General information for g5927.t16
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative General transcription factor IIH subunit 3.
Parent gene
- The parent gene g5927 is located on chr_2: 12881941..12882919 (+ 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 | g5927 | g5927.t16 | isoform | g5927.t16 | 12881941 | 12882919 |
| chr_2 | g5927 | g5927.t16 | TSS | g5927.t16 | 12881941 | 12881941 |
| chr_2 | g5927 | g5927.t16 | exon | g5927.t16.exon1 | 12881941 | 12882324 |
| chr_2 | g5927 | g5927.t16 | cds | g5927.t16.CDS1 | 12882076 | 12882324 |
| chr_2 | g5927 | g5927.t16 | exon | g5927.t16.exon2 | 12882386 | 12882919 |
| chr_2 | g5927 | g5927.t16 | cds | g5927.t16.CDS2 | 12882386 | 12882622 |
| chr_2 | g5927 | g5927.t16 | TTS | g5927.t16 | 12882946 | 12882946 |
Sequences
>g5927.t16 Gene=g5927 Length=918
GAAAATACATCGGACGACCCTAGTTTATTAGTTATTGCTGTAGATACTAACCCATCTCAA
ATAGTAATCAGAAAAAATCCAGATGCTTTGACAAAAATTATAAATTCAATTTCGGCATTT
GGAAATGCTCATTTAATGCAAAAACCTCAAAACAAATTGGCTGTAGTTGCATGTCATCAT
CATGAAAGTAAATTTCTTTATCCGTCCGCTGAAAAACCTCAAGAATTTCGACAAATTGAT
GGTCAATATGAGTTTTTTACATTTGTGGAAAAGTCAATTAAAAATAACTTGTCTGAATTG
ATAAAAAATGCTCCTAATATTTCAAATAATAGCGAAAGTTTATTGGCTGGATGTCTTGCT
ATGATATTGTGCTATATATTAAGAATCAAGAAATCCCAACCAACAGGAAGTAATTTAAAC
ACACGAATACTTGTTGTAACTGGCAGTGAAGACTCAGCCCATCAATACATGACTTATATG
AATGTATTCTTTACAGCACAAAAAGAAAGAGTTGCTATTGACATTTGTGCTCTGGACAAT
ACTTTAGTTTTACTTCAACAAGGTTGCGATATCACAGGAGGACATGTAATAATTTTTAAT
TTAAGAATAGTGATCTATTAACATTTGAATTTTGTCTTTTAGTATTTAAAAGTTCCTCAG
CTTGATGGACTTTTGCAATATTTACTCTGGATTTTTCTTCCTGATCCATCAATTCGGTCT
AAGCTTGCACTTCCGCCGCCCGTTAAAGTTGATTATCGTGCAGCATGCTTCTGTCATCGA
GAACTAATTGACATCGGATTTGTATGTTCTGTCTGTCTTTCAATCTTTTGCAAATTTTCT
CCTATTTGTACCACTTGTTCAACCGTCTTCAAAGTTCCATTACCTATTAAGCCTAAGAAA
AAGAAACTAAAAACTTAA
>g5927.t16 Gene=g5927 Length=161
MQKPQNKLAVVACHHHESKFLYPSAEKPQEFRQIDGQYEFFTFVEKSIKNNLSELIKNAP
NISNNSESLLAGCLAMILCYILRIKKSQPTGSNLNTRILVVTGSEDSAHQYMTYMNVFFT
AQKERVAIDICALDNTLVLLQQGCDITGGHVIIFNLRIVIY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g5927.t16 | Gene3D | G3DSA:3.40.50.410 | - | 1 | 155 | 1.5E-41 |
| 2 | g5927.t16 | PANTHER | PTHR12831 | TRANSCRIPTION INITIATION FACTOR IIH TFIIH , POLYPEPTIDE 3-RELATED | 3 | 150 | 8.6E-34 |
| 1 | g5927.t16 | Pfam | PF03850 | Transcription factor Tfb4 | 2 | 150 | 8.9E-41 |
| 5 | g5927.t16 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 67 | - |
| 6 | g5927.t16 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 68 | 84 | - |
| 4 | g5927.t16 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 85 | 161 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5927/g5927.t16; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5927.t16.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006355 | regulation of transcription, DNA-templated | BP |
| 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.
