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Q9Y2V3

- RX_HUMAN

UniProt

Q9Y2V3 - RX_HUMAN

Protein

Retinal homeobox protein Rx

Gene

RAX

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 125 (01 Oct 2014)
      Sequence version 2 (18 May 2010)
      Previous versions | rss
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    Functioni

    Plays a critical role in eye formation by regulating the initial specification of retinal cells and/or their subsequent proliferation. Binds to the photoreceptor conserved element-I (PCE-1/Ret 1) in the photoreceptor cell-specific arrestin promoter.

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    DNA bindingi136 – 19560HomeoboxPROSITE-ProRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. RNA polymerase II core promoter proximal region sequence-specific DNA binding Source: NTNU_SB
    2. RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription Source: NTNU_SB

    GO - Biological processi

    1. camera-type eye development Source: Ensembl
    2. hypothalamus development Source: Ensembl
    3. limb development Source: Ensembl
    4. pattern specification process Source: Ensembl
    5. positive regulation of transcription from RNA polymerase II promoter Source: NTNU_SB
    6. visual perception Source: ProtInc

    Keywords - Molecular functioni

    Developmental protein

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    DNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Retinal homeobox protein Rx
    Alternative name(s):
    Retina and anterior neural fold homeobox protein
    Gene namesi
    Name:RAX
    Synonyms:RX
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome 18

    Organism-specific databases

    HGNCiHGNC:18662. RAX.

    Subcellular locationi

    GO - Cellular componenti

    1. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Involvement in diseasei

    Microphthalmia, isolated, 3 (MCOP3) [MIM:611038]: A disorder of eye formation, ranging from small size of a single eye to complete bilateral absence of ocular tissues. Ocular abnormalities like opacities of the cornea and lens, scaring of the retina and choroid, and other abnormalities may also be present.1 Publication
    Note: The disease is caused by mutations affecting the gene represented in this entry.
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti192 – 1921R → Q in MCOP3; does not affect nuclear localization; reduces DNA binding activity. 1 Publication
    VAR_034905

    Keywords - Diseasei

    Disease mutation, Microphthalmia

    Organism-specific databases

    MIMi611038. phenotype.
    Orphaneti2542. Isolated anophthalmia - microphthalmia.
    PharmGKBiPA38626.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 346346Retinal homeobox protein RxPRO_0000049276Add
    BLAST

    Proteomic databases

    PaxDbiQ9Y2V3.
    PRIDEiQ9Y2V3.

    PTM databases

    PhosphoSiteiQ9Y2V3.

    Expressioni

    Tissue specificityi

    Expressed in the developing eye and weakly expressed in the adult retina.

    Gene expression databases

    ArrayExpressiQ9Y2V3.
    BgeeiQ9Y2V3.
    CleanExiHS_RAX.
    GenevestigatoriQ9Y2V3.

    Interactioni

    Protein-protein interaction databases

    BioGridi119034. 1 interaction.
    STRINGi9606.ENSP00000334813.

    Structurei

    3D structure databases

    ProteinModelPortaliQ9Y2V3.
    SMRiQ9Y2V3. Positions 142-192.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi33 – 408Octapeptide motif
    Motifi323 – 33614OARAdd
    BLAST
    Motifi329 – 3335Nuclear localization signalSequence Analysis

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi276 – 2827Poly-Pro

    Sequence similaritiesi

    Contains 1 homeobox DNA-binding domain.PROSITE-ProRule annotation

    Keywords - Domaini

    Homeobox

    Phylogenomic databases

    eggNOGiNOG261733.
    HOGENOMiHOG000231518.
    HOVERGENiHBG021349.
    InParanoidiQ9Y2V3.
    KOiK09332.
    OMAiCGPGFGD.
    PhylomeDBiQ9Y2V3.
    TreeFamiTF315976.

