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VAX1 Gene

protein-coding GIFtS: 47

GC10M118878

ventral anterior homeobox 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
MGC126743 ^²
MGC126745 ^²
OTTHUMP00000058791 ^²
OTTHUMP00000180555 ^²

Descriptions
ventral anterior homeobox 1 ^²

External Ids
HGNC: 12660¹
Entrez Gene: 11023²
UniProtKB: Q5SQQ9³
Ensembl: ENSG00000148704⁷

Search outside databases for aliases for VAX1 gene

Previous GC identifers: GC10M117812 GC10U900019 GC10M118552

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

EntrezGene summary for VAX1:

This gene encodes a homeo-domain containing protein from a class of homeobox transcription factors

which are conserved in vertebrates. Genes of this family are involved in the regulation of body

development and morphogenesis. The most conserved genes, called HOX genes are found in special

gene clusters. This gene belongs to the VAX subfamily and lies in the vicinity of the EMX homeobox

gene family. Another member of VAX family is located on chromosome 2. The encoded protein may play

an important role in the development of anterior ventral forebrain and visual system. Multiple

transcript variants encoding different isoforms have been found for this gene. [provided by

RefSeq]

UniProtKB/Swiss-Prot: VAX1_HUMAN, Q5SQQ9

Function: Required for axon guidance and major tract formation in the developing forebrain. May

contribute to the differentiation of the neuroretina, pigmented epithelium and optic stalk (By

similarity)

Gene Wiki entry for VAX1

(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 VAX1 gene

Entrez Gene cytogenetic band: 10q26.1 Ensembl cytogenetic band: 10q25.3 HGNC cytogenetic band: 10q26.11

VAX1 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 10 GeneLoc Exon Structure

GeneLoc location for GC10M118878: (about GC identifiers)

Start:	118,878,022 bp from pter
End:	118,887,802 bp from pter
Size:	9,781 bases
Orientation:	minus strand

RefSeq DNA sequence:

NC_000010.9 NT_030059.12

(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)
About This Section

UniProtKB/Swiss-Prot: VAX1_HUMAN, Q5SQQ9 (See protein sequence)

Recommended Name: Ventral anterior homeobox 1

Size: 334 amino acids; 34713 Da

Subcellular location: Nucleus (By similarity)

Secondary accessions: Q6ZSX0

Alternative splicing: 2 isoforms: Q5SQQ9-1 Q5SQQ9-2

REFSEQ proteins (2 alternative transcripts):

NP_001106175.1 NP_954582.1

ENSEMBL proteins:

ENSP00000277905 ENSP00000358207

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 (VAX1)
	Human Recombinant Proteins from Abnova (VAX1)

OriGene Purified Recombinant Human Protein: VAX1

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0005634	nucleus	IEA	--

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Antibodies for VAX1:

	Browse Antibodies Central at Invitrogen
	Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
	Sigma-Aldrich Antibodies for VAX1
	Browse R&D Systems for Antibodies
	Antibodies from Abcam (VAX1), each with their Abpromise^SM
	Browse Abnova for Monoclonal and Polyclonal Antibodies
	Search Novus for antibodies for VAX1

Assays for VAX1:

	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

Graphical View of Domain Structure for InterPro Entry Q5SQQ9

ProtoNet protein and cluster: Q5SQQ9

1 Blocks protein family: IPB000047 Lambda and other repressor helix-turn-helix signature

UniProtKB/Swiss-Prot: VAX1_HUMAN, Q5SQQ9

Similarity: Belongs to the EMX homeobox family

Similarity: Contains 1 homeobox DNA-binding domain

(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.)
About This Section

Inhib. RNA:		Invitrogen RNAi Products for gene knock-down (VAX1)
		Browse for Gene Knock-down Tools from Millipore
		Abnova Chimera RNAi Products for Gene knock-down (VAX1)

OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_199131

Applied Biosystems Silencer® siRNAs for VAX1

Sigma-Aldrich siRNA for VAX1

Sigma-Aldrich shRNA for VAX1

Explore Sigma-Aldrich super-pooled esiRNAs

Clones:		Invitrogen Clones for VAX1
		Browse Clones for the Expression of Recombinant Proteins Available from Millipore

OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_001112704
Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_001112704
untagged cDNA clones in CMV expression vector (see all 2): NM_001112704

Primers:

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

OriGene genome-wide validated SYBR primer pairs: NM_001112704

UniProtKB/Swiss-Prot: VAX1_HUMAN, Q5SQQ9

Function: Required for axon guidance and major tract formation in the developing forebrain. May

contribute to the differentiation of the neuroretina, pigmented epithelium and optic stalk (By

ventral anterior homeobox 1,specifically expressed in the developing basal forebrain and optic

nerve,tightly linked to EMX2 in mouse and human

8 MGI mutant phenotypes (inferred from 2 alleles) (MGI details for Vax1):

craniofacial	digestive/alimentary	lethality-postnatal	lethality-prenatal/perinatal	life span-post-weaning/aging
nervous system	skeleton	vision/eye

