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    RBM19 RNA binding motif protein 19 [ Homo sapiens (human) ]

    Gene ID: 9904, updated on 27-Nov-2024

    Summary

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    Official Symbol
    RBM19provided by HGNC
    Official Full Name
    RNA binding motif protein 19provided by HGNC
    Primary source
    HGNC:HGNC:29098
    See related
    Ensembl:ENSG00000122965 MIM:616444; AllianceGenome:HGNC:29098
    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
    Mrd1
    Summary
    This gene encodes a nucleolar protein that contains six RNA-binding motifs. The encoded protein may be involved in regulating ribosome biogenesis. Multiple alternatively spliced variants, encoding the same protein, have been identified.[provided by RefSeq, Apr 2009]
    Expression
    Ubiquitous expression in testis (RPKM 6.2), spleen (RPKM 5.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RBM19 in Genome Data Viewer
    Location:
    12q24.13-q24.21
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (113816740..113966325, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (113792564..113942186, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (114254545..114404130, complement)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1234 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:114206803-114207314 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24661 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:114215183-114215682 Neighboring gene NANOG hESC enhancer GRCh37_chr12:114222326-114222862 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:114243165-114243665 Neighboring gene dynein light chain LC8-type 1 pseudogene 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:114255753-114256680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:114256681-114257606 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:114294867-114295368 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr12:114295369-114295868 Neighboring gene uncharacterized LOC124903025 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr12:114300792-114301991 Neighboring gene H3K27ac hESC enhancer GRCh37_chr12:114348209-114348709 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:114369155-114369838 Neighboring gene VISTA enhancer hs1673 Neighboring gene tRNA-Glu (anticodon CTC) 16-1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7075 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7076 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:114402552-114403480 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:114403481-114404408 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_24787 Neighboring gene uncharacterized LOC105369993 Neighboring gene CRE2 enhancer downstream of TBX5 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:114501919-114502507 Neighboring gene uncharacterized LOC105369994

    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. Rbm19 is a nucleolar protein expressed in crypt/progenitor cells of the intestinal epithelium. Lorenzen JA, et al. Gene Expr Patterns, 2005 Dec. PMID 16027046
    2. Nil per os encodes a conserved RNA recognition motif protein required for morphogenesis and cytodifferentiation of digestive organs in zebrafish. Mayer AN, et al. Development, 2003 Sep. PMID 12874115
    3. A non-proteolytic role for ubiquitin in deadenylation of MHC-I mRNA by the RNA-binding E3-ligase MEX-3C. Cano F, et al. Nat Commun, 2015 Oct 16. PMID 26471122, Free PMC Article
    4. A protein array screen for Kaposi's sarcoma-associated herpesvirus LANA interactors links LANA to TIP60, PP2A activity, and telomere shortening. Shamay M, et al. J Virol, 2012 May. PMID 22379092, Free PMC Article
    5. Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations. Xie T, et al. Neurobiol Aging, 2014 Jul. PMID 24529757

    See all (70) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    2. Clinical trial and genome-wide association study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Molecular genetics of successful smoking cessation: convergent genome-wide association study results.
    3. Primarily a zebrafish paper but shows an alignment of human RBM19
      Title: Nil per os encodes a conserved RNA recognition motif protein required for morphogenesis and cytodifferentiation of digestive organs in zebrafish.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling.
    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

    EBI GWAS Catalog

    Description
    Genome-wide association study combining pathway analysis for typical sporadic amyotrophic lateral sclerosis in Chinese Han populations.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of RNA binding motif protein 19 (RBM19) by siRNA inhibits HIV-1 replication in HeLa P4/R5 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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    Markers

    Homology

    Clone Names

    • KIAA0682, DKFZp586F1023

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables RNA binding HDA PubMed 
    enables RNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in positive regulation of embryonic development ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in membrane HDA PubMed 
    is_active_in nuclear speck IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleolus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    probable RNA-binding protein 19

    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_001146698.2 → NP_001140170.1  probable RNA-binding protein 19

      See identical proteins and their annotated locations for NP_001140170.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 3' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AA594568, AC090669, AK291444, AL117547, BC004289, DB096676
      Consensus CDS
      CCDS9172.1
      UniProtKB/Swiss-Prot
      A8K5X9, Q9BPY6, Q9UFN5, Q9Y4C8
      Related
      ENSP00000376344.3, ENST00000392561.7
      Conserved Domains (6) summary
      cd12318
      Location:730 → 809
      RRM5_RBM19_like; RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins
      cd12502
      Location:294 → 365
      RRM2_RMB19; RNA recognition motif 2 (RRM2) found in RNA-binding protein 19 (RBM19) and similar proteins
      cd12564
      Location:2 → 77
      RRM1_RBM19; RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins
      cd12567
      Location:400 → 478
      RRM3_RBM19; RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and similar proteins
      cd12569
      Location:587 → 658
      RRM4_RBM19; RNA recognition motif 4 (RRM4) found in RNA-binding protein 19 (RBM19) and similar proteins
      cd12571
      Location:832 → 910
      RRM6_RBM19; RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19) and similar proteins

