Rbm4 RNA binding motif protein 4 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Rbm4provided by MGI
Official Full Name: RNA binding motif protein 4provided by MGI
Primary source: MGI:MGI:1100865
See related: Ensembl:ENSMUSG00000094936 AllianceGenome:MGI:1100865
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: lark; Lark1; Mlark; Rbm4a; 4921506I22Rik
Summary: Enables mRNA 3'-UTR binding activity and pre-mRNA binding activity. Involved in circadian regulation of translation; entrainment of circadian clock by photoperiod; and regulation of nucleocytoplasmic transport. Acts upstream of or within several processes, including insulin secretion involved in cellular response to glucose stimulus; regulation of gene expression; and regulation of insulin receptor signaling pathway. Located in nucleolus and perinuclear region of cytoplasm. Is expressed in several structures, including alimentary system; brain; genitourinary system; respiratory system; and sensory organ. Orthologous to human RBM4 (RNA binding motif protein 4). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in whole brain E14.5 (RPKM 23.3), CNS E14 (RPKM 23.0) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 19 A; 19 4.11 cM

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	19	NC_000085.7 (4834321..4844037, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	19	NC_000085.6 (4784293..4794009, complement)

Chromosome 19 - NC_000085.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The N6-methyladenosine demethylase FTO is required for odontoblast differentiation in vitro and dentine formation in mice by promoting RUNX2 exon 5 inclusion through RBM4.
Title: The N6-methyladenosine demethylase FTO is required for odontoblast differentiation in vitro and dentine formation in mice by promoting RUNX2 exon 5 inclusion through RBM4.
Activation of TrkB signaling mitigates cerebellar anomalies caused by Rbm4-Bdnf deficiency.
Title: Activation of TrkB signaling mitigates cerebellar anomalies caused by Rbm4-Bdnf deficiency.
Overexpression of mm9_circ_013935 alleviates renal inflammation and fibrosis in diabetic nephropathy via the miR-153-3p/NFIC axis.
Title: Overexpression of mm9_circ_013935 alleviates renal inflammation and fibrosis in diabetic nephropathy via the miR-153-3p/NFIC axis.
Rbm24 regulates inner-ear-specific alternative splicing and is essential for maintaining auditory and motor coordination.
Title: Rbm24 regulates inner-ear-specific alternative splicing and is essential for maintaining auditory and motor coordination.
RBM4 regulates M1 macrophages polarization through targeting STAT1-mediated glycolysis.
Title: RBM4 regulates M1 macrophages polarization through targeting STAT1-mediated glycolysis.
Data suggest that LARK is a conserved G4-binding protein and that the G4 structure may have developed into an elaborate epigenetic mechanism of gene transcription regulation during evolution.
Title: Identification of LARK as a novel and conserved G-quadruplex binding protein in invertebrates and vertebrates.
RBM4 plays a role in neuronal migration via modulating the expression of Dab1 splice isoforms. This finding implies that RBM4 is necessary during brain development and that its deficiency may lead to developmental brain abnormality.
Title: RBM4 Modulates Radial Migration via Alternative Splicing of Dab1 during Cortex Development.
Our studies demonstrated that RBM4a-regulated alternative splicing constituted another regulatory mechanism for strengthening the influence of PRDM16 on the development of brown adipocytes.
Title: RBM4a modulates the impact of PRDM16 on development of brown adipocytes through an alternative splicing mechanism.
Study identified a novel splicing network composed of RBM4a, SRSF3, and MAP4K4 in brown adipogenesis and subsequently manipulating the effect of downstream JNK signaling which contributes to insulin resistance and reduced metabolism.
Title: RBM4a-SRSF3-MAP4K4 Splicing Cascade Constitutes a Molecular Mechanism for Regulating Brown Adipogenesis.
RBM4 depletion reduced the expression of the proneural gene Mash1, and such reduction was reversed by an RBM4-induced Numb isoform containing exon 3 but lacking exon 9. RBM4 was also essential for neurite outgrowth from cortical neurons in vitro. Neurite outgrowth defects of RBM4-depleted neurons were rescued by RBM4-induced exon 9-lacking Numb isoforms. RBM4 modulates exon selection of Numb.
Title: RBM4 promotes neuronal differentiation and neurite outgrowth by modulating Numb isoform expression.

