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    RBM42 RNA binding motif protein 42 [ Homo sapiens (human) ]

    Gene ID: 79171, updated on 3-Nov-2024

    Summary

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    Official Symbol
    RBM42provided by HGNC
    Official Full Name
    RNA binding motif protein 42provided by HGNC
    Primary source
    HGNC:HGNC:28117
    See related
    Ensembl:ENSG00000126254 MIM:613232; AllianceGenome:HGNC:28117
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Enables RNA binding activity. Predicted to act upstream of or within negative regulation of mRNA splicing, via spliceosome. Part of U4/U6 x U5 tri-snRNP complex. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in fat (RPKM 19.0), spleen (RPKM 16.6) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RBM42 in Genome Data Viewer
    Location:
    19q13.12
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (35629036..35637685)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (38173991..38182639)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (36119938..36128587)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene HAUS5 divergent transcript Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:36103371-36103926 Neighboring gene HAUS augmin like complex subunit 5 Neighboring gene tRNA-undetermined (NNN) 10-1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:36118908-36119435 Neighboring gene Sharpr-MPRA regulatory region 5913 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:36132803-36133518 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10530 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10531 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14489 Neighboring gene ETS variant transcription factor 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14490 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14491 Neighboring gene cytochrome c oxidase subunit 6B1

    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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    Related articles in PubMed

    1. Biallelic variants in RBM42 cause a multisystem disorder with neurological, facial, cardiac, and musculoskeletal involvement. Chen Y, et al. Protein Cell, 2024 Jan 3. PMID 37294900, Free PMC Article
    2. Discovery of a splicing regulator required for cell cycle progression. Suvorova ES, et al. PLoS Genet, 2013. PMID 23437009, Free PMC Article
    3. hnRNP K interacts with RNA binding motif protein 42 and functions in the maintenance of cellular ATP level during stress conditions. Fukuda T, et al. Genes Cells, 2009 Feb. PMID 19170760
    4. Mechanism of 5' splice site transfer for human spliceosome activation. Charenton C, et al. Science, 2019 Apr 26. PMID 30975767, Free PMC Article
    5. The SWI/SNF chromatin remodeling factor DPF3 regulates metastasis of ccRCC by modulating TGF-β signaling. Cui H, et al. Nat Commun, 2022 Aug 9. PMID 35945219, Free PMC Article

    See all (61) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Biallelic variants in RBM42 cause a multisystem disorder with neurological, facial, cardiac, and musculoskeletal involvement.
      Title: Biallelic variants in RBM42 cause a multisystem disorder with neurological, facial, cardiac, and musculoskeletal involvement.
    2. hnRNP K and RBM42 have a role in the maintenance of cellular ATP level in the stress conditions possibly through protecting their target mRNAs.
      Title: hnRNP K interacts with RNA binding motif protein 42 and functions in the maintenance of cellular ATP level during stress conditions.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev interacting protein, RNA binding motif protein 42 (RBM42), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells 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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    Homology

    Clone Names

    • MGC10433

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in mRNA splicing, via spliceosome NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in negative regulation of mRNA splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    part_of U4/U6 x U5 tri-snRNP complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    RNA-binding protein 42

    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_001319113.2 → NP_001306042.1  RNA-binding protein 42 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an in-frame exon and uses an alternate in-frame splice site in the 5' coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      BC002868, HY031737
      UniProtKB/TrEMBL
      K7EP90
      Related
      ENSP00000466044.1, ENST00000588161.5
      Conserved Domains (1) summary
      cd12383
      Location:346 → 428
      RRM_RBM42; RNA recognition motif in RNA-binding protein 42 (RBM42) and similar proteins

    2. NM_024321.5 → NP_077297.2  RNA-binding protein 42 isoform 1

      See identical proteins and their annotated locations for NP_077297.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      BC004204, HY031737
      Consensus CDS
      CCDS12468.1
      UniProtKB/Swiss-Prot
      O00320, Q8N5R7, Q9BTD8, Q9BU66
      UniProtKB/TrEMBL
      K7EP90
      Related
      ENSP00000262633.3, ENST00000262633.9
      Conserved Domains (1) summary
      cd12383
      Location:375 → 457
      RRM_RBM42; RNA recognition motif (RRM) found in RNA-binding protein 42 (RBM42) and similar proteins

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      35629036..35637685
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      38173991..38182639
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BTD8.1 GenPept UniProtKB/Swiss-Prot:Q9BTD8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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