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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

RBMY1D Gene

protein-coding   GIFtS: 30
GCID: GC0YM024026

RNA Binding Motif Protein, Y-Linked, Family 1, Member D

  See related disease
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
RNA Binding Motif Protein, Y-Linked, Family 1, Member D1 2
RNA-Binding Motif Protein, Y Chromosome, Family 1 Member D2

External Ids:    HGNC: 239151   Entrez Gene: 3789492   Ensembl: ENSG000002443957   UniProtKB: P0C7P13   

Export aliases for RBMY1D gene to outside databases

Previous GC identifers: GC0YU900271 GC0YM022435


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

Entrez Gene summary for RBMY1D Gene:
This gene encodes a protein containing an RNA-binding motif in the N-terminus and four SRGY (serine, arginine,
glycine, tyrosine) boxes in the C-terminus. Multiple copies of this gene are found in the AZFb azoospermia factor
region of chromosome Y and the encoded protein is thought to be involved in spermatogenesis. Most copies of this
locus are pseudogenes, although six highly similar copies have full-length ORFs and are considered functional.
Four functional copies of this gene are found within inverted repeat IR2; two functional copies of this gene are
found in palindrome P3, along with two copies of PTPN13-like, Y-linked. (provided by RefSeq, Jul 2008)

GeneCards Summary for RBMY1D Gene: 
RBMY1D (RNA binding motif protein, Y-linked, family 1, member D) is a protein-coding gene. Diseases associated with RBMY1D include azoospermia. GO annotations related to this gene include RNA binding and nucleotide binding. An important paralog of this gene is RBMY1J.

UniProtKB/Swiss-Prot: RBY1D_HUMAN, P0C7P1
Function: RNA-binding protein which may be involved in spermatogenesis. Required for sperm development, possibly
by participating in pre-mRNA splicing in the testis




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RBMY1D gene promoter:
         POU2F1   POU2F1b   POU2F1a   POU2F1c   CUTL1   GATA-1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for RBMY1D

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RBMY1D


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: Yq11.223   Ensembl cytogenetic band:  Yq11.223   HGNC cytogenetic band: Yq11.223

RBMY1D Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RBMY1D gene location

GeneLoc information about chromosome Y         GeneLoc Exon Structure

GeneLoc location for GC0YM024026:  view genomic region     (about GC identifiers)

Start:
24,026,223 bp from pter      End:
24,040,673 bp from pter
Size:
14,451 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: RBY1D_HUMAN, P0C7P1 (See protein sequence)
Recommended Name: RNA-binding motif protein, Y chromosome, family 1 member D  
Size: 496 amino acids; 55775 Da
Subunit: Interacts with splicing factor proteins SFRS3/SRP20, TRA2B/SFRS10, KHDRBS1/SAM68 and KHDRBS3
Subcellular location: Nucleus
Developmental stage: Expressed in all of the transcriptionally active stages of germ cell development from
spermatogonia through spermatocytes to round spermatids
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

Explore the universe of human proteins at neXtProt for RBMY1D: NX_P0C7P1

Explore proteomics data for RBMY1D at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_P0C7P1

  • RBMY1D Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    RBMY1D Protein Expression
    REFSEQ proteins: NP_001006120.2  
    ENSEMBL proteins: 
     ENSP00000372099   ENSP00000372127   ENSP00000372124   ENSP00000399181  

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    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--

    RBMY1D for ontologies           About GeneDecksing



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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    HGNC Gene Families: 
    RBM: RNA binding motif (RRM) containing

    3 InterPro protein domains:
     IPR012604 RBM1CTR
     IPR012677 Nucleotide-bd_a/b_plait
     IPR000504 RRM_dom

    Graphical View of Domain Structure for InterPro Entry P0C7P1

    ProtoNet protein and cluster: P0C7P1

    UniProtKB/Swiss-Prot: RBY1D_HUMAN, P0C7P1
    Similarity: Contains 1 RRM (RNA recognition motif) domain


    RBMY1D for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RBY1D_HUMAN, P0C7P1
    Function: RNA-binding protein which may be involved in spermatogenesis. Required for sperm development, possibly
    by participating in pre-mRNA splicing in the testis

         Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166nucleotide binding IEA--
    GO:0003676nucleic acid binding ----
    GO:0003723RNA binding IEA--
         
    RBMY1D for ontologies           About GeneDecksing


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    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for RBMY1D

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006397mRNA processing IEA--
    GO:0008380RNA splicing IEA--

    RBMY1D for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section
    Browse Small Molecules at EMD Millipore
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    Browse Tocris compounds for RBMY1D (RBY1D)

