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Q9Y2V3

- RX_HUMAN

UniProt

Q9Y2V3 - RX_HUMAN

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Protein

Retinal homeobox protein Rx

Gene

RAX

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli

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
Complete GO annotation...

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-KW
Complete GO annotation...

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

BgeeiQ9Y2V3.
CleanExiHS_RAX.
ExpressionAtlasiQ9Y2V3. differential.
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.
GeneTreeiENSGT00760000118958.
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

        10         20         30         40         50
MHLPGCAPAM ADGSFSLAGH LLRSPGGSTS RLHSIEAILG FTKDDGILGT
60 70 80 90 100
FPAERGARGA KERDRRLGAR PACPKAPEEG SEPSPPPAPA PAPEYEAPRP
110 120 130 140 150
YCPKEPGEAR PSPGLPVGPA TGEAKLSEEE QPKKKHRRNR TTFTTYQLHE
160 170 180 190 200
LERAFEKSHY PDVYSREELA GKVNLPEVRV QVWFQNRRAK WRRQEKLEVS
210 220 230 240 250
SMKLQDSPLL SFSRSPPSAT LSPLGAGPGS GGGPAGGALP LESWLGPPLP
260 270 280 290 300
GGGATALQSL PGFGPPAQSL PASYTPPPPP PPFLNSPPLG PGLQPLAPPP
310 320 330 340
PSYPCGPGFG DKFPLDEADP RNSSIAALRL KAKEHIQAIG KPWQAL
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.
GeneTreei ENSGT00760000118958.
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

Bgeei Q9Y2V3.
CleanExi HS_RAX.
ExpressionAtlasi Q9Y2V3. differential.
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

« Hide 'large scale' publications
  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 29, 2014
This is version 126 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