Xpc (XPC complex subunit, DNA damage recognition and repair factor) - Rat Genome Database

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Gene: Xpc (XPC complex subunit, DNA damage recognition and repair factor) Rattus norvegicus
Analyze
Symbol: Xpc
Name: XPC complex subunit, DNA damage recognition and repair factor
RGD ID: 1305760
Description: 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); PARTICIPATES IN altered nucleotide excision repair pathway; nucleotide excision repair pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; amphetamine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: DNA repair protein complementing XP-C cells; LOC312560; xeroderma pigmentosum, complementation group C
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84125,550,833 - 125,578,084 (-)NCBIGRCr8
mRatBN7.24123,993,670 - 124,020,922 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4123,993,666 - 124,021,010 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4129,459,646 - 129,486,894 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04125,234,074 - 125,261,322 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04123,858,628 - 123,885,876 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04123,134,457 - 123,161,985 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4123,134,457 - 123,161,985 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04187,383,715 - 187,411,243 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44125,672,674 - 125,699,925 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14125,917,926 - 125,944,347 (-)NCBI
Celera4112,913,130 - 112,940,381 (-)NCBICelera
Cytogenetic Map4q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-dexrazoxane  (ISO)
(S)-colchicine  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4,6-tribromophenol  (ISO)
2-acetamidofluorene  (ISO)
2-hydroxypropanoic acid  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
4-hydroxynon-2-enal  (ISO)
5-aza-2'-deoxycytidine  (ISO)
acrolein  (ISO)
adenine  (ISO)
aflatoxin B1  (ISO)
alpha-pinene  (ISO)
amphetamine  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
asbestos  (ISO)
ascaridole  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
Bisphenol A diglycidyl ether  (ISO)
buspirone  (EXP)
buta-1,3-diene  (ISO)
cadmium dichloride  (ISO)
caffeine  (ISO)
carbazoles  (ISO)
carbon nanotube  (ISO)
carboplatin  (ISO)
CGP 52608  (ISO)
chloroacetaldehyde  (ISO)
chloroethene  (ISO)
chlorpromazine  (EXP)
cidofovir anhydrous  (ISO)
cisplatin  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
coumarin  (ISO)
cyclophosphamide  (EXP,ISO)
cyclosporin A  (EXP,ISO)
cylindrospermopsin  (ISO)
diarsenic trioxide  (ISO)
Dibutyl phosphate  (ISO)
dibutyl phthalate  (EXP,ISO)
diethylstilbestrol  (ISO)
dioxygen  (ISO)
doxorubicin  (ISO)
ethyl methanesulfonate  (ISO)
fenofibrate  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
FR900359  (ISO)
furan  (EXP)
gentamycin  (EXP)
glafenine  (EXP)
gold atom  (ISO)
gold(0)  (ISO)
hydrogen peroxide  (ISO)
hydroxyurea  (ISO)
idarubicin  (ISO)
ifosfamide  (ISO)
imiquimod  (ISO)
metformin  (EXP)
methyl methanesulfonate  (ISO)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
nefazodone  (EXP)
nimesulide  (EXP)
nimustine  (ISO)
Nonidet P-40  (ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
picoxystrobin  (ISO)
pifithrin-?  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
Ptaquiloside  (ISO)
quercetin  (EXP,ISO)
rac-lactic acid  (ISO)
resveratrol  (EXP,ISO)
rotenone  (EXP)
scopoletin  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
sterigmatocystin  (ISO)
tetrachloromethane  (EXP,ISO)
troglitazone  (EXP)
tungsten  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
Y-27632  (ISO)
zidovudine  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. TFIIH: when transcription met DNA repair. Compe E and Egly JM, Nat Rev Mol Cell Biol. 2012 May 10;13(6):343-54. doi: 10.1038/nrm3350.
2. Detecting pathway-based gene-gene and gene-environment interactions in pancreatic cancer. Duell EJ, etal., Cancer Epidemiol Biomarkers Prev. 2008 Jun;17(6):1470-9.
3. Xeroderma pigmentosum complementation group C single-nucleotide polymorphisms in the nucleotide excision repair pathway correlate with prolonged progression-free survival in advanced ovarian cancer. Fleming ND, etal., Cancer. 2012 Feb 1;118(3):689-97. doi: 10.1002/cncr.26329. Epub 2011 Jul 12.
4. 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.
5. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
6. 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.
7. DNA repair proteins and telomerase reverse transcriptase in the cochlear lateral wall of cisplatin-treated rats. Guthrie OW J Chemother. 2009 Feb;21(1):74-9.
8. Preincision complex-I from the excision nuclease reaction among cochlear spiral limbus and outer hair cells. Guthrie OW J Mol Histol. 2008 Dec;39(6):617-25. Epub 2008 Nov 1.
9. 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.
10. Characterization of molecular defects in xeroderma pigmentosum group C. Li L, etal., Nat Genet. 1993 Dec;5(4):413-7.
11. The role of XPC: implications in cancer and oxidative DNA damage. Melis JP, etal., Mutat Res. 2011 Nov-Dec;728(3):107-17. doi: 10.1016/j.mrrev.2011.07.001. Epub 2011 Jul 7.
12. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
13. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
14. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
15. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
16. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
17. Comprehensive gene review and curation RGD comprehensive gene curation
Additional References at PubMed
PMID:8077226   PMID:8168482   PMID:9067411   PMID:9734359   PMID:10873465   PMID:11259578   PMID:11279143   PMID:12509299   PMID:12555660   PMID:12815074   PMID:15010313   PMID:15533840  
PMID:17049932   PMID:17088560   PMID:18682493   PMID:19615386   PMID:19941824   PMID:20539233   PMID:22431748   PMID:23376485   PMID:25901318   PMID:29973595   PMID:31527837  


