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VAX2 Gene

protein-coding GIFtS: 56

GC02P070981

ventral anterior homeobox 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)
About This Section

Aliases
DRES93 ^¹, ²

Descriptions
ventral anterior homeobox 2 ^²

External Ids
HGNC: 12661¹
Entrez Gene: 25806²
UniProtKB: Q9UIW0³
Ensembl: ENSG00000116035⁷

Search outside databases for aliases for VAX2 gene

Previous GC identifers: GC02P071137 GC02P071338 GC02P071085 GC02P071102 GC02P071039

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

EntrezGene summary for VAX2:

This gene encodes a homeobox protein and is almost exclusively expressed in the ventral portion of

the retina during development. In mouse studies, this gene was found to be required for the

correct formation of the optic fissure and other aspects of retinal development. [provided by

RefSeq]

UniProtKB/Swiss-Prot: VAX2_HUMAN, Q9UIW0

Function: Plays a crucial role in eye development and, in particular, in the specification of the

ventral optic vesicle (By similarity). May be a regulator of axial polarization in the retina

(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 VAX2 gene

Entrez Gene cytogenetic band: 2p13 Ensembl cytogenetic band: 2p13.3 HGNC cytogenetic band: 2p13.3

VAX2 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 2 GeneLoc Exon Structure

GeneLoc location for GC02P070981: (about GC identifiers)

Start:	70,981,228 bp from pter
End:	71,014,084 bp from pter
Size:	32,857 bases
Orientation:	plus strand

RefSeq DNA sequence:

NC_000002.10 NT_022184.14

(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: VAX2_HUMAN, Q9UIW0 (See protein sequence)

Recommended Name: Ventral anterior homeobox 2

Size: 290 amino acids; 30874 Da

Subcellular location: Nucleus (Probable)

Developmental stage: Expressed in the ventral part of the optic vesicles at 7 week dpc

Post-translational modifications:

View phosphorylation sites using PhosphoSite²

REFSEQ proteins: NP_036608.1

ENSEMBL proteins:

ENSP00000234392

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 (VAX2)
	Human Recombinant Proteins from Abnova (VAX2)

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	IEA	--
GO:0005737	cytoplasm	IEA	--

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Antibodies for VAX2:

	Browse Antibodies Central at Invitrogen
	Browse Millipore's Extensive Line of Mono- and Polyclonal Antibodies
	Sigma-Aldrich Antibodies for VAX2
	Browse R&D Systems for Antibodies
	Antibodies from Abcam (VAX2), each with their Abpromise^SM
	Monoclonal and Polyclonal Antibodies from Abnova (VAX2)
	Novus Biologicals Antibody for DRES93

Assays for VAX2:

	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 Q9UIW0

ProtoNet protein and cluster: Q9UIW0

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

UniProtKB/Swiss-Prot: VAX2_HUMAN, Q9UIW0

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 (VAX2)
		Browse for Gene Knock-down Tools from Millipore
		Abnova Chimera RNAi Products for Gene knock-down (VAX2)

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_012476

Applied Biosystems Silencer® siRNAs for VAX2

Sigma-Aldrich siRNA for VAX2

Sigma-Aldrich shRNA for VAX2

Explore Sigma-Aldrich super-pooled esiRNAs

Clones:		Invitrogen Clones for VAX2
		Browse Clones for the Expression of Recombinant Proteins Available from Millipore

OriGene GFP tagged cDNA clone in CMV expression vector: NM_012476
Myc/DDK tagged cDNA clone in CMV expression vector: NM_012476
untagged cDNA clone in CMV expression vector: NM_012476

Primers:

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

OriGene genome-wide validated SYBR primer pairs: NM_012476

UniProtKB/Swiss-Prot: VAX2_HUMAN, Q9UIW0

Function: Plays a crucial role in eye development and, in particular, in the specification of the

ventral optic vesicle (By similarity). May be a regulator of axial polarization in the retina

Genatlas biochemistry entry for VAX2:

ventral anterior homeobox 2,specifically expressed in the developing vertebral eye,controlling the

patterning of the eye dorsoventral axis

7 MGI mutant phenotypes (inferred from 2 alleles) (MGI details for Vax2):

behavior/neurological	craniofacial	digestive/alimentary	growth/size	lethality-prenatal/perinatal
nervous system	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	NAS	10485894
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.)
About This Section

4 Interacting proteins for VAX2 (ENSP00000234392³) via UniProtKB, MINT, and/or STRING

Interactant		Interaction Details
GeneCard	External ID(s)	Interaction Details
TBX5	ENSP00000309913³	STRING (score=.736)
PAX2	ENSP00000359317³	STRING (score=.732)
ALDH1A3	ENSP00000332256³	STRING (score=.728)
EFNB2	ENSP00000245323³	STRING (score=.714)

About this table

5/9 Gene Ontology (GO) biological process terms (links to tree view) (see all 9 ):

