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Q5SQQ9 (VAX1_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 87. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (5) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Alt products·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Ventral anterior homeobox 1
Gene names
Name:VAX1
OrganismHomo sapiens (Human) [Reference proteome]
Taxonomic identifier9606 [NCBI]
Taxonomic lineageEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo

Protein attributes

Sequence length334 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Transcription factor that may function in dorsoventral specification of the forebrain. 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.

Subcellular location

Nucleus By similarity.

Involvement in disease

Microphthalmia, syndromic, 11 (MCOPS11) [MIM:614402]: A rare clinical entity including as main characteristics microphthalmia and small optic nerves, cleft lip and palate, absence of corpus callosum, hippocampal malformations, and absence of the pineal gland. Microphthalmia is a disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues (anophthalmia). In many cases, microphthalmia/anophthalmia occurs in association with syndromes that include non-ocular abnormalities.
Note: The disease is caused by mutations affecting the gene represented in this entry. Ref.5

Sequence similarities

Belongs to the EMX homeobox family.

Contains 1 homeobox DNA-binding domain.

Ontologies

Keywords
   Biological processTranscription
Transcription regulation
   Cellular componentNucleus
   Coding sequence diversityAlternative splicing
   DiseaseDisease mutation
Microphthalmia
   DomainHomeobox
   LigandDNA-binding
   Molecular functionDevelopmental protein
   Technical termComplete proteome
Reference proteome
Gene Ontology (GO)
   Biological_processaxon guidance

Inferred from electronic annotation. Source: Ensembl

brain development

Inferred from electronic annotation. Source: Ensembl

camera-type eye development

Inferred from electronic annotation. Source: Ensembl

negative regulation of neuroblast proliferation

Inferred from electronic annotation. Source: Ensembl

negative regulation of transcription from RNA polymerase II promoter

Inferred from electronic annotation. Source: Ensembl

neuron migration

Inferred from electronic annotation. Source: Ensembl

palate development

Inferred from electronic annotation. Source: Ensembl

skeletal muscle cell differentiation

Inferred from electronic annotation. Source: Ensembl

transcription, DNA-templated

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular_componentnucleus

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular_functionchromatin DNA binding

Inferred from electronic annotation. Source: Ensembl

sequence-specific DNA binding transcription factor activity

Inferred from electronic annotation. Source: Ensembl

transcription regulatory region sequence-specific DNA binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Alternative products

This entry describes 2 isoforms produced by alternative splicing. [Align] [Select]
Isoform 1 (identifier: Q5SQQ9-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.
Isoform 2 (identifier: Q5SQQ9-2)

The sequence of this isoform differs from the canonical sequence as follows:
     144-334: VKVWFQNRRT...KEGAEKKALD → ANSEENNERF...DSGGRGWQPL

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 334334Ventral anterior homeobox 1
PRO_0000240522

Regions

DNA binding100 – 15960Homeobox
Compositional bias216 – 26853Ala-rich

Natural variations

Alternative sequence144 – 334191VKVWF…KKALD → ANSEENNERFKRGIKKQKKK RKKEPANDESRRGDSGGRGW QPL in isoform 2.
VSP_019396
Natural variant1521R → S in MCOPS11; loss of function mutation. Ref.5
VAR_067307

Sequences

Sequence LengthMass (Da)Tools
Isoform 1 [UniParc].

