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Category Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21

GIFtS
-

XRCC6BP1 Gene

protein-coding GIFtS: 44
GCID: GC12P058335

XRCC6 binding protein 1

Explore 2 diseases affiliated with
XRCC6BP1 via

MalaCards

our new
Human Malady Compendium

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc, ⁷Ensembl, ⁸DME, ⁹miRBase, and/or ¹⁰fRNAdb)
About This Section

Aliases
XRCC6 Binding Protein 1¹ ²		Ku70 Binding Protein 3²
KUB3¹ ² ³		Mitochondrial Inner Membrane Protease ATP23 Homolog²
Ku70-Binding Protein 3² ³		EC 3.4.24.-³
XRCC6-Binding Protein 1² ³		EC 3.4.24⁸

External Ids:	HGNC: 29452¹	Entrez Gene: 91419²	Ensembl: ENSG00000166896⁷	UniProtKB: Q9Y6H3³

Export aliases for XRCC6BP1 gene to outside databases

Previous GC identifers: GC12P056625 GC12P055372

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section

RefSeq DNA sequence:

NC_000012.11 NC_018923.1 NT_029419.12

Regulatory elements:

SABiosciences Regulatory transcription factor binding sites in the XRCC6BP1 gene promoter:
Elk-1 HNF-1A c-Rel NRF-2 FOXJ2 (long isoform) HNF-1 Chx10 FOXJ2 Pax-4a LyF-1
Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: XRCC6BP1 promoter sequence

Search SABiosciences Chromatin IP Primers for XRCC6BP1

Epigenetics:

QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat XRCC6BP1

Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 12q14.1 Ensembl cytogenetic band: 12q14.1 HGNC cytogenetic band: 12q14.1

XRCC6BP1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
XRCC6BP1 gene location

GeneLoc information about chromosome 12 GeneLoc Exon Structure

GeneLoc location for GC12P058335: view genomic region (about GC identifiers)

Start:	58,335,324 bp from pter	End:	58,351,052 bp from pter
Size:	15,729 bases	Orientation:	plus strand

1 alternative location:

Chr12-,PATCHES 58,466,585-58,482,192

(According to ¹UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to ²PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: ATP23_HUMAN, Q9Y6H3 (See protein sequence)

Recommended Name: Mitochondrial inner membrane protease ATP23 homolog

Size: 246 amino acids; 28081 Da

Subunit: Interacts with XRCC6

Sequence caution: Sequence=AAD31085.1; Type=Erroneous initiation;

Secondary accessions: Q1RLM4 Q96E81

Explore the universe of human proteins at neXtProt for XRCC6BP1: NX_Q9Y6H3

3 DME Specific Peptides for XRCC6BP1 (Q9Y6H3)

RHLACSE

HAFDHCR

RAANLSGDC

XRCC6BP1 Protein expression data from MOPED and PaxDb: About this image

REFSEQ proteins: NP_150592.1

ENSEMBL proteins:

ENSP00000300145 ENSP00000449550

Human Recombinant Protein Products:

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	Uscn Proteins for XRCC6BP1

Gene Ontology (GO): 1 cellular component term (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005958	DNA-dependent protein kinase-DNA ligase 4 complex	NAS	10219089

XRCC6BP1 for ontologies About GeneDecksing

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(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section

XRCC6BP1 for domains About GeneDecksing

1 InterPro domain/family:

IPR019165 Peptidase_M76_ATP23

Graphical View of Domain Structure for InterPro Entry Q9Y6H3

ProtoNet protein and cluster: Q9Y6H3

UniProtKB/Swiss-Prot: ATP23_HUMAN, Q9Y6H3

Similarity: Belongs to the peptidase M76 family

(According to ¹UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or ²DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
About This Section

Enzyme Numbers (IUBMB): EC 3.4.24.-¹ EC 3.4.24²

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In Situ Assay
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Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0004222	metalloendopeptidase activity	IEA	--
GO:0004677	DNA-dependent protein kinase activity	TAS	10219089
GO:0046872	metal ion binding	IEA	--

XRCC6BP1 for ontologies About GeneDecksing

(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to ¹UniProtKB, ²MINT, ³I2D, and/or ⁴STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene).
About This Section

Interactions:

Search SABiosciences Gene Network Central^TM Interacting Genes and Proteins Networks for XRCC6BP1

STRING Interaction Network Preview (showing 5 interactants - click image to see 14)

5/34 Interacting proteins for XRCC6BP1 (Q9Y6H3³ ENSP00000300145⁴) via UniProtKB, MINT, STRING, and/or I2D (see all 34)

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
XRCC6	P12956³, ENSP00000352257⁴	I2D: score=2 STRING: ENSP00000352257
UQCRFS1	P47985³, ENSP00000306397⁴	I2D: score=1 STRING: ENSP00000306397
PHB	P35232³, ENSP00000300408⁴	I2D: score=1 STRING: ENSP00000300408
PHB2	Q99623³, ENSP00000382362⁴	I2D: score=1 STRING: ENSP00000382362
BCS1L	Q9Y276³, ENSP00000352219⁴	I2D: score=1 STRING: ENSP00000352219

