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XRCC6BP1 Gene

protein-coding GIFtS: 47

GC12P056625

XRCC6 binding protein 1
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc , and/or ⁷Ensembl, ⁸miRBase)
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Aliases
EC 3.4.24.- ^³
KUB3 ^¹, ², ³
MGC134817 ^²
MGC134818 ^²

Descriptions
Ku70 binding protein 3 ^²
Ku70-binding protein 3 ^², ³
XRCC6 binding protein 1 ^²
XRCC6-binding protein 1 ^³

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

Search outside databases for aliases for XRCC6BP1 gene

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

(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 36),
and/or miRBase,
Genomic Views according to UCSC and Ensembl, Transcription factor binding sites according to SABiosciences)
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Genomic View:

UCSC Golden Path with GeneCards custom track

Transcription factor binding sites upstream to the XRCC6BP1 gene

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)

GeneLoc gene densities for chromosome 12 GeneLoc Exon Structure

GeneLoc location for GC12P056625: (about GC identifiers)

Start:	56,621,627 bp from pter
End:	56,637,319 bp from pter
Size:	15,693 bases
Orientation:	plus strand

RefSeq DNA sequence:

NC_000012.10 NT_029419.11

(According to ¹UniProtKB, and/or Ensembl, Phosphorylation sites according to ²Phosphosite, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Enzo Life Sciences, Abnova, OriGene and/or, Abcam,
Biochemical Assays by Invitrogen, Millipore, R&D Systems, Cell Signaling Technology, and/or Enzo Life Sciences, Ontologies according to Gene Ontology Consortium 01 Apr 2009 and Entrez Gene, Antibodies by Invitrogen, Millipore, Sigma-Aldrich, R&D Systems, Cell Signaling Technology, Abcam, Abnova, and/or Novus Biologicals)
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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

Secondary accessions: Q1RLM4 Q96E81

REFSEQ proteins: NP_150592.1

ENSEMBL proteins:

ENSP00000300145

Human Recombinant Proteins

	Browse Drug Discovery Central at Invitrogen for human recombinant proteins
	Browse Purified and Recombinant Proteins at Millipore
	Browse Human Recombinant Proteins at Sigma-Aldrich
	Browse R&D Systems for human recombinant proteins
	Browse recombinant and purified proteins available from Enzo Life Sciences
	Browse Abcam for Recombinant Proteins
	Human Recombinant Proteins from Abnova (XRCC6BP1)

Browse Origene for full length recombinant human proteins expressed in human HEK293 cells

1 Gene Ontology (GO) cellular component term (links to tree view):

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

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Antibodies for XRCC6BP1:

	Browse Antibodies Central at Invitrogen
	Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
	Sigma-Aldrich Antibodies for XRCC6BP1
	Browse R&D Systems for Antibodies
	Search for antibodies at Abcam and the World's Antibody Gateway (free search engine of over 150 antibody companies)
	Monoclonal and Polyclonal Antibodies from Abnova (XRCC6BP1)
	Novus Biologicals Antibodies for XRCC6BP1

Assays for XRCC6BP1:

	Browse Invitrogen for biochemical assays
	Browse Kits and Assays available from Millipore
	Browse R&D Systems for biochemical assays
	Browse biochemical assays available from Enzo Life Sciences

(According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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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 MGI Jun 06 2009, UniProtKB, IUBMB,and/or Genatlas,
shRNA from OriGene, Sigma-Aldrich, RNAi from Sigma-Aldrich,
RNAi Products, Clones, and Q-PCR Products from Invitrogen, Millipore, OriGene, and/or Abnova, siRNAs from Applied Biosystems, SYBR primers from OriGene, Cell-based Assays from Millipore, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (XRCC6BP1)
		Browse for Gene Knock-down Tools from Millipore
		Abnova Chimera RNAi Products for Gene knock-down (XRCC6BP1)

