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

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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 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); 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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


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)
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)
paracetamol  (ISO)
paraquat  (ISO)
phenacetin  (ISO)
PhIP  (ISO)
pirinixic acid  (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 arsenite  (ISO)
sulfadimethoxine  (EXP)
tamoxifen  (EXP)
testosterone  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
tributylstannane  (EXP)
trichloroethene  (EXP)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
valproic acid  (ISO)
vorinostat  (ISO)
Y-27632  (ISO)
zidovudine  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

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 (-)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
(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
(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
(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
(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
260 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
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)5228222669540447Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51887394763873947Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51887394774251464Rat
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)52122674466226744Rat
1578767Stresp17Stress response QTL 174.30.01blood aldosterone amount (VT:0005346)plasma aldosterone level (CMO:0000551)52795544072955440Rat
1578776Stresp18Stress response QTL 182.9thymus mass (VT:0004954)thymus wet weight (CMO:0000855)52795544072955440Rat
6903292Stl28Serum triglyceride level QTL 282.60.0073blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)52851548973515489Rat
6903306Scl35Serum cholesterol QTL 352.60.0073blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)52851548973515489Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
1598807Glom12Glomerulus QTL 122.7kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)53321566578215665Rat
1298067Scl15Serum cholesterol level QTL 154.80.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53321566578215665Rat
1302786Kidm8Kidney mass QTL 828.15kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)53321566578215665Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)534730116104251008Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)534944474113558310Rat
1641922Alcrsp8Alcohol response QTL 8alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)53518915368564008Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1331773Scl26Serum cholesterol level QTL 263.065blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)54372665686724018Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
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)546711509161317411Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)54786906290099692Rat
9589025Epfw7Epididymal fat weight QTL 720.660.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)54946360094463600Rat
7411561Bw134Body weight QTL 134240.001body mass (VT:0001259)body weight gain (CMO:0000420)54946360094463600Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
2303615Vencon7Ventilatory control QTL 70.001respiration trait (VT:0001943)respiration rate (CMO:0000289)55098389595983895Rat
2303574Gluco42Glucose level QTL 422blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)55349671998496719Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)555715622100715622Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)558829236128034027Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
2316954Rf57Renal function QTL 570kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)55979352890450144Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)559793528113558156Rat
61386Bp49Blood pressure QTL 4916.6cerebrum integrity trait (VT:0010549)brain infarction volume (CMO:0001013)56029343498603051Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat

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
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 renal system reproductive system respiratory system appendage
High
Medium 1 4 6 4 4 2
Low 2 43 53 41 13 41 8 11 70 35 37 9 8
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000064685   ⟹   ENSRNOP00000059280
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl560,431,673 - 60,475,726 (-)Ensembl
Rnor_6.0 Ensembl561,749,767 - 61,792,928 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000108242   ⟹   ENSRNOP00000080582
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl560,451,144 - 60,475,726 (-)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:
RefSeq 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
RefSeq 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
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
  ENSRNOT00000064685.2 UniProtKB/TrEMBL
  ENSRNOT00000108242 ENTREZGENE
  ENSRNOT00000108242.1 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
KEGG Report rno:298074 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
  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