About this table

Gene Ontology (GO): 2 biological process terms (GO ID links to tree view): About this table

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0006303	double-strand break repair via nonhomologous end joining	TAS	10219089
GO:0006508	proteolysis	IEA	--

XRCC6BP1 for ontologies About GeneDecksing

(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section

Browse Small Molecules at EMD Millipore

Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for XRCC6BP1
Search CenterWatch for drugs/clinical trials and news about XRCC6BP1 / ATP23

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 235 Homo sapiens; Mar 10 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
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Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for XRCC6BP1 gene:

NM_033276.2

Unigene Cluster for XRCC6BP1:

XRCC6 binding protein 1

Hs.61188 [show with all ESTs]

Unigene Representative Sequence: AF078164

4 Ensembl transcripts including schematic representations, and UCSC links where relevant:

ENST00000551997 ENST00000300145(uc001sqp.3) ENST00000549257 ENST00000546709

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Additional cDNA sequence:

AF078164.2 BC012776.2 BC115381.1 BC115382.1

3 DOTS entries:

DT.111826 DT.40301434 DT.97839013

24/68 AceView cDNA sequences (see all 68):

AI559269 AI540267 AI857832 AA627751 CB141563 BQ437666 BC012776 AA909432

BX094549 AI860137 AA806615 AI184361 BU729777 AI338259 AI340350 BI825524

BM796770 AA453588 BM702722 AI348117 AI871538 BU601924 BG765139 AA025281

GeneLoc Exon Structure

5 Alternative Splicing Database (ASD) splice patterns (SP) for XRCC6BP1 About this scheme

ExUns:	1a	·	1b	·	1c	·	1d	·	1e	^	2	^	3	^	4	^	5	^	6a	·	6b	^	7	^	8a	·	8b	·	8c
SP1:									-						-
SP2:									-						-		-
SP3:															-		-
SP4:																	-
SP5:									-		-				-		-

ECgene alternative splicing isoforms for XRCC6BP1

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

XRCC6BP1 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS
CGAP TAG: --

About this image

XRCC6BP1 expression in embryonic tissues and stem cells

Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine About this table

Stem Cell Differentiation: 1 LifeMap Cell

Name

Category

Definitive endoderm-like cells (A scalable, suspensi...)

Expression:

Positive

Negative

Selective marker

Experimental details:

Curated

Microarrays

In-situ hybridization

See XRCC6BP1 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for XRCC6BP1

SOURCE GeneReport for Unigene cluster: Hs.61188

SABiosciences Expression via Pathway-Focused PCR Array including XRCC6BP1:

DNA Repair in human mouse rat

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In Situ
Assay Products:

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(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD , ⁵MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or ⁶Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of eukaryotes.

Orthologs for XRCC6BP1 gene from 8/26 species (see all 26) About this table

Organism	Taxonomic classification	Gene	Description	Human Similarity	Orthology Type	Details
mouse (Mus musculus)	Mammalia	Xrcc6bp1^{1 , 5}	XRCC6 binding protein 1^{1, 5}	79.95(n)¹ 80.49(a)¹		10 (73.84 cM)⁵ 68876¹ NM_001159559.1¹ NP_001153031.1¹ 126868430⁵
chicken (Gallus gallus)	Aves	XRCC6BP1¹	XRCC6 binding protein 1	71.55(n) 66.81(a)		417812 NM_001199554.1 NP_001186483.1
lizard (Anolis carolinensis)	Reptilia	XRCC6BP1⁶	--	65(a)	1 ↔ 1	5(52926178-52936222)
African clawed frog (Xenopus laevis)	Amphibia	kub3-prov²	Ku70-binding protein 3	76.59(n)		BC056096.1
zebrafish (Danio rerio)	Actinopterygii	zgc:162885¹	zgc:162885	64.57(n) 65.69(a)		100004177 NM_001083580.1 NP_001077049.1
fruit fly (Drosophila melanogaster)	Insecta	CG5131¹	CG5131	52.64(n) 45.9(a)		35057 NM_136001.1 NP_609845.1
thale cress (Arabidopsis thaliana)	eudicotyledons	AT3G03420¹	ku70-binding-like protein	52.52(n) 41.86(a)		821258 NM_111213.2 NP_566205.1
rice (Oryza sativa)	Liliopsida	Os12g0288900¹	hypothetical protein	47.35(n) 40.13(a)		4352004 NM_001073127.1 NP_001066595.1

ENSEMBL Gene Tree for XRCC6BP1 (if available)
TreeFam Gene Tree for XRCC6BP1 (if available)

(Paralogs according to ¹HomoloGene,
²Ensembl, and ³SIMAP, Pseudogenes according to ⁴Pseudogene.org Build 68)
About This Section