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_033276

Applied Biosystems Silencer® siRNAs for XRCC6BP1

Sigma-Aldrich siRNA for XRCC6BP1

Sigma-Aldrich shRNA for XRCC6BP1

Explore Sigma-Aldrich super-pooled esiRNAs

Clones:		Invitrogen Clones for XRCC6BP1
		Browse Clones for the Expression of Recombinant Proteins Available from Millipore

OriGene GFP tagged cDNA clone in CMV expression vector: NM_033276
Myc/DDK tagged cDNA clone in CMV expression vector: NM_033276
untagged cDNA clone in CMV expression vector: NM_033276

Primers:

Browse Quantitative PCR Central at Invitrogen for Q-PCR LUX™ Primers

OriGene genome-wide validated SYBR primer pairs: NM_033276

5 Gene Ontology (GO) molecular function terms (links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0004677	DNA-dependent protein kinase activity	TAS	10219089
GO:0008233	peptidase activity	IEA	--
GO:0008237	metallopeptidase activity	IEA	--
GO:0008270	zinc ion binding	IEA	--
GO:0046872	metal ion binding	IEA	--

About this table

(Pathways according to Invitrogen (maps by GeneGo), Millipore, Cell Signaling Technology, Sigma-Aldrich, KEGG and/or UniProtKB,
Sets of similar genes according to GeneDecks, Proteins Network according to SABiosciences, Interactions according to ¹UniProtKB, ²MINT, and/or ³STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2009 via Entrez Gene.)
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3 Interacting proteins for XRCC6BP1 (ENSP00000300145³) via UniProtKB, MINT, and/or STRING

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
XRCC4	ENSP00000342011³	STRING (score=.955)
PRKDC	ENSP00000313420³	STRING (score=.899)
XRCC6	ENSP00000352257³	STRING (score=.814)

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2 Gene Ontology (GO) biological process terms (links to tree view):

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

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(Chemical Compounds according to UniProtKB, Enzo Life Sciences, Sigma-Aldrich, Tocris Bioscience, and/or Novoseek and Drugs according to Enzo Life Sciences and/or PharmGKB)
About This Section

Browse drugs & compounds from Enzo Life Sciences

Browse Small Molecules at Sigma-Aldrich

Browse Tocris compounds for XRCC6BP1

(GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 219 Homo sapiens; Jun 2 2009) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView,
non coding RNAs according to RNAdb,
ESTs according to GeneTide,
exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from Invitrogen, Millipore, and/or Abnova,
siRNAs from Applied Biosystems, Sigma-Aldrich,
shRNA from Sigma-Aldrich, OriGene,
Tagged/untagged cDNA clones from OriGene,
Expression Assays from Applied Biosystems)
About This Section

Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (XRCC6BP1)
		Browse for Gene Knock-down Tools from Millipore
		Abnova Chimera RNAi Products for Gene knock-down (XRCC6BP1)

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_033276

Sigma-Aldrich siRNA for XRCC6BP1

Sigma-Aldrich shRNA for XRCC6BP1

Explore Sigma-Aldrich super-pooled esiRNAs

Applied Biosystems Silencer® siRNAs:

NM_033276

REFSEQ mRNAs for XRCC6BP1 gene:

NM_033276.2

Applied Biosystems TaqMan ® Gene Expression Assays:

NM_033276

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_033276
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_033276
                                 untagged cDNA clone in CMV expression vector: NM_033276

Additional cDNA sequence:

AF078164.2 BC012776.2 BC033881.1 BC115381.1 BC115382.1

3 DOTS entries:

DT.111826 DT.40301434 DT.97839013

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

AI540267 CB141563 BX094549 BQ437666 BC012776 AI559269 AI857832 AA909432

AA627751 AI860137 AA806615 AA862367 AI760916 AA968628 BM702722 AI500004

AI338259 AA731250 BE790505 BU729777 BM796770 AI348117 BM557436 AI340350

highest scoring ESTs for XRCC6BP1:

