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Analyze GeneStrainQTL List |
 Gene Annotator (Functional Annotation) unavailable |
 Gene Annotator (Annotation Distribution) unavailable |
 Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable |
Gene Annotator (Functional Annotation) |
Gene Annotator (Annotation Distribution) |
Variant Visualizer (Genomic Variants) |
 InterViewer (Protein-Protein Interactions) unavailable |
 Gviewer (Genome Viewer) unavailable |
 Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable |
InterViewer (Protein-Protein Interactions) |
GViewer (Genome Viewer) |
Variant Visualizer (Damaging Variants) |
 Gene Annotator (Annotation Comparison) unavailable |
 OLGA (Gene List Generator) unavailable |
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Gene Annotator (Annotation Comparison) |
OLGA (Gene List Generator) |
Excel (Download) |
 MOET (Multi-Ontology Enrichement) unavailable |
 GOLF (Gene-Ortholog Location Finder) unavailable |
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MOET (Multi-Ontology Enrichement) |
GOLF (Gene-Ortholog Location Finder) |
Imported Annotations - ClinVar | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Term | Qualifier | Evidence | With | Reference | Notes | Source | Original Reference(s) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Common Variable Immunodeficiency 4 | ISO | RGD:732846 | 8554872 | ClinVar Annotator: match by term: Common variable immunodeficiency 4 | ClinVar | PMID:19666484, PMID:28492532 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Gene-Chemical Interaction AnnotationsGene Ontology AnnotationsMolecular Pathway AnnotationsDisease Annotations
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Gene-Chemical Interaction Annotations
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Gene Ontology Annotations
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Molecular Pathway AnnotationsReferences - curated| 1. | Bakalkin G, etal., Neuroreport. 1998 Jun 22;9(9):2147-51. |
| 2. | Endoh D, etal., Radiat Res. 2001 Feb;155(2):320-7. |
| 3. | Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27. |
| 4. | GOA data from the GO Consortium |
| 5. | Hammer F, etal., Endocrinology 2004 Feb;145(2):901-12. Epub 2003 Oct 23. |
| 6. | Higashiura M, etal., Exp Cell Res. 1992 Aug;201(2):444-51. |
| 7. | Lieber MR Annu Rev Biochem. 2010;79:181-211. doi: 10.1146/annurev.biochem.052308.093131. |
| 8. | MGD data from the GO Consortium |
| 9. | Okui T, etal., Radiat Res 2002 May;157(5):553-61. |
| 10. | Online Mendelian Inheritance in Man, OMIM (TM). |
| 11. | Parrella P, etal., J Clin Pathol. 2006 Nov;59(11):1181-5. Epub 2006 Feb 23. |
| 12. | Pipeline to import KEGG annotations from KEGG into RGD |
| 13. | RGD automated data pipeline |
| 14. | RGD automated import pipeline for gene-chemical interactions |
| 15. | Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11. |
References - uncurated| PubMed | 8621488 10409678 10716994 10783163 11751629 12145306 12377759 12604618 15159402 15979950 18162465 18378183 18809223 19121380 19135898 19723106 19946888 20150414 20383123 21568942 22019940 22504299 22658674 22681889 24095731 25852083 25941166 26359349 27621182 27829214 28712728 |
Comparative Map Data| Xrcc6 (Rattus norvegicus - Norway rat) |
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| XRCC6 (Homo sapiens - human) |
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| Xrcc6 (Mus musculus - house mouse) |
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| Xrcc6 (Chinchilla lanigera - long-tailed chinchilla) |
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| XRCC6 (Canis lupus familiaris - dog) |
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| Xrcc6 (Ictidomys tridecemlineatus - thirteen-lined ground squirrel) |
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| XRCC6 (Sus scrofa - pig) |
