General information for g11399.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as General transcription factor IIH subunit 1.
Parent gene
- The parent gene g11399 is located on chr_1: 15964128..15965941 (+ 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_1 | g11399 | g11399.t1 | TSS | g11399.t1 | 15963969 | 15963969 |
| chr_1 | g11399 | g11399.t1 | isoform | g11399.t1 | 15964128 | 15965941 |
| chr_1 | g11399 | g11399.t1 | exon | g11399.t1.exon1 | 15964128 | 15964284 |
| chr_1 | g11399 | g11399.t1 | cds | g11399.t1.CDS1 | 15964128 | 15964284 |
| chr_1 | g11399 | g11399.t1 | exon | g11399.t1.exon2 | 15964341 | 15965941 |
| chr_1 | g11399 | g11399.t1 | cds | g11399.t1.CDS2 | 15964341 | 15965941 |
| chr_1 | g11399 | g11399.t1 | TTS | g11399.t1 | 15966290 | 15966290 |
Sequences
>g11399.t1 Gene=g11399 Length=1758
ATGGCTCAGAAGAAAGTAGAAGATGTTTTGTTGCAAATTCCACAAGTTAGATATAAAAAG
AGCGATGGAACTTTATATATTATGAAAGAACGAGTGGTGTTTATGCTAGAGAACAAAGAT
CAAATCGCTGTATCTCATAGCTTCTATGATATAAAGATGCAAAAAATTTCACCGGAAGGT
AAACCAAAAATTCAATTGCAACTTGTTCTTCAGGATGGCGGTAACTCCACATTTCATTTT
GTAAATAAAAATGGGACTCAGCATCAAATGCATGATCGTGAAAGAGTAAAAGAACTTATT
CAATCAATATTGCCAAATTTCAAGCGAAAAATTGATACCGAACTAGAACAAAAAAATAAA
CTACTTACAGAAAATCCGAAATTACTACAACTCTACAAAGACTTGGTTATATCGAAAGTT
ATAACATCTGAAGAATTTTGGACTATTCATGGAAAAGATTTACAAAATATTCAAAATGTT
TCGTCAAAACAAGAAATTGGAGTTTCGGGAAATTTTCTTACTGAAATCAAACCAATTAAC
GATGGTTGTAATCAATTTAAATATAATCTCACACCTGAAGTTATCGAATCAGTTTTTCGT
GCATATCCAGCTGTAAAAAAGAAACATGCAGAACACGTTCCAAACAAACTTACTGAATCC
GAATTTTGGACTAAATTTTTTCAATCGCATTATTTTCATCGTGATCGTATTACTACTGGA
ATGAAAGACTTGTTTGCAGAATGTGGTAAAATGGATGAAAGTATGTTAAAGAAAGATATA
AAAAAATCTAACGATCCTTTATTAAATCTATCAAAATTTGGTGATAATACAATTGAAGAA
GGTTTTTGCAGTTCGAGTTTAGTTGACAATAAAATTGACAATGCCGGCAACATTGTTCAT
CAAAATATTATCAAGCGATTTAATCAGCATTCTTTCCTTATTTTAAAAACTTGTAAAGAG
CAACAGAAAAATTCAGAAGCAAATCCAATTACAGATGAGCAGCAAGACAAGAAAAATAAT
AGCATAGAAGGATCAAATAAAAGACAAAAAAATGTTGATAATGAAGTAGTTCCTATTCAA
ACAGAAGAGGAGAGGAATGAACAAGTTCAAAAAAAGAAAATGAGAATTGCAGAGAAGATT
CATTATGATGATCTTGGGAATGATTTAACACAGCAAAATAAAGACATGTCAACTGTTACA
AATATAAATTTAGACAAACTAGAGAGGTATTTATATGGTCCAATGCCTTCGAATGAAAAC
TCTTTTGTAAACAGTAATAAATATAAAGTCGCGCCAATTGATGTAGTTGATATGACTATT
AGAAAAAATACTTCTGAATGGAGTCAACGAGTTACGCACAAGCAATTGATCAATCCTACA
GCAGCTGTGAATGCGCTTGGTGAATTGAGCCCGGGAGGTGTTTTAATGAGTGGCTATCAT
GACCACAATCTATCGCAATTTGTGCCAACTGAGGTTGAAAAAGAGCTCAATAATCTTTAT
TTATCAGCTGGTGAGTTGTTACATGAATTTTGGCTTTGTTTTCCACCAATTACTCCAGAG
CTAGAGATGAAATTACTAAAAATGCACGATACAATACAACGATTTAATTCCTCAAAAATC
