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

Gene ID: 9904, updated on 5-Mar-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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Location:
12q24.13-q24.21
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (113816740..113966325, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (113792564..113942186, complement)
105.20220307 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 (62) 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)

Genotypes

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 mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
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_2023_10

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

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