    Search CenterWatch for drugs/clinical trials and news about RBMY1D / RBY1D

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
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    About This Section

    REFSEQ mRNAs for RBMY1D gene: 
    NM_001006120.2  

    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000382653(uc010nxc.1) ENST00000382680(uc004fuu.3 uc011nbe.2 uc010nxb.2 uc004fuv.3)
    ENST00000382677 ENST00000418956
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    GeneLoc Exon Structure


    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    RBMY1D expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    RBMY1D Expression
    About this image


    See RBMY1D Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RBMY1D

    UniProtKB/Swiss-Prot: RBY1D_HUMAN, P0C7P1
    Tissue specificity: Testis-specific

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RBMY1D

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for RBMY1D gene from 4/10 species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves RBMX6
    heterogeneous nuclear ribonucleoprotein G
    59(a)
    1 → many
    4(4390057-4400409)
    zebrafish
    (Danio rerio)
    Actinopterygii rbmx6
    RNA binding motif protein, X-linked
    50(a)
    1 → many
    14(32725471-32732600)
    fruit fly
    (Drosophila melanogaster)
    Insecta tra26
    transformer 2
    12(a)
    1 → many
    2R(10489509-10491857)
    worm
    (Caenorhabditis elegans)
    Secernentea rsp-86
    Protein RSP-8, isoform a
    11(a)
    1 → many
    III(11826215-11831475)
            Species with no ortholog for RBMY1D

    ENSEMBL Gene Tree for RBMY1D (if available)
    TreeFam Gene Tree for RBMY1D (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RBMY1D gene
    RBMY1E1 2  RBMY1A11 2  RBMY1B1 2  RBMY1F1 2  RBMY1J1 2  TRA2B2  RBMXL22  RBMXL32  
    RBMXL12  CIRBP2  RBM32  RBMX2  TRA2A2  
    17 SIMAP similar genes for RBMY1D using alignment to 2 protein entries:     RBY1D_HUMAN (see all proteins):
    RBMY1C    RBMY1E    RBMY1B    RBMY1F    RBMY1J    RBMY1A1
    RBM    YRRM    RBMX    PABPC4    CIRBP    RBMXL2
    RBM38    RBMXL1    RBM3    SFRS3    SRSF5

    RBMY1D for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section
    Structural Variations
         Database of Genomic Variants (DGV) 9 variations for RBMY1D:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv819669CNV Insertion19587683
    nsv469635CNV Loss16826518
    nsv10026CNV Gain18304495
    nsv471611CNV Gain+Loss15918152
    essv23856CNV CNV17122850
    nsv469695CNV Complex16826518
    dgv2503e1CNV Complex17122850
    dgv2502e1CNV Complex17122850
    dgv2501e1CNV Complex17122850

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    2 diseases for RBMY1D:    About MalaCards
    azoospermia    


    RBMY1D for disorders           About GeneDecksing


    Export disorders for RBMY1D gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for RBMY1D gene integrated from 9 sources:
    (articles sorted by number of sources associating them with RBMY1D)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. (PubMed id 12815422)1, 2, 3 Skaletsky H.... Page D.C. (2003)
    2. RBMY, a male germ cell-specific RNA-binding protein, activated in human liver cancers and transforms rodent fibroblasts. (PubMed id 15184870)1 Tsuei D.J....Chang M.H. (2004)
    3. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
    4. Structure and organization of the RBMY genes on the human Y chromosome: transposition and amplification of an ancestral autosomal hnRNPG gene. (PubMed id 9598316)1 Chai N.-N.... Yen P.H. (1998)
    5. Degeneracy in human multicopy RBM (YRRM), a candidate spermatogenesis gene. (PubMed id 8875892)1 Prosser J.... Cooke H.J. (1996)
    6. A Y chromosome gene family with RNA-binding protein homology: candidates for the azoospermia factor AZF controlling human spermatogenesis. (PubMed id 8269511)1 Ma K.... Jobling M. (1993)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    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, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 378949 HGNC: 23915 Ensembl:ENSG00000244395 euGenes: HUgn378949 ECgene: RBMY1D
    H-InvDB: RBMY1D

    (According to HUGE)
    About This Section
      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for RBMY1D Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for RBMY1D gene:
    Search GeneIP for patents involving RBMY1D

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
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    About This Section

     
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    Category
    (GIFtS: 73)
    transforming growth factor, beta 1
    GIFtS Group
    The GeneCards human gene database gene index: 1 3 5 6 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 


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