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VCX Gene

protein-coding GIFtS: 40

GC0XP007770

variable charge, X-linked
(Previous names: variable charge, X chromosome )
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)
About This Section

Aliases
MGC118975 ^²
OTTHUMP00000027889 ^²
VCX-10r ^¹, ², ³
VCX-B1 ^¹, ², ³
VCX1 ^¹, ², ³
VCX10R ^¹, ², ³, ⁵
VCXB1 ^², ³, ⁵

Descriptions
Variable charge protein on X with ten repeats ^³
Variably charged protein X-B1 ^³
variable charge, X chromosome ^¹, ²
variable charge, X-linked ^²

External Ids
HGNC: 12667¹
Entrez Gene: 26609²
UniProtKB: Q9H320³
Ensembl: ENSG00000182583⁷

Search outside databases for aliases for VCX gene

Previous GC identifers: GC0XP006659 GC0XP007169 GC0XP007221 GC0XP007620

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

EntrezGene summary for VCX:

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 10 repeats of the 30-bp unit. [provided by

RefSeq]

UniProtKB/Swiss-Prot: VCX1_HUMAN, Q9H320

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

Gene Wiki entry for VCX

(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 VCX gene

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

VCX 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 GC0XP007770: (about GC identifiers)

Start:	7,770,303 bp from pter
End:	7,772,184 bp from pter
Size:	1,882 bases
Orientation:	plus 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: VCX1_HUMAN, Q9H320 (See protein sequence)

Recommended Name: Variable charge X-linked protein 1

Size: 206 amino acids; 22289 Da

Secondary accessions: Q9P0H3

REFSEQ proteins: NP_038480.2

ENSEMBL proteins:

ENSP00000370447 ENSP00000344144 ENSP00000372332

Human Recombinant Proteins

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

2 Gene Ontology (GO) cellular component terms (links to tree view):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005634	nucleus	IDA	12862317
GO:0005730	nucleolus	IDA	12862317

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Antibodies for VCX:

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Assays for VCX:

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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: Q9H320

UniProtKB/Swiss-Prot: VCX1_HUMAN, Q9H320

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_013452

Applied Biosystems Silencer® siRNAs for VCX

Sigma-Aldrich siRNA for VCX

Sigma-Aldrich shRNA for VCX

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_013452
Myc/DDK tagged cDNA clone in CMV expression vector: NM_013452
untagged cDNA clone in CMV expression vector: NM_013452

Primers:

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

OriGene genome-wide validated SYBR primer pairs: NM_013452

UniProtKB/Swiss-Prot: VCX1_HUMAN, Q9H320

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

Genatlas biochemistry entry for VCX:

basic protein variable charge X/Y on chromosome X,testis specific,most likely present in germ

cells,included in the CRI-S232 sequence flanking the STS gene

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0003682	chromatin binding	TAS	12862317
GO:0005515	protein binding	NAS	12862317

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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2 Interacting proteins for VCX (ENSP00000344144³) via UniProtKB, MINT, and/or STRING

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
VCX3B	ENSP00000370420³	STRING (score=.96)
STS	ENSP00000217961³	STRING (score=.787)

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0006325	establishment or maintenance of chromatin architecture	TAS	12862317
GO:0007283	spermatogenesis	IEP	12862317
GO:0042255	ribosome assembly	NAS	12862317

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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 VCX

(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)
About This Section

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_013452

Sigma-Aldrich siRNA for VCX

Sigma-Aldrich shRNA for VCX

Explore Sigma-Aldrich super-pooled esiRNAs

Applied Biosystems Silencer® siRNAs:

NM_013452

REFSEQ mRNAs for VCX gene:

NM_013452.2

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_013452
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_013452
                                 untagged cDNA clone in CMV expression vector: NM_013452

Additional cDNA sequence:

AF159129.1 AF167081.2 BC098123.1 BC126903.1

2 DOTS entries:

DT.313846 DT.313845

11 AceView cDNA sequences:

AF167081 AF159129 AA565702 NM_013452 AA206042 BE504628 BF885187 AU099954

AA897187 BV184446 AI824821

highest scoring ESTs for VCX:

DB367564 DB445503 BF885449 CN263392 AA206042 AA565702 AF167081 BE504628 BC126903 AF159129

Unigene Cluster for VCX:

Variable charge, X-linked

Hs.567503 [show with all ESTs]

Unigene Representative Sequence: AF167081

GeneLoc Exon Structure

3 Ensembl transcripts including schematic representations:

ENST00000381059 ENST00000341408 ENST00000382879

(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 )
About This Section

VCX expression in normal and diseased human tissues

¹ / ²

4 probe-sets matching VCX 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	U133-A	8	0.91	0.18	--	--	--	--	--	--	--
211403_x_at²	U133-A	8	0.91	0.18	--	--	--	--	--	--	--
207281_x_at²	U133Plus2	8	0.91	0.18	--	--	--	--	--	--	--
211403_x_at²	U133Plus2	8	0.91	0.18	--	--	--	--	--	--	--

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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.567503
UniProtKB/Swiss-Prot: VCX1_HUMAN, Q9H320
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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ENSEMBL Gene Tree for VCX

