General information for g4136.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as General transcription and DNA repair factor IIH helicase subunit XPD.
Parent gene
- The parent gene g4136 is located on chr_3: 30891773..30893551 (+ 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 | g4136 | g4136.t2 | isoform | g4136.t2 | 30885175 | 30891003 |
| chr_3 | g4136 | g4136.t2 | exon | g4136.t2.exon1 | 30885175 | 30886871 |
| chr_3 | g4136 | g4136.t2 | exon | g4136.t2.exon2 | 30886933 | 30887168 |
| chr_3 | g4136 | g4136.t2 | exon | g4136.t2.exon3 | 30887234 | 30887305 |
| chr_3 | g4136 | g4136.t2 | exon | g4136.t2.exon4 | 30887371 | 30887421 |
| chr_3 | g4136 | g4136.t2 | exon | g4136.t2.exon5 | 30887822 | 30887916 |
| chr_3 | g4136 | g4136.t2 | exon | g4136.t2.exon6 | 30890137 | 30891003 |
| chr_3 | g4136 | g4136.t2 | cds | g4136.t2.CDS1 | 30890226 | 30891002 |
| chr_3 | g4136 | g4136.t2 | TTS | g4136.t2 | 30891836 | 30891836 |
| chr_3 | g4136 | g4136.t2 | TSS | g4136.t2 | NA | NA |
Sequences
>g4136.t2 Gene=g4136 Length=3018
GCTACCTACTTTACCTACTTTTCATACAAAAATCTACTTTCTACTTTTCCAACTCTGATT
GTGAGCTTGTTTCTGCCAAAATAAAAGTGATTTTTATTTCTCGATTTCTTGGGGCTTTTT
CCAATAATAAAACATAGAAATTTAATCAAATCTGAACTACCACGTTTTCTAAATTGTTAT
ATCAATAACTTTTGTTTGATAAAAGCTTTATATGTATATCGTGTATTAAGCAAAAATTAA
ATTCAATTCTTTTATTTGCATTCTTCTTTTTTTCGTTTCAATTTAATTTCTTATTTTTTG
GTGCGATTTTTAGTTTGTCAAATATCGTGAAACTTGTTGCAACTTGATCTTTCATGAAAG
GGTACTAACAAAGTGTTTTAGAACAGGTCTGGTCGATTTTATATACAGGAACATAATTCA
AATTTAGTTATATATACTTATACATTTTTTATTCCTATATTAAGTATTCTTTACTTCAAC
ATATGGAATATTGTACTTTCTGTTGAAATTCGTAATCTTCTTTTGTATAGAAATTATAAT
AAGTCTCATCGATTGAAACTAAAAGAGATATATATCACTGGTTATTTTACAATTTTGCAT
ATTGTGTGAATTTTTTTTCAATCTTTTTACTACTTACTTGATTTTTTAATTGACAACTTA
ATTGTTGAGAAAATAAGGAAAATTGATGAATTGATTATTTGAAGAAATTGATTTGGATTA
CATTATTATTTGTCACAGCAAATAAAGTTAATGTTCAAGTTTTTTTACCATGATGAGAAT
TTTCATGAAAATGCTTTCTCAATTCAATATCTTAACTCAAAATTATTACTTTTTGGCAAC
AAAAAACTCTTTTTATTTATGCATTTTACTAGAAATGCACAAAACGTAATTTCTCTCTCG
TTGAATGCAATGTGAAAAAATATATATCATATACATATACATAGATTTCTTATTTGATCG
TACACGTATTATTTTAAATATATCATATATATGTTTTAAAGAAAAACGAGGAAATTTACT
CAAGAATATGTAAAAGAAGGGAAAGTTAAGAGAATTAAAGAGGTAATTAATAAGAAATTG
AGATATTTTTTTCAATTATTAGGAATTTATGCTTCTCTTCTTACGAATTTATGTGCTCCT
AAAGTCTGTTAATTGAGATGCGCTAGGGTTAAAGTCATGCATTGTATGATGTGCATAAAC
GATTCCAGATGACATTGCAGGCAATTCTCTAGGATATGGTGGTGATGAAGTTGCTGCATG
AATGCTTGTGATCGAATCTTTTTGTATAACATTTAGATGATGAAAAGGTGCTTTGGTTAG
CTTATTGTCTTCAAATGAGAGCTGTGAGCTGTTTGTTGCTGCCACTACCGGAGATGTTAG
TGAGAGACTTTTATTTCTCTCATTATTGTGCAAAAGATATTTAAAGAATTCATATGTTGA
CCAACACACAGCAGTTGCTGGCATTTGATATAGCACACGAGCTTGTAATCCTTTGAAAAA
TCCTGACATTCCCGCAACACGATAAACTTTACGTATGGCGTCAAAAAGTCCCTTTGTTGT
CCCAACTCCCTGTTCTTGTGTATTCAAGAGAGTTTTGCATACATCTAAGGGCGTCGTAAA
AGCAGCTGCTGCTGCACCTGCTGCACCACCAGCGACCACATGAGCCAATGGTGAGTATTT
CTTCTCTTTATTCAACTAATTTCTTGAAAGAATTCATACGTTGAGAAGTGAATAGCTTGA
TAAGGCAGATTCATCACAAGTTGAGTTGTATATGAGCGATAAAAAGCACCGAAACCTTCT
