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VCX2 Gene

protein-coding GIFtS: 37

GC0XM008097

variable charge, X-linked 2
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
MGC118977 ^²
MGC125729 ^²
MGC125794 ^²
MGC125795 ^²
OTTHUMP00000022871 ^²
VCX-2R ^¹
VCX-2r ^¹, ², ³
VCX-B ^³
VCX2R ^², ³, ⁵
VCXB ^², ³, ⁵

Descriptions
Variable charge protein on X with two repeats ^², ³
Variably charged protein X-B ^³
variable charge, X-linked 2 ^²
variably charged X-B ^²

External Ids
HGNC: 18158¹
Entrez Gene: 51480²
UniProtKB: Q9H322³
Ensembl: ENSG00000177504⁷

Search outside databases for aliases for VCX2 gene

Previous GC identifers: GC0XM007550 GC0XM007947

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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EntrezGene summary for VCX2:

This gene belongs to the VCX/Y gene family, which has multiple members on both X and Y chromosomes,

and all are expressed exclusively in male germ cells. The X-linked members are clustered on

chromosome Xp22 and Y-linked members are two identical copies of the gene within a palindromic

region on Yq11. The family members share a high degree of sequence identity, with the exception

that a 30-bp unit is tandemly repeated in X-linked members but occurs only once in Y-linked

members. The VCX gene cluster is polymorphic in terms of copy number; different individuals may

have a different number of VCX genes. VCX/Y genes encode small and highly charged proteins of

unknown function. The presence of a putative bipartite nuclear localization signal suggests that

VCX/Y members are nuclear proteins. This gene contains 2 repeats of the 30-bp unit. [provided by

RefSeq]

UniProtKB/Swiss-Prot: VCX2_HUMAN, Q9H322

Function: May mediate a process in spermatogenesis or may play a role in sex ratio distortion

(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)
About This Section

Genomic View:

UCSC Golden Path with GeneCards custom track

Transcription factor binding sites upstream to the VCX2 gene

Entrez Gene cytogenetic band: Xp22.32 Ensembl cytogenetic band: Xp22.31 HGNC cytogenetic band: Xp22.32

VCX2 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 X GeneLoc Exon Structure

GeneLoc location for GC0XM008097: (about GC identifiers)

Start:	8,097,985 bp from pter
End:	8,099,308 bp from pter
Size:	1,324 bases
Orientation:	minus strand

RefSeq DNA sequence:

NC_000023.9 NT_011757.15

(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: VCX2_HUMAN, Q9H322 (See protein sequence)

Recommended Name: Variable charge X-linked protein 2

Size: 139 amino acids; 14647 Da

Secondary accessions: A3KPB6 Q4V9T2 Q9P0H5

REFSEQ proteins: NP_057462.2

ENSEMBL proteins:

ENSP00000321309

Human Recombinant Proteins

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005575	cellular_component	ND	--

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Antibodies for VCX2:

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Assays for VCX2:

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	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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ProtoNet protein and cluster: Q9H322

UniProtKB/Swiss-Prot: VCX2_HUMAN, Q9H322

Similarity: Belongs to the VCX/VCY 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:		Browse Invitrogen for RNAi
		Browse for Gene Knock-down Tools from Millipore
		Browse Abnova for Chimera RNAi Products

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_016378

Applied Biosystems Silencer® siRNAs for VCX2

Sigma-Aldrich siRNA for VCX2

Browse shRNA at Sigma-Aldrich

Explore Sigma-Aldrich super-pooled esiRNAs

Clones:		Browse Clone Ranger at Invitrogen for clones
		Browse Clones for the Expression of Recombinant Proteins Available from Millipore

OriGene GFP tagged cDNA clone in CMV expression vector: NM_016378
Myc/DDK tagged cDNA clone in CMV expression vector: NM_016378
untagged cDNA clone in CMV expression vector: NM_016378

Primers:

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

OriGene genome-wide validated SYBR primer pairs: NM_016378

UniProtKB/Swiss-Prot: VCX2_HUMAN, Q9H322

Function: May mediate a process in spermatogenesis or may play a role in sex ratio distortion

1 Gene Ontology (GO) molecular function term (links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0003674	molecular_function	ND	--

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(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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1 Interacting protein for VCX2 (ENSP00000321309³) via UniProtKB, MINT, and/or STRING

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
STS	ENSP00000217961³	STRING (score=.823)

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1 Gene Ontology (GO) biological process term (links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0008150	biological_process	ND	--

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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 VCX2

