Xpc XPC complex subunit, DNA damage recognition and repair factor [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Xpcprovided by RGD
Official Full Name: XPC complex subunit, DNA damage recognition and repair factorprovided by RGD
Primary source: RGD:1305760
See related: EnsemblRapid:ENSRNOG00000008274 AllianceGenome:RGD:1305760
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable several functions, including DNA binding activity; DNA damage sensor activity; and transcription coactivator activity. Involved in response to auditory stimulus and response to xenobiotic stimulus. Predicted to be located in several cellular components, including cytosol; mitochondrion; and nuclear lumen. Predicted to be part of XPC complex and nucleotide-excision repair factor 2 complex. Predicted to be active in cytoplasm and site of DNA damage. Human ortholog(s) of this gene implicated in pancreatic cancer; serous cystadenocarcinoma; xeroderma pigmentosum; and xeroderma pigmentosum group C. Orthologous to human XPC (XPC complex subunit, DNA damage recognition and repair factor). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Adrenal (RPKM 184.9), Kidney (RPKM 156.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 4q34

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (125550833..125578084, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (123993670..124020922, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (123134457..123161985, complement)

Chromosome 4 - NC_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

XP mRNA levels were up to 95% (XPA) and 69% (XPC) of the respective maximum expression capacity of each gene; in addition, these cochlear levels were up to sixfold (XPC) and threefold (XPA)
Title: Real-time quantification of Xeroderma pigmentosum mRNA from the mammalian cochlea.
study examined XPA and XPC immunoreactivity among outer hair cells and spiral limbus cells; data show that outer hair cells failed to acclimate to cisplatin treatment cycles by regulating XPA and XPC immunoreactivity
Title: Preincision complex-I from the excision nuclease reaction among cochlear spiral limbus and outer hair cells.

Submit: New GeneRIF Correction

General gene information

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Markers

RH133911 (e-PCR)
- UniSTS:217194

RH36905 (e-PCR)
- UniSTS:87932

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables DNA damage sensor activity	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables damaged DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables damaged DNA binding	ISO Inferred from Sequence Orthology more info
enables protein-containing complex binding	ISO Inferred from Sequence Orthology more info
enables single-stranded DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables single-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription coactivator activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA damage response	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within DNA repair	ISO Inferred from Sequence Orthology more info
involved_in UV-damage excision repair	ISO Inferred from Sequence Orthology more info
involved_in mismatch repair	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within mitotic intra-S DNA damage checkpoint signaling	ISO Inferred from Sequence Orthology more info
involved_in nucleotide-excision repair	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within nucleotide-excision repair	ISO Inferred from Sequence Orthology more info
involved_in nucleotide-excision repair	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within pyrimidine dimer repair by nucleotide-excision repair	ISO Inferred from Sequence Orthology more info
involved_in regulation of mitotic cell cycle phase transition	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to UV-B	ISO Inferred from Sequence Orthology more info
involved_in response to auditory stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to xenobiotic stimulus	IEP Inferred from Expression Pattern more info	PubMed

Component	Evidence Code	Pubs
part_of XPC complex	IBA Inferred from Biological aspect of Ancestor more info
part_of XPC complex	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in intracellular membrane-bounded organelle	ISO Inferred from Sequence Orthology more info
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	ISO Inferred from Sequence Orthology more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
part_of nucleotide-excision repair complex	ISO Inferred from Sequence Orthology more info
part_of nucleotide-excision repair factor 2 complex	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in site of DNA damage	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: DNA repair protein complementing XP-C cells

Names: xeroderma pigmentosum, complementation group C

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001107874.1 → NP_001101344.1 DNA repair protein complementing XP-C cells

See identical proteins and their annotated locations for NP_001101344.1

Status: PROVISIONAL

Source sequence(s)

CH473957

UniProtKB/TrEMBL

A6IBA2, D4A3D8

Related

ENSRNOP00000011490.4, ENSRNOT00000011490.5

Conserved Domains (6) summary

smart01032
Location:745 → 819

BHD_3; Rad4 beta-hairpin domain 3

smart01030
Location:624 → 675

BHD_1; Rad4 beta-hairpin domain 1

smart01031
Location:678 → 737

BHD_2; Rad4 beta-hairpin domain 2

pfam07404
Location:399 → 489

TEBP_beta; Telomere-binding protein beta subunit (TEBP beta)

TIGR00605
Location:144 → 860

rad4; DNA repair protein rad4

pfam03835
Location:525 → 620

Rad4; Rad4 transglutaminase-like domain