TGCTTAAAAACTTTTCGTGCACAATCCGTTACAGATTTGTATGGTGAATCATACATCTGT
AGTCGCTGTTTTATGACTTCTGTTGGATTTGAAATTGCATCGTGTATGAGAGTAGCTGAC
GTCGCACTTATTAGATAATTTATGTTATCATTAATTTTTAATTTAGCCAAACTTGACTTT
GTGAATTCGTATGAACTGAAATATAATGCATGGGCTGGTCCAGCTCCGAGTACGACTGCT
GATGCTCCTCTTAAAGCCTAAGAATACCTTCTTGCCGAATCATATCTCTCAACACACCAC
CAATTGTGTTACTTGCATGCGACAAACTCTGCATTCTCGTCTAGAATAAAATTGCAGATG
TTGTTTCTAAAGAGTTGATAAAAGAATCTGTGGTTGTTTGTGATGAGGCGCACAATATTG
ATAACGTCTGTGTCGATTCAATGAGTGTTCGTATTAATAAGCGTGTGATTGAAAGAGGAA
CACAAGCATTGGGTACATTAGAAAAGCTGGTACAGGAAATGAAAGAAGATGATCAACAGA
GACTTCAAGATGAATATGCTAAAATGGTTCAAGGACTGCGTGATGCTTATCAAGCTCGTG
AGACAGATAAAATGCTAGCTAATCCAGTTCTTCCCGATGACATATTGCAAGAAGCAGTTC
CAGGAAATATTCGTCATGCGGATCATTTTCTAGGTTTCTTAAATCGTTTTATTGCATATT
TGAAAACGAGATTGAGAGTTCAGCATGTCGTTCAAGAATCACCAGCAGGTTTTTTAAAAG
ACATTCATTCGAAAGTATGTATAGATCGAAAACCACTTCGATTTTGTGCCGAAAGATTAC
AATCTCTTTTAAGAACATTAGAAATCACTGATTTAACTGATTATGGTGGTCTTACTGTAA
TTACACATTTTGCAACTCTCGTATCAACATATACGCAAGGATTTACAATTATTATTGAGC
CATTTGATGATAAAACACCAACTGTTTCAAATCCAATTCTCTACTTCAGCTGTCTTGATT
CATCGATCGCAATGAGACCAATTTTTAGACGTTTTCAATCAGTTGTTATTACATCAGGTA
CGTTAAGTCCTATGGATATGTATCCAAAAATTCTCGATTTTGATCCAGTTGTTATGAGTT
CATTTACTATGACTTTATCTCGACCATGTTTGCTACCAATGGTTGTTACTCGTGGAAATG
ATCAAGTTGCAATAAGTT
>g4136.t2 Gene=g4136 Length=259
MSVRINKRVIERGTQALGTLEKLVQEMKEDDQQRLQDEYAKMVQGLRDAYQARETDKMLA
NPVLPDDILQEAVPGNIRHADHFLGFLNRFIAYLKTRLRVQHVVQESPAGFLKDIHSKVC
IDRKPLRFCAERLQSLLRTLEITDLTDYGGLTVITHFATLVSTYTQGFTIIIEPFDDKTP
TVSNPILYFSCLDSSIAMRPIFRRFQSVVITSGTLSPMDMYPKILDFDPVVMSSFTMTLS
RPCLLPMVVTRGNDQVAIS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g4136.t2 | PANTHER | PTHR11472 | DNA REPAIR DEAD HELICASE RAD3/XP-D SUBFAMILY MEMBER | 1 | 259 | 0 |
| 3 | g4136.t2 | PANTHER | PTHR11472:SF1 | GENERAL TRANSCRIPTION AND DNA REPAIR FACTOR IIH HELICASE SUBUNIT XPD | 1 | 259 | 0 |
| 8 | g4136.t2 | PRINTS | PR00852 | Xeroderma pigmentosum group D protein signature | 27 | 46 | 0 |
| 9 | g4136.t2 | PRINTS | PR00852 | Xeroderma pigmentosum group D protein signature | 62 | 80 | 0 |
| 6 | g4136.t2 | PRINTS | PR00852 | Xeroderma pigmentosum group D protein signature | 87 | 108 | 0 |
| 4 | g4136.t2 | PRINTS | PR00852 | Xeroderma pigmentosum group D protein signature | 126 | 148 | 0 |
| 7 | g4136.t2 | PRINTS | PR00852 | Xeroderma pigmentosum group D protein signature | 157 | 175 | 0 |
| 5 | g4136.t2 | PRINTS | PR00852 | Xeroderma pigmentosum group D protein signature | 246 | 259 | 0 |
| 1 | g4136.t2 | Pfam | PF06777 | Helical and beta-bridge domain | 24 | 167 | 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:0005634 | nucleus | CC |
| GO:0003677 | DNA binding | MF |
| GO:0005524 | ATP binding | MF |
| GO:0016818 | hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides | MF |
| GO:0003678 | DNA helicase activity | MF |
| GO:0006289 | nucleotide-excision repair | BP |
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.
