XPA (XPA, DNA damage recognition and repair factor) - Rat Genome Database

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Gene: XPA (XPA, DNA damage recognition and repair factor) Canis lupus familiaris
Analyze
Symbol: XPA
Name: XPA, DNA damage recognition and repair factor
RGD ID: 12255150
Description: ENCODES a protein that exhibits damaged DNA binding (inferred); DNA binding (inferred); metal ion binding (inferred); INVOLVED IN DNA repair (ortholog); intrinsic apoptotic signaling pathway in response to DNA damage (ortholog); multicellular organism growth (ortholog); PARTICIPATES IN altered nucleotide excision repair pathway; nucleotide excision repair pathway; ASSOCIATED WITH basal cell carcinoma (ortholog); Cockayne syndrome (ortholog); congenital disorder of glycosylation Ii (ortholog); FOUND IN DNA replication factor A complex (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: DNA repair protein complementing XP-A cells
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11154,976,978 - 54,996,140 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1154,976,976 - 54,996,065 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1153,406,654 - 53,430,263 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01156,085,046 - 56,108,618 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1156,088,588 - 56,108,630 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11154,581,396 - 54,605,007 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01154,611,286 - 54,634,866 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01155,307,954 - 55,331,573 (-)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
XPA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11154,976,978 - 54,996,140 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1154,976,976 - 54,996,065 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1153,406,654 - 53,430,263 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01156,085,046 - 56,108,618 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1156,088,588 - 56,108,630 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11154,581,396 - 54,605,007 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01154,611,286 - 54,634,866 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01155,307,954 - 55,331,573 (-)NCBIUU_Cfam_GSD_1.0
XPA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38997,654,398 - 97,697,340 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl997,674,909 - 97,697,340 (-)EnsemblGRCh38hg38GRCh38
GRCh379100,437,191 - 100,459,622 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36999,477,012 - 99,499,512 (-)NCBINCBI36Build 36hg18NCBI36
Build 34997,516,746 - 97,539,194NCBI
Celera970,951,417 - 70,973,928 (-)NCBICelera
Cytogenetic Map9q22.33NCBI
HuRef970,038,231 - 70,060,725 (-)NCBIHuRef
CHM1_19100,583,626 - 100,606,139 (-)NCBICHM1_1
T2T-CHM13v2.09109,826,339 - 109,869,281 (-)NCBIT2T-CHM13v2.0
Xpa
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39446,175,222 - 46,196,317 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl446,155,347 - 46,196,311 (-)EnsemblGRCm39 Ensembl
GRCm38446,175,220 - 46,196,344 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl446,155,347 - 46,196,311 (-)EnsemblGRCm38mm10GRCm38
MGSCv37446,188,094 - 46,209,183 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36446,196,339 - 46,217,411 (-)NCBIMGSCv36mm8
Celera446,197,357 - 46,218,441 (-)NCBICelera
Cytogenetic Map4B1NCBI
cM Map424.49NCBI
Xpa
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8565,227,281 - 65,275,784 (-)NCBIGRCr8
mRatBN7.2560,431,673 - 60,475,726 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl560,431,673 - 60,475,726 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx562,404,102 - 62,448,198 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0564,223,605 - 64,267,701 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0564,192,858 - 64,236,954 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0561,749,767 - 61,793,641 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl561,749,767 - 61,792,928 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0566,266,229 - 66,310,103 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4562,706,719 - 62,750,771 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1562,726,371 - 62,750,949 (-)NCBI
Celera558,992,396 - 59,036,208 (-)NCBICelera
Cytogenetic Map5q22NCBI
Xpa
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541927,751,043 - 27,774,917 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541927,751,042 - 27,774,917 (+)NCBIChiLan1.0ChiLan1.0
XPA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21141,759,709 - 41,823,406 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1941,762,094 - 41,825,789 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0968,726,723 - 68,788,049 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1996,866,303 - 96,909,260 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl996,886,795 - 96,909,254 (-)Ensemblpanpan1.1panPan2
Xpa
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947169,920,223 - 169,945,978 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365246,465,104 - 6,493,610 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365246,467,365 - 6,493,556 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
XPA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1239,532,272 - 239,568,570 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11239,532,331 - 239,568,589 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21267,660,926 - 267,694,917 (-)NCBISscrofa10.2Sscrofa10.2susScr3
XPA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11241,711,872 - 41,735,024 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1241,711,943 - 41,725,698 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603838,764,911 - 38,788,051 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Xpa
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248253,137,823 - 3,162,294 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248253,138,386 - 3,162,774 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in XPA
207 total Variants

Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system adipose tissue
High
Medium 4 17 1 2 1 6 9 8 9 5
Low 1 5 5 5 4 5 6 3 1 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSCAFT00000003869   ⟹   ENSCAFP00000003578
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1154,976,976 - 54,996,065 (-)Ensembl
RefSeq Acc Id: ENSCAFT00000063948   ⟹   ENSCAFP00000066750
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl1154,983,813 - 54,996,065 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845025919   ⟹   ENSCAFP00845020434
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl1156,088,588 - 56,108,630 (-)Ensembl
RefSeq Acc Id: XM_038490776   ⟹   XP_038346704
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.11154,581,396 - 54,605,007 (-)NCBI
RefSeq Acc Id: XM_038552904   ⟹   XP_038408832
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.01155,307,954 - 55,331,573 (-)NCBI
RefSeq Acc Id: XM_038616767   ⟹   XP_038472695
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.01154,611,286 - 54,634,866 (-)NCBI
RefSeq Acc Id: XM_038682234   ⟹   XP_038538162
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.01156,085,046 - 56,108,618 (-)NCBI
RefSeq Acc Id: XM_538745   ⟹   XP_538745
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.11154,976,978 - 54,996,131 (-)NCBI
Dog10K_Boxer_Tasha1153,406,654 - 53,430,263 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_538745   ⟸   XM_538745
- UniProtKB: A0A8C0MAC1 (UniProtKB/TrEMBL),   A0A8C0L1G5 (UniProtKB/TrEMBL),   A0A8I3NWC3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000066750   ⟸   ENSCAFT00000063948
RefSeq Acc Id: ENSCAFP00000003578   ⟸   ENSCAFT00000003869
RefSeq Acc Id: XP_038346704   ⟸   XM_038490776
RefSeq Acc Id: XP_038472695   ⟸   XM_038616767
RefSeq Acc Id: XP_038538162   ⟸   XM_038682234
- UniProtKB: A0A8C0MAC1 (UniProtKB/TrEMBL),   A0A8C0L1G5 (UniProtKB/TrEMBL),   A0A8I3NWC3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038408832   ⟸   XM_038552904
- UniProtKB: A0A8C0L1G5 (UniProtKB/TrEMBL),   A0A8C0MAC1 (UniProtKB/TrEMBL),   A0A8I3NWC3 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845020434   ⟸   ENSCAFT00845025919
Protein Domains
XPA C-terminal

Promoters
RGD ID:13685270
Promoter ID:EPDNEW_C3338
Type:initiation region
Name:XPA_1
Description:XPA, DNA damage recognition and repair factor
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.11154,996,113 - 54,996,173EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000002454 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030004430 UniProtKB/TrEMBL
  ENSCAFG00040017866 UniProtKB/TrEMBL
  ENSCAFG00845014486 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000003869.6 UniProtKB/TrEMBL
  ENSCAFT00030008123.1 UniProtKB/TrEMBL
  ENSCAFT00040032982.1 UniProtKB/TrEMBL
  ENSCAFT00845025919 ENTREZGENE
  ENSCAFT00845025919.1 UniProtKB/TrEMBL
Gene3D-CATH 3.90.530.10 UniProtKB/TrEMBL
InterPro DNA-bd_dom_put_sf UniProtKB/TrEMBL
  XPA UniProtKB/TrEMBL
  XPA_C UniProtKB/TrEMBL
  XPA_CS UniProtKB/TrEMBL
  XPA_sf UniProtKB/TrEMBL
  Znf_XPA_CS UniProtKB/TrEMBL
KEGG Report cfa:481623 UniProtKB/TrEMBL
NCBI Gene XPA ENTREZGENE
PANTHER DNA REPAIR PROTEIN COMPLEMENTING XP-A CELLS UniProtKB/TrEMBL
  PTHR10142 UniProtKB/TrEMBL
Pfam XPA_C UniProtKB/TrEMBL
  XPA_N UniProtKB/TrEMBL
PROSITE XPA_1 UniProtKB/TrEMBL
  XPA_2 UniProtKB/TrEMBL
Superfamily-SCOP Glucocorticoid receptor-like (DNA-binding domain) UniProtKB/TrEMBL
  SSF46955 UniProtKB/TrEMBL
UniProt A0A8C0L1G5 ENTREZGENE
  A0A8C0MAC1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3NWC3 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:48455 ENTREZGENE