(SNPs/Variants according to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

SNP ID	Valid	Clinical significance	Chr 12 pos	Sequence	#	AA Chg	Type	More	#	Allele freq	Pop	Total sample	More
Genomic Data					Transcription Related Data				Allele Frequencies
				--	--	--		--	--
rs11357155^1,2	C	--	55384300(+)	`AAAAA-/AAAAAA`	1	--	int¹ trp³		0	--	--	--	--
rs183640052^1,2		--	58333463(+)	`TTATGC/TATACA`	1	--	us2k¹		0	--	--	--	--
rs112480071^1,2	C,F,	--	58333527(+)	`CATGGT/ATGGAG`	1	--	us2k¹		2		WA CSA	4
rs187682572^1,2		--	58333630(+)	`ACGTGC/GACATA`	1	--	us2k¹		0	--	--	--	--
rs2888287^1,2	C,F,A,H,	--	58333725(-)	`tgaacA/Gttgta`	1	--	us2k¹		6		NS NA WA EA	482
rs192366545^1,2		--	58333798(+)	`TAAACA/CTACAC`	1	--	us2k¹		0	--	--	--	--
rs149633039^1,2		--	58333805(+)	`ACACAC/TAAACC`	1	--	us2k¹		0	--	--	--	--
rs201479321^1,2	C	--	58333851(-)	`ATTTGA/GATTTT`	1	--	us2k¹		0	--	--	--	--
rs144344828^1,2		--	58333860(+)	`ATAGTA/GTTTCA`	1	--	us2k¹		0	--	--	--	--
rs2888286^1,2	C,F,A,H,	--	58333869(-)	`ATATAC/TATTTG`	1	--	us2k¹		10		NS EA NA WA	768

HapMap Linkage Disequilibrium report for XRCC6BP1 (58335324 - 58351052 bp)
Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
Database of Genomic Variants (DGV) variations for XRCC6BP1: --

SABiosciences Cancer Mutation PCR Assays

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section

XRCC6BP1 for disorders About GeneDecksing

2 diseases for XRCC6BP1: About MalaCards

glioblastoma malaria

Export disorders for XRCC6BP1 gene to outside databases

(in PubMed. Associations of this gene to articles via ¹Entrez Gene, ²UniProtKB/Swiss-Prot, ³HGNC, ⁴GAD, ⁵PharmGKB, ⁶HMDB, ⁷DrugBank, ⁸UniProtKB/TrEMBL, ⁹ Novoseek, and/or ¹⁰fRNAdb)
About This Section

PubMed articles for XRCC6BP1 gene integrated from 9 sources:
(articles sorted by number of sources associating them with XRCC6BP1)

Utopia: connect your pdf to the dynamic
world of online information

Isolation of Ku70-binding proteins (KUBs). (PubMed id 10219089)^{1, 2, 3} Yang C.R.... Boothman D.A. (1999)
KUB3 amplification and overexpression in human gliomas. (PubMed id 11571779)^{1, 9} Fischer U....Meese E. (2001)
The finished DNA sequence of human chromosome 12. (PubMed id 16541075)² Scherer S.E.... Gibbs R.A. (2006)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)² Gerhard D.S....Malek J. (2004)
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)¹ Strausberg R.L....Marra M.A. (2002)
Amplicons on chromosome 12q13-21 in glioblastoma recu rrences. (PubMed id 19839052)⁹ Fischer U....Meese E. (2010)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		AND	OR
Aliases
Free Text

Query String		PubMed OMIM NCBI Bookshelf
	(Note: In FireFox, select the above section and copy using Ctrl-C)

(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
About This Section

Entrez Gene: 91419	HGNC: 29452	AceView: KUB3	Ensembl:ENSG00000166896	euGenes: HUgn91419
ECgene: XRCC6BP1	H-InvDB: XRCC6BP1

(According to HUGE)
About This Section

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section

Name	Description
PharmGKB entry for XRCC6BP1	Pharmacogenomics, SNPs, Pathways

Intellectual Property for XRCC6BP1 gene
(Patent information from GeneIP, Licensable technologies from WIS Yeda, Salk, Tufts, IP news from LifeMap Sciences, Inc.)

About This Section

Patent Information for XRCC6BP1 gene:
Search GeneIP for patents involving XRCC6BP1

GeneCards and IP:
Japan Patent Office Licenses GeneCards European Patent Office Licenses GeneCards Improving the IP Search

(Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
In Situ Hybridization Assays from
Advanced Cell Diagnostics
About This Section


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	QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat XRCC6BP1
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	GenScript Custom Purified and Recombinant Proteins Services for XRCC6BP1		GenScript cDNA clones with any tag delivered in your preferred vector for XRCC6BP1
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GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 27 Apr 2013

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Category			VWF (GIFTS: 73) von Willebrand factor
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The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

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Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

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XRCC6BP1 Gene

XRCC6 binding protein 1

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XRCC6BP1 Gene

XRCC6 binding protein 1

Aliasesfor XRCC6BP1 gene

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Genomic Viewsfor XRCC6BP1 gene

Proteinsfor XRCC6BP1 gene

Protein Domains /Familiesfor XRCC6BP1 gene

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