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

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0003700	transcription factor activity	IEA	--
GO:0031490	chromatin DNA binding	IEA	--
GO:0043565	sequence-specific DNA 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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5/10 Gene Ontology (GO) biological process terms (links to tree view) (see all 10 ):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	IEA	--
GO:0001764	neuron migration	IEA	--
GO:0006355	regulation of transcription, DNA-dependent	IEA	--
GO:0007275	multicellular organismal development	IEA	--
GO:0007406	negative regulation of neuroblast proliferation	IEA	--

About this table

(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 VAX1

(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 (VAX1)
		Browse for Gene Knock-down Tools from Millipore
		Abnova Chimera RNAi Products for Gene knock-down (VAX1)

OriGene 29mer shRNA kit in GFP-retroviral vectors (see all 2): NM_199131

Sigma-Aldrich siRNA for VAX1

Sigma-Aldrich shRNA for VAX1

Explore Sigma-Aldrich super-pooled esiRNAs

Applied Biosystems Silencer® siRNAs:

NM_001112704 NM_199131

REFSEQ mRNAs for VAX1 gene (2 alternative transcripts):

NM_001112704.1 NM_199131.2

Applied Biosystems TaqMan ® Gene Expression Assays:

NM_001112704 NM_199131

               OriGene GFP tagged cDNA clones in CMV expression vector (see all 2): NM_001112704
                                 Myc/DDK tagged cDNA clones in CMV expression vector (see all 2): NM_001112704
                                 untagged cDNA clones in CMV expression vector (see all 2): NM_001112704

Additional cDNA sequence:

AK127095.1 BC101694.1 BC101696.1

3 DOTS entries:

DT.101977837 DT.99978132 DT.97815810

3 AceView cDNA sequences:

BU740757 NM_199131 AK127095

highest scoring ESTs for VAX1:

AK127095 NM_199131 BC101694 BC101696 DA244166 AI015025 BM682748 BM727523 BU740757 DB306041

Unigene Cluster for VAX1:

Ventral anterior homeobox 1

Hs.441536 [show with all ESTs]

Unigene Representative Sequence: NM_199131

GeneLoc Exon Structure

2 Ensembl transcripts including schematic representations:

ENST00000277905 ENST00000369206

(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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VAX1 expression in normal and diseased human tissues

Applied Biosystems TaqMan ® Gene Expression Assays for VAX1

¹ Data from GNF BioGPS
About these images

About these images

CGAP SAGE TAG: GAAGCTGAAA

SOURCE GeneReport for Unigene cluster: Hs.441536

(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)
About This Section

Orthologs for VAX1 gene from 5/7 species (see all 7 )

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
dog (Canis familiaris)	VAX1¹	--	ventral anterior homeobox 1	88.68(n) 91.98(a)	486906 XM_859942.1 XP_865035.1
chimpanzee (Pan troglodytes)	VAX1¹	--	ventral anterior homeobox 1	99.46(n) 99.46(a)	740057 XM_001151780.1 XP_001151780.1
cow (Bos taurus)	VAX1¹	--	ventral anterior homeobox 1	86.83(n) 90.74(a)	782056 XM_001250207.1 XP_001250208.1
rat (Rattus norvegicus)	Vax1¹	--	ventral anterior homeobox 1	84.16(n) 88.89(a)	64571 NM_022636.1 NP_072158.1
mouse (Mus musculus)	Vax1^{1, 5}	19 (53.50 cM)⁵	ventral anterior homeobox containing gene 1^{1, 5}	85.19(n)¹ 88.89(a)¹	22326¹ NM_009501.1¹ NP_033527.1¹ AB020495⁵ AF064554⁵ (see all 7)

About this table Species with no ortholog for VAX1

ENSEMBL Gene Tree for VAX1

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

Paralogs for VAX1 gene

VAX2²

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

10/42 NCBI SNPs in VAX1 are shown (see all 42 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay) (see all 25)

AB	SNP ID	Valid	Chr 10 pos	Sequence	Recs	AA Chg	Type	More	Recs	Allele freq	Pop	Total sample	More
AB	Genomic Data				Transcription Data				Allele Frequencies
				--	--	--		--	--				--
	rs10787760^1,2	A,C,F,H	118880683(+)	`AAGAAG/ATAATG`	1	--	ut3¹ ese³ trp³		8		EU EA WA NA	778
	rs6585429^1,2	A,C,F,H	118883221(+)	`GGGTCG/AGGGCA`	2	--	int¹ ut3¹		4		EU EA WA	412
	rs7086344^1,2	A,C,F,H	118880563(+)	`GAGGGC/TCCCAG`	1	--	ut3¹ ese³		6		EU EA WA NA	594
	rs10787761^1,2	A,C,H	118888370(+)	`CCTGCA/GCACCC`	1	--	ng3¹		1		WA	120
	rs11197907^1,2	C,H	118888627(+)	`TTGTAC/TTCAGA`	1	--	ng3¹		4		EU EA WA	418
	rs7911294^1,2	H	118881280(+)	`GGAGGT/GCTCTT`	1	--	ut3¹ ese³		4		EU EA WA	418
	rs12573179^1,2	H	118878762(+)	`cgttcC/Gtaagc`	1	--	ut3¹ ese³		4		EU EA WA	420
	rs1871345^1,2	A,C,F	118885358(-)	`GGCCAA/GTGATG`	1	--	int¹		0	--	--	--	--
	rs751231^1,2	A,C,F	118886654(-)	`AGATCT/GCCGGG`	1	--	int¹		1		MN	184
	rs751232^1,2	C,F	118886601(-)	`GACTCC/GGGAGG`	1	--	int¹		1		MN	184