GO ID	Qualified GO term	Evidence	PubMed IDs
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	IEA	--
GO:0006355	regulation of transcription, DNA-dependent	IEA	--
GO:0007275	multicellular organismal development	IEA	--
GO:0007398	ectoderm development	TAS	10485894
GO:0007409	axonogenesis	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 VAX2

(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 (VAX2)
		Browse for Gene Knock-down Tools from Millipore
		Abnova Chimera RNAi Products for Gene knock-down (VAX2)

OriGene 29mer shRNA kit in GFP-retroviral vector: NM_012476

Sigma-Aldrich siRNA for VAX2

Sigma-Aldrich shRNA for VAX2

Explore Sigma-Aldrich super-pooled esiRNAs

Applied Biosystems Silencer® siRNAs:

NM_012476

REFSEQ mRNAs for VAX2 gene:

NM_012476.2

Applied Biosystems TaqMan ® Gene Expression Assays:

NM_012476

              OriGene GFP tagged cDNA clone in CMV expression vector: NM_012476
                                 Myc/DDK tagged cDNA clone in CMV expression vector: NM_012476
                                 untagged cDNA clone in CMV expression vector: NM_012476

Additional cDNA sequence:

BC006336.2 BT007035.1 Y17791.1

1 DOTS entry:

DT.75152909

13 AceView cDNA sequences:

Y17791 BC006336 BM710832 NM_012476 BG601065 H92142 BF037978 BT007035

BQ637322 BF685044 BF684283 BQ957193 H92143

highest scoring ESTs for VAX2:

BC006336 BG601065 BM710832 BT007035 H92143 Y17791 BF037978 BF685044 BQ637322 BQ957193

Unigene Cluster for VAX2:

Ventral anterior homeobox 2

Hs.249170 [show with all ESTs]

Unigene Representative Sequence: Y17791

GeneLoc Exon Structure

2 Alternative Splicing Database (ASD) splice patterns (SP) for VAX2

ExUns:	1	^	2a	·	2b	^	3	^	4a	·	4b
SP1:
SP2:							-

About this scheme

ECgene alternative splicing isoforms for VAX2

1 Ensembl transcript including schematic representation:

ENST00000234392

(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

VAX2 expression in normal and diseased human tissues

Applied Biosystems TaqMan ® Gene Expression Assays for VAX2

¹ / ² / ³

3 probe-sets matching VAX2 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
39527_at*²^{, 3}	U95-A	9	1.00	0.11	1.00	1.00	AF090102	0.40	0.05	0.29	2
220443_s_at²^{, 3}	U133-A	1	1.00	1.00	--	--	NM_012476	0.60	1.00	0.82	1
220443_s_at²	U133Plus2	1	1.00	1.00	--	--	--	--	--	--	--

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Data from

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

CGAP SAGE TAG: GGCGATGGGG

SOURCE GeneReport for Unigene cluster: Hs.249170

(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 VAX2 gene from 5/6 species (see all 6 )

Organism	Gene	Locus	Description	Human Similarity	NCBI accessions
chimpanzee (Pan troglodytes)	VAX2¹	--	ventral anterior homeobox 2	99.2(n) 99.31(a)	470400 XM_525781.2 XP_525781.2
cow (Bos taurus)	VAX2¹	--	ventral anterior homeobox 2	88.5(n) 87.68(a)	539808 XM_589627.2 XP_589627.2
rat (Rattus norvegicus)	Vax2¹	--	ventral anterior homeobox 2	84.89(n) 86.16(a)	64572 NM_022637.1 NP_072159.1
mouse (Mus musculus)	Vax2^{1, 5}	6 (35.50 cM)⁵	ventral anterior homeobox containing gene 2^{1, 5}	86.04(n)¹ 88.24(a)¹	24113¹ NM_011912.2¹ NP_036042.1¹ AB020498⁵ AB221556⁵ (see all 10)
zebrafish (Danio rerio)	vax2²	--	ventral anterior homeobox 2	74.21(n)	373869 AY183363.1

About this table Species with no ortholog for VAX2

ENSEMBL Gene Tree for VAX2

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

Paralogs for VAX2 gene

VAX1²

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

10/257 NCBI SNPs in VAX2 are shown (see all 257 )
(Click for Applied Biosystems TaqMan ® Genotyping Assay) (see all 117)