Genomics

Comparative Map Data
Xpc
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr84125,550,833 - 125,578,084 (-)NCBIGRCr8
mRatBN7.24123,993,670 - 124,020,922 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4123,993,666 - 124,021,010 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4129,459,646 - 129,486,894 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.04125,234,074 - 125,261,322 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.04123,858,628 - 123,885,876 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.04123,134,457 - 123,161,985 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4123,134,457 - 123,161,985 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04187,383,715 - 187,411,243 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44125,672,674 - 125,699,925 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14125,917,926 - 125,944,347 (-)NCBI
Celera4112,913,130 - 112,940,381 (-)NCBICelera
Cytogenetic Map4q34NCBI
XPC
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38314,145,147 - 14,178,601 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl314,145,147 - 14,178,621 (-)EnsemblGRCh38hg38GRCh38
GRCh37314,186,647 - 14,220,101 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36314,161,648 - 14,195,143 (-)NCBINCBI36Build 36hg18NCBI36
Build 34314,161,650 - 14,195,143NCBI
Celera314,124,954 - 14,158,401 (-)NCBICelera
Cytogenetic Map3p25.1NCBI
HuRef314,121,624 - 14,155,151 (-)NCBIHuRef
CHM1_1314,137,033 - 14,170,557 (-)NCBICHM1_1
T2T-CHM13v2.0314,147,095 - 14,180,465 (-)NCBIT2T-CHM13v2.0
Xpc
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39691,466,287 - 91,492,870 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl691,466,287 - 91,492,870 (-)EnsemblGRCm39 Ensembl
GRCm38691,489,305 - 91,515,888 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl691,489,305 - 91,515,888 (-)EnsemblGRCm38mm10GRCm38
MGSCv37691,439,299 - 91,465,882 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36691,455,347 - 91,481,299 (-)NCBIMGSCv36mm8
Celera693,382,596 - 93,409,179 (-)NCBICelera
Cytogenetic Map6D1NCBI
cM Map640.55NCBI
Xpc
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542916,935,901 - 16,955,845 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542916,935,901 - 16,968,285 (-)NCBIChiLan1.0ChiLan1.0
XPC
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2214,122,786 - 14,156,247 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1314,127,548 - 14,160,963 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0314,063,499 - 14,097,023 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1314,403,958 - 14,437,373 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl314,403,958 - 14,437,377 (-)Ensemblpanpan1.1panPan2
XPC
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1204,299,644 - 4,328,826 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl204,300,386 - 4,328,768 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha204,337,538 - 4,366,720 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0204,320,982 - 4,350,180 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl204,224,655 - 4,350,191 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1204,040,484 - 4,069,665 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0204,362,780 - 4,391,947 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0204,327,193 - 4,356,396 (-)NCBIUU_Cfam_GSD_1.0
Xpc
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494218,769,774 - 18,812,350 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936602118,188 - 139,675 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936602118,173 - 139,884 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
XPC
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1370,348,864 - 70,397,772 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11370,348,841 - 70,397,194 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21377,746,524 - 77,794,867 (+)NCBISscrofa10.2Sscrofa10.2susScr3
XPC
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12250,088,019 - 50,121,584 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2250,085,353 - 50,121,542 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666041116,374,068 - 116,407,591 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Xpc
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248721,438,769 - 1,466,642 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248721,438,673 - 1,467,206 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Xpc
98 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:426
Count of miRNA genes:234
Interacting mature miRNAs:285
Transcripts:ENSRNOT00000011490
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
2293840Kiddil9Kidney dilation QTL 92.9kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)4120926564148090731Rat
61434Cia3Collagen induced arthritis QTL 34.8joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)4103194656148194656Rat
70177Xhs1X-ray hypersensitivity QTL 125.1intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)482798864152731274Rat
70200Alc18Alcohol consumption QTL 189.2drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)456647873149491524Rat
70201Gcr1Gastric cancer resistance QTL 12.7stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)4120260281147278687Rat
1578655Bmd11Bone mineral density QTL 1111femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)490850165135850165Rat
2303168Bp330Blood pressure QTL 3304.250.017arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)45214602146446691Rat
