Gene loci information

Transcript annotation

  • This transcript has been annotated as General transcription and DNA repair factor IIH helicase subunit XPD.

Parent gene

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.t4 TSS g4136.t4 30889217 30889217
chr_3 g4136 g4136.t4 isoform g4136.t4 30890137 30891773
chr_3 g4136 g4136.t4 exon g4136.t4.exon1 30890137 30891032
chr_3 g4136 g4136.t4 cds g4136.t4.CDS1 30890226 30891032
chr_3 g4136 g4136.t4 exon g4136.t4.exon2 30891360 30891773
chr_3 g4136 g4136.t4 cds g4136.t4.CDS2 30891360 30891773
chr_3 g4136 g4136.t4 TTS g4136.t4 30891836 30891836

Sequences

>g4136.t4 Gene=g4136 Length=1310
TTGCAGATGTTGTTTCTAAAGAGTTGATAAAAGAATCTGTGGTTGTTTGTGATGAGGCGC
ACAATATTGATAACGTCTGTGTCGATTCAATGAGTGTTCGTATTAATAAGCGTGTGATTG
AAAGAGGAACACAAGCATTGGGTACATTAGAAAAGCTGGTACAGGAAATGAAAGAAGATG
ATCAACAGAGACTTCAAGATGAATATGCTAAAATGGTTCAAGGACTGCGTGATGCTTATC
AAGCTCGTGAGACAGATAAAATGCTAGCTAATCCAGTTCTTCCCGATGACATATTGCAAG
AAGCAGTTCCAGGAAATATTCGTCATGCGGATCATTTTCTAGGTTTCTTAAATCGTTTTA
TTGCATATTTGAAAACGAGATTGAGAGTTCAGCATGTCGTTCAAGAATCACCAGCAGGTT
TTTTAAAAGACATTCATTCGAAAGTATGTATAGATCGAAAACCACTTCGATTTTGTGCCG
AAAGATTACAATCTCTTTTAAGAACATTAGAAATCACTGATTTAACTGATTATGGTGGTC
TTACTGTAATTACACATTTTGCAACTCTCGTATCAACATATACGCAAGGATTTACAATTA
TTATTGAGCCATTTGATGATAAAACACCAACTGTTTCAAATCCAATTCTCTACTTCAGCT
GTCTTGATTCATCGATCGCAATGAGACCAATTTTTAGACGTTTTCAATCAGTTGTTATTA
CATCAGGTACGTTAAGTCCTATGGATATGTATCCAAAAATTCTCGATTTTGATCCAGTTG
TTATGAGTTCATTTACTATGACTTTATCTCGACCATGTTTGCTACCAATGGTTGTTACTC
GTGGAAATGATCAAGTTGCAATAAGTTCTAAATTTGAATCACGTGAAGATACAGCTTATG
TCTATACACAATCACGAATTTTGAAAGCACGTTTAGAATATCTTCGAGATCAATTTCAAA
TTAAAGAGAATGATTTTCTTACATTTGATGCTCTTCGTCATGCTGCACAATGTGTCGGTC
GTGCTATTAGAGGAAAAACTGATTATGGTATTATGATATTTGCTGATAAGAGATTCGCTC
GTCAAGATAAGCGTGGAAAACTACCAAAGTGGATTCAAGAATATCTTACCGATAATTATG
TAAATTTGAGCACTGAAGAGGCAATGCAGTTAGCAAAAATATGGCTTAGACAAATGGCTC
AACCTTTCTCACGTGAAGATCAATTAGGCTTATCTTTATTAACTGTTGAGCAATTAAAAA
GTAATGAAAAACAAATCATTGAGAAACATTTAAAACCACAAACTATTTGA

>g4136.t4 Gene=g4136 Length=406
MSVRINKRVIERGTQALGTLEKLVQEMKEDDQQRLQDEYAKMVQGLRDAYQARETDKMLA
NPVLPDDILQEAVPGNIRHADHFLGFLNRFIAYLKTRLRVQHVVQESPAGFLKDIHSKVC
IDRKPLRFCAERLQSLLRTLEITDLTDYGGLTVITHFATLVSTYTQGFTIIIEPFDDKTP
TVSNPILYFSCLDSSIAMRPIFRRFQSVVITSGTLSPMDMYPKILDFDPVVMSSFTMTLS
RPCLLPMVVTRGNDQVAISSKFESREDTAYVYTQSRILKARLEYLRDQFQIKENDFLTFD
ALRHAAQCVGRAIRGKTDYGIMIFADKRFARQDKRGKLPKWIQEYLTDNYVNLSTEEAMQ
LAKIWLRQMAQPFSREDQLGLSLLTVEQLKSNEKQIIEKHLKPQTI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g4136.t4 Gene3D G3DSA:3.40.50.300 - 268 344 0
3 g4136.t4 PANTHER PTHR11472 DNA REPAIR DEAD HELICASE RAD3/XP-D SUBFAMILY MEMBER 1 269 0
5 g4136.t4 PANTHER PTHR11472:SF1 GENERAL TRANSCRIPTION AND DNA REPAIR FACTOR IIH HELICASE SUBUNIT XPD 1 269 0
4 g4136.t4 PANTHER PTHR11472 DNA REPAIR DEAD HELICASE RAD3/XP-D SUBFAMILY MEMBER 269 392 0
6 g4136.t4 PANTHER PTHR11472:SF1 GENERAL TRANSCRIPTION AND DNA REPAIR FACTOR IIH HELICASE SUBUNIT XPD 269 392 0
11 g4136.t4 PRINTS PR00852 Xeroderma pigmentosum group D protein signature 27 46 0
12 g4136.t4 PRINTS PR00852 Xeroderma pigmentosum group D protein signature 62 80 0
9 g4136.t4 PRINTS PR00852 Xeroderma pigmentosum group D protein signature 87 108 0
8 g4136.t4 PRINTS PR00852 Xeroderma pigmentosum group D protein signature 126 148 0
10 g4136.t4 PRINTS PR00852 Xeroderma pigmentosum group D protein signature 157 175 0
7 g4136.t4 PRINTS PR00852 Xeroderma pigmentosum group D protein signature 246 263 0
2 g4136.t4 Pfam PF06777 Helical and beta-bridge domain 24 167 0
1 g4136.t4 Pfam PF13307 Helicase C-terminal domain 271 344 0
13 g4136.t4 SMART SM00491 Cxpdneu3 199 331 0
15 g4136.t4 TIGRFAM TIGR00604 rad3: DNA repair helicase (rad3) 1 271 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:0006139 nucleobase-containing compound metabolic process BP
GO:0004386 helicase activity MF
GO:0006289 nucleotide-excision repair BP
GO:0003676 nucleic acid binding MF
GO:0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides MF
GO:0003678 DNA helicase activity MF

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.

Raw TPM values