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

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Xpa (XPA, DNA damage recognition and repair factor) Rattus norvegicus
Analyze
Symbol: Xpa
Name: XPA, DNA damage recognition and repair factor
RGD ID: 1308769
Description: 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 nucleus. 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); PARTICIPATES IN altered nucleotide excision repair pathway; nucleotide excision repair pathway; INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: DNA repair protein complementing XP-A cells; LOC298074; xeroderma pigmentosum, complementation group A
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8565,227,281 - 65,275,784 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl565,227,281 - 65,272,425 (-)EnsemblGRCr8
mRatBN7.2560,431,673 - 60,475,726 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl560,431,673 - 60,475,726 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx562,404,102 - 62,448,198 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0564,223,605 - 64,267,701 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0564,192,858 - 64,236,954 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0561,749,767 - 61,793,641 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl561,749,767 - 61,792,928 (-)Ensemblrn6Rnor6.0
Rnor_5.0566,266,229 - 66,310,103 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4562,706,719 - 62,750,771 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera558,992,396 - 59,036,208 (-)NCBICelera
RGSC_v3.1562,726,371 - 62,750,949 (-)NCBI
Cytogenetic Map5q22NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
(+)-taxifolin  (ISO)
(-)-quinic acid  (ISO)
1,1'-azobis(N,N-dimethylformamide)  (ISO)
1,2-dichloroethane  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,6-dinitrotoluene  (EXP)
2-hydroxypropanoic acid  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
6-propyl-2-thiouracil  (EXP)
7,12-dimethyltetraphene  (ISO)
acetamide  (EXP)
acrylamide  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amitrole  (EXP)
antimony trichloride  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (EXP,ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
Butylbenzyl phthalate  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
chloroethene  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
diethylstilbestrol  (ISO)
doxorubicin  (ISO)
ebselen  (ISO)
epoxiconazole  (ISO)
folic acid  (ISO)
furan  (EXP)
gentamycin  (EXP)
gold atom  (ISO)
gold(0)  (ISO)
hydrogen peroxide  (ISO)
indole-3-methanol  (EXP)
indometacin  (ISO)
irinotecan  (ISO)
isoprenaline  (ISO)
kainic acid  (EXP)
lead diacetate  (ISO)
lipopolysaccharide  (ISO)
lovastatin  (EXP)
metam  (ISO)
methimazole  (EXP)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
mitomycin C  (ISO)
ozone  (EXP)
paracetamol  (ISO)
paraquat  (ISO)
phenacetin  (ISO)
PhIP  (ISO)
pirinixic acid  (ISO)
quinoline yellow  (ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
Se-methyl-L-selenocysteine  (ISO)
Se-methylselenocysteine  (ISO)
selenocystine  (ISO)
selenomethionine  (ISO)
senecionine  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sulfadimethoxine  (EXP)
tamoxifen  (EXP)
testosterone  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
titanium dioxide  (ISO)
tributylstannane  (EXP)
trichloroethene  (EXP)
trichostatin A  (ISO)
triphenyl phosphate  (EXP,ISO)
valproic acid  (ISO)
vorinostat  (ISO)
Y-27632  (ISO)
zidovudine  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. An Xpb mouse model for combined xeroderma pigmentosum and cockayne syndrome reveals progeroid features upon further attenuation of DNA repair. Andressoo JO, etal., Mol Cell Biol. 2009 Mar;29(5):1276-90. doi: 10.1128/MCB.01229-08. Epub 2008 Dec 29.
2. The genetic association database. Becker KG, etal., Nat Genet. 2004 May;36(5):431-2.
3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Noise exposure potentiates the subcellular distribution of nucleotide excision repair proteins within spiral ganglion neurons. Guthrie OW and Xu H, Hear Res. 2012 Dec;294(1-2):21-30. doi: 10.1016/j.heares.2012.09.001. Epub 2012 Sep 27.
6. Nucleotide excision repair: new tricks with old bricks. Kamileri I, etal., Trends Genet. 2012 Nov;28(11):566-73. doi: 10.1016/j.tig.2012.06.004. Epub 2012 Jul 22.
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
9. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
10. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
11. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
13. Comprehensive gene review and curation RGD comprehensive gene curation
14. The multi-replication protein A (RPA) system--a new perspective. Sakaguchi K, etal., FEBS J. 2009 Feb;276(4):943-63. doi: 10.1111/j.1742-4658.2008.06841.x. Epub 2009 Jan 12.
