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RBMY1J Gene

protein-coding   GIFtS: 34
GCID: GC0YP024456

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

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(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
RNA Binding Motif Protein, Y-Linked, Family 1, Member J1 2
Y Chromosome RNA Recognition Motif 22 3
RNA-Binding Motif Protein, Y Chromosome, Family 1 Member F/J2
YRRM23

External Ids:    HGNC: 239171   Entrez Gene: 3789512   Ensembl: ENSG000002269417   UniProtKB: Q154153   

Export aliases for RBMY1J gene to outside databases

Previous GC identifers: GC0YU900273 GC0YP022959 GC0YP022866


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for RBMY1J 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 RBMY1J Gene:
RBMY1J (RNA binding motif protein, Y-linked, family 1, member J) is a protein-coding gene. GO annotations related to this gene include RNA binding and nucleotide binding. An important paralog of this gene is RBMY1E.

UniProtKB/Swiss-Prot: RBY1F_HUMAN, Q15415
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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the RBMY1J gene promoter:
         POU2F1   POU2F1a   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for RBMY1J

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat RBMY1J


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

RBMY1J Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RBMY1J gene location

GeneLoc information about chromosome Y         GeneLoc Exon Structure

GeneLoc location for GC0YP024456:  view genomic region     (about GC identifiers)

Start:
24,454,970 bp from pter      End:
24,564,028 bp from pter
Size:
109,059 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: RBY1F_HUMAN, Q15415 (See protein sequence)
Recommended Name: RNA-binding motif protein, Y chromosome, family 1 member F/J  
Size: 496 amino acids; 55728 Da
Subunit: Interacts with splicing factor proteins SFRS3/SRP20, TRA2B/SFRS10, KHDRBS1/SAM68 and KHDRBS3
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
Secondary accessions: B2R916
Alternative splicing: 2 isoforms:  Q15415-1   Q15415-2   

Explore the universe of human proteins at neXtProt for RBMY1J: NX_Q15415

Explore proteomics data for RBMY1J at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See RBMY1J Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001006117.2  
    ENSEMBL proteins: 
     ENSP00000250831   ENSP00000405745   ENSP00000389621  

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    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 Q15415

    ProtoNet protein and cluster: Q15415

    2 Blocks protein domains:
    IPB000504 RNA-binding region RNP-1 (RNA recognition motif)
    IPB012604 RBM1CTR


    UniProtKB/Swiss-Prot: RBY1F_HUMAN, Q15415
    Similarity: Contains 1 RRM (RNA recognition motif) domain


    Find genes that share domains with RBMY1J           About GenesLikeMe


    (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,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: RBY1F_HUMAN, Q15415
    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:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166nucleotide binding IEA--
    GO:0003676nucleic acid binding ----
    GO:0003723RNA binding NAS8269511
         
    Find genes that share ontologies with RBMY1J           About GenesLikeMe


    Animal Models:
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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    RBY1F_HUMAN, Q15415: Nucleus
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol2

    Gene Ontology (GO): 2 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005575cellular_component ND--
    GO:0005634nucleus IEA--

    Find genes that share ontologies with RBMY1J           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for RBMY1J
    Interactions:

        Search GeneGlobe Interaction Network for RBMY1J

    STRING Interaction Network Preview (showing 5 interactants - click image to see 11)

    Selected Interacting proteins for RBMY1J (Q154153 ENSP000002508314) via UniProtKB, MINT, STRING, and/or I2D (see all 12)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HNRNPKP619783I2D: score=1 
    CRNKL1ENSP000003665574STRING: ENSP00000366557
    ISY1ENSP000003769734STRING: ENSP00000376973
    PLRG1ENSP000003031914STRING: ENSP00000303191
    RBM22ENSP000001998144STRING: ENSP00000199814
    About this table

    Gene Ontology (GO): 3 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006397mRNA processing IEA--
    GO:0007283spermatogenesis NAS8269511
    GO:0008380RNA splicing IEA--

    Find genes that share ontologies with RBMY1J           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for RBMY1J (RBY1F)



    (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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    REFSEQ mRNAs for RBMY1J gene: 
    NM_001006117.2  

    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000470460 ENST00000250831(uc004fve.3) ENST00000414629(uc004fvd.3)
    ENST00000445779(uc011nbh.2)
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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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    RBMY1J expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    RBMY1J Expression
    About this image

    RBMY1J Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    RBMY1J Protein Expression

    UniProtKB/Swiss-Prot: RBY1F_HUMAN, Q15415
    Tissue specificity: Testis-specific

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    In Situ
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    (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)
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    This gene was present in the common ancestor of animals.