AB	SNP ID	Valid	Chr 2 pos	Sequence	Recs	AA Chg	Type	More	Recs	Allele freq	Pop	Total sample	More
AB	Genomic Data				Transcription Data				Allele Frequencies
				--	--	--		--	--				--
	rs2234500^1,2	C,F,H	71013730(+)	`GGCCCC/GGCTCC`	1	P/R	mis¹ ese³		9		EA NA EU WA	1558
	rs2270262^1,2	C,F	71013929(+)	`CCGGAC/GAGGAG`	1	--	ut3¹ ese³ trp³		1		EA	738
	rs1861076^1,2	C	70980233(+)	`CCGCAA/CGCCTC`	1	--	ng5¹		0	--	--	--	--
--	rs2234495^1,2	C,F	70981302(+)	`CGCGCC/AGGGCG`	1	R/R	syn¹ ese³		1		EA	1474
	rs2234501^1,2	C	71013794(+)	`TGGCTA/GGAACG`	1	L/L	syn¹ ese³		1		NA	76
	rs1981719^1,2	A,C,F,H,O	71012756(+)	`TGCCAC/TGGTCC`	1	--	int¹		12		EU EA WA NA	1050
	rs722285^1,2	A,C,F,H	70990702(+)	`ttgtcA/Gatttt`	1	--	int¹		8		EU EA WA	828
	rs10168442^1,2	A,C,F,H	70992069(+)	`aactaC/Tgccaa`	1	--	int¹		8		EU EA WA	836
	rs959053^1,2	C,F,H,O	71009080(+)	`AGCCCG/ATATGT`	1	--	int¹		12		MN NA EU EA WA	1162
	rs959054^1,2	C,F,H,O	71009360(+)	`ACTCCC/TCCACT`	1	--	int¹		12		NA EA MN EU WA	1267

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HapMap Linkage Disequilibrium images for VAX2 (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: 604295

Human Genome Epidemiology Navigator: VAX2 (1 document)

(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

6 PubMed articles for VAX2 gene:

A homeobox gene, vax2, controls the patterning of the eye dorsoventral axis. (PubMed id 10485894)^{1, 2, 3, 4} Barbieri A.M....Banfi S. (1999)
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)
Classification and nomenclature of all human homeobox genes. (PubMed id 17963489)³ Holland P.W....Bruford E.A. (2007)
Analysis of candidate genes on chromosome 2 in oral cleft case-parent trios from three populations. (PubMed id 16953426)³ Beaty T.H....Scott A.F. (2006)
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)
The level of BMP4 signaling is critical for the regulation of distinct T-box gene expression domains and growth along the dorso-ventral axis of the optic cup. (PubMed id 17173667)¹ Behesti H....Sowden J.C. (2006)

(in PubMed, OMIM, and NCBI Bookshelf)
About This Section

		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: 25806	HGNC: 12661	AceView: VAX2	Ensembl:ENSG00000116035	euGenes: HUgn25806
ECgene: VAX2	H-InvDB: VAX2

(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)
About This Section

Licensable Technologies for VAX2
(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)
About This Section

Products for VAX2:

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 VAX2-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 VAX2		Antibodies for VAX2
	Explore super-pooled esiRNAs		Browse proteins at Sigma-Aldrich
	Lentivirus-delivered shRNAs for VAX2		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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VAX2 Gene

protein-coding GIFtS: 56

Aliases &
Descriptions
for VAX2

Summaries
for VAX2

Genomic Location
for VAX2

Proteins
for VAX2

Protein Domains/
Families
for VAX2

Gene Function
for VAX2

Pathways & Interactions
for VAX2

Drugs & Compounds
for VAX2

Transcripts
for VAX2

Expression
for VAX2

Orthologs
for VAX2

Paralogs
for VAX2

SNPs/Variants
for VAX2

Disorders & Mutations
for VAX2

Medical News
for VAX2

Publications
for VAX2

Search for VAX2

Genome Databases showing VAX2

Other Databases showing VAX2

Specialized Databases showing VAX2

Licensable Technologies
for VAX2

Services
for VAX2

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

VAX2 Gene

protein-coding GIFtS: 56

Aliases & Descriptionsfor VAX2

Summariesfor VAX2

Genomic Locationfor VAX2

Proteinsfor VAX2

Protein Domains/Familiesfor VAX2

Gene Functionfor VAX2

Pathways & Interactionsfor VAX2

Drugs & Compoundsfor VAX2

Transcriptsfor VAX2

Expression for VAX2

Orthologsfor VAX2

Paralogsfor VAX2

SNPs/Variantsfor VAX2

Disorders & Mutationsfor VAX2

Medical Newsfor VAX2

Publicationsfor VAX2

Search for VAX2

Genome Databases showing VAX2

Other Databases showing VAX2

Specialized Databases showing VAX2

Licensable Technologiesfor VAX2

Servicesfor VAX2

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 VAX2

Summaries
for VAX2

Genomic Location
for VAX2

Proteins
for VAX2

Protein Domains/
Families
for VAX2

Gene Function
for VAX2

Pathways & Interactions
for VAX2

Drugs & Compounds
for VAX2

Transcripts
for VAX2

Expression
for VAX2

Orthologs
for VAX2

Paralogs
for VAX2

SNPs/Variants
for VAX2

Disorders & Mutations
for VAX2

Medical News
for VAX2

Publications
for VAX2

Licensable Technologies
for VAX2

Services
for VAX2