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P0DJD3

- RBY1A_HUMAN

UniProt

P0DJD3 - RBY1A_HUMAN

Protein

RNA-binding motif protein, Y chromosome, family 1 member A1

Gene

RBMY1A1

Organism
Homo sapiens (Human)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 25 (01 Oct 2014)
      Sequence version 1 (22 Feb 2012)
      Previous versions | rss
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    Functioni

    RNA-binding protein involved in pre-mRNA splicing. Required for sperm development. Acts additively with TRA2B to promote exon 7 inclusion of the survival motor neuron SMN. Binds non-specifically to mRNAs.2 Publications

    GO - Molecular functioni

    1. mRNA binding Source: UniProtKB
    2. nucleotide binding Source: InterPro
    3. protein binding Source: UniProtKB

    GO - Biological processi

    1. mRNA processing Source: UniProtKB-KW
    2. regulation of alternative mRNA splicing, via spliceosome Source: UniProtKB
    3. RNA splicing Source: UniProtKB-KW

    Keywords - Molecular functioni

    Activator

    Keywords - Biological processi

    mRNA processing, mRNA splicing

    Keywords - Ligandi

    RNA-binding

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    RNA-binding motif protein, Y chromosome, family 1 member A1
    Alternative name(s):
    RNA-binding motif protein 1
    RNA-binding motif protein 2
    Y chromosome RNA recognition motif 1
    Short name:
    hRBMY
    Gene namesi
    Name:RBMY1A1
    Synonyms:RBM1, RBM2, YRRM1, YRRM2
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    ProteomesiUP000005640: Chromosome Y

    Organism-specific databases

    HGNCiHGNC:9912. RBMY1A1.

    Subcellular locationi

    Nucleus 1 Publication

    GO - Cellular componenti

    1. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Nucleus

    Pathology & Biotechi

    Organism-specific databases

    Orphaneti1646. Partial chromosome Y deletion.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 496496RNA-binding motif protein, Y chromosome, family 1 member A1PRO_0000081899Add
    BLAST

    Proteomic databases

    PRIDEiP0DJD3.

    Expressioni

    Tissue specificityi

    Testis-specific.1 Publication

    Developmental stagei

    Expressed in all of the transcriptionally active stages of germ cell development from spermatogonia through spermatocytes to round spermatids.1 Publication

    Gene expression databases

    BgeeiP0DJD3.
    CleanExiHS_RBMY1A1.

    Organism-specific databases

    HPAiHPA001534.

    Interactioni

    Subunit structurei

    Interacts with splicing factor proteins SFRS3/SRP20, TRA2B/SFRS10, KHDRBS1/SAM68 and KHDRBS3.5 Publications

    Protein-protein interaction databases

    IntActiP0DJD3. 1 interaction.

    Structurei

    Secondary structure

    1
    496
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi9 – 135
    Turni16 – 183
    Helixi21 – 299
    Beta strandi35 – 406
    Turni43 – 453
    Beta strandi50 – 545
    Helixi58 – 6710
    Beta strandi74 – 774
    Beta strandi79 – 824
    Beta strandi89 – 935

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    2FY1NMR-A1-109[»]
    ProteinModelPortaliP0DJD3.
    SMRiP0DJD3. Positions 1-108.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini8 – 8578RRMPROSITE-ProRule annotationAdd
    BLAST

    Compositional bias

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Compositional biasi254 – 34087Arg-richAdd
    BLAST

    Sequence similaritiesi

    Contains 1 RRM (RNA recognition motif) domain.PROSITE-ProRule annotation

    Phylogenomic databases

    OrthoDBiEOG780RPD.
    PhylomeDBiP0DJD3.
    TreeFamiTF331833.

    Family and domain databases

    Gene3Di3.30.70.330. 1 hit.
    InterProiIPR012677. Nucleotide-bd_a/b_plait.
    IPR012604. RBM1CTR.
    IPR000504. RRM_dom.
    [Graphical view]
    PfamiPF08081. RBM1CTR. 1 hit.
    PF00076. RRM_1. 1 hit.
    [Graphical view]
    SMARTiSM00360. RRM. 1 hit.
    [Graphical view]
    PROSITEiPS50102. RRM. 1 hit.
    [Graphical view]

    Sequences (3)i

    Sequence statusi: Complete.