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| XRCC6 (Chlorocebus sabaeus - African green monkey) |
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| Xrcc6 (Heterocephalus glaber - naked mole-rat) |
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Position Markers| RH131971 |
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| AI230026 |
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QTLs in Region (Rnor_6.0)| The following QTLs overlap with this region. |  | Full Report | | CSV | | TAB | | Printer | | Gviewer |
miRNA Target Status
| 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. |
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RNA-SEQ Expression| 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 | 3 | 26 | 56 | 40 | 19 | 40 | 2 | 5 | 74 | 35 | 41 | 11 | 2 |
| Low | 17 | 1 | 1 | 1 | 6 | 6 | 6 | ||||||
| Below cutoff |
Nucleotide Sequences| RefSeq Transcripts | NM_139080 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| XM_008765671 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| GenBank Nucleotide | AAHX01051863 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| AAHX01051864 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AB066102 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| AC128377 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| BC061528 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| BC078718 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles | |
| CH473950 | (Get FASTA) | NCBI Sequence Viewer | Search GEO for Microarray Profiles |
| RefSeq Acc Id: | ENSRNOT00000008819 ⟹ ENSRNOP00000008819 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| RefSeq Acc Id: | ENSRNOT00000066849 ⟹ ENSRNOP00000061920 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| RefSeq Acc Id: | NM_139080 ⟹ NP_620780 | ||||||||||||||||||||
| RefSeq Status: | VALIDATED | ||||||||||||||||||||
| Type: | CODING | ||||||||||||||||||||
| Position: |
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| Sequence: |
GAGACCTGGAGCCCGCGTGGAAGTGGCGCCCACCCTCTTCTGTCCCAGTGGCGCTCTCGCCTCChide sequence |
| RefSeq Acc Id: | XM_008765671 ⟹ XP_008763893 | ||||||||
| RefSeq Status: | |||||||||
| Type: | CODING | ||||||||
| Position: |
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| Sequence: |
TGATTGGACGAGAGACCTGGAGCCCGCGTGGAAGTGGCGCCCACCCTCTTCTGTCCCAGTGGCGhide sequence |
Protein Sequences| Protein RefSeqs | NP_620780 | (Get FASTA) | NCBI Sequence Viewer |
| XP_008763893 | (Get FASTA) | NCBI Sequence Viewer | |
| GenBank Protein | AAH78718 | (Get FASTA) | NCBI Sequence Viewer |
| BAB83858 | (Get FASTA) | NCBI Sequence Viewer | |
| EDM15680 | (Get FASTA) | NCBI Sequence Viewer | |
| EDM15681 | (Get FASTA) | NCBI Sequence Viewer |
| RefSeq Acc Id: | NP_620780 ⟸ NM_139080 |
| - UniProtKB: | Q6AZ64 (UniProtKB/TrEMBL) |
| - Sequence: |
MSEWESYYKTEGEEEEEEEQSPDTNGEYKYSGRDSLIFLVDASRAMFESQGEDELTPFDMSIQChide sequence |
| RefSeq Acc Id: | XP_008763893 ⟸ XM_008765671 |
| - Peptide Label: | isoform X1 |
| - Sequence: |
MSEWESYYKTEGEEEEEEEQSPDTNGEYKYSGRDSLIFLVDASRAMFESQGEDELTPFDMSIQChide sequence |
| RefSeq Acc Id: | ENSRNOP00000008819 ⟸ ENSRNOT00000008819 |
| RefSeq Acc Id: | ENSRNOP00000061920 ⟸ ENSRNOT00000066849 |
TranscriptomePromoters| RGD ID: | 13695525 | ||||||||
| Promoter ID: | EPDNEW_R6049 | ||||||||
| Type: | multiple initiation site | ||||||||
| Name: | Xrcc6_1 | ||||||||
| Description: | X-ray repair cross complementing 6 | ||||||||
| SO ACC ID: | SO:0000170 | ||||||||
| Source: | EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/) | ||||||||
| Experiment Methods: | Single-end sequencing. | ||||||||
| Position: |
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Strain Sequence Variants (Rnor 6.0)
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Damaging Variants| Chromosome | Start Pos | End Pos | Reference Nucleotide | Variant Nucleotide | Variant Type | Strain |