2302049Pia32Pristane induced arthritis QTL 325.10.001blood autoantibody amount (VT:0003725)serum immunoglobulin G-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002112)4105789505150789505Rat
61476Aia3Adjuvant induced arthritis QTL 33.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)486730991131730991Rat
724535Cm18Cardiac mass QTL 182.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)4118856416163856416Rat
731165Uae21Urinary albumin excretion QTL 212.40.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)4106649412151649412Rat
1331759Hrtrt13Heart rate QTL 133.54628heart pumping trait (VT:2000009)heart rate (CMO:0000002)4110275411168266883Rat
737821Hcar9Hepatocarcinoma resistance QTL 93.7liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)4109866907167139601Rat
1298082Stresp4Stress response QTL 4blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)450119848146803430Rat
631646Stl4Serum triglyceride level QTL 46.50.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)473169846132642728Rat
631674Iddm14Insulin dependent diabetes mellitus QTL 14blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)464528739157573521Rat
631689Scl4Serum cholesterol level QTL 41.90.008blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)495174120140174120Rat
1331802Srn5Serum renin concentration QTL 53.045renin activity (VT:0005581)plasma renin activity level (CMO:0000116)4119428175157578333Rat
1582232Gluco25Glucose level QTL 253.60.0023blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)485253748148090731Rat
738009Sach4Saccharine consumption QTL 44.90.000016consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)459948935154902892Rat
738015Pia9Pristane induced arthritis QTL 94.50.048joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)480694870125694870Rat
738016Alc16Alcohol consumption QTL 163.60.00015consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
738031Alc14Alcohol consumption QTL 147.60.00003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)459948935154902892Rat
1641919Alc22Alcohol consumption QTL 220.0005drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)481192555126192555Rat
634334Xhs3X-ray hypersensitivity QTL 310intestine integrity trait (VT:0010554)post-insult time to onset of moribundity (CMO:0001896)484728680129854654Rat
634335Anxrr16Anxiety related response QTL 167.22locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)493308457167139447Rat
634347Hcar8Hepatocarcinoma resistance QTL 85.8liver integrity trait (VT:0010547)liver tumorous lesion area to total liver area ratio (CMO:0001075)4123143783168143783Rat
1576305Emca6Estrogen-induced mammary cancer QTL 65.8mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)444463720155883716Rat
1576316Ept5Estrogen-induced pituitary tumorigenesis QTL 53.8pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)483428419177635233Rat
1641833Alc21Alcohol consumption QTL 218.60.0001drinking behavior trait (VT:0001422)ethanol drink intake rate (CMO:0001407)456698790126192555Rat
1578662Bss15Bone structure and strength QTL 1519.6femur width (VT:1000666)femoral neck width (CMO:0001695)487327165132327165Rat
1578670Bss14Bone structure and strength QTL 1416.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)487327165132327165Rat
1300116Hrtrt5Heart rate QTL 53.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)4116179486151161268Rat
1358352Srcrt3Stress Responsive Cort QTL 32.29blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)438465774146803430Rat
1354612Foco1Food consumption QTL 18.87eating behavior trait (VT:0001431)food intake rate (CMO:0000427)444463908148090542Rat
1354660Salc1Saline consumption QTL 111.26drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)444463908148090542Rat
2316958Gluco58Glucose level QTL 5810blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)411320076180699135Rat
1358202Gluco11Glucose level QTL 112.40.02adipocyte glucose uptake trait (VT:0004185)absolute change in adipocyte glucose uptake (CMO:0000873)485379421167139601Rat
2312567Glom19Glomerulus QTL 191.90.006kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)445456990146803430Rat
1549832Bss3Bone structure and strength QTL 311femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)4109827074154827074Rat
61330Eau1Experimental allergic uveoretinitis QTL 10.0003uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)470362013132642728Rat
61406Scwia1Streptococcal cell wall induced arthritis QTL 12.3joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)4106805662151805662Rat
61418Pia5Pristane induced arthritis QTL 54.5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)462277855128289560Rat
6478760Anxrr45Anxiety related response QTL 450.06717locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
6478763Anxrr46Anxiety related response QTL 460.07428locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)4110870972155870972Rat
7207480Bss105Bone structure and strength QTL 1058.1femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)4109827074154827074Rat
12798519Anxrr54Anxiety related response QTL 542.540.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4114627026159627026Rat
12798527Anxrr58Anxiety related response QTL 584.110.05locomotor behavior trait (VT:0001392)distance moved per unit of time into, out of or within a discrete space in an experimental apparatus (CMO:0001493)4119463257147278687Rat
12798523Anxrr56Anxiety related response QTL 562.830.05locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)485253748150276390Rat