Submit: New GeneRIF Correction See all GeneRIFs (16)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Rbm4 (e-PCR), detects polymorphism
- UniSTS:479234

AW536637 (e-PCR)
- UniSTS:181173

NoName (e-PCR)
- UniSTS:492235

Readthrough Gm21992

Readthrough gene: Gm21992, Included gene: Rbm14

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables cyclin binding	ISO Inferred from Sequence Orthology more info
enables mRNA 3'-UTR binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables miRNA binding	ISO Inferred from Sequence Orthology more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables pre-mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables pre-mRNA intronic binding	ISO Inferred from Sequence Orthology more info
enables pre-mRNA intronic pyrimidine-rich binding	ISO Inferred from Sequence Orthology more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in IRES-dependent translational initiation of linear mRNA	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within RNA splicing	IEA Inferred from Electronic Annotation more info
involved_in cap-independent translational initiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cell differentiation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within circadian regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in circadian regulation of translation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within enteroendocrine cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in entrainment of circadian clock by photoperiod	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within glucose homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within insulin secretion involved in cellular response to glucose stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in miRNA-mediated gene silencing by inhibition of translation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of translation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of translation in response to stress	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of translational initiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within pancreas development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of muscle cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of translation	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of alternative mRNA splicing, via spliceosome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of alternative mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of insulin receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of nucleocytoplasmic transport	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of nucleocytoplasmic transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulatory ncRNA-mediated gene silencing	IEA Inferred from Electronic Annotation more info
involved_in response to arsenic-containing substance	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic stress granule	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
is_active_in nuclear speck	IBA Inferred from Biological aspect of Ancestor more info
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: RNA-binding protein 4

Names: RNA-binding motif protein 4a; lark homolog

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)

NM_001290122.1 → NP_001277051.1 RNA-binding protein 4 isoform a

See identical proteins and their annotated locations for NP_001277051.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 all encode isoform a.

Source sequence(s)

AK049659, BM932360, CN670081, DV660645

Consensus CDS

CCDS29436.1

UniProtKB/Swiss-Prot

O08752, Q8BN66, Q8C7Q4

UniProtKB/TrEMBL

A1L3S3, B7ZN14

Related

ENSMUSP00000137174.3, ENSMUST00000179189.9

Conserved Domains (3) summary

smart00343
Location:161 → 176

ZnF_C2HC; zinc finger

cd12606
Location:2 → 68

RRM1_RBM4; RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

cd12607
Location:78 → 144

RRM2_RBM4; RNA recognition motif 2 in vertebrate RNA-binding protein 4 (RBM4)
NM_001290123.1 → NP_001277052.1 RNA-binding protein 4 isoform a

See identical proteins and their annotated locations for NP_001277052.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 all encode isoform a.

Source sequence(s)

AK049659, BM932360, CN670081, DV660645

Consensus CDS

CCDS29436.1

UniProtKB/Swiss-Prot

O08752, Q8BN66, Q8C7Q4

UniProtKB/TrEMBL

A1L3S3, B7ZN14

Conserved Domains (3) summary

smart00343
Location:161 → 176

ZnF_C2HC; zinc finger

cd12606
Location:2 → 68

RRM1_RBM4; RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

cd12607
Location:78 → 144

RRM2_RBM4; RNA recognition motif 2 in vertebrate RNA-binding protein 4 (RBM4)
NM_001290124.1 → NP_001277053.1 RNA-binding protein 4 isoform b

See identical proteins and their annotated locations for NP_001277053.1

Status: VALIDATED

Description

Transcript Variant: This variant (4) differs in the 5' UTR, and lacks an alternate exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (b) has a distinct and shorter C-terminus, compared to isoform a. Both variants 4 and 5 encode isoform b.

Source sequence(s)

AK049659, BM932360, CK331622, CN670081

Consensus CDS

CCDS79671.1

UniProtKB/TrEMBL

A0A494BAP6, Q5CZX8

Related

ENSMUSP00000129745.3, ENSMUST00000164209.9

Conserved Domains (1) summary

cl17169
Location:78 → 138

RRM_SF; RNA recognition motif (RRM) superfamily
NM_001290125.1 → NP_001277054.1 RNA-binding protein 4 isoform b

See identical proteins and their annotated locations for NP_001277054.1

Status: VALIDATED

Description

Transcript Variant: This variant (5) lacks an alternate exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (b) has a distinct and shorter C-terminus, compared to isoform a. Both variants 4 and 5 encode isoform b.

Source sequence(s)

AK049659, BC090633, BM932