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.t5 isoform g4136.t5 30890299 30891773
chr_3 g4136 g4136.t5 exon g4136.t5.exon1 30890299 30891773
chr_3 g4136 g4136.t5 cds g4136.t5.CDS1 30890304 30891773
chr_3 g4136 g4136.t5 TTS g4136.t5 30891836 30891836
chr_3 g4136 g4136.t5 TSS g4136.t5 NA NA

Sequences

>g4136.t5 Gene=g4136 Length=1475
AGGAAATGAAAGAAGATGATCAACAGAGACTTCAAGATGAATATGCTAAAATGGTTCAAG
GACTGCGTGATGCTTATCAAGCTCGTGAGACAGATAAAATGCTAGCTAATCCAGTTCTTC
CCGATGACATATTGCAAGAAGCAGTTCCAGGAAATATTCGTCATGCGGATCATTTTCTAG
GTTTCTTAAATCGTTTTATTGCATATTTGAAAACGAGATTGAGAGTTCAGCATGTCGTTC
AAGAATCACCAGCAGGTTTTTTAAAAGACATTCATTCGAAAGTATGTATAGATCGAAAAC
CACTTCGATTTTGTGCCGAAAGATTACAATCTCTTTTAAGAACATTAGAAATCACTGATT
TAACTGATTATGGTGGTCTTACTGTAATTACACATTTTGCAACTCTCGTATCAACATATA
CGCAAGGATTTACAATTATTATTGAGCCATTTGATGATAAAACACCAACTGTTTCAAATC
CAATTCTCTACTTCAGCTGTCTTGATTCATCGATCGCAATGAGACCAATTTTTAGACGTT
TTCAATCAGTTGTTATTACATCAGGTACGTTAAGTCCTATGGATATGTATCCAAAAATTC
TCGATTTTGATCCAGTTGTTATGAGTTCATTTACTATGACTTTATCTCGACCATGTTTGC
TACCAATGGTTGTTACTCGTGGAAATGATCAAGTTGCAATAAGTTCTAAATTTGAATCAC
GTGAAGATACAGCTGTAACAAGAAATTATGGTCAATTACTTGTAGAAACGGCAAAAATTG
TGCCTGATGGAATTGTTTGTTTCTTTACATCATATTTATATTTAGAATCAGTTGTCGCAT
CATGGTATGATCAAGGAATCATTGATACATTATTAAAATACAAGTTGCTATTTATTGAAA
CACAAGATGCGGCTGAAACTTCTTATGCGCTAATGAATTATGTAAAAGCATGTGACTGTG
GAAGAGGAGCTGTTTTACTAGCTGTTGCAAGAGGAAAGGTGTCTGAGGGAGTAGATTTTG
ATCATCATTTAGGACGAGCTGTTCTTATGTTTGGCATACCTTATGTCTATACACAATCAC
GAATTTTGAAAGCACGTTTAGAATATCTTCGAGATCAATTTCAAATTAAAGAGAATGATT
TTCTTACATTTGATGCTCTTCGTCATGCTGCACAATGTGTCGGTCGTGCTATTAGAGGAA
AAACTGATTATGGTATTATGATATTTGCTGATAAGAGATTCGCTCGTCAAGATAAGCGTG
GAAAACTACCAAAGTGGATTCAAGAATATCTTACCGATAATTATGTAAATTTGAGCACTG
AAGAGGCAATGCAGTTAGCAAAAATATGGCTTAGACAAATGGCTCAACCTTTCTCACGTG
AAGATCAATTAGGCTTATCTTTATTAACTGTTGAGCAATTAAAAAGTAATGAAAAACAAA
TCATTGAGAAACATTTAAAACCACAAACTATTTGA

>g4136.t5 Gene=g4136 Length=489
MKEDDQQRLQDEYAKMVQGLRDAYQARETDKMLANPVLPDDILQEAVPGNIRHADHFLGF
LNRFIAYLKTRLRVQHVVQESPAGFLKDIHSKVCIDRKPLRFCAERLQSLLRTLEITDLT
DYGGLTVITHFATLVSTYTQGFTIIIEPFDDKTPTVSNPILYFSCLDSSIAMRPIFRRFQ
SVVITSGTLSPMDMYPKILDFDPVVMSSFTMTLSRPCLLPMVVTRGNDQVAISSKFESRE
DTAVTRNYGQLLVETAKIVPDGIVCFFTSYLYLESVVASWYDQGIIDTLLKYKLLFIETQ
DAAETSYALMNYVKACDCGRGAVLLAVARGKVSEGVDFDHHLGRAVLMFGIPYVYTQSRI
LKARLEYLRDQFQIKENDFLTFDALRHAAQCVGRAIRGKTDYGIMIFADKRFARQDKRGK
LPKWIQEYLTDNYVNLSTEEAMQLAKIWLRQMAQPFSREDQLGLSLLTVEQLKSNEKQII
EKHLKPQTI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g4136.t5 CDD cd18788 SF2_C_XPD 216 412 0
14 g4136.t5 Gene3D G3DSA:3.40.50.300 - 226 427 0
3 g4136.t5 PANTHER PTHR11472 DNA REPAIR DEAD HELICASE RAD3/XP-D SUBFAMILY MEMBER 1 475 0
4 g4136.t5 PANTHER PTHR11472:SF1 GENERAL TRANSCRIPTION AND DNA REPAIR FACTOR IIH HELICASE SUBUNIT XPD 1 475 0
5 g4136.t5 PRINTS PR00852 Xeroderma pigmentosum group D protein signature 1 20 0
6 g4136.t5 PRINTS PR00852 Xeroderma pigmentosum group D protein signature 36 54 0
7 g4136.t5 PRINTS PR00852 Xeroderma pigmentosum group D protein signature 61 82 0
10 g4136.t5 PRINTS PR00852 Xeroderma pigmentosum group D protein signature 100 122 0
8 g4136.t5 PRINTS PR00852 Xeroderma pigmentosum group D protein signature 131 149 0
12 g4136.t5 PRINTS PR00852 Xeroderma pigmentosum group D protein signature 220 237 0
11 g4136.t5 PRINTS PR00852 Xeroderma pigmentosum group D protein signature 364 386 0
9 g4136.t5 PRINTS PR00852 Xeroderma pigmentosum group D protein signature 435 455 0
2 g4136.t5 Pfam PF06777 Helical and beta-bridge domain 1 141 0
1 g4136.t5 Pfam PF13307 Helicase C-terminal domain 252 427 0
13 g4136.t5 SMART SM00491 Cxpdneu3 270 414 0
15 g4136.t5 TIGRFAM TIGR00604 rad3: DNA repair helicase (rad3) 2 436 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

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.

Raw TPM values