15. Analysis of a human DNA excision repair gene involved in group A xeroderma pigmentosum and containing a zinc-finger domain. Tanaka K, etal., Nature. 1990 Nov 1;348(6296):73-6.
16. Immunohistochemical analysis of nucleotide excision repair factors XPA and XPB in adult rat brain. Yang SZ, etal., Anat Rec (Hoboken). 2008 Jul;291(7):775-80. doi: 10.1002/ar.20713.
Additional References at PubMed
PMID:1601884   PMID:7700386   PMID:8197175   PMID:9661901   PMID:10843671   PMID:11005836   PMID:11408355   PMID:11950998   PMID:12509265   PMID:12815074   PMID:17720715   PMID:18443001  
PMID:18979173   PMID:20539233   PMID:21148310   PMID:22323595   PMID:25907855   PMID:26493720   PMID:28056182  


Genomics

Comparative Map Data
Xpa
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8565,227,281 - 65,275,784 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl565,227,281 - 65,272,425 (-)EnsemblGRCr8
mRatBN7.2560,431,673 - 60,475,726 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl560,431,673 - 60,475,726 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx562,404,102 - 62,448,198 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0564,223,605 - 64,267,701 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0564,192,858 - 64,236,954 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0561,749,767 - 61,793,641 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl561,749,767 - 61,792,928 (-)Ensemblrn6Rnor6.0
Rnor_5.0566,266,229 - 66,310,103 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4562,706,719 - 62,750,771 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera558,992,396 - 59,036,208 (-)NCBICelera
RGSC_v3.1562,726,371 - 62,750,949 (-)NCBI
Cytogenetic Map5q22NCBI
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 (-)Ensemblhg38GRCh38
GRCh379100,437,191 - 100,459,622 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36999,477,012 - 99,499,512 (-)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm38446,175,220 - 46,196,344 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl446,155,347 - 46,196,311 (-)Ensemblmm10GRCm38
MGSCv37446,188,094 - 46,209,183 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36446,196,339 - 46,217,411 (-)NCBIMGSCv36mm8
Celera446,197,357 - 46,218,441 (-)NCBICelera
Cytogenetic Map4B1NCBI
cM Map424.49NCBI
Xpa
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541927,751,043 - 27,774,917 (+)Ensembl
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 (-)EnsemblpanPan2panpan1.1
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 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1153,406,654 - 53,430,263 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01156,085,046 - 56,108,618 (-)NCBIROS_Cfam_1.0ROS_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_1.0UU_Cfam_GSD_1.0
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 (-)EnsemblSpeTri2.0 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 (-)EnsemblsusScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248253,138,386 - 3,162,774 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Xpa
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11321,906 - 342,143 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Xpa
527 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:150
Count of miRNA genes:114
Interacting mature miRNAs:124
Transcripts:ENSRNOT00000064685
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)53275164977751649Rat
1298067Scl15Serum cholesterol level QTL 154.80.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53801167083011670Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)55266537294894052Rat
6907115Mcs29Mammary carcinoma susceptibility QTL 29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)53800433183004331Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)544924861153890773Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)52367149379046465Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)538207390136631402Rat
61386Bp49Blood pressure QTL 4916.6cerebrum integrity trait (VT:0010549)brain infarction volume (CMO:0001013)565089051103648916Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)548523123134369373Rat
1598807Glom12Glomerulus QTL 122.7kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)53801167083011670Rat
1302786Kidm8Kidney mass QTL 828.15kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)53801167083011670Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)565089051166764498Rat
1331782Rf36Renal function QTL 363.296kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)539019942102105896Rat