| 7 | 123254123 | 123254124 | C | T | snv | HTX/Kyo (KyushuU), SDLEF7/Barth (UDEL), SBN/Ygl (MCW), SBH/Ygl (MCW) |
| Chromosome | Start Pos | End Pos | Reference Nucleotide | Variant Nucleotide | Variant Type | Strain |
| 7 | 123269458 | 123269459 | C | T | snv | SBN/Ygl (MCW), SBH/Ygl (MCW), SBN/Ygl (RGD), SBH/Ygl (RGD) |
| Chromosome | Start Pos | End Pos | Reference Nucleotide | Variant Nucleotide | Variant Type | Strain |
| 7 | 120411768 | 120411769 | C | T | snv | SBH/Ygl (ICL), SBN/Ygl (ICL) |
External Database Links| Database | Acc Id | Source(s) |
| AGR Gene | RGD:2643 | AgrOrtholog |
| Ensembl Genes | ENSRNOG00000006392 | Ensembl, ENTREZGENE, UniProtKB/TrEMBL |
| Ensembl Protein | ENSRNOP00000008819 | ENTREZGENE, UniProtKB/TrEMBL |
| ENSRNOP00000061920 | UniProtKB/TrEMBL | |
| Ensembl Transcript | ENSRNOT00000008819 | ENTREZGENE, UniProtKB/TrEMBL |
| ENSRNOT00000066849 | UniProtKB/TrEMBL | |
| Gene3D-CATH | 1.10.720.30 | UniProtKB/TrEMBL |
| 2.40.290.10 | UniProtKB/TrEMBL | |
| 3.40.50.410 | UniProtKB/TrEMBL | |
| 4.10.970.10 | UniProtKB/TrEMBL | |
| IMAGE_CLONE | IMAGE:7115290 | IMAGE-MGC_LOAD |
| InterPro | DNA_helicase_ATP-dep_Ku | UniProtKB/TrEMBL |
| DNA_helicase_ATP-dep_Ku70 | UniProtKB/TrEMBL | |
| Ku70_bridge/pillars_dom | UniProtKB/TrEMBL | |
| Ku_C | UniProtKB/TrEMBL | |
| Ku_N | UniProtKB/TrEMBL | |
| SAP_DNA-bd | UniProtKB/TrEMBL | |
| SAP_dom_sf | UniProtKB/TrEMBL | |
| SPOC-like | UniProtKB/TrEMBL | |
| vWFA_dom_sf | UniProtKB/TrEMBL | |
| KEGG Report | rno:25019 | UniProtKB/TrEMBL |
| MGC_CLONE | MGC:93146 | IMAGE-MGC_LOAD |
| NCBI Gene | 25019 | ENTREZGENE |
| Pfam | Ku_C | UniProtKB/TrEMBL |
| Ku_N | UniProtKB/TrEMBL | |
| PF02735 | UniProtKB/TrEMBL | |
| SAP | UniProtKB/TrEMBL | |
| PhenoGen | Xrcc6 | PhenoGen |
| PIRSF | Ku70 | UniProtKB/TrEMBL |
| PROSITE | SAP | UniProtKB/TrEMBL |
| SMART | Ku78 | UniProtKB/TrEMBL |
| SAP | UniProtKB/TrEMBL | |
| Superfamily-SCOP | SPOC-like | UniProtKB/TrEMBL |
| SSF53300 | UniProtKB/TrEMBL | |
| SSF68906 | UniProtKB/TrEMBL | |
| TIGRFAMs | ku70 | UniProtKB/TrEMBL |
| UniGene | Rn.161996 | ENTREZGENE |
| UniProt | E9PT85_RAT | UniProtKB/TrEMBL |
| Q6AZ64 | ENTREZGENE, UniProtKB/TrEMBL |
Nomenclature History| Date | Current Symbol | Current Name | Previous Symbol | Previous Name | Description | Reference | Status |
|---|---|---|---|---|---|---|---|
| 2016-06-08 | Xrcc6 | X-ray repair cross complementing 6 | Xrcc6 | X-ray repair complementing defective repair in Chinese hamster cells 6 | Nomenclature updated to reflect human and mouse nomenclature | 1299863 | APPROVED |
| 2006-03-30 | Xrcc6 | X-ray repair complementing defective repair in Chinese hamster cells 6 | G22p1 | thyroid autoantigen | Symbol and Name updated | 1299863 | APPROVED |
| 2002-11-06 | G22p1 | thyroid autoantigen | Ku70 DNA-binding component of DNA-dependent proteinkinase complex (thyroid autoantigen 70 kDa) | Name updated | 625702 | APPROVED | |
| 2002-06-10 | G22p1 | Ku70 DNA-binding component of DNA-dependent proteinkinase complex (thyroid autoantigen 70 kDa) | Symbol and Name status set to approved | 70586 | APPROVED |
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| More on Xrcc6 | |
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Alliance Gene |
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NCBI Gene |
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Ensembl Gene |
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JBrowse: rn5 rn6 |
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NCBI Genome Data Viewer |
| RGD Object Information | |
| RGD ID: | 2643 |
| Created: | 2000-05-25 |
| Species: | Rattus norvegicus |
| Last Modified: | 2020-05-05 |
| Status: | ACTIVE |
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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.
