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RBMY1D RNA binding motif protein Y-linked family 1 member D [ Homo sapiens (human) ]

Gene ID: 378949, updated on 3-Apr-2024

Summary

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Official Symbol
RBMY1Dprovided by HGNC
Official Full Name
RNA binding motif protein Y-linked family 1 member Dprovided by HGNC
Primary source
HGNC:HGNC:23915
See related
Ensembl:ENSG00000244395 AllianceGenome:HGNC:23915
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
RBM1; RBM2; YRRM1; YRRM2; hRBMY; RBMY1A1
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 likely functions as a splicing factor 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 6.2) See more
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Genomic context

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Location:
Yq11.223
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (21868431..21900746, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (22703948..22736261, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (24026223..24040673, complement)

Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105377236 Neighboring gene OFD1 pseudogene 16 Y-linked Neighboring gene uncharacterized LOC105377237 Neighboring gene RNA binding motif protein Y-linked family 1 member E Neighboring gene RNA binding motif protein Y-linked family 2 member A, pseudogene

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
  • 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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Related articles in PubMed

  1. RBMY, a male germ cell-specific RNA-binding protein, activated in human liver cancers and transforms rodent fibroblasts. Tsuei DJ, et al. Oncogene, 2004 Jul 29. PMID 15184870
  2. Degeneracy in human multicopy RBM (YRRM), a candidate spermatogenesis gene. Prosser J, et al. Mamm Genome, 1996 Nov. PMID 8875892
  3. A Y chromosome gene family with RNA-binding protein homology: candidates for the azoospermia factor AZF controlling human spermatogenesis. Ma K, et al. Cell, 1993 Dec 31. PMID 8269511
  4. Structure and organization of the RBMY genes on the human Y chromosome: transposition and amplification of an ancestral autosomal hnRNPG gene. Chai NN, et al. Genomics, 1998 Apr 15. PMID 9598316
  5. A Genome-Wide CRISPR Screen Identifies Genes Critical for Resistance to FLT3 Inhibitor AC220. Hou P, et al. Cancer Res, 2017 Aug 15. PMID 28625976, Free PMC Article

See all (8) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

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

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
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
  
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 D
Names
RNA-binding motif protein 1
RNA-binding motif protein 2
RNA-binding motif protein, Y chromosome, family 1 member A1
Y chromosome RNA recognition motif 1

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.

mRNA and Protein(s)

  1. NM_001006120.3 → NP_001006120.2  RNA-binding motif protein, Y chromosome, family 1 member D isoform 1

    See identical proteins and their annotated locations for NP_001006120.2

    Status: REVIEWED

    Source sequence(s)
    AC007322
    Consensus CDS
    CCDS35480.1
    UniProtKB/Swiss-Prot
    B7ZMD9, P0C7P1, P0DJD4
    Related
    ENSP00000372127.1, ENST00000382680.5
    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_001320949.1 → NP_001307878.1  RNA-binding motif protein, Y chromosome, family 1 member D isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC007322
    Consensus CDS
    CCDS83521.1
    UniProtKB/TrEMBL
    B7ZMC0
    Related
    ENSP00000399181.2, ENST00000418956.2
    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

  3. NM_001320950.1 → NP_001307879.1  RNA-binding motif protein, Y chromosome, family 1 member D isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) encodes isoform 3, which has a distinct N-terminus compared to isoform 1.
    Source sequence(s)
    AC007322, BC144423
    UniProtKB/TrEMBL
    B7ZMC0
    Conserved Domains (3) summary
    COG0724
    Location:20 → 165
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    pfam08081
    Location:150 → 194
    RBM1CTR; RBM1CTR (NUC064) family
    cl17169
    Location:17 → 61
    RRM_SF; RNA recognition motif (RRM) superfamily

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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
    21868431..21900746 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011531487.4 → XP_011529789.1  RNA-binding motif protein, Y chromosome, family 1 member D isoform X2

    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

  2. XM_011531488.4 → XP_011529790.1  RNA-binding motif protein, Y chromosome, family 1 member D isoform X3

    See identical proteins and their annotated locations for XP_011529790.1

    UniProtKB/Swiss-Prot
    P0DJD4
    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

  3. XM_011531486.2 → XP_011529788.1  RNA-binding motif protein, Y chromosome, family 1 member D isoform X1

    See identical proteins and their annotated locations for XP_011529788.1

    UniProtKB/Swiss-Prot
    B7ZMD9, P0C7P1, P0DJD4
    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

  4. XM_011531489.2 → XP_011529791.1  RNA-binding motif protein, Y chromosome, family 1 member D isoform X4

    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

  5. XM_047442737.1 → XP_047298693.1  RNA-binding motif protein, Y chromosome, family 1 member D isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060948.1 Alternate T2T-CHM13v2.0

    Range
    22703948..22736261 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054328301.1 → XP_054184276.1  RNA-binding motif protein, Y chromosome, family 1 member D isoform X6

  2. XM_054328300.1 → XP_054184275.1  RNA-binding motif protein, Y chromosome, family 1 member D isoform X1

    UniProtKB/Swiss-Prot
    P0DJD3, Q15376, Q15377, Q15414, Q6NSB5, Q86VU6, Q8NHR0

  3. XM_054328302.1 → XP_054184277.1  RNA-binding motif protein, Y chromosome, family 1 member D isoform X7

  4. XM_054328303.1 → XP_054184278.1  RNA-binding motif protein, Y chromosome, family 1 member D isoform X8

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P0C7P1.1 GenPept UniProtKB/Swiss-Prot:P0C7P1

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