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RBM4B RNA binding motif protein 4B [ Homo sapiens (human) ]

Gene ID: 83759, updated on 14-Nov-2024

Summary

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Official Symbol
RBM4Bprovided by HGNC
Official Full Name
RNA binding motif protein 4Bprovided by HGNC
Primary source
HGNC:HGNC:28842
See related
Ensembl:ENSG00000173914 AllianceGenome:HGNC:28842
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
Also known as
RBM30; RBM4L; ZCRB3B; ZCCHC15; ZCCHC21B
Summary
Enables RNA binding activity. Predicted to be involved in entrainment of circadian clock by photoperiod; mRNA splicing, via spliceosome; and regulation of gene expression. Predicted to act upstream of or within positive regulation of gene expression. Located in cytosol and nucleoplasm. Part of protein-containing complex. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in ovary (RPKM 14.9), endometrium (RPKM 13.1) and 25 other tissues See more
Orthologs
all
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Genomic context

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See RBM4B in Genome Data Viewer
Location:
11q13.2
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (66664998..66677887, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (66661244..66674135, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (66432469..66445358, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5053 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:66384051-66384984 Neighboring gene RBM14-RBM4 readthrough Neighboring gene RNA, U4 small nuclear 39, pseudogene Neighboring gene hESC enhancers GRCh37_chr11:66405625-66406338 and GRCh37_chr11:66406339-66407050 Neighboring gene RNA binding motif protein 14 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66410755-66411278 Neighboring gene MPRA-validated peak1306 silencer Neighboring gene RNA binding motif protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3599 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3600 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66453249-66453749 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:66462288-66462788 Neighboring gene spectrin beta, non-erythrocytic 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66487347-66488304 Neighboring gene RNA, 7SL, cytoplasmic 12, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:66511467-66511967 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3601 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5056 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3602 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5057 Neighboring gene TOP6B like initiator of meiotic double strand breaks Neighboring gene fragile site, folic acid type, rare, fra(11)(q13.3) Neighboring gene complement C1q binding protein pseudogene 2

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. The LARK/RBM4a protein is highly expressed in cerebellum as compared to cerebrum. Pfuhl T, et al. Neurosci Lett, 2008 Oct 17. PMID 18708123
  2. A novel splicing regulator shares a nuclear import pathway with SR proteins. Lai MC, et al. EMBO J, 2003 Mar 17. PMID 12628928, Free PMC Article
  3. Physical interaction and functional coupling between ACDP4 and the intracellular ion chaperone COX11, an implication of the role of ACDP4 in essential metal ion transport and homeostasis. Guo D, et al. Mol Pain, 2005 Apr 19. PMID 15840172, Free PMC Article
  4. Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4. Psychiatric GWAS Consortium Bipolar Disorder Working Group. Nat Genet, 2011 Sep 18. PMID 21926972, Free PMC Article
  5. Functional proteomic analysis of human nucleolus. Scherl A, et al. Mol Biol Cell, 2002 Nov. PMID 12429849, Free PMC Article

See all (65) citations in PubMed

GeneRIFs: Gene References Into Functions

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
Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4.
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)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC10871, DKFZp586F1322

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
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in circadian regulation of gene expression ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in circadian rhythm ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in entrainment of circadian clock by photoperiod ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of gene expression IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of translation ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in cytosol IDA
Inferred from Direct Assay
more info
  
is_active_in nuclear speck IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleolus IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
RNA-binding protein 4B
Names
RNA-binding motif protein 30
zinc finger CCHC-type and RNA binding motif 3B

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_001286135.2 → NP_001273064.1  RNA-binding protein 4B isoform 2

    See identical proteins and their annotated locations for NP_001273064.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    BC004951, BQ428264
    Consensus CDS
    CCDS66144.1
    UniProtKB/TrEMBL
    E9PLB0, E9PM61
    Related
    ENSP00000435239.1, ENST00000531969.5
    Conserved Domains (1) summary
    cl17169
    Location:78 → 141
    RRM_SF; RNA recognition motif (RRM) superfamily

  2. NM_031492.4 → NP_113680.1  RNA-binding protein 4B isoform 1

    See identical proteins and their annotated locations for NP_113680.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    BC004951, BQ428264
    Consensus CDS
    CCDS8149.1
    UniProtKB/Swiss-Prot
    B3KT83, Q9BQ04
    Related
    ENSP00000310471.4, ENST00000310046.9
    Conserved Domains (4) summary
    PTZ00368
    Location:145 → 181
    PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional
    smart00343
    Location:161 → 176
    ZnF_C2HC; zinc finger
    cd12606
    Location:2 → 68
    RRM1_RBM4; RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 4 (RBM4)
    cd12607
    Location:78 → 144
    RRM2_RBM4; RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 4 (RBM4)

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    66664998..66677887 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011545297.4 → XP_011543599.1  RNA-binding protein 4B isoform X1

    See identical proteins and their annotated locations for XP_011543599.1

    UniProtKB/Swiss-Prot
    B3KT83, Q9BQ04
    Conserved Domains (4) summary
    PTZ00368
    Location:145 → 181
    PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional
    smart00343
    Location:161 → 176
    ZnF_C2HC; zinc finger
    cd12606
    Location:2 → 68
    RRM1_RBM4; RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 4 (RBM4)
    cd12607
    Location:78 → 144
    RRM2_RBM4; RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 4 (RBM4)

  2. XM_017018402.3 → XP_016873891.1  RNA-binding protein 4B isoform X1

    UniProtKB/Swiss-Prot
    B3KT83, Q9BQ04
    Conserved Domains (4) summary
    PTZ00368
    Location:145 → 181
    PTZ00368; universal minicircle sequence binding protein (UMSBP); Provisional
    smart00343
    Location:161 → 176
    ZnF_C2HC; zinc finger
    cd12606
    Location:2 → 68
    RRM1_RBM4; RNA recognition motif 1 (RRM1) found in vertebrate RNA-binding protein 4 (RBM4)
    cd12607
    Location:78 → 144
    RRM2_RBM4; RNA recognition motif 2 (RRM2) found in vertebrate RNA-binding protein 4 (RBM4)

RNA

  1. XR_247214.4 RNA Sequence

  2. XR_247213.4 RNA Sequence

  3. XR_007062509.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    66661244..66674135 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054370145.1 → XP_054226120.1  RNA-binding protein 4B isoform X1

    UniProtKB/Swiss-Prot
    B3KT83, Q9BQ04

  2. XM_054370144.1 → XP_054226119.1  RNA-binding protein 4B isoform X1

    UniProtKB/Swiss-Prot
    B3KT83, Q9BQ04

RNA

  1. XR_008488466.1 RNA Sequence

  2. XR_008488465.1 RNA Sequence

  3. XR_008488467.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BQ04.1 GenPept UniProtKB/Swiss-Prot:Q9BQ04

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