AAGCCATTTGAAGATCGAATTATACGAGACTTGTCACCATTGGGATCACAGTTAGTGTCA
CATATAAATCTACTTATTGATACGGCATTCAGAAAATTCAGTTCTTGGAAAGAAAAGAAA
GTAGGCAAAGTCAAATAG
>g11399.t1 Gene=g11399 Length=585
MAQKKVEDVLLQIPQVRYKKSDGTLYIMKERVVFMLENKDQIAVSHSFYDIKMQKISPEG
KPKIQLQLVLQDGGNSTFHFVNKNGTQHQMHDRERVKELIQSILPNFKRKIDTELEQKNK
LLTENPKLLQLYKDLVISKVITSEEFWTIHGKDLQNIQNVSSKQEIGVSGNFLTEIKPIN
DGCNQFKYNLTPEVIESVFRAYPAVKKKHAEHVPNKLTESEFWTKFFQSHYFHRDRITTG
MKDLFAECGKMDESMLKKDIKKSNDPLLNLSKFGDNTIEEGFCSSSLVDNKIDNAGNIVH
QNIIKRFNQHSFLILKTCKEQQKNSEANPITDEQQDKKNNSIEGSNKRQKNVDNEVVPIQ
TEEERNEQVQKKKMRIAEKIHYDDLGNDLTQQNKDMSTVTNINLDKLERYLYGPMPSNEN
SFVNSNKYKVAPIDVVDMTIRKNTSEWSQRVTHKQLINPTAAVNALGELSPGGVLMSGYH
DHNLSQFVPTEVEKELNNLYLSAGELLHEFWLCFPPITPELEMKLLKMHDTIQRFNSSKI
KPFEDRIIRDLSPLGSQLVSHINLLIDTAFRKFSSWKEKKVGKVK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g11399.t1 | CDD | cd13229 | PH_TFIIH | 10 | 105 | 2.79063E-28 |
| 9 | g11399.t1 | Coils | Coil | Coil | 359 | 379 | - |
| 8 | g11399.t1 | Gene3D | G3DSA:2.30.29.30 | - | 1 | 112 | 1.8E-40 |
| 13 | g11399.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 324 | 355 | - |
| 14 | g11399.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 330 | 350 | - |
| 3 | g11399.t1 | PANTHER | PTHR12856 | TRANSCRIPTION INITIATION FACTOR IIH-RELATED | 9 | 580 | 1.2E-137 |
| 4 | g11399.t1 | PANTHER | PTHR12856:SF0 | GENERAL TRANSCRIPTION FACTOR IIH SUBUNIT 1 | 9 | 580 | 1.2E-137 |
| 1 | g11399.t1 | Pfam | PF08567 | TFIIH p62 subunit, N-terminal domain | 17 | 101 | 9.5E-19 |
| 2 | g11399.t1 | Pfam | PF03909 | BSD domain | 183 | 236 | 4.4E-16 |
| 15 | g11399.t1 | ProSiteProfiles | PS50858 | BSD domain profile. | 105 | 148 | 10.489 |
| 16 | g11399.t1 | ProSiteProfiles | PS50858 | BSD domain profile. | 182 | 234 | 14.193 |
| 11 | g11399.t1 | SMART | SM00751 | wurzfinal6 | 103 | 158 | 1.0E-6 |
| 12 | g11399.t1 | SMART | SM00751 | wurzfinal6 | 182 | 234 | 5.3E-16 |
| 5 | g11399.t1 | SUPERFAMILY | SSF50729 | PH domain-like | 5 | 110 | 6.15E-27 |
| 7 | g11399.t1 | SUPERFAMILY | SSF140383 | BSD domain-like | 109 | 148 | 8.63E-12 |
| 6 | g11399.t1 | SUPERFAMILY | SSF140383 | BSD domain-like | 178 | 233 | 9.16E-7 |
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:0006351 | transcription, DNA-templated | BP |
| GO:0006289 | nucleotide-excision repair | BP |
| GO:0000439 | transcription factor TFIIH core complex | CC |
KEGG
Orthology
- This transcript has been annotated with K03141 (transcription initiation factor TFIIH subunit 1)
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.