About this table

HapMap Linkage Disequilibrium images for VAX1 (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: 604294

GeneTests: VAX1

Anophthalmia/Microphthalmia

(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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8 PubMed articles for VAX1 gene:

The DNA sequence and comparative analysis of human chromosome 10. (PubMed id 15164054)^{3, 4} Deloukas P.... Rogers J. (2004)
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)
Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)^{3, 4} Ota T....Sugano S. (2004)
A homeobox gene, vax2, controls the patterning of the eye dorsoventral axis. (PubMed id 10485894)^{2, 3} Barbieri A.M....Banfi S. (1999)
Vax1 is a novel homeobox-containing gene expressed in the developing anterior ventral forebrain. (PubMed id 9636075)^{2, 3} Hallonet M....Gruss P. (1998)
Classification and nomenclature of all human homeobox genes. (PubMed id 17963489)³ Holland P.W....Bruford E.A. (2007)
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)
Normalization and subtraction: two approaches to facilitate gene discovery. (PubMed id 8889548)³ Bonaldo M.F....Soares M.B. (1996)

(in PubMed, OMIM, and NCBI Bookshelf)
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		AND	OR
Aliases
Disorders
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: 11023	HGNC: 12660	AceView: VAX1	Ensembl:ENSG00000148704	euGenes: HUgn11023
ECgene: VAX1	H-InvDB: VAX1

(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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Name	Description
GeneReviews	http://www.genetests.org/query?gene=VAX1

Licensable Technologies for VAX1
(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 VAX1:

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 VAX1-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 VAX1		Antibodies for VAX1
	Explore super-pooled esiRNAs		Browse proteins at Sigma-Aldrich
	Lentivirus-delivered shRNAs for VAX1		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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	Tagged/untagged cDNA clones
	Validated SYBR primer pairs
	Purified proteins from HEK293T cells
	Western blot validated antibodies
	shRNA in GFP-retroviral vector

Search Tocris compounds for VAX1

Search www.enzolifesicences.com for proteins, assays, substrates, inhibitors & antibodies

Search Novus for antibodies for VAX1

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VAX1 Gene

protein-coding GIFtS: 47

Aliases &
Descriptions
for VAX1

Summaries
for VAX1

Genomic Location
for VAX1

Proteins
for VAX1

Protein Domains/
Families
for VAX1

Gene Function
for VAX1

Pathways & Interactions
for VAX1

Drugs & Compounds
for VAX1

Transcripts
for VAX1

Expression
for VAX1

Orthologs
for VAX1

Paralogs
for VAX1

SNPs/Variants
for VAX1

Disorders & Mutations
for VAX1

Medical News
for VAX1

Publications
for VAX1

Search for VAX1

Genome Databases showing VAX1

Other Databases showing VAX1

Specialized Databases showing VAX1

Licensable Technologies
for VAX1

Services
for VAX1

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

VAX1 Gene

protein-coding GIFtS: 47

Aliases & Descriptionsfor VAX1

Summariesfor VAX1

Genomic Locationfor VAX1

Proteinsfor VAX1

Protein Domains/Familiesfor VAX1

Gene Functionfor VAX1

Pathways & Interactionsfor VAX1

Drugs & Compoundsfor VAX1

Transcriptsfor VAX1

Expression for VAX1

Orthologsfor VAX1

Paralogsfor VAX1

SNPs/Variantsfor VAX1

Disorders & Mutationsfor VAX1

Medical Newsfor VAX1

Publicationsfor VAX1

Search for VAX1

Genome Databases showing VAX1

Other Databases showing VAX1

Specialized Databases showing VAX1

Licensable Technologiesfor VAX1

Servicesfor VAX1

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 VAX1

Summaries
for VAX1

Genomic Location
for VAX1

Proteins
for VAX1

Protein Domains/
Families
for VAX1

Gene Function
for VAX1

Pathways & Interactions
for VAX1

Drugs & Compounds
for VAX1

Transcripts
for VAX1

Expression
for VAX1

Orthologs
for VAX1

Paralogs
for VAX1

SNPs/Variants
for VAX1

Disorders & Mutations
for VAX1

Medical News
for VAX1

Publications
for VAX1

Licensable Technologies
for VAX1

Services
for VAX1