    Family and domain databases

    Gene3Di1.10.10.60. 1 hit.
    InterProiIPR017970. Homeobox_CS.
    IPR001356. Homeobox_dom.
    IPR009057. Homeodomain-like.
    IPR003654. OAR_dom.
    [Graphical view]
    PfamiPF00046. Homeobox. 1 hit.
    PF03826. OAR. 1 hit.
    [Graphical view]
    SMARTiSM00389. HOX. 1 hit.
    [Graphical view]
    SUPFAMiSSF46689. SSF46689. 1 hit.
    PROSITEiPS00027. HOMEOBOX_1. 1 hit.
    PS50071. HOMEOBOX_2. 1 hit.
    PS50803. OAR. 1 hit.
    [Graphical view]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: Q9Y2V3-1) [UniParc]FASTAAdd to Basket

    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.

    « Hide

    MHLPGCAPAM ADGSFSLAGH LLRSPGGSTS RLHSIEAILG FTKDDGILGT    50
    FPAERGARGA KERDRRLGAR PACPKAPEEG SEPSPPPAPA PAPEYEAPRP 100
    YCPKEPGEAR PSPGLPVGPA TGEAKLSEEE QPKKKHRRNR TTFTTYQLHE 150
    LERAFEKSHY PDVYSREELA GKVNLPEVRV QVWFQNRRAK WRRQEKLEVS 200
    SMKLQDSPLL SFSRSPPSAT LSPLGAGPGS GGGPAGGALP LESWLGPPLP 250
    GGGATALQSL PGFGPPAQSL PASYTPPPPP PPFLNSPPLG PGLQPLAPPP 300
    PSYPCGPGFG DKFPLDEADP RNSSIAALRL KAKEHIQAIG KPWQAL 346
    Length:346
    Mass (Da):36,676
    Last modified:May 18, 2010 - v2
    Checksum:iFEDA196F6A326F31
    GO
    Isoform 2 (identifier: Q9Y2V3-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         97-104: APRPYCPK → GVVPEPTG
         105-346: Missing.

    Show »
    Length:104
    Mass (Da):10,651
    Checksum:iD35EB2FD1A253508
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti107 – 1071G → W in AAD23438. (PubMed:10625658)Curated

    Natural variant

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Natural varianti44 – 441D → E.1 Publication
    Corresponds to variant rs2271733 [ dbSNP | Ensembl ].
    VAR_020150
    Natural varianti192 – 1921R → Q in MCOP3; does not affect nuclear localization; reduces DNA binding activity. 1 Publication
    VAR_034905

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei97 – 1048APRPYCPK → GVVPEPTG in isoform 2. 2 PublicationsVSP_053558
    Alternative sequencei105 – 346242Missing in isoform 2. 2 PublicationsVSP_053559Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF115392 mRNA. Translation: AAD23438.1.
    AB593018 mRNA. Translation: BAJ83973.1.
    AC067859 Genomic DNA. No translation available.
    BC051901 mRNA. Translation: AAH51901.1.
    CCDSiCCDS11972.1. [Q9Y2V3-1]
    RefSeqiNP_038463.2. NM_013435.2. [Q9Y2V3-1]
    UniGeneiHs.278957.

    Genome annotation databases

    EnsembliENST00000256852; ENSP00000256852; ENSG00000134438. [Q9Y2V3-2]
    ENST00000334889; ENSP00000334813; ENSG00000134438. [Q9Y2V3-1]
    GeneIDi30062.
    KEGGihsa:30062.
    UCSCiuc002lhx.3. human. [Q9Y2V3-1]
    uc010dpp.3. human.

    Polymorphism databases

    DMDMi296452886.

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AF115392 mRNA. Translation: AAD23438.1 .
    AB593018 mRNA. Translation: BAJ83973.1 .
    AC067859 Genomic DNA. No translation available.
    BC051901 mRNA. Translation: AAH51901.1 .
    CCDSi CCDS11972.1. [Q9Y2V3-1 ]
    RefSeqi NP_038463.2. NM_013435.2. [Q9Y2V3-1 ]
    UniGenei Hs.278957.

    3D structure databases

    ProteinModelPortali Q9Y2V3.
    SMRi Q9Y2V3. Positions 142-192.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 119034. 1 interaction.
    STRINGi 9606.ENSP00000334813.

    PTM databases

    PhosphoSitei Q9Y2V3.

    Polymorphism databases

    DMDMi 296452886.

    Proteomic databases

    PaxDbi Q9Y2V3.
    PRIDEi Q9Y2V3.