AA025281 AA025321 AA453588 AA476668 AA731250 AA775482 AA806615 AA861720 AA862367 AA909432

Unigene Cluster for XRCC6BP1:

XRCC6 binding protein 1

Hs.61188 [show with all ESTs]

Unigene Representative Sequence: AF078164

GeneLoc Exon Structure

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

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

About this scheme

ECgene alternative splicing isoforms for XRCC6BP1

1 Ensembl transcript including schematic representation:

ENST00000300145

(Experimental results according to ¹GeneNote and GNF BioGPS,
probe sets-to-genes annotations according to ²GeneAnnot , ³GeneTide , Sets of similar genes according to GeneDecks, Electronic Northern calculations according to data from UniGene (Build 219 Homo sapiens), SAGE tags according to CGAP, plus additional links to SOURCE, and/or GNF BioGPS, and/or EXPOLDB, and/or UniProtKB,
Expression Assays from Applied Biosystems )
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XRCC6BP1 expression in normal and diseased human tissues

Applied Biosystems TaqMan ® Gene Expression Assays for XRCC6BP1

¹ / ² / ³

4 probe-sets matching XRCC6BP1 gene

Affymetrix probe-set	Array	# genes	Sensitivity	Specificity	Correlation	Length	Gb_Accession	Consensus	Uniqueness	Score	Rank
Affymetrix probe-set	Array	GeneAnnot data			GeneNote data		GeneTide data
53933_at²^{, 3}	U95-B	1	1.00	1.00	1.00	1.00	AI525818	0.80	1.00	0.91	1
227678_at²^{, 3}	U133-B	1	1.00	1.00	--	--	AI628122	0.80	1.00	0.91	1
227678_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--
1554349_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--

GeneDecks XRCC6BP1 for binary patterns associated with the probe-sets selected above

About GeneDecksing

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Data from

(Publications) and GNF BioGPS
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About these images

CGAP SAGE TAG: --

SOURCE GeneReport for Unigene cluster: Hs.61188

(Orthologs according to ^1,2HomoloGene (²older version, for species not in ¹newer version), ³euGenes, ⁴SGD and/or ⁵MGI Jun 06 2009, with possible further links to Flybase and/or WormBase, Gene Trees according to Ensembl)
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Orthologs for XRCC6BP1 gene from 5/14 species (see all 14 )

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
dog (Canis familiaris)	XRCC6BP1¹	--	XRCC6 binding protein 1	88.33(n) 85.83(a)	474422 XM_531653.2 XP_531653.2
chimpanzee (Pan troglodytes)	XRCC6BP1¹	--	XRCC6 binding protein 1	99.19(n) 98.78(a)	452031 XM_509179.2 XP_509179.2
rat (Rattus norvegicus)	Xrcc6bp1¹	--	XRCC6 binding protein 1	79.27(n) 79.67(a)	299828 XM_216903.4 XP_216903.4
mouse (Mus musculus)	Xrcc6bp1^{1, 5}	10⁵	XRCC6 binding protein 1^{1, 5}	81.19(n)¹ 78.77(a)¹	68876¹ NM_026858.2¹ NP_081134.2¹ AA691755⁵ AI852984⁵ (see all 14)
chicken (Gallus gallus)	XRCC6BP1¹	--	XRCC6 binding protein 1	71.55(n) 66.81(a)	417812 XM_416054.1 XP_416054.1

About this table Species with no ortholog for XRCC6BP1

ENSEMBL Gene Tree for XRCC6BP1

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

(According to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
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10/128 NCBI SNPs in XRCC6BP1 are shown (see all 128 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay) (see all 62)

