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VCX3A Gene

protein-coding GIFtS: 46

GC0XM006461

variable charge, X-linked 3A
(Previous names: variable charge, X-linked 3 )
Symbol approved by the HUGO Gene Nomenclature Committee (HGNC) database
(Previous symbol: VCX3)

(According to ¹HGNC, ²Entrez Gene,
³UniProtKB/Swiss-Prot, ⁴UniProtKB/TrEMBL, ⁵OMIM, ⁶GeneLoc , and/or ⁷Ensembl, ⁸miRBase)
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Aliases
MGC118976 ^²
MGC125730 ^²
MGC125796 ^²
OTTHUMP00000022866 ^²
VCX-8R ^¹
VCX-8r ^¹, ², ³
VCX-A ^¹, ², ³
VCX3 ^², ³
VCX8R ^², ³, ⁵
VCXA ^², ³, ⁵

Descriptions
Variable charge protein on X with eight repeats ^², ³
Variably charged protein X-A ^³
variable charge, X-linked 3 ^¹
variable charge, X-linked 3A ^²
variably charged X-A ^²

External Ids
HGNC: 18159¹
Entrez Gene: 51481²
UniProtKB: Q9NNX9³
Ensembl: ENSG00000169059⁷

Search outside databases for aliases for VCX3A gene

Previous GC identifers: GC0XP007622 GC0XP007623

(According to Entrez Gene, Wikipedia's Gene Wiki,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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EntrezGene summary for VCX3A:

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

RefSeq]

UniProtKB/Swiss-Prot: VCX3_HUMAN, Q9NNX9

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 VCX3A gene

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

VCX3A 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 GC0XM006461: (about GC identifiers)

Start:	6,461,659 bp from pter
End:	6,463,159 bp from pter
Size:	1,501 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: VCX3_HUMAN, Q9NNX9 (See protein sequence)

Recommended Name: Variable charge X-linked protein 3

Size: 186 amino acids; 20020 Da

Secondary accessions: Q9P0H4

REFSEQ proteins: NP_057463.2

ENSEMBL proteins:

ENSP00000370479 ENSP00000381713

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
	Recombinant Proteins from Abcam (VCX3A)
	Human Recombinant Proteins from Abnova (VCX3A)

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	ISS	--
GO:0005730	nucleolus	ISS	--

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Antibodies for VCX3A:

	Browse Antibodies Central at Invitrogen
	Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
	Sigma-Aldrich Antibodies for VCX3A
	Browse R&D Systems for Antibodies
	Antibodies from Abcam (VCX3A), each with their Abpromise^SM
	Monoclonal and Polyclonal Antibodies from Abnova (VCX3A)
	Novus Biologicals Antibodies for VCX3A

Assays for VCX3A:

	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)
About This Section

ProtoNet protein and cluster: Q9NNX9

UniProtKB/Swiss-Prot: VCX3_HUMAN, Q9NNX9

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
		Abnova Chimera RNAi Products for Gene knock-down (VCX3A)

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_016379

Applied Biosystems Silencer® siRNAs for VCX3A

Sigma-Aldrich siRNA for VCX3A

Sigma-Aldrich shRNA for VCX3A

Explore Sigma-Aldrich super-pooled esiRNAs

Clones:		Invitrogen Clones for VCX3A
		Browse Clones for the Expression of Recombinant Proteins Available from Millipore

OriGene GFP tagged cDNA clone in CMV expression vector: NM_016379
Myc/DDK tagged cDNA clone in CMV expression vector: NM_016379
untagged cDNA clone in CMV expression vector: NM_016379

Primers:

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

OriGene genome-wide validated SYBR primer pairs: NM_016379

UniProtKB/Swiss-Prot: VCX3_HUMAN, Q9NNX9

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

(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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5/10 Interacting proteins for VCX3A (ENSP00000370479³) via UniProtKB, MINT, and/or STRING (see all 10 )

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
VCX3B	ENSP00000370420³	STRING (score=.925)
DCP2	ENSP00000373715³	STRING (score=.903)
DCPS	ENSP00000263579³	STRING (score=.852)
PRKX	ENSP00000262848³	STRING (score=.835)
KAL1	ENSP00000262648³	STRING (score=.833)

