Xpa XPA, DNA damage recognition and repair factor [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Xpaprovided by RGD
Official Full Name: XPA, DNA damage recognition and repair factorprovided by RGD
Primary source: RGD:1308769
See related: EnsemblRapid:ENSRNOG00000009576 AllianceGenome:RGD:1308769
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable DNA binding activity; protein domain specific binding activity; and protein homodimerization activity. Involved in response to auditory stimulus. Predicted to be located in intercellular bridge and nucleoplasm. Predicted to be part of DNA replication factor A complex and nucleotide-excision repair factor 1 complex. Human ortholog(s) of this gene implicated in xeroderma pigmentosum and xeroderma pigmentosum group A. Orthologous to human XPA (XPA, DNA damage recognition and repair factor). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Thymus (RPKM 33.2), Kidney (RPKM 29.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q22

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (65227281..65275784, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (60431673..60475726, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (61749767..61793641, complement)

Chromosome 5 - NC_086023.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: 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?

This current study tested the hypothesis that noise stress would alter the expression pattern of EGFR/XPA within the auditory nerve. In both the apical and middle cochlear coils, the noise stress depleted EGFR+XPA expression. Furthermore, there was a reduction in the proportion of neurons that expressed XPA-alone in the middle coils.
Title: Noise Stress Induces an Epidermal Growth Factor Receptor/Xeroderma Pigmentosum-A Response in the Auditory Nerve.
A population of spiral ganglion neurons that constitutively express XPA may also express the EGFR in rat.
Title: Localization and distribution of neurons that co-express xeroderma pigmentosum-A and epidermal growth factor receptor within Rosenthal's canal.
This study showed that spontaneous Xpa mutations causing cerebellar pathology are impaired in motor functions during the neonatal period.
Title: Behavioral effects of neonatal lesions on the cerebellar system.
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.
nucleotide excision repair (NER) factors XPA and XPB exist in the nuclei of neurons in the brain, suggesting that the NER may play important roles in the process of DNA repair in adult brain neurons
Title: Immunohistochemical analysis of nucleotide excision repair factors XPA and XPB in adult rat brain.

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General gene information

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Markers

BE108357 (e-PCR)
- UniSTS:247737

RH130418 (e-PCR)
- UniSTS:213702

RH132739 (e-PCR)
- UniSTS:216022

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
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 metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein domain specific binding	ISO Inferred from Sequence Orthology more info
enables protein homodimerization activity	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA repair	ISO Inferred from Sequence Orthology more info
involved_in DNA repair	ISO Inferred from Sequence Orthology more info
involved_in UV protection	ISO Inferred from Sequence Orthology more info
involved_in UV-damage excision repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in base-excision repair	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within intrinsic apoptotic signaling pathway in response to DNA damage	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within multicellular organism growth	ISO Inferred from Sequence Orthology 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 nucleotide-excision repair involved in interstrand cross-link repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in nucleotide-excision repair, DNA damage recognition	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within positive regulation of transcription initiation by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in protein localization to nucleus	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of autophagy	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to UV	ISO Inferred from Sequence Orthology more info
involved_in response to auditory stimulus	IEP Inferred from Expression Pattern more info	PubMed
acts_upstream_of_or_within response to oxidative stress	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to toxic substance	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of DNA replication factor A complex	ISO Inferred from Sequence Orthology more info
located_in intercellular bridge	IEA Inferred from Electronic Annotation more info
located_in intercellular bridge	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 factor 1 complex	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: DNA repair protein complementing XP-A cells

Names: xeroderma pigmentosum, complementation group A

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_001106656.1 → NP_001100126.1 DNA repair protein complementing XP-A cells isoform 2

See identical proteins and their annotated locations for NP_001100126.1

Status: PROVISIONAL

Source sequence(s)

CH473962

UniProtKB/TrEMBL

A6IJB2, D4A981

Related

ENSRNOP00000059280.1, ENSRNOT00000064685.3

Conserved Domains (2) summary

pfam01286
Location:104 → 133

XPA_N; XPA protein N-terminal

pfam05181
Location:135 → 186

XPA_C; XPA protein C-terminus
NM_001399041.1 → NP_001385970.1 DNA repair protein complementing XP-A cells isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

A0A8I6G6T5, A6IJB3

Related

ENSRNOP00000100893.1, ENSRNOT00000127599.1

Conserved Domains (1) summary

TIGR00598
Location:105 → 273

rad14; DNA repair protein

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086023.1 Reference GRCr8

Range

65227281..65275784 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039109456.2 → XP_038965384.1 DNA repair protein complementing XP-A cells isoform X3

Conserved Domains (1) summary

cd21076
Location:120 → 226

DBD_XPA; DNA-binding domain found in DNA repair protein complementing XP-A cells (XPA) and similar proteins
XM_063287331.1 → XP_063143401.1 DNA repair protein complementing XP-A cells isoform X6
XM_063287332.1 → XP_063143402.1 DNA repair protein complementing XP-A cells isoform X6
XM_006238035.4 → XP_006238097.1 DNA repair protein complementing XP-A cells isoform X1

Related

ENSRNOP00000108065.1, ENSRNOT00000141451.1

Conserved Domains (3) summary

TIGR00598
Location:124 → 292

rad14; DNA repair protein

pfam01286
Location:123 → 152

XPA_N; XPA protein N-terminal

pfam05181
Location:154 → 205

XPA_C; XPA protein C-terminus
XM_039109457.2 → XP_038965385.1 DNA repair protein complementing XP-A cells isoform X4

Conserved Domains (1) summary

cd21076
Location:120 → 226

DBD_XPA; DNA-binding domain found in DNA repair protein complementing XP-A cells (XPA) and similar proteins
XM_017593241.2 → XP_017448730.1 DNA repair protein complementing XP-A cells isoform X2
XM_008763697.3 → XP_008761919.1 DNA repair protein complementing XP-A cells isoform X5

Conserved Domains (2) summary

pfam01286
Location:123 → 152

XPA_N; XPA protein N-terminal

pfam05181
Location:154 → 205

XPA_C; XPA protein C-terminus