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

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_016378

Sigma-Aldrich siRNA for VCX2

Browse shRNA at Sigma-Aldrich

Explore Sigma-Aldrich super-pooled esiRNAs

Applied Biosystems Silencer® siRNAs:

NM_016378

REFSEQ mRNAs for VCX2 gene:

NM_016378.2

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_016378
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_016378
                                 untagged cDNA clone in CMV expression vector: NM_016378

Additional cDNA sequence:

AF159127.1 AF167079.1 BC096715.1 BC098101.1 BC098113.1 BC098163.1 BC104153.2 BC104167.1

BC104168.1

2 DOTS entries:

DT.313845 DT.313846

11 AceView cDNA sequences:

AF167081 NM_013452 AA565702 AF159129 AA206042 BE504628 BF885187 AU099954

AA897187 AI824821 BV184446

highest scoring ESTs for VCX2:

AA992247 AI015625 AI018550 AI693508 BF592902 AA921797 BC096715 BC098101 BC098113 BC098163

Unigene Cluster for VCX2:

Variable charge, X-linked 2

Hs.279737 [show with all ESTs]

Unigene Representative Sequence: AF167079

GeneLoc Exon Structure

1 Ensembl transcript including schematic representation:

ENST00000317103

(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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VCX2 expression in normal and diseased human tissues

¹ / ² / ³

4 probe-sets matching VCX2 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
207281_x_at²^{, 3}	U133-A	8	1.00	0.28	--	--	NM_016378	0.40	1.00	0.76	1
211403_x_at²^{, 3}	U133-A	8	1.00	0.27	--	--	AF167079	0.60	0.83	0.73	1
207281_x_at²	U133Plus2	8	1.00	0.28	--	--	--	--	--	--	--
211403_x_at²	U133Plus2	8	1.00	0.27	--	--	--	--	--	--	--

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Data from

(Publications) and GNF BioGPS
About these images
About these images

CGAP SAGE TAG: --

SOURCE GeneReport for Unigene cluster: Hs.279737
UniProtKB/Swiss-Prot: VCX2_HUMAN, Q9H322
Tissue specificity: Expressed exclusively in testis

(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 VCX2 gene from 1 species

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
chimpanzee (Pan troglodytes)	VCX2¹	--	variable charge, X-linked 2	94.24(n) 87.05(a)	740797 XM_001140030.1 XP_001140030.1

About this table Species with no ortholog for VCX2

ENSEMBL Gene Tree for VCX2

(Paralogs according to ¹HomoloGene
and ²Ensembl, Pseudogenes according to ³Pseudogene.org)
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Paralogs for VCX2 gene

VCY² VCX3B² VCX² VCX3A² ENSG00000214950² VCY1B²

(According to the ¹NCBI SNP Database, ²Ensembl, ³PupaSUITE, and UniProtKB, Linkage Disequilibrium by HapMap, Genotyping Reagents from Applied Biosystems)
About This Section

10/35 NCBI SNPs in VCX2 are shown (see all 35 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay) (see all 1)

AB	SNP ID	Valid	Chr X pos	Sequence	Recs	AA Chg	Type	More	Recs	Allele freq	Pop	Total sample	More
AB	Genomic Data				Transcription Data				Allele Frequencies
				--	--	--		--	--				--
--	rs1869586^1,2	A,C,F,H	8099581(-)	`tgagtG/Caatgt`	1	--	ng3¹		4		EU EA WA	418
--	rs3761599^1,2	A,C,F,H	8101017(-)	`CCCATG/AAAACA`	1	--	ng3¹ tfbs³		8		EU EA WA	724
--	rs1058239^1,2	C,F,H	8098080(-)	`GAGCAG/CCGACT`	1	S/T	mis¹ ese³		4		EU EA WA	408
--	rs1058238^1,2	F	8098160(-)	`GTGGAG/AGAACC`	1	E/E	syn¹		2		MN	368
--	rs4066727^1,2	--	8099187(-)	`TCGTAC/TAGCCC`	1	--	ut5¹ ese³		0	--	--	--	--
--	rs67598627^1,2	--	8100158(+)	`AATGT-/GTTTTTTT`	1	--	ng3¹		0	--	--	--	--
--	rs41305169^1,2	--	8098182(+)	`GACTCA/GGGGGG`	1	L/P	mis¹		0	--	--	--	--
--	rs4066726^1,2	--	8099201(-)	`GATGAC/TTGACG`	1	--	ut5¹ ese³		0	--	--	--	--
--	rs67059971^1,2	--	8100472(+)	`ACCAG-/TTTTCC`	1	--	ng3¹		0	--	--	--	--
--	rs1058237^1,2	--	8098165(-)	`GCGAGC/GTGGAA`	1	V/L	mis¹ ese³		0	--	--	--	--