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0007283	spermatogenesis	ISS	--
GO:0007399	nervous system development	IEP	10903929
GO:0007420	brain development	IMP	10903929

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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 VCX3A

(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
		Abnova Chimera RNAi Products for Gene knock-down (VCX3A)

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_016379

Sigma-Aldrich siRNA for VCX3A

Sigma-Aldrich shRNA for VCX3A

Explore Sigma-Aldrich super-pooled esiRNAs

Applied Biosystems Silencer® siRNAs:

NM_016379

REFSEQ mRNAs for VCX3A gene:

NM_016379.3

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_016379
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_016379
                                 untagged cDNA clone in CMV expression vector: NM_016379

Additional cDNA sequence:

AF159128.1 AF167078.1 BC039722.1 BC098149.1 BC126902.1

5 DOTS entries:

DT.120654203 DT.443460 DT.91679712 DT.121292751 DT.313846

10 AceView cDNA sequences:

BQ212742 BC039722 BV206645 NM_016379 CB160710 AF167078 BV184444 AF159128

AA994122 AA897187

highest scoring ESTs for VCX3A:

AF167078 AA897187 AA994122 NM_016379 CR749002 DB461930 AF159128 BC039722 BQ212742 CB160710

Unigene Clusters for VCX3A:

Variable charge, X-linked 3A

Hs.170076 [show with all ESTs], Hs.278906 [show with all ESTs]

Unigene Representative Sequences: BU595028, AF167078

GeneLoc Exon Structure

2 Ensembl transcripts including schematic representations:

ENST00000381089 ENST00000398729

(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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VCX3A expression in normal and diseased human tissues

¹ / ² / ³

4 probe-sets matching VCX3A 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^{, 3}	U133-A	8	0.91	0.18	--	--	AF167079	0.20	0.17	0.18	2
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: GAGGGATTTT

SOURCE GeneReport for Unigene clusters: Hs.170076 Hs.278906
UniProtKB/Swiss-Prot: VCX3_HUMAN, Q9NNX9
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 VCX3A

(Paralogs according to ¹HomoloGene
and ²Ensembl, Pseudogenes according to ³Pseudogene.org)
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Paralogs for VCX3A gene

VCX3B¹ ² VCX¹ 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

10/35 NCBI SNPs in VCX3A are shown (see all 35 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay) (see all 8)

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
				--	--	--		--	--				--
--	rs12011876^1,2	A,C,F,H	6464813(+)	`ATTTTG/ACTTTT`	1	--	ng3¹		4		EU EA WA	392
--	rs5934292^1,2	C	6462036(-)	`CCCCCC/TGAGTC`	1	L/P	mis¹		0	--	--	--	--
--	rs1058244^1,2	F	6461778(-)	`GGCCAT/GCTACT`	1	--	ut3¹		1		MN	184
--	rs7882075^1,2	H	6464397(+)	`CGTTAC/TTAAAC`	1	--	ng3¹		4		EU EA WA	404
--	rs5989511^1,2	C	6461799(-)	`AGAACC/TACCGA`	1	L/P	mis¹ ese³		0	--	--	--	--
--	rs61534132^1,2	--	6464049(+)	`ACTAA-/CTAA GTGTA`	1	--	ng3¹		0	--	--	--	--
--	rs67643849^1,2	--	6464790(+)	`AACAG-/TATAGAA`	1	--	ng3¹		0	--	--	--	--
--	rs35666104^1,2	--	6464044(+)	`CCAGT-/ACTA ACTAA`	1	--	ng3¹		0	--	--	--	--
--	rs34652879^1,2	--	6461779(-)	`CGGCC-/AAGCTA`	1	--	ut3¹		0	--	--	--	--
--	rs60478994^1,2	--	6464112(+)	`TTTTT-/TCACCA`	1	--	ng3¹		0	--	--	--	--

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HapMap Linkage Disequilibrium images for VCX3A (up to first 250kb)

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

OMIM: 300533

UniProtKB/Swiss-Prot: VCX3_HUMAN, Q9NNX9

Defects in VCX3A are associated with some forms of X-linked nonspecific mental retardation

2 Novoseek disease relationships for VCX3A gene

Disease	Score	Articles	PubMed IDs for Articles with Shared Sentences (# sentences)
ichthyosis x-linked	91.13	4	15888481 (1), 18076704 (1)
mental retardation	70.02	9	10903929 (2), 15888481 (2), 16470742 (1), 18076704 (1)