AB	SNP ID	Valid	Chr 12 pos	Sequence	Recs	AA Chg	Type	More	Recs	Allele freq	Pop	Total sample	More
AB	Genomic Data				Transcription Data				Allele Frequencies
				--	--	--		--	--				--
	rs2888286^1,2	A,C,F,H	56620136(-)	`ATATAC/TATTTG`	1	--	ng5¹		4		EU EA WA	404
	rs3751325^1,2	A,C,F,H	56621893(-)	`GTTGCA/TGGTGA`	1	S/C	mis¹ ese³		13		EA NA EU WA	2504
	rs2888287^1,2	A,C,F,H	56619992(-)	`tgaacA/Gttgta`	1	--	ng5¹		1		WA	120
	rs4590915^1,2	A,C,F	56621397(+)	`GGGAGA/GGCAGC`	1	--	ng5¹		4		EA NA	204
	rs3751326^1,2	A,C	56621597(-)	`GGAGGC/GGGCTT`	1	--	ng5¹ tfbs³		0	--	--	--	--
	rs4760346^1,2	A,C	56621010(+)	`GGTAAA/GCGAAT`	1	--	ng5¹		0	--	--	--	--
	rs4760345^1,2	H	56620278(+)	`TCCTAG/CATAAA`	1	--	ng5¹		4		EU EA WA	420
--	rs4509811^1,2	C	56621409(+)	`GCGAAA/GTCCGC`	1	--	ng5¹		0	--	--	--	--
	rs10122^1,2	A,C,F,H,O	56636898(+)	`GCTCAT/CAGAGA`	1	H/H	syn¹ ese³		14		MN NA EU EA WA	1424
	rs17120203^1,2	C,F,H	56631873(+)	`GAGCTT/CATTCA`	1	L/L	syn¹		8		NA EU EA WA	634

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HapMap Linkage Disequilibrium images for XRCC6BP1 (up to first 250kb)

(in which this Gene is Involved, According to OMIM, UniProtKB, PharmGKB, Genatlas, GeneTests, Blood group antigen gene mutations by BGMUT, HGMD, GAD, HuGE Navigator, BCGD, and/or TGDB.)
About This Section

(Possibly Related Articles in Doctor's Guide)
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(in PubMed. Associations of this gene to articles via ¹Novoseek, ²HGNC, ³Entrez Gene, ⁴UniProtKB/Swiss-Prot, ⁵UniProtKB/TrEMBL, ⁶GAD, and/or ⁷PharmGKB)
About This Section

5 PubMed articles for XRCC6BP1 gene:

Isolation of Ku70-binding proteins (KUBs). (PubMed id 10219089)^{2, 3, 4} Yang C.R.... Boothman D.A. (1999)
KUB3 amplification and overexpression in human gliomas. (PubMed id 11571779)^{1, 3} Fischer U....Meese E. (2001)
The finished DNA sequence of human chromosome 12. (PubMed id 16541075)⁴ 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)⁴ 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)³ Strausberg R.L....Marra M.A. (2002)

(in PubMed, OMIM, and NCBI Bookshelf)
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		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, and/or H-InvDB)
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Entrez Gene: 91419	HGNC: 29452	AceView: KUB3	Ensembl:ENSG00000166896	euGenes: HUgn91419
ECgene: XRCC6BP1	H-InvDB: XRCC6BP1

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

Licensable Technologies for XRCC6BP1
(Available from WIS Yeda, Salk, Tufts)

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(Reagents available from Applied Biosystems, Antibodies and assays by Cell Signaling Technology, Abcam, Novus Biologicals,
Sigma-Aldrich, R&D Systems, Millipore, Abnova, and/or Invitrogen, Clones available from OriGene,and/or Invitrogen, Drugs and/or compounds by Sigma-Aldrich,
Enzo Life Sciences, and/or Tocris Bioscience)
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Products for XRCC6BP1:

TaqMan ® Gene Expression Assays

TaqMan ® Genotyping Assays

Free SNP selection tool

Invitrogen iPath Pathways	Invitrogen BLOCK-iT™ RNAi
Invitrogen Antibodies	Invitrogen Assays
Invitrogen Clones	Invitrogen Q-PCR Products
Invitrogen Human Recombinant Kinases	Invitrogen Custom Antibody and Peptide Service
Invitrogen Proteins / Assays / Screening Services	Search Invitrogen catalog for XRCC6BP1-related products

