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    RBMY1A1 RNA binding motif protein Y-linked family 1 member A1 [ Homo sapiens (human) ]

    Gene ID: 5940, updated on 2-Nov-2024

    Summary

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    Official Symbol
    RBMY1A1provided by HGNC
    Official Full Name
    RNA binding motif protein Y-linked family 1 member A1provided by HGNC
    Primary source
    HGNC:HGNC:9912
    See related
    Ensembl:ENSG00000234414 MIM:400006; AllianceGenome:HGNC:9912
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RBM; RBM1; RBM2; RBMY; YRRM1; YRRM2; RBMY1C
    Summary
    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. This protein is thought to function as a splicing regulator during spermatogenesis. Multiple closely related paralogs of this gene are found in a gene cluster in the AZFb azoospermia factor region of chromosome Y. Most of these related copies are thought to be pseudogenes, though several likely encode functional proteins. [provided by RefSeq, Mar 2016]
    Expression
    Restricted expression toward testis (RPKM 10.4) See more
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    Genomic context

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    See RBMY1A1 in Genome Data Viewer
    Location:
    Yq11.223
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (21534879..21559683)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (22410130..22434934)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (23696765..23711212)

    Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene RNA binding motif protein Y-linked family 1 member H, pseudogene Neighboring gene RNA binding motif protein Y-linked family 1 member B Neighboring gene testis expressed transcript, Y-linked 13 Neighboring gene elongin C pseudogene 5

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PIM1-Induced Cytoplasmic Expression of RBMY Mediates Hepatocellular Carcinoma Metastasis.
      Title: PIM1-Induced Cytoplasmic Expression of RBMY Mediates Hepatocellular Carcinoma Metastasis.
    2. Potential dual functional roles of the Y-linked RBMY in hepatocarcinogenesis.
      Title: Potential dual functional roles of the Y-linked RBMY in hepatocarcinogenesis.
    3. genetic association study in population in southwest China: Data suggest that copy number variation in RBMY1 is associated with sperm motility and asthenozoospermia; RBMY1 functional copy dosage is positively correlated with sperm motility; dosage insufficiency is independent genetic risk factor for asthenozoospermia; RBMY1 is an important candidate for male infertility in azoospermia factor (AZF) region of Y-chromosome.
      Title: Copy number variation of functional RBMY1 is associated with sperm motility: an azoospermia factor-linked candidate for asthenozoospermia.
    4. RBMY is a novel oncofetal protein that plays a key role in attenuating glycogen synthase kinase 3beta activity, leading to aberrant activation of Wnt/beta-catenin signaling, which facilitates malignant hepatic stemness.
      Title: RBMY, a novel inhibitor of glycogen synthase kinase 3β, increases tumor stemness and predicts poor prognosis of hepatocellular carcinoma.
    5. results imply that different alternative splicing may happen in testis cells and probably difference of RBMY function during spermatogenesis is due to the differential expression of RBMY protein isoforms.
      Title: Expression analysis of RNA-binding motif gene on Y chromosome (RBMY) protein isoforms in testis tissue and a testicular germ cell cancer-derived cell line (NT2).
    6. One possible function of RBMY could be its involvement in sperm motility.
      Title: Cellular ontogeny of RBMY during human spermatogenesis and its role in sperm motility.
    7. investigation of role of RBMY in spermatogenesis: isolation and identification of RBMY target mRNAs in testis; RBMY binds to only transcript variant 2 of Nek10; RBMY may take part in alternative splicing of Nek10
      Title: Identifying mRNAs bound by human RBMY protein in the testis.
    8. regulates germline-specific splicing events; ectopic expression stimulated the inclusion of a testis-enriched exon
      Title: Human RBMY regulates germline-specific splicing events by modulating the function of the serine/arginine-rich proteins 9G8 and Tra2-{beta}.
    9. germ cell-specific RBMY and hnRNP G-T proteins were more efficient in stimulating TLE4-T incorporation than somatically expressed hnRNP G protein.
      Title: The germ cell nuclear proteins hnRNP G-T and RBMY activate a testis-specific exon.
    10. Patients with complete Sertoli cell-only syndrome (SCOS) did not exhibit RBMY1 gene expression.
      Title: Quantification of DDX3Y, RBMY1, DAZ and TSPY mRNAs in testes of patients with severe impairment of spermatogenesis.
    Submit: New GeneRIF Correction See all GeneRIFs (15)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Spermatogenic failure, Y-linked, 2
    MedGen: C1839071 OMIM: 415000 GeneReviews: Y Chromosome Infertility
    		not available