    This entry describes 3 isoformsi produced by alternative splicing. Align

    Isoform 1 (identifier: P0DJD3-1) [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

    MVEADHPGKL FIGGLNRETN EKMLKAVFGK HGPISEVLLI KDRTSKSRGF    50
    AFITFENPAD AKNAAKDMNG KSLHGKAIKV EQAKKPSFQS GGRRRPPASS 100
    RNRSPSGSLR SARGSRGGTR GWLPSHEGHL DDGGYTPDLK MSYSRGLIPV 150
    KRGPSSRSGG PPPKKSAPSA VARSNSWMGS QGPMSQRREN YGVPPRRATI 200
    SSWRNDRMST RHDGYATNDG NHPSCQETRD YAPPSRGYAY RDNGHSNRDE 250
    HSSRGYRNHR SSRETRDYAP PSRGHAYRDY GHSRRDESYS RGYRNRRSSR 300
    ETREYAPPSR GHGYRDYGHS RRHESYSRGY RNHPSSRETR DYAPPHRDYA 350
    YRDYGHSSWD EHSSRGYSYH DGYGEALGRD HSEHLSGSSY RDALQRYGTS 400
    HGAPPARGPR MSYGGSTCHA YSNTRDRYGR SWESYSSCGD FHYCDREHVC 450
    RKDQRNPPSL GRVLPDPREA CGSSSYVASI VDGGESRSEK GDSSRY 496
    Length:496
    Mass (Da):55,784
    Last modified:February 22, 2012 - v1
    Checksum:i3E493C52C7BA9E7E
    GO
    Isoform 2 (identifier: P0DJD3-2) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         327-363: Missing.

    Show »
    Length:459
    Mass (Da):51,292
    Checksum:iF3C0267BBEF99E55
    GO
    Isoform 3 (identifier: P0DJD3-3) [UniParc]FASTAAdd to Basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-140: Missing.

    Show »
    Length:356
    Mass (Da):40,651
    Checksum:i96D4EAB0E82A3C1C
    GO

    Alternative sequence

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Alternative sequencei1 – 140140Missing in isoform 3. 1 PublicationVSP_042315Add
    BLAST
    Alternative sequencei327 – 36337Missing in isoform 2. 1 PublicationVSP_042316Add
    BLAST

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X76059 mRNA. Translation: CAA53659.1.
    BC047768 mRNA. Translation: AAH47768.1.
    BC070298 mRNA. Translation: AAH70298.1.
    AC010141 Genomic DNA. No translation available.
    CCDSiCCDS14796.1. [P0DJD3-1]
    PIRiA49418.
    RefSeqiNP_005049.1. NM_005058.2. [P0DJD3-1]
    XP_005262573.1. XM_005262516.1. [P0DJD3-2]
    UniGeneiHs.380450.

    Genome annotation databases

    EnsembliENST00000303902; ENSP00000303712; ENSG00000234414. [P0DJD3-1]
    ENST00000382707; ENSP00000372154; ENSG00000234414. [P0DJD3-1]
    GeneIDi5940.
    KEGGihsa:5940.
    UCSCiuc004fur.4. human. [P0DJD3-1]
    uc010nxa.3. human. [P0DJD3-2]

    Polymorphism databases

    DMDMi378522864.

    Keywords - Coding sequence diversityi

    Alternative splicing

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X76059 mRNA. Translation: CAA53659.1 .
    BC047768 mRNA. Translation: AAH47768.1 .
    BC070298 mRNA. Translation: AAH70298.1 .
    AC010141 Genomic DNA. No translation available.
    CCDSi CCDS14796.1. [P0DJD3-1 ]
    PIRi A49418.
    RefSeqi NP_005049.1. NM_005058.2. [P0DJD3-1 ]
    XP_005262573.1. XM_005262516.1. [P0DJD3-2 ]
    UniGenei Hs.380450.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    2FY1 NMR - A 1-109 [» ]
    ProteinModelPortali P0DJD3.
    SMRi P0DJD3. Positions 1-108.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    IntActi P0DJD3. 1 interaction.

    Polymorphism databases

    DMDMi 378522864.

    Proteomic databases

    PRIDEi P0DJD3.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    Ensembli ENST00000303902 ; ENSP00000303712 ; ENSG00000234414 . [P0DJD3-1 ]
    ENST00000382707 ; ENSP00000372154 ; ENSG00000234414 . [P0DJD3-1 ]
    GeneIDi 5940.
    KEGGi hsa:5940.
    UCSCi uc004fur.4. human. [P0DJD3-1 ]
    uc010nxa.3. human. [P0DJD3-2 ]

    Organism-specific databases

    CTDi 5940.
    GeneCardsi GC0YP023675.
    GeneReviewsi RBMY1A1.
    HGNCi HGNC:9912. RBMY1A1.
    HPAi HPA001534.
    MIMi 400006. gene.
    neXtProti NX_P0DJD3.
    Orphaneti 1646. Partial chromosome Y deletion.
    GenAtlasi Search...