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

VCX3A¹ ² VCX3B¹ ² VCY² VCX2² ENSG00000214950² VCY1B²

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

10/34 NCBI SNPs in VCX are shown (see all 34 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay) (see all 6)

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
				--	--	--		--	--				--
	rs12688826^1,2	H	7769028(+)	`AATTAG/ACAGGA`	1	--	ng5¹		4		EU EA WA	418
--	rs6639946^1,2	C	7771645(+)	`GAGCGC/GGCCAG`	1	A/G	mis¹		0	--	--	--	--
--	rs2529876^1,2	A	7770800(-)	`TACCCA/GGTTTC`	1	--	int¹		0	--	--	--	--
--	rs35791291^1,2	--	7769344(+)	`TGGTG-/AAAAAA`	1	--	ng5¹		0	--	--	--	--
--	rs3046978^1,2	--	7770156(+)	`CACAC-/ACAC TCACA`	1	--	ng5¹		0	--	--	--	--
--	rs34898862^1,2	--	7770124(+)	`ATATT-/ACACACA`	1	--	ng5¹		0	--	--	--	--
--	rs56142947^1,2	--	7769355(+)	`AAAAA-/AACCAGT`	1	--	ng5¹		0	--	--	--	--
--	rs56202916^1,2	--	7769083(+)	`CTGTGC/TTCTTA`	1	--	ng5¹		0	--	--	--	--
--	rs1637792^1,2	--	7771824(-)	`CTCCAC/GCTGGC`	1	V/L	mis¹ ese³		0	--	--	--	--
--	rs59815537^1,2	--	7770154(+)	`CACAC-/ACAC TCACA`	1	--	ng5¹		0	--	--	--	--

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HapMap Linkage Disequilibrium images for VCX (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: 300229

(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

8 PubMed articles for VCX gene:

A member of a gene family on Xp22.3, VCX-A, is deleted in patients with X-linked nonspecific mental retardation. (PubMed id 10903929)^{2, 3, 4} Fukami M....Rappold G.A. (2000)
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)
A shared promoter region suggests a common ancestor for the human VCX/Y, SPANX, and CSAG gene families and the murine CYPT family. (PubMed id 17342728)³ Hansen M.A....Leffers H. (2008)
Expression and localization of VCX/Y proteins and their possible involvement in regulation of ribosome assembly during spermatogenesis. (PubMed id 12862317)³ Zou S.W....Wang L.F. (2003)
Genetic alterations of lung adenocarcinoma in relation to smoking and ethnicity. (PubMed id 12826317)³ Sy S.M....Yim A.P. (2003)
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)
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)
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)

(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: 26609	HGNC: 12667	AceView: VCX	Ensembl:ENSG00000182583	euGenes: HUgn26609
ECgene: VCX	H-InvDB: VCX

(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 VCX
(Available from WIS Yeda, Salk, Tufts)

About This Section

(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 VCX:

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 VCX-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 VCX		Browse antibodies at Sigma-Aldrich
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	Lentivirus-delivered shRNAs for VCX		Browse small molecules at Sigma-Aldrich
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	Recombinant & Natural Proteins

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Search Novus for antibodies for VCX

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VCX Gene

protein-coding GIFtS: 40

Aliases &
Descriptions
for VCX

Summaries
for VCX

Genomic Location
for VCX

Proteins
for VCX

Protein Domains/
Families
for VCX

Gene Function
for VCX

Pathways & Interactions
for VCX

Drugs & Compounds
for VCX

Transcripts
for VCX

Expression
for VCX

Orthologs
for VCX

Paralogs
for VCX

SNPs/Variants
for VCX

Disorders & Mutations
for VCX

Medical News
for VCX

Publications
for VCX

Search for VCX

Genome Databases showing VCX

Other Databases showing VCX

Specialized Databases showing VCX

Licensable Technologies
for VCX

Services
for VCX

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

VCX Gene

protein-coding GIFtS: 40

Aliases & Descriptionsfor VCX

Summariesfor VCX

Genomic Locationfor VCX

Proteinsfor VCX

Protein Domains/Familiesfor VCX

Gene Functionfor VCX

Pathways & Interactionsfor VCX

Drugs & Compoundsfor VCX

Transcriptsfor VCX

Expression for VCX

Orthologsfor VCX

Paralogsfor VCX

SNPs/Variantsfor VCX

Disorders & Mutationsfor VCX

Medical Newsfor VCX

Publicationsfor VCX

Search for VCX

Genome Databases showing VCX

Other Databases showing VCX

Specialized Databases showing VCX

Licensable Technologiesfor VCX

Servicesfor VCX

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 VCX

Summaries
for VCX

Genomic Location
for VCX

Proteins
for VCX

Protein Domains/
Families
for VCX

Gene Function
for VCX

Pathways & Interactions
for VCX

Drugs & Compounds
for VCX

Transcripts
for VCX

Expression
for VCX

Orthologs
for VCX

Paralogs
for VCX

SNPs/Variants
for VCX

Disorders & Mutations
for VCX

Medical News
for VCX

Publications
for VCX

Licensable Technologies
for VCX

Services
for VCX