6903292Stl28Serum triglyceride level QTL 282.60.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)53331167378311673Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)551657967166600247Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)53275164977751649Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555124766172190305Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)53998594884985948Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)5692228281330203Rat
6903306Scl35Serum cholesterol QTL 352.60.0073blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53331167378311673Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)53952692484526924Rat
1331773Scl26Serum cholesterol level QTL 263.065blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)54852312391770353Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)560601597137492949Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)51001906491770353Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)560511627105511627Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5706553574335773Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)536460764136631402Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)564589016109589016Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)51001906487027358Rat
8552954Pigfal14Plasma insulin-like growth factor 1 level QTL 149blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)52602321171023211Rat
2316954Rf57Renal function QTL 570kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)56458901693503770Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)556546393101546393Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)52367149368671493Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)56458901691762830Rat

Markers in Region
RH130418  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2560,448,117 - 60,448,322 (+)MAPPERmRatBN7.2
Rnor_6.0561,766,212 - 61,766,416NCBIRnor6.0
Rnor_5.0566,282,674 - 66,282,878UniSTSRnor5.0
RGSC_v3.4562,723,164 - 62,723,368UniSTSRGSC3.4
Celera559,008,841 - 59,009,045UniSTS
RH 3.4 Map5381.7UniSTS
Cytogenetic Map5q22UniSTS
RH132739  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2560,448,546 - 60,448,738 (+)MAPPERmRatBN7.2
Rnor_6.0561,766,641 - 61,766,832NCBIRnor6.0
Rnor_5.0566,283,103 - 66,283,294UniSTSRnor5.0
RGSC_v3.4562,723,593 - 62,723,784UniSTSRGSC3.4
Celera559,009,270 - 59,009,461UniSTS
RH 3.4 Map5379.2UniSTS
Cytogenetic Map5q22UniSTS
BE108357  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2560,448,117 - 60,448,273 (+)MAPPERmRatBN7.2
Rnor_6.0561,766,212 - 61,766,367NCBIRnor6.0
Rnor_5.0566,282,674 - 66,282,829UniSTSRnor5.0
RGSC_v3.4562,723,164 - 62,723,319UniSTSRGSC3.4
Celera559,008,841 - 59,008,996UniSTS
RH 3.4 Map5389.2UniSTS
Cytogenetic Map5q22UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000064685   ⟹   ENSRNOP00000059280
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl565,227,281 - 65,271,333 (-)Ensembl
mRatBN7.2 Ensembl560,431,673 - 60,475,726 (-)Ensembl
Rnor_6.0 Ensembl561,749,767 - 61,792,928 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000108242   ⟹   ENSRNOP00000080582
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl565,241,699 - 65,271,333 (-)Ensembl
mRatBN7.2 Ensembl560,451,144 - 60,475,726 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000127599   ⟹   ENSRNOP00000100893
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl565,246,086 - 65,271,333 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000136647   ⟹   ENSRNOP00000108314
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl565,234,974 - 65,271,333 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000138011   ⟹   ENSRNOP00000102576
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl565,246,754 - 65,272,425 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000141451   ⟹   ENSRNOP00000108065
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl565,246,754 - 65,271,187 (-)Ensembl
RefSeq Acc Id: NM_001106656   ⟹   NP_001100126
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8565,227,281 - 65,271,333 (-)NCBI
mRatBN7.2560,431,673 - 60,475,726 (-)NCBI
Rnor_6.0561,749,767 - 61,792,928 (-)NCBI
Rnor_5.0566,266,229 - 66,310,103 (-)NCBI
RGSC_v3.4562,706,719 - 62,750,771 (-)RGD
Celera558,992,396 - 59,036,208 (-)RGD
Sequence:
RefSeq Acc Id: NM_001399041   ⟹   NP_001385970
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8565,246,754 - 65,271,332 (-)NCBI
mRatBN7.2560,451,146 - 60,475,725 (-)NCBI
RefSeq Acc Id: XM_006238035   ⟹   XP_006238097
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8565,246,755 - 65,271,101 (-)NCBI
mRatBN7.2560,451,144 - 60,475,494 (-)NCBI
Rnor_6.0561,769,240 - 61,792,696 (-)NCBI
Rnor_5.0566,266,229 - 66,310,103 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008763697   ⟹   XP_008761919
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8565,251,905 - 65,271,101 (-)NCBI
mRatBN7.2560,456,298 - 60,475,494 (-)NCBI