	Millipore Custom Antibody & Bulk Services
	Millipore Preclinical / Clinical Development Services
	Millipore Immunoassay Services
	Millipore Target Screening & Profiling Services

	Predesigned and custom siRNAs for XRCC6BP1		Antibodies for XRCC6BP1
	Explore super-pooled esiRNAs		Browse proteins at Sigma-Aldrich
	Lentivirus-delivered shRNAs for XRCC6BP1		Browse small molecules at Sigma-Aldrich
	"Your Favorite Gene" Pathways		feedback

	Antibodies		Primer Pairs
	Cell Culture Products		ELISAs
	Flow Cytometry Kits		Protease Activity Assays & Reagents
	Cell Selection/Detection Kits & Reagents		ELISA/Assay Development Kits & Reagents
	Multiplex/Array Assay Kits & Reagents		ELISpot Kits & Development Modules
	Recombinant & Natural Proteins

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	Custom Service for Rabbit Pab from Full-length Protein

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XRCC6BP1 Gene

protein-coding GIFtS: 47

Aliases &
Descriptions
for XRCC6BP1

Summaries
for XRCC6BP1

Genomic Location
for XRCC6BP1

Proteins
for XRCC6BP1

Protein Domains/
Families
for XRCC6BP1

Gene Function
for XRCC6BP1

Pathways & Interactions
for XRCC6BP1

Drugs & Compounds
for XRCC6BP1

Transcripts
for XRCC6BP1

Expression
for XRCC6BP1

Orthologs
for XRCC6BP1

Paralogs
for XRCC6BP1

SNPs/Variants
for XRCC6BP1

Disorders & Mutations
for XRCC6BP1

Medical News
for XRCC6BP1

Publications
for XRCC6BP1

Search for XRCC6BP1

Genome Databases showing XRCC6BP1

Other Databases showing XRCC6BP1

Specialized Databases showing XRCC6BP1

Licensable Technologies
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Services
for XRCC6BP1

Gene Index: 3 5 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

XRCC6BP1 Gene

protein-coding GIFtS: 47

Aliases & Descriptionsfor XRCC6BP1

Summariesfor XRCC6BP1

Genomic Locationfor XRCC6BP1

Proteinsfor XRCC6BP1

Protein Domains/Familiesfor XRCC6BP1

Gene Functionfor XRCC6BP1

Pathways & Interactionsfor XRCC6BP1

Drugs & Compoundsfor XRCC6BP1

Transcriptsfor XRCC6BP1

Expression for XRCC6BP1

Orthologsfor XRCC6BP1

Paralogsfor XRCC6BP1

SNPs/Variantsfor XRCC6BP1

Disorders & Mutationsfor XRCC6BP1

Medical Newsfor XRCC6BP1

Publicationsfor XRCC6BP1

Search for XRCC6BP1

Genome Databases showing XRCC6BP1

Other Databases showing XRCC6BP1

Specialized Databases showing XRCC6BP1

Licensable Technologiesfor XRCC6BP1

Servicesfor XRCC6BP1

Gene Index: 3 5 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

Aliases &
Descriptions
for XRCC6BP1

Summaries
for XRCC6BP1

Genomic Location
for XRCC6BP1

Proteins
for XRCC6BP1

Protein Domains/
Families
for XRCC6BP1

Gene Function
for XRCC6BP1

Pathways & Interactions
for XRCC6BP1

Drugs & Compounds
for XRCC6BP1

Transcripts
for XRCC6BP1

Expression
for XRCC6BP1

Orthologs
for XRCC6BP1

Paralogs
for XRCC6BP1

SNPs/Variants
for XRCC6BP1

Disorders & Mutations
for XRCC6BP1

Medical News
for XRCC6BP1

Publications
for XRCC6BP1

Licensable Technologies
for XRCC6BP1

Services
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