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Vpu vpu HIV-1 Vpu is identified to have a physical interaction with RNA binding motif protein, Y-linked, family 1, member A1 (RBMY1A1) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Clone Names

    • MGC181956

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables mRNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in positive regulation of mRNA splicing, via spliceosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in regulation of alternative mRNA splicing, via spliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    part_of spliceosomal complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    RNA-binding motif protein, Y chromosome, family 1 member A1
    Names
    RNA-binding motif protein 2
    RNA-binding motif protein, Y chromosome, family 1 member A1/C
    Y chromosome RNA recognition motif 1
    Y chromosome RNA recognition motif 2

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_012805.2 RefSeqGene

      Range
      5002..19449
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001320944.2 → NP_001307873.1  RNA-binding motif protein, Y chromosome, family 1 member A1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      BC070298, BX119894, CB107177
      UniProtKB/TrEMBL
      B7ZMC0
      Conserved Domains (3) summary
      COG0724
      Location:1 → 189
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12382
      Location:7 → 85
      RRM_RBMX_like; RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins
      pfam08081
      Location:174 → 218
      RBM1CTR; RBM1CTR (NUC064) family

    2. NM_001320945.2 → NP_001307874.1  RNA-binding motif protein, Y chromosome, family 1 member A1 isoform 3

      Status: REVIEWED

      Source sequence(s)
      BC047768, CB107177
      UniProtKB/Swiss-Prot
      P0DJD3
      Conserved Domains (1) summary
      pfam08081
      Location:34 → 78
      RBM1CTR; RBM1CTR (NUC064) family

    3. NM_005058.4 → NP_005049.1  RNA-binding motif protein, Y chromosome, family 1 member A1 isoform 1

      See identical proteins and their annotated locations for NP_005049.1

      Status: REVIEWED

      Source sequence(s)
      BX119894, CB107177, X76059
      Consensus CDS
      CCDS14796.1
      UniProtKB/Swiss-Prot
      P0DJD3, P0DJD4, Q15376, Q15377, Q15414, Q6NSB5, Q86VU6, Q8NHR0
      Related
      ENSP00000372154.2, ENST00000382707.6
      Conserved Domains (3) summary
      COG0724
      Location:1 → 189
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12382
      Location:7 → 85
      RRM_RBMX_like; RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins
      pfam08081
      Location:174 → 218
      RBM1CTR; RBM1CTR (NUC064) family

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000024.10 Reference GRCh38.p14 Primary Assembly

      Range
      21534879..21559683
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011531437.3 → XP_011529739.1  RNA-binding motif protein, Y chromosome, family 1 member A1 isoform X1

      UniProtKB/Swiss-Prot
      P0DJD4
      Conserved Domains (4) summary
      PHA02896
      Location:247 → 362
      PHA02896; A-type inclusion like protein; Provisional
      COG0724
      Location:1 → 189
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12382
      Location:7 → 85
      RRM_RBMX_like; RNA recognition motif in heterogeneous nuclear ribonucleoprotein G (hnRNP G), Y chromosome RNA recognition motif 1 (hRBMY), testis-specific heterogeneous nuclear ribonucleoprotein G-T (hnRNP G-T) and similar proteins
      pfam08081
      Location:174 → 218
      RBM1CTR; RBM1CTR (NUC064) family

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060948.1 Alternate T2T-CHM13v2.0

      Range
      22410130..22434934
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054328317.1 → XP_054184292.1  RNA-binding motif protein, Y chromosome, family 1 member A1 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P0DJD3.1 GenPept UniProtKB/Swiss-Prot:P0DJD3

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