Rnor_6.0561,769,241 - 61,792,696 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593241   ⟹   XP_017448730
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8565,246,983 - 65,271,101 (-)NCBI
mRatBN7.2560,451,375 - 60,475,494 (-)NCBI
Rnor_6.0561,769,241 - 61,792,696 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039109456   ⟹   XP_038965384
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8565,230,806 - 65,271,101 (-)NCBI
mRatBN7.2560,434,389 - 60,475,494 (-)NCBI
RefSeq Acc Id: XM_039109457   ⟹   XP_038965385
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8565,246,755 - 65,271,101 (-)NCBI
mRatBN7.2560,451,198 - 60,475,494 (-)NCBI
RefSeq Acc Id: XM_063287331   ⟹   XP_063143401
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8565,246,755 - 65,271,371 (-)NCBI
RefSeq Acc Id: XM_063287332   ⟹   XP_063143402
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8565,246,755 - 65,271,227 (-)NCBI
RefSeq Acc Id: XR_010066350
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8565,246,918 - 65,271,101 (-)NCBI
RefSeq Acc Id: XR_010066351
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8565,246,918 - 65,275,784 (-)NCBI
RefSeq Acc Id: NP_001100126   ⟸   NM_001106656
- Peptide Label: isoform 2
- UniProtKB: D4A981 (UniProtKB/TrEMBL),   A6IJB2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006238097   ⟸   XM_006238035
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008761919   ⟸   XM_008763697
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017448730   ⟸   XM_017593241
- Peptide Label: isoform X2
- Sequence:
Ensembl Acc Id: ENSRNOP00000059280   ⟸   ENSRNOT00000064685
RefSeq Acc Id: XP_038965384   ⟸   XM_039109456
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038965385   ⟸   XM_039109457
- Peptide Label: isoform X4
Ensembl Acc Id: ENSRNOP00000080582   ⟸   ENSRNOT00000108242
RefSeq Acc Id: NP_001385970   ⟸   NM_001399041
- Peptide Label: isoform 1
- UniProtKB: A0A8I6G6T5 (UniProtKB/TrEMBL),   A6IJB3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063143401   ⟸   XM_063287331
- Peptide Label: isoform X6
RefSeq Acc Id: XP_063143402   ⟸   XM_063287332
- Peptide Label: isoform X6
Ensembl Acc Id: ENSRNOP00000108314   ⟸   ENSRNOT00000136647
Ensembl Acc Id: ENSRNOP00000108065   ⟸   ENSRNOT00000141451
Ensembl Acc Id: ENSRNOP00000100893   ⟸   ENSRNOT00000127599
Ensembl Acc Id: ENSRNOP00000102576   ⟸   ENSRNOT00000138011
Protein Domains
XPA C-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A981-F1-model_v2 AlphaFold D4A981 1-241 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13693711
Promoter ID:EPDNEW_R4235
Type:multiple initiation site
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:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0561,792,953 - 61,793,013EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308769 AgrOrtholog
BioCyc Gene G2FUF-41414 BioCyc
Ensembl Genes ENSRNOG00000009576 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064685 ENTREZGENE
  ENSRNOT00000064685.3 UniProtKB/TrEMBL
  ENSRNOT00000108242.2 UniProtKB/TrEMBL
  ENSRNOT00000127599 ENTREZGENE
  ENSRNOT00000127599.1 UniProtKB/TrEMBL
  ENSRNOT00000136647.1 UniProtKB/TrEMBL
  ENSRNOT00000138011.1 UniProtKB/TrEMBL
  ENSRNOT00000141451 ENTREZGENE
  ENSRNOT00000141451.1 UniProtKB/TrEMBL
Gene3D-CATH 3.90.530.10 UniProtKB/TrEMBL
InterPro DNA-bd_dom_put UniProtKB/TrEMBL
  XPA UniProtKB/TrEMBL
  XPA_C UniProtKB/TrEMBL
  XPA_C_sf UniProtKB/TrEMBL
  XPA_CS UniProtKB/TrEMBL
  Znf_XPA_CS UniProtKB/TrEMBL
NCBI Gene 298074 ENTREZGENE
PANTHER DNA REPAIR PROTEIN COMPLEMENTING XP-A CELLS UniProtKB/TrEMBL
  PTHR10142 UniProtKB/TrEMBL
Pfam XPA_C UniProtKB/TrEMBL
  XPA_N UniProtKB/TrEMBL
PhenoGen Xpa PhenoGen
PROSITE XPA_1 UniProtKB/TrEMBL
  XPA_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000009576 RatGTEx
Superfamily-SCOP Glucocorticoid receptor-like (DNA-binding domain) UniProtKB/TrEMBL
  Putativ_DNA_bind UniProtKB/TrEMBL
UniProt A0A8I6G6T5 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0L7F6_RAT UniProtKB/TrEMBL
  A0ABK0LMC0_RAT UniProtKB/TrEMBL
  A0ABK0M073_RAT UniProtKB/TrEMBL
  A0ABK0M0X7_RAT UniProtKB/TrEMBL
  A6IJB2 ENTREZGENE, UniProtKB/TrEMBL
  A6IJB3 ENTREZGENE, UniProtKB/TrEMBL
  D4A981 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-03 Xpa  XPA, DNA damage recognition and repair factor  Xpa  xeroderma pigmentosum, complementation group A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Xpa  xeroderma pigmentosum, complementation group A   Xpa_predicted  xeroderma pigmentosum, complementation group A (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Xpa_predicted  xeroderma pigmentosum, complementation group A (predicted)      Symbol and Name status set to approved 70820 APPROVED