Last modified December 21, 2004. Version 1.
Checksum: 927FCADCFE937C12

FASTA33434,713
        10         20         30         40         50         60 
MFGKPDKMDV RCHSDAEAAR VSKNAHKESR ESKGAEGNLP AAFLKEPQGA FSASGAAEDC 

        70         80         90        100        110        120 
NKSKSNSAAD PDYCRRILVR DAKGSIREII LPKGLDLDRP KRTRTSFTAE QLYRLEMEFQ 

       130        140        150        160        170        180 
RCQYVVGRER TELARQLNLS ETQVKVWFQN RRTKQKKDQG KDSELRSVVS ETAATCSVLR 

       190        200        210        220        230        240 
LLEQGRLLSP PGLPALLPPC ATGALGSALR GPSLPALGAG AAAGSAAAAA AAAPGPAGAA 

       250        260        270        280        290        300 
SPHPPAVGGA PGPGPAGPGG LHAGAPAAGH SLFSLPVPSL LGSVASRLSS APLTMAGSLA 

       310        320        330 
GNLQELSARY LSSSAFEPYS RTNNKEGAEK KALD 

« Hide

Isoform 2 [UniParc].

Checksum: 71D7F3F0256F2B72
Show »

FASTA18621,044

References

« Hide 'large scale' references
[1]"Complete sequencing and characterization of 21,243 full-length human cDNAs."
Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S. expand/collapse author list , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
Tissue: Brain.
[2]"The DNA sequence and comparative analysis of human chromosome 10."
Deloukas P., Earthrowl M.E., Grafham D.V., Rubenfield M., French L., Steward C.A., Sims S.K., Jones M.C., Searle S., Scott C., Howe K., Hunt S.E., Andrews T.D., Gilbert J.G.R., Swarbreck D., Ashurst J.L., Taylor A., Battles J. expand/collapse author list , Bird C.P., Ainscough R., Almeida J.P., Ashwell R.I.S., Ambrose K.D., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Bates K., Beasley H., Bray-Allen S., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Cahill P., Camire D., Carter N.P., Chapman J.C., Clark S.Y., Clarke G., Clee C.M., Clegg S., Corby N., Coulson A., Dhami P., Dutta I., Dunn M., Faulkner L., Frankish A., Frankland J.A., Garner P., Garnett J., Gribble S., Griffiths C., Grocock R., Gustafson E., Hammond S., Harley J.L., Hart E., Heath P.D., Ho T.P., Hopkins B., Horne J., Howden P.J., Huckle E., Hynds C., Johnson C., Johnson D., Kana A., Kay M., Kimberley A.M., Kershaw J.K., Kokkinaki M., Laird G.K., Lawlor S., Lee H.M., Leongamornlert D.A., Laird G., Lloyd C., Lloyd D.M., Loveland J., Lovell J., McLaren S., McLay K.E., McMurray A., Mashreghi-Mohammadi M., Matthews L., Milne S., Nickerson T., Nguyen M., Overton-Larty E., Palmer S.A., Pearce A.V., Peck A.I., Pelan S., Phillimore B., Porter K., Rice C.M., Rogosin A., Ross M.T., Sarafidou T., Sehra H.K., Shownkeen R., Skuce C.D., Smith M., Standring L., Sycamore N., Tester J., Thorpe A., Torcasso W., Tracey A., Tromans A., Tsolas J., Wall M., Walsh J., Wang H., Weinstock K., West A.P., Willey D.L., Whitehead S.L., Wilming L., Wray P.W., Young L., Chen Y., Lovering R.C., Moschonas N.K., Siebert R., Fechtel K., Bentley D., Durbin R.M., Hubbard T., Doucette-Stamm L., Beck S., Smith D.R., Rogers J.
Nature 429:375-381(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA] (ISOFORM 1).
[3]Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M., Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J., Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S., Turner R. expand/collapse author list , Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H., Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K., Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D., Hunkapiller M.W., Myers E.W., Venter J.C.
Submitted (SEP-2005) to the EMBL/GenBank/DDBJ databases
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[4]"The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
The MGC Project Team
Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
Tissue: Brain.
[5]"VAX1 mutation associated with microphthalmia, corpus callosum agenesis, and orofacial clefting: The first description of a VAX1 phenotype in humans."
Slavotinek A.M., Chao R., Vacik T., Yahyavi M., Abouzeid H., Bardakjian T., Schneider A., Shaw G., Sherr E.H., Lemke G., Youssef M., Schorderet D.F.
Hum. Mutat. 33:364-368(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: VARIANT MCOPS11 SER-152, CHARACTERIZATION OF VARIANT MCOPS11 SER-152.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
AK127095 mRNA. Translation: BAC86826.1.
CH471066 Genomic DNA. Translation: EAW49433.1.
BC101694 mRNA. Translation: AAI01695.1.
BC101696 mRNA. Translation: AAI01697.1.
AL731557 Genomic DNA. Translation: CAI14824.1.
AL731557 Genomic DNA. Translation: CAI14825.1.
CCDSCCDS44483.1. [Q5SQQ9-1]
CCDS7597.1. [Q5SQQ9-2]
RefSeqNP_001106175.1. NM_001112704.1. [Q5SQQ9-1]
NP_954582.1. NM_199131.2. [Q5SQQ9-2]
UniGeneHs.441536.