    Orthologs for RBMY1J gene from Selected species (see all 11)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves RBMX6
    Gallus gallus RNA binding motif protein, X-linked ...
    62(a)
    1 → many
    4(4390057-4400409)
    lizard
    (Anolis carolinensis)
    Reptilia --
    Uncharacterized protein
    45(a)
    many ↔ many
    GL343252.1(14484-20512)
    zebrafish
    (Danio rerio)
    Actinopterygii rbmx6
    RNA binding motif protein, X-linked
    51(a)
    1 → many
    14(32725471-32732600) ENSDARG00000014244
    fruit fly
    (Drosophila melanogaster)
    Insecta tra26
    transformer 2
    15(a)
    1 → many
    2R(10489509-10491857)
    worm
    (Caenorhabditis elegans)
    Secernentea rsp-86
    Protein RSP-8, isoform a
    19(a)
    1 → many
    III(11826215-11831475) WBGene00004705
            Species with no ortholog for RBMY1J

    ENSEMBL Gene Tree for RBMY1J (if available)
    TreeFam Gene Tree for RBMY1J (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for RBMY1J gene
    RBMY1F1 2  RBMY1A11 2  RBMY1B1 2  RBMY1D1 2  RBMY1E1 2  TRA2B2  RBMXL22  RBMXL32  
    RBMXL12  CIRBP2  RBM32  RBMX2  TRA2A2  
    Selected SIMAP similar genes for RBMY1J using alignment to 2 protein entries:     RBY1F_HUMAN (see all proteins) (see all similar genes):
    RBMY1B    RBMY1A1    RBMY1C    RBMY1D    RBMY1E    RBMY1F
    RBM    BOLL    YRRM    RBMX    PABPC4    PABPC1
    CIRBP    RBMXL2    RBM38    RBMXL1    RBM3    SFRS3

    Find genes that share paralogs with RBMY1J           About GenesLikeMe


    Selected Pseudogenes.org Pseudogenes for RBMY1J (see all 12)
    PGOHUM00000233690 PGOHUM00000233697 PGOHUM00000233717 PGOHUM00000261024 PGOHUM00000233796


    (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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    6 SNPs for RBMY1J    About this table                                 

    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr Y posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1995290991,2
    ----24553925(+) TGTTCC/GTTTGT 1 -- int10--------
    rs3738099401,2
    ----24553622(+) CTACTC/TCTGTA 1 -- int10--------
    rs1999979461,2
    ----24553995(+) TGGCTC/TACTGC 1 -- int10--------

    HapMap Linkage Disequilibrium report for RBMY1J (24454970 - 24564028 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for RBMY1J:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv10031CNV Gain18304495
    nsv10029CNV Gain18304495
    essv15983CNV CNV17122850
    essv11423CNV CNV17122850
    dgv2501e1CNV Complex17122850

    Site Specific Mutation Identification with PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for RBMY1J

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    2 diseases from the University of Copenhagen DISEASES database for RBMY1J:
    Gonadoblastoma     Turner syndrome

    Find genes that share disorders with RBMY1J           About GenesLikeMe


    Export disorders for RBMY1J 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)
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    PubMed articles for RBMY1J gene integrated from 10 sources:
    (articles sorted by number of sources associating them with RBMY1J)
        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. (Nature 2003)
    2. A Y chromosome gene family with RNA-binding protein homology: candidates for the azoospermia factor AZF controlling human spermatogenesis. (PubMed id 8269511)1, 2 Ma K.... Jobling M. (Cell 1993)
    3. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    4. 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. (Oncogene 2004)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (Nat. Genet. 2004)
    6. 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. (Genomics 1998)
    7. Degeneracy in human multicopy RBM (YRRM), a candidate spermatogenesis gene. (PubMed id 8875892)1 Prosser J.... Cooke H.J. (Mamm. Genome 1996)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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)
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    Entrez Gene: 378951 HGNC: 23917 Ensembl:ENSG00000226941 euGenes: HUgn378951 ECgene: RBMY1J
    H-InvDB: RBMY1J

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for RBMY1J Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for RBMY1J gene:
    Search GeneIP for patents involving RBMY1J

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    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, eBioscience, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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