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Human Gene Mutation Database: VCX3A

(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)
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10/14 PubMed articles for VCX3A gene (see all 14 ):

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 member of a gene family on Xp22.3, VCX-A, is deleted in patients with X-linked nonspecific mental retardation. (PubMed id 10903929)^{1, 3, 4} Fukami M....Rappold G.A. (2000)
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, 3} Cuevas-Covarrubias S.A. and Gonzalez-Huerta L.M. (2008)
The LIFEdb database in 2006. (PubMed id 16381901)³ Mehrle A....Wiemann S. (2006)
Identification of an mRNA-decapping regulator implicated in X-linked mental retardation. (PubMed id 17157254)³ Jiao X....Kiledjian M. (2006)
From ORFeome to biology: a functional genomics pipeline. (PubMed id 15489336)³ Wiemann S....Poustka A. (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)
DNA cloning using in vitro site-specific recombination. (PubMed id 11076863)³ Hartley J.L....Brasch M.A. (2000)
Characterization of a low copy repetitive element S232 involved in the generation of frequent deletions of the distal short arm of the human X chromosome. (PubMed id 1549475)³ Li X.M....Shapiro L.J. (1992)
Deletions of VCX-A and NLGN4: a variable phenotype including normal intellect. (PubMed id 17391250)¹ Macarov M....Meiner V. (2007)

(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: 51481	HGNC: 18159	AceView: VCX3	Ensembl:ENSG00000169059	euGenes: HUgn51481
ECgene: VCX3A	H-InvDB: VCX3A

(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)
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Licensable Technologies for VCX3A
(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 VCX3A:

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 VCX3A-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 VCX3A		Antibodies for VCX3A
	Explore super-pooled esiRNAs		Browse proteins at Sigma-Aldrich
	Lentivirus-delivered shRNAs for VCX3A		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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VCX3A Gene

protein-coding GIFtS: 46

Aliases &
Descriptions
for VCX3A

Summaries
for VCX3A

Genomic Location
for VCX3A

Proteins
for VCX3A

Protein Domains/
Families
for VCX3A

Gene Function
for VCX3A

Pathways & Interactions
for VCX3A

Drugs & Compounds
for VCX3A

Transcripts
for VCX3A

Expression
for VCX3A

Orthologs
for VCX3A

Paralogs
for VCX3A

SNPs/Variants
for VCX3A

Disorders & Mutations
for VCX3A

Medical News
for VCX3A

Publications
for VCX3A

Search for VCX3A

Genome Databases showing VCX3A

Other Databases showing VCX3A

Specialized Databases showing VCX3A

Licensable Technologies
for VCX3A

Services
for VCX3A

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

VCX3A Gene

protein-coding GIFtS: 46

Aliases & Descriptionsfor VCX3A

Summariesfor VCX3A

Genomic Locationfor VCX3A

Proteinsfor VCX3A

Protein Domains/Familiesfor VCX3A

Gene Functionfor VCX3A

Pathways & Interactionsfor VCX3A

Drugs & Compoundsfor VCX3A

Transcriptsfor VCX3A

Expression for VCX3A

Orthologsfor VCX3A

Paralogsfor VCX3A

SNPs/Variantsfor VCX3A

Disorders & Mutationsfor VCX3A

Medical Newsfor VCX3A

Publicationsfor VCX3A

Search for VCX3A

Genome Databases showing VCX3A

Other Databases showing VCX3A

Specialized Databases showing VCX3A

Licensable Technologiesfor VCX3A

Servicesfor VCX3A

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 VCX3A

Summaries
for VCX3A

Genomic Location
for VCX3A

Proteins
for VCX3A

Protein Domains/
Families
for VCX3A

Gene Function
for VCX3A

Pathways & Interactions
for VCX3A

Drugs & Compounds
for VCX3A

Transcripts
for VCX3A

Expression
for VCX3A

Orthologs
for VCX3A

Paralogs
for VCX3A

SNPs/Variants
for VCX3A

Disorders & Mutations
for VCX3A

Medical News
for VCX3A

Publications
for VCX3A

Licensable Technologies
for VCX3A

Services
for VCX3A