    Phylogenomic databases

    OrthoDBi EOG780RPD.
    PhylomeDBi P0DJD3.
    TreeFami TF331833.

    Miscellaneous databases

    GenomeRNAii 5940.
    NextBioi 23158.
    PROi P0DJD3.
    SOURCEi Search...

    Gene expression databases

    Bgeei P0DJD3.
    CleanExi HS_RBMY1A1.

    Family and domain databases

    Gene3Di 3.30.70.330. 1 hit.
    InterProi IPR012677. Nucleotide-bd_a/b_plait.
    IPR012604. RBM1CTR.
    IPR000504. RRM_dom.
    [Graphical view ]
    Pfami PF08081. RBM1CTR. 1 hit.
    PF00076. RRM_1. 1 hit.
    [Graphical view ]
    SMARTi SM00360. RRM. 1 hit.
    [Graphical view ]
    PROSITEi PS50102. RRM. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "A Y chromosome gene family with RNA-binding protein homology: candidates for the azoospermia factor AZF controlling human spermatogenesis."
      Ma K., Inglis J.D., Sharkey A., Bickmore W.A., Hill R.E., Prosser E.J., Speedson R.M., Thomson E.J., Jobling M.
      Cell 75:1287-1295(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), FUNCTION, TISSUE SPECIFICITY.
      Tissue: Testis.
    2. "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] (ISOFORMS 2 AND 3).
      Tissue: Brain and Testis.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    4. "Structure and organization of the RBMY genes on the human Y chromosome: transposition and amplification of an ancestral autosomal hnRNPG gene."
      Chai N.-N., Zhou H., Hernandez J., Najmabadi H., Bhasin S., Yen P.H.
      Genomics 49:283-289(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION.
    5. "Expression of RBM in the nuclei of human germ cells is dependent on a critical region of the Y chromosome long arm."
      Elliott D.J., Millar M.R., Oghene K., Ross A., Kiesewetter F., Pryor J., McIntyre M., Hargreave T.B., Saunders P.T.K., Vogt P.H., Chandley A.C., Cooke H.
      Proc. Natl. Acad. Sci. U.S.A. 94:3848-3853(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE.
    6. "T-STAR/ETOILE: a novel relative of SAM68 that interacts with an RNA-binding protein implicated in spermatogenesis."
      Venables J.P., Vernet C., Chew S.L., Elliott D.J., Cowmeadow R.B., Wu J., Cooke H.J., Artzt K., Eperon I.C.
      Hum. Mol. Genet. 8:959-969(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH KHDRBS3.
    7. "RBMY, a probable human spermatogenesis factor, and other hnRNP G proteins interact with Tra2beta and affect splicing."
      Venables J.P., Elliott D.J., Makarova O.V., Makarov E.M., Cooke H.J., Eperon E.C.
      Hum. Mol. Genet. 9:685-694(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH TRA2B.
      Tissue: Testis.
    8. "hnRNP-G promotes exon 7 inclusion of survival motor neuron (SMN) via direct interaction with Htra2-beta1."
      Hofmann Y., Wirth B.
      Hum. Mol. Genet. 11:2037-2049(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, INTERACTION WITH TRA2B, RNA-BINDING.
    9. "The role of potential splicing factors including RBMY, RBMX, hnRNPG-T and STAR proteins in spermatogenesis."
      Elliott D.J.
      Int. J. Androl. 27:328-334(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH KHDRBS1.
    10. "The testis-specific human protein RBMY recognizes RNA through a novel mode of interaction."
      Skrisovska L., Bourgeois C.F., Stefl R., Grellscheid S.-N., Kister L., Wenter P., Elliott D.J., Stevenin J., Allain F.H.-T.
      EMBO Rep. 8:372-379(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: STRUCTURE BY NMR OF 1-109 IN COMPLEX WITH RNA.

    Entry informationi

    Entry nameiRBY1A_HUMAN
    AccessioniPrimary (citable) accession number: P0DJD3
    Secondary accession number(s): Q15376
    , Q15377, Q15414, Q6NSB5, Q86VU6, Q8NHR0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 22, 2012
    Last sequence update: February 22, 2012
    Last modified: October 1, 2014
    This is version 25 of the entry and version 1 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

    Miscellaneous

    The RBMY1 proteins are encoded by repeated regions of the Y chromosome, mostly within the AZFb region. The exact number of functional copies is unclear and may vary between individuals, and some of them may represent pseudogenes. The proteins are very similar, which makes the characterization of each protein difficult. Thus, most experiments do not discriminate between the different members. One can therefore suppose that reported interactions with a RBMY1 protein involve all the proteins.

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Human chromosome Y
      Human chromosome Y: entries, gene names and cross-references to MIM
    2. MIM cross-references
      Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3