t1 | TTS | g5035.t1 | 6544492 | 6544492 |
Sequences
>g5035.t1 Gene=g5035 Length=222
ATGGTAAATGTTCTTAAAGGAGTTTTAGTTGAATGTGATCCGGCAATGAAACAATTTCTT
TTACATTTAGATGAAAAATTGATATTGGGTCGAAAATTTATTCTACAAGAATTAGACGAG
AAGCATTTGTTTATCGCATCTGACATTGTTGAAACATTACAAGCAAAAATTGATGATTTA
ATGGACCGCATTAGTTTTCCATTGCACGAAAAGGATAATTAA
>g5035.t1 Gene=g5035 Length=73
MVNVLKGVLVECDPAMKQFLLHLDEKLILGRKFILQELDEKHLFIASDIVETLQAKIDDL
MDRISFPLHEKDN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5035.t1 | Gene3D | G3DSA:3.30.70.1220 | General transcription factor iih | 1 | 71 | 0 |
| 2 | g5035.t1 | PANTHER | PTHR28580 | GENERAL TRANSCRIPTION FACTOR IIH SUBUNIT 5 | 1 | 67 | 0 |
| 1 | g5035.t1 | Pfam | PF06331 | Transcription factor TFIIH complex subunit Tfb5 | 1 | 67 | 0 |
| 4 | g5035.t1 | SMART | SM01395 | Tbf5_2 | 1 | 68 | 0 |
| 3 | g5035.t1 | SUPERFAMILY | SSF142897 | TFB5-like | 6 | 70 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5035/g5035.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5035.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006367 | transcription initiation from RNA polymerase II promoter | BP |
| GO:0006289 | nucleotide-excision repair | BP |
| GO:0000439 | transcription factor TFIIH core complex | CC |
KEGG
Orthology
- This transcript has been annotated with K10845 (TFIIH basal transcription factor complex TTD-A subunit)
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.
