Xndc1 (Xrcc1 N-terminal domain containing 1) - Rat Genome Database

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Gene: Xndc1 (Xrcc1 N-terminal domain containing 1) Mus musculus
Analyze
Symbol: Xndc1
Name: Xrcc1 N-terminal domain containing 1
RGD ID: 8548915
MGI Page MGI
Description: ; FOUND IN chromosome (ortholog); nucleolus (ortholog); INTERACTS WITH (1->4)-beta-D-glucan; bisphenol A; bisphenol F
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Xndr; XRCC1 N-terminal domain-related
RGD Orthologs
Human
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm397101,714,698 - 101,732,969 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl7101,714,718 - 101,732,972 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm387102,065,491 - 102,083,762 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl7102,065,511 - 102,083,765 (+)Ensemblmm10GRCm38
Celera7102,440,643 - 102,453,462 (+)NCBICelera
Cytogenetic Map7E2NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
chromosome  (ISO)
nucleolus  (ISO)

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References
Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:14610273   PMID:16141072   PMID:16141073   PMID:18799693   PMID:21677750   PMID:21854574  


Genomics

Comparative Map Data
Xndc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm397101,714,698 - 101,732,969 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl7101,714,718 - 101,732,972 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm387102,065,491 - 102,083,762 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl7102,065,511 - 102,083,765 (+)Ensemblmm10GRCm38
Celera7102,440,643 - 102,453,462 (+)NCBICelera
Cytogenetic Map7E2NCBI
XNDC1N
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381171,865,509 - 71,928,594 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1171,865,504 - 71,928,654 (-)Ensemblhg38GRCh38
GRCh371171,576,555 - 71,639,640 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map11q13.4NCBI
HuRef1167,870,352 - 67,933,221 (-)NCBIHuRef
CHM1_11171,460,458 - 71,523,333 (-)NCBICHM1_1
T2T-CHM13v2.01171,792,417 - 71,855,483 (-)NCBIT2T-CHM13v2.0
Xndc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81165,852,276 - 165,872,591 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1165,857,557 - 165,885,055 (+)EnsemblGRCr8
mRatBN7.21156,440,284 - 156,460,609 (+)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx1164,417,925 - 164,438,196 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01171,598,016 - 171,618,284 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01164,475,341 - 164,495,596 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01167,158,720 - 167,180,052 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01173,347,626 - 173,368,947 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera1154,508,701 - 154,528,942 (+)NCBICelera
Cytogenetic Map1q32NCBI
XNDC1N
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2972,806,135 - 72,878,985 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11173,849,411 - 73,921,250 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01166,934,597 - 67,009,499 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11170,209,063 - 70,233,594 (-)NCBIPanPan1.1PanPan1.1panPan2
TRPC2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12126,163,641 - 26,202,938 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2125,954,186 - 25,972,451 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02126,393,446 - 26,411,710 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2126,393,446 - 26,411,710 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12126,184,856 - 26,203,094 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02126,400,905 - 26,419,148 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02126,302,824 - 26,321,080 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Xndc1n
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494759,665,600 - 59,691,690 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049364981,265,136 - 1,291,007 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TRPC2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.196,449,641 - 6,488,707 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.297,210,605 - 7,250,215 (-)NCBISscrofa10.2Sscrofa10.2susScr3
XNDC1N
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1163,096,260 - 63,132,158 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604362,767,605 - 62,796,359 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Xndc1n
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v12100,360,427 - 100,380,267 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Xndc1
1141 total Variants

QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357460Vtbt4_mvertebral trabecular bone trait 4 (mouse)Not determined7101693381135693530Mouse
25314307Mlh1fc2_mMLH1 foci count 2 (mouse)76502999133501729Mouse
27226781Tibl3_mtibia length 3, 5 week (mouse)774849748122199223Mouse
25314305Vmm6_mvariable multisystem mineralization 6, eye (mouse)761849748102749207Mouse
27226778Femd11_mfemur midshaft diameter 11, 16 week (mouse)756949748134001729Mouse
1301781Capsq3_mcapsaicin sensitivity related QTL 3 (mouse)Not determined787143137119485380Mouse
14746989Manh62_mmandible shape 62 (mouse)775742528109742528Mouse
11039524Tbbr3_mTrypanosoma brucei brucei response 3 (mouse)7100750722134750843Mouse
27226769Tibl12_mtibia length 12, 10 week (mouse)787249208126499172Mouse
10043926Bw1n_mbody weight 1 in NSY (mouse)Not determined745161966118693530Mouse
27226765Tibl18_mtibia length 18, 16 week (mouse)781849748126499172Mouse
27226763Feml20_mfemur length 20, 16 week (mouse)785049208124199223Mouse
4142500Morq1_mmodifier of Rs1 QTL 1 (mouse)Not determined80551681114551791Mouse
1301647Elpt_melevated leptin (mouse)Not determined786500186120500329Mouse
13208555Lgth10_mbody length 10 (mouse)751649748125599172Mouse
26884408Bzwq13_mbi-zygomatic width QTL 13, 16 week (mouse)761749748121399223Mouse
1301937Skull10_mskull morphology 10 (mouse)Not determined791482996125483156Mouse
1300528Ssial3_msusceptibility to sialadenitis 3 (mouse)Not determined793391848127392041Mouse
1300791Abbp3_mA/J and C57BL/6 blood pressure 3 (mouse)Not determined739673887103510010Mouse
1301566Adip3_madiposity 3 (mouse)Not determined775394215109394346Mouse
26884404Huml1_mhumerus length 1, 5 week (mouse)730199425108999207Mouse
1301155Bpq7_mblood pressure QTL 7 (mouse)Not determined770143137104143379Mouse
26884398Humsd6_mhumerus midshaft diameter 6, 16 week (mouse)778649748136901729Mouse
1301158Eae4_msusceptibility to experimental allergic encephalomyelitis 4 (mouse)Not determined719147398141919804Mouse
10412199Sst2_msusceptibility to tuberculosis 2 (mouse)Not determined718728794119485380Mouse
27226790Feml15_mfemur length 15, 10 week (mouse)787249208126499172Mouse
13524850Asrq7_macoustic startle response 7 (mouse)798394974132394974Mouse
1300654Bomd1_mbone mineral density 1 (mouse)Not determined768365595102365702Mouse
1302062Stheal6_msoft tissue heal 6 (mouse)Not determined787043932121044066Mouse
26884440Sklq4_mskull length QTL 4, 5 week (mouse)765249748126499172Mouse
27095903Scvln10_msacral vertebrae length 2, 10 week (mouse)781449748126499172Mouse
27226715Metcl3_mmetatarsal-calcaneal length 3, 5 week (mouse)767849748119499223Mouse
26884444Sklq8_mskull length QTL 8, 10 week (mouse)767849748124199223Mouse
25823170Hrsq7_mhost response to SARS QTL 7, log titer (mouse)754819589116822815Mouse
1301082Bbaa16_mB.burgdorferi-associated arthritis 16 (mouse)Not determined736280015116416877Mouse
10412110Cctq1_mcentral corneal thickness QTL 1 (mouse)Not determined780551681114551791Mouse
12792978Fbmd3_mfemoral bone mineral density 3, females only (mouse)77050288142367832Mouse
1301447Fembm3_mfemoral bone morphometry 3 (mouse)Not determined7100993261134993342Mouse
10412104Tons2_mtongue size 2 (mouse)Not determined799837716133837716Mouse
1301188Heal6_mwound healing/regeneration 6 (mouse)Not determined787043932121044066Mouse
26884418Bzwq7_mbi-zygomatic width QTL 7, 10 week (mouse)767849748105449207Mouse
10043973Obq29_mobesity QTL 29 (mouse)Not determined772263372106263372Mouse
27226751Femd5_mfemur midshaft diameter 5, 10 week (mouse)753249748143153737Mouse
27095933Ulnl3_mulna length 3, 5 week (mouse)773149748143153737Mouse
1301105Cfld4_mcystic fibrosis lung disease 4 (mouse)Not determined7101693381135693530Mouse
1300721Cfbw3_mcystic fibrosis body weight 3 (mouse)Not determined7101693381135693530Mouse
27095929Pglq8_mpelvic girdle length QTL 8, 10 week (mouse)787849208108099207Mouse
27226745Metcl9_mmetatarsal-calcaneal length 9, 10 week (mouse)774849748122199223Mouse
27095930Ulnl10_mulna length 10, 16 week (mouse)780849748126699172Mouse
27095923Pglq3_mpelvic girdle length QTL 3, 5 week (mouse)781249748124199223Mouse
27095916Scvln15_msacral vertebrae length 2, 16 week (mouse)761749748123699223Mouse
13464255Ifvrq2_minfluenza virus resistance QTL 2 (mouse)792500698106455693Mouse
1357664Nba3_mNew Zealand Black autoimmunity 3 (mouse)Not determined791482996125483156Mouse
1301478Eae26_msusceptibility to experimental allergic encephalomyelitis 26 (mouse)Not determined798164922132165010Mouse
26884451Sklq14_mskull length QTL 14, 16 week (mouse)767849748124999172Mouse
27095910Pglq13_mpelvic girdle length QTL 13, 16 week (mouse)773049748125699172Mouse
13463473Hbbcq4_mhemoglobin concentration QTL 4 (mouse)787043932121044066Mouse
11553869Stmm2b_mskin tumor modifier of MSM 2a (mouse)773725965107725965Mouse
27095907Scvln4_msacral vertebrae length 2, 5 week (mouse)769949748120499223Mouse
1301997Cia7_mcollagen induced arthritis QTL 7 (mouse)Not determined785365595112533819Mouse