    Protocols and materials databases

    DNASUi 30062.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000256852 ; ENSP00000256852 ; ENSG00000134438 . [Q9Y2V3-2 ]
    ENST00000334889 ; ENSP00000334813 ; ENSG00000134438 . [Q9Y2V3-1 ]
    GeneIDi 30062.
    KEGGi hsa:30062.
    UCSCi uc002lhx.3. human. [Q9Y2V3-1 ]
    uc010dpp.3. human.

    Organism-specific databases

    CTDi 30062.
    GeneCardsi GC18M056909.
    GeneReviewsi RAX.
    H-InvDB HIX0202674.
    HGNCi HGNC:18662. RAX.
    MIMi 601881. gene.
    611038. phenotype.
    neXtProti NX_Q9Y2V3.
    Orphaneti 2542. Isolated anophthalmia - microphthalmia.
    PharmGKBi PA38626.
    GenAtlasi Search...

    Phylogenomic databases

    eggNOGi NOG261733.
    HOGENOMi HOG000231518.
    HOVERGENi HBG021349.
    InParanoidi Q9Y2V3.
    KOi K09332.
    OMAi CGPGFGD.
    PhylomeDBi Q9Y2V3.
    TreeFami TF315976.

    Miscellaneous databases

    ChiTaRSi RAX. human.
    GenomeRNAii 30062.
    NextBioi 52852.
    PROi Q9Y2V3.
    SOURCEi Search...

    Gene expression databases

    ArrayExpressi Q9Y2V3.
    Bgeei Q9Y2V3.
    CleanExi HS_RAX.
    Genevestigatori Q9Y2V3.

    Family and domain databases

    Gene3Di 1.10.10.60. 1 hit.
    InterProi IPR017970. Homeobox_CS.
    IPR001356. Homeobox_dom.
    IPR009057. Homeodomain-like.
    IPR003654. OAR_dom.
    [Graphical view ]
    Pfami PF00046. Homeobox. 1 hit.
    PF03826. OAR. 1 hit.
    [Graphical view ]
    SMARTi SM00389. HOX. 1 hit.
    [Graphical view ]
    SUPFAMi SSF46689. SSF46689. 1 hit.
    PROSITEi PS00027. HOMEOBOX_1. 1 hit.
    PS50071. HOMEOBOX_2. 1 hit.
    PS50803. OAR. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Both PCE-1/RX and OTX/CRX interactions are necessary for photoreceptor-specific gene expression."
      Kimura A., Singh D., Wawrousek E.F., Kikuchi M., Nakamura M., Shinohara T.
      J. Biol. Chem. 275:1152-1160(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
      Tissue: Retina.
    2. "Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping method."
      Oshikawa M., Tsutsui C., Ikegami T., Fuchida Y., Matsubara M., Toyama S., Usami R., Ohtoko K., Kato S.
      Invest. Ophthalmol. Vis. Sci. 52:6662-6670(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
      Tissue: Retinoblastoma.
    3. 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: Eye.
    5. "Mutations in the human RAX homeobox gene in a patient with anophthalmia and sclerocornea."
      Voronina V.A., Kozhemyakina E.A., O'Kernick C.M., Kahn N.D., Wenger S.L., Linberg J.V., Schneider A.S., Mathers P.H.
      Hum. Mol. Genet. 13:315-322(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: VARIANT MCOP3 GLN-192, VARIANT GLU-44, CHARACTERIZATION OF VARIANT GLU-44, CHARACTERIZATION OF VARIANT MCOP3 GLN-192.

    Entry informationi

    Entry nameiRX_HUMAN
    AccessioniPrimary (citable) accession number: Q9Y2V3
    Secondary accession number(s): Q86V11
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: September 26, 2001
    Last sequence update: May 18, 2010
    Last modified: October 1, 2014
    This is version 125 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (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.

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Human chromosome 18
      Human chromosome 18: entries, gene names and cross-references to MIM
    2. Human entries with polymorphisms or disease mutations
      List of human entries with polymorphisms or disease mutations
    3. Human polymorphisms and disease mutations
      Index of human polymorphisms and disease mutations
    4. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    5. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3