    2. NM_001146699.2 → NP_001140171.1  probable RNA-binding protein 19

      See identical proteins and their annotated locations for NP_001140171.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AC009731, AC090669, AI218902, AK291444, DB096676
      Consensus CDS
      CCDS9172.1
      UniProtKB/Swiss-Prot
      A8K5X9, Q9BPY6, Q9UFN5, Q9Y4C8
      Related
      ENSP00000442053.2, ENST00000545145.6
      Conserved Domains (6) summary
      cd12318
      Location:730 → 809
      RRM5_RBM19_like; RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins
      cd12502
      Location:294 → 365
      RRM2_RMB19; RNA recognition motif 2 (RRM2) found in RNA-binding protein 19 (RBM19) and similar proteins
      cd12564
      Location:2 → 77
      RRM1_RBM19; RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins
      cd12567
      Location:400 → 478
      RRM3_RBM19; RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and similar proteins
      cd12569
      Location:587 → 658
      RRM4_RBM19; RNA recognition motif 4 (RRM4) found in RNA-binding protein 19 (RBM19) and similar proteins
      cd12571
      Location:832 → 910
      RRM6_RBM19; RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19) and similar proteins

    3. NM_016196.4 → NP_057280.2  probable RNA-binding protein 19

      See identical proteins and their annotated locations for NP_057280.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
      Source sequence(s)
      AC009731, AC090669, AL117547, DB096676
      Consensus CDS
      CCDS9172.1
      UniProtKB/Swiss-Prot
      A8K5X9, Q9BPY6, Q9UFN5, Q9Y4C8
      Related
      ENSP00000261741.5, ENST00000261741.10
      Conserved Domains (6) summary
      cd12318
      Location:730 → 809
      RRM5_RBM19_like; RNA recognition motif 5 (RRM5) found in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins
      cd12502
      Location:294 → 365
      RRM2_RMB19; RNA recognition motif 2 (RRM2) found in RNA-binding protein 19 (RBM19) and similar proteins
      cd12564
      Location:2 → 77
      RRM1_RBM19; RNA recognition motif 1 (RRM1) found in RNA-binding protein 19 (RBM19) and similar proteins
      cd12567
      Location:400 → 478
      RRM3_RBM19; RNA recognition motif 3 (RRM3) found in RNA-binding protein 19 (RBM19) and similar proteins
      cd12569
      Location:587 → 658
      RRM4_RBM19; RNA recognition motif 4 (RRM4) found in RNA-binding protein 19 (RBM19) and similar proteins
      cd12571
      Location:832 → 910
      RRM6_RBM19; RNA recognition motif 6 (RRM6) found in RNA-binding protein 19 (RBM19) 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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      113816740..113966325 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017020281.2 → XP_016875770.1  probable RNA-binding protein 19 isoform X1

      Conserved Domains (8) summary
      COG0724
      Location:453 → 777
      RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
      cd12318
      Location:706 → 785
      RRM5_RBM19_like; RNA recognition motif 5 in RNA-binding protein 19 (RBM19 or RBD-1) and similar proteins
      cd12564
      Location:2 → 77
      RRM1_RBM19; RNA recognition motif 1 in RNA-binding protein 19 (RBM19) and similar proteins
      cd12567
      Location:376 → 454
      RRM3_RBM19; RNA recognition motif 3 in RNA-binding protein 19 (RBM19) and similar proteins
      cd12569
      Location:563 → 634
      RRM4_RBM19; RNA recognition motif 4 in RNA-binding protein 19 (RBM19) and similar proteins
      cd12571
      Location:808 → 886
      RRM6_RBM19; RNA recognition motif 6 in RNA-binding protein 19 (RBM19) and similar proteins
      pfam16651
      Location:82 → 286
      RRM_u2; Unstructured region on RNA-binding-domain protein
      cl17169
      Location:294 → 341
      RRM_SF; RNA recognition motif (RRM) superfamily

    2. XM_047429936.1 → XP_047285892.1  probable RNA-binding protein 19 isoform X1

    RNA

    1. XR_001748932.2 RNA Sequence

    2. XR_944848.3 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      113792564..113942186 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054373952.1 → XP_054229927.1  probable RNA-binding protein 19 isoform X1

    2. XM_054373951.1 → XP_054229926.1  probable RNA-binding protein 19 isoform X1

    3. XM_054373950.1 → XP_054229925.1  probable RNA-binding protein 19 isoform X1

    4. XM_054373948.1 → XP_054229923.1  probable RNA-binding protein 19 isoform X2

    5. XM_054373947.1 → XP_054229922.1  probable RNA-binding protein 19 isoform X2

    6. XM_054373949.1 → XP_054229924.1  probable RNA-binding protein 19 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y4C8.3 GenPept UniProtKB/Swiss-Prot:Q9Y4C8

    Gene LinkOut

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

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