Markers in Region
RH133911  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24124,022,682 - 124,022,894 (+)MAPPERmRatBN7.2
Rnor_6.04123,163,746 - 123,163,957NCBIRnor6.0
Rnor_5.04187,381,743 - 187,381,954UniSTSRnor5.0
RGSC_v3.44125,701,686 - 125,701,897UniSTSRGSC3.4
Celera4112,942,142 - 112,942,353UniSTS
RH 3.4 Map4736.07UniSTS
Cytogenetic Map4q34UniSTS
RH36905  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.24124,015,064 - 124,015,949 (+)MAPPERmRatBN7.2
Rnor_6.04123,156,128 - 123,157,012NCBIRnor6.0
Rnor_5.04187,388,687 - 187,389,572NCBIRnor5.0
RGSC_v3.44125,694,068 - 125,694,952UniSTSRGSC3.4
Celera4112,934,524 - 112,935,408UniSTS
Cytogenetic Map4q34UniSTS


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 2 12 39 23 19 23 1 1 74 35 36 11 1
Low 1 31 18 18 18 7 10 5 7
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000011490   ⟹   ENSRNOP00000011490
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl4123,993,666 - 124,021,010 (-)Ensembl
Rnor_6.0 Ensembl4123,134,457 - 123,161,985 (-)Ensembl
RefSeq Acc Id: NM_001107874   ⟹   NP_001101344
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr84125,550,833 - 125,578,084 (-)NCBI
mRatBN7.24123,993,670 - 124,020,922 (-)NCBI
Rnor_6.04123,134,457 - 123,161,985 (-)NCBI
Rnor_5.04187,383,715 - 187,411,243 (+)NCBI
RGSC_v3.44125,672,674 - 125,699,925 (-)RGD
Celera4112,913,130 - 112,940,381 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001101344 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL91370 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000011490
  ENSRNOP00000011490.3
RefSeq Acc Id: NP_001101344   ⟸   NM_001107874
- UniProtKB: D4A3D8 (UniProtKB/TrEMBL),   A6IBA2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000011490   ⟸   ENSRNOT00000011490
Protein Domains
Rad4 beta-hairpin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A3D8-F1-model_v2 AlphaFold D4A3D8 1-933 view protein structure

Transcriptome

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

Promoters
RGD ID:13693252
Promoter ID:EPDNEW_R3776
Type:initiation region
Name:Xpc_1
Description:XPC complex subunit, 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_6.04123,161,965 - 123,162,025EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305760 AgrOrtholog
BioCyc Gene G2FUF-43720 BioCyc
Ensembl Genes ENSRNOG00000008274 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000011490 ENTREZGENE
  ENSRNOT00000011490.4 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.2460 UniProtKB/TrEMBL
  3.90.260.10 UniProtKB/TrEMBL
  Rad4, beta-hairpin domain BHD1 UniProtKB/TrEMBL
InterPro DNA_repair_Rad4 UniProtKB/TrEMBL
  DNA_repair_Rad4_DNA-bd_1 UniProtKB/TrEMBL
  DNA_repair_Rad4_DNA-bd_2 UniProtKB/TrEMBL
  DNA_repair_Rad4_DNA-bd_3 UniProtKB/TrEMBL
  DNA_repair_Rad4_subg UniProtKB/TrEMBL
  DNA_repair_Rad4_transGln-dom UniProtKB/TrEMBL
  Papain_like_cys_pep_sf UniProtKB/TrEMBL
  Rad4_BHD3_sf UniProtKB/TrEMBL
  Transglutaminase-like_sf UniProtKB/TrEMBL
KEGG Report rno:312560 UniProtKB/TrEMBL
NCBI Gene 312560 ENTREZGENE
PANTHER DNA REPAIR PROTEIN COMPLEMENTING XP-C CELLS UniProtKB/TrEMBL
  Rad4 UniProtKB/TrEMBL
Pfam BHD_1 UniProtKB/TrEMBL
  BHD_2 UniProtKB/TrEMBL
  BHD_3 UniProtKB/TrEMBL
  Rad4 UniProtKB/TrEMBL
PhenoGen Xpc PhenoGen
RatGTEx ENSRNOG00000008274 RatGTEx
SMART BHD_1 UniProtKB/TrEMBL
  BHD_2 UniProtKB/TrEMBL
  BHD_3 UniProtKB/TrEMBL
Superfamily-SCOP SSF54001 UniProtKB/TrEMBL
UniProt A6IBA2 ENTREZGENE, UniProtKB/TrEMBL
  D4A3D8 ENTREZGENE, UniProtKB/TrEMBL


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