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HapMap Linkage Disequilibrium images for VCX2 (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

OMIM: 300532

(Possibly Related Articles in Doctor's Guide)
About This Section

(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

9 PubMed articles for VCX2 gene:

A human sex-chromosomal gene family expressed in male germ cells and encoding variably charged proteins. (PubMed id 10607842)^{2, 3, 4} Lahn B.T. and Page D.C. (2000)
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)^{3, 4} Gerhard D.S....Malek J. (2004)
A member of a gene family on Xp22.3, VCX-A, is deleted in patients with X-linked nonspecific mental retardation. (PubMed id 10903929)^{3, 4} Fukami M....Rappold G.A. (2000)
The DNA sequence of the human X chromosome. (PubMed id 15772651)⁴ Ross M.T.... Bentley D.R. (2005)
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)
Identification and characterization of the potential promoter regions of 1031 kinds of human genes. (PubMed id 11337467)³ Suzuki Y....Sugano S. (2001)
Analysis of the VCX3A, VCX2 and VCX3B genes shows that VCX3A gene deletion is not sufficient to result in mental retardation in X-linked ichthyosis. (PubMed id 18076704)¹ Cuevas-Covarrubias S.A. and Gonzalez-Huerta L.M. (2008)
Deletion of VCX-A due to NAHR plays a major role in the occurrence of mental retardation in patients with X-linked ichthyosis. (PubMed id 15888481)¹ Van Esch H....Froyen G. (2005)
Molecular cytogenetic analysis of a familial interstitial deletion Xp22.2-22.3 with a highly variable phenotype in female carriers. (PubMed id 16470742)¹ Chocholska S....Kehrer-Sawatzki H. (2006)

(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)
About This Section

Entrez Gene: 51480	HGNC: 18158	AceView: VCX	Ensembl:ENSG00000177504	euGenes: HUgn51480
ECgene: VCX2	H-InvDB: VCX2

(According to HUGE)
About This Section

(According to ATLAS, HORDE, IMGT, MTDB, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
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Licensable Technologies for VCX2
(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 VCX2:

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 VCX2-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 VCX2		Browse antibodies at Sigma-Aldrich
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VCX2 Gene

protein-coding GIFtS: 37

Aliases &
Descriptions
for VCX2

Summaries
for VCX2

Genomic Location
for VCX2

Proteins
for VCX2

Protein Domains/
Families
for VCX2

Gene Function
for VCX2

Pathways & Interactions
for VCX2

Drugs & Compounds
for VCX2

Transcripts
for VCX2

Expression
for VCX2

Orthologs
for VCX2

Paralogs
for VCX2

SNPs/Variants
for VCX2

Disorders & Mutations
for VCX2

Medical News
for VCX2

Publications
for VCX2

Search for VCX2

Genome Databases showing VCX2

Other Databases showing VCX2

Specialized Databases showing VCX2

Licensable Technologies
for VCX2

Services
for VCX2

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

VCX2 Gene

protein-coding GIFtS: 37

Aliases & Descriptionsfor VCX2

Summariesfor VCX2

Genomic Locationfor VCX2

Proteinsfor VCX2

Protein Domains/Familiesfor VCX2

Gene Functionfor VCX2

Pathways & Interactionsfor VCX2

Drugs & Compoundsfor VCX2

Transcriptsfor VCX2

Expression for VCX2

Orthologsfor VCX2

Paralogsfor VCX2

SNPs/Variantsfor VCX2

Disorders & Mutationsfor VCX2

Medical Newsfor VCX2

Publicationsfor VCX2

Search for VCX2

Genome Databases showing VCX2

Other Databases showing VCX2

Specialized Databases showing VCX2

Licensable Technologiesfor VCX2

Servicesfor VCX2

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 VCX2

Summaries
for VCX2

Genomic Location
for VCX2

Proteins
for VCX2

Protein Domains/
Families
for VCX2

Gene Function
for VCX2

Pathways & Interactions
for VCX2

Drugs & Compounds
for VCX2

Transcripts
for VCX2

Expression
for VCX2

Orthologs
for VCX2

Paralogs
for VCX2

SNPs/Variants
for VCX2

Disorders & Mutations
for VCX2

Medical News
for VCX2

Publications
for VCX2

Licensable Technologies
for VCX2

Services
for VCX2