3D structure databases

ProteinModelPortalQ5SQQ9.
SMRQ5SQQ9. Positions 102-157.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING9606.ENSP00000358207.

PTM databases

PhosphoSiteQ5SQQ9.

Polymorphism databases

DMDM74743553.

Proteomic databases

PaxDbQ5SQQ9.
PRIDEQ5SQQ9.

Protocols and materials databases

DNASU11023.
StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblENST00000277905; ENSP00000277905; ENSG00000148704. [Q5SQQ9-2]
ENST00000369206; ENSP00000358207; ENSG00000148704. [Q5SQQ9-1]
GeneID11023.
KEGGhsa:11023.
UCSCuc001ldb.1. human. [Q5SQQ9-2]
uc009xyx.3. human. [Q5SQQ9-1]

Organism-specific databases

CTD11023.
GeneCardsGC10M118878.
GeneReviewsVAX1.
HGNCHGNC:12660. VAX1.
HPAHPA028946.
MIM604294. gene.
614402. phenotype.
neXtProtNX_Q5SQQ9.
PharmGKBPA37283.
GenAtlasSearch...

Phylogenomic databases

eggNOGNOG323848.
HOGENOMHOG000049217.
HOVERGENHBG007558.
InParanoidQ5SQQ9.
KOK09318.
OMASISTFDK.
OrthoDBEOG71ZP35.
PhylomeDBQ5SQQ9.
TreeFamTF319504.

Gene expression databases

BgeeQ5SQQ9.
CleanExHS_VAX1.
GenevestigatorQ5SQQ9.

Family and domain databases

Gene3D1.10.10.60. 1 hit.
InterProIPR017970. Homeobox_CS.
IPR001356. Homeobox_dom.
IPR009057. Homeodomain-like.
IPR000047. HTH_motif.
[Graphical view]
PfamPF00046. Homeobox. 1 hit.
[Graphical view]
PRINTSPR00031. HTHREPRESSR.
SMARTSM00389. HOX. 1 hit.
[Graphical view]
SUPFAMSSF46689. SSF46689. 1 hit.
PROSITEPS00027. HOMEOBOX_1. 1 hit.
PS50071. HOMEOBOX_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Other

GeneWikiVAX1.
GenomeRNAi11023.
NextBio41888.
PROQ5SQQ9.
SOURCESearch...

Entry information

Entry nameVAX1_HUMAN
AccessionPrimary (citable) accession number: Q5SQQ9
Secondary accession number(s): B1AVW5, Q6ZSX0
Entry history
Integrated into UniProtKB/Swiss-Prot: June 27, 2006
Last sequence update: December 21, 2004
Last modified: July 9, 2014
This is version 87 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Relevant documents

SIMILARITY comments

Index of protein domains and families

MIM cross-references

Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot

Human polymorphisms and disease mutations

Index of human polymorphisms and disease mutations

Human entries with polymorphisms or disease mutations

List of human entries with polymorphisms or disease mutations

Human chromosome 10

Human chromosome 10: entries, gene names and cross-references to MIM