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000094130   ⟹   ENSMUSP00000091680
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl7101,714,965 - 101,732,288 (+)Ensembl
GRCm38.p6 Ensembl7102,065,758 - 102,083,081 (+)Ensembl
Ensembl Acc Id: ENSMUST00000106950   ⟹   ENSMUSP00000102563
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl7101,714,718 - 101,732,969 (+)Ensembl
GRCm38.p6 Ensembl7102,065,511 - 102,083,762 (+)Ensembl
Ensembl Acc Id: ENSMUST00000125197
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl7101,725,124 - 101,728,473 (+)Ensembl
GRCm38.p6 Ensembl7102,075,917 - 102,079,266 (+)Ensembl
Ensembl Acc Id: ENSMUST00000140395
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl7101,730,265 - 101,731,798 (+)Ensembl
GRCm38.p6 Ensembl7102,081,058 - 102,082,591 (+)Ensembl
Ensembl Acc Id: ENSMUST00000141646
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl7101,714,729 - 101,719,210 (+)Ensembl
GRCm38.p6 Ensembl7102,065,522 - 102,070,003 (+)Ensembl
Ensembl Acc Id: ENSMUST00000142629   ⟹   ENSMUSP00000121475
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl7101,727,991 - 101,732,972 (+)Ensembl
GRCm38.p6 Ensembl7102,078,784 - 102,083,765 (+)Ensembl
Ensembl Acc Id: ENSMUST00000143839
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl7101,730,268 - 101,731,728 (+)Ensembl
GRCm38.p6 Ensembl7102,081,061 - 102,082,521 (+)Ensembl
Ensembl Acc Id: ENSMUST00000146450   ⟹   ENSMUSP00000117300
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl7101,714,800 - 101,727,087 (+)Ensembl
GRCm38.p6 Ensembl7102,065,593 - 102,077,880 (+)Ensembl
Ensembl Acc Id: ENSMUST00000153176
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl7101,714,727 - 101,729,502 (+)Ensembl
GRCm38.p6 Ensembl7102,065,520 - 102,080,295 (+)Ensembl
RefSeq Acc Id: NM_001286689   ⟹   NP_001273618
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm397101,714,698 - 101,732,969 (+)NCBI
GRCm387102,065,491 - 102,083,762 (+)NCBI
Celera7102,440,643 - 102,453,462 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001286690   ⟹   NP_001273619
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm397101,714,698 - 101,732,969 (+)NCBI
GRCm387102,065,491 - 102,083,762 (+)NCBI
Celera7102,440,643 - 102,453,462 (+)NCBI
Sequence:
RefSeq Acc Id: NP_001273618   ⟸   NM_001286689
- UniProtKB: E9PVR2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001273619   ⟸   NM_001286690
- UniProtKB: E9PVR2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSMUSP00000117300   ⟸   ENSMUST00000146450
Ensembl Acc Id: ENSMUSP00000102563   ⟸   ENSMUST00000106950
Ensembl Acc Id: ENSMUSP00000091680   ⟸   ENSMUST00000094130
Ensembl Acc Id: ENSMUSP00000121475   ⟸   ENSMUST00000142629
Protein Domains
DNA-repair protein Xrcc1 N-terminal

Promoters
RGD ID:8665007
Promoter ID:EPDNEW_M10535
Type:multiple initiation site
Name:Xndc1_1
Description:Mus musculus Xrcc1 N-terminal domain containing 1 , transcriptvariant 2, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm387102,065,501 - 102,065,561EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:5546359 AgrOrtholog
Ensembl Genes ENSMUSG00000070425 UniProtKB/TrEMBL
  ENSMUSG00000099481 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000094130 ENTREZGENE
  ENSMUST00000094130.4 UniProtKB/TrEMBL
  ENSMUST00000106950 ENTREZGENE
  ENSMUST00000106950.8 UniProtKB/TrEMBL
  ENSMUST00000123372.8 UniProtKB/TrEMBL
  ENSMUST00000142629.8 UniProtKB/TrEMBL
  ENSMUST00000146450.8 UniProtKB/TrEMBL
Gene3D-CATH Galactose-binding domain-like UniProtKB/TrEMBL
InterPro Galactose-bd-like UniProtKB/TrEMBL
  Xrcc1_N UniProtKB/TrEMBL
KEGG Report mmu:102443350 UniProtKB/TrEMBL
MGD MGI:5546359 ENTREZGENE
NCBI Gene Xndc1 ENTREZGENE
PANTHER DNA-REPAIR PROTEIN XRCC1 UniProtKB/TrEMBL
  XRCC1_N DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
Pfam XRCC1_N UniProtKB/TrEMBL
PhenoGen Xndc1 PhenoGen
Superfamily-SCOP SSF49785 UniProtKB/TrEMBL
UniProt D3Z526_MOUSE UniProtKB/TrEMBL
  E9PVR2 ENTREZGENE, UniProtKB/TrEMBL
  F6R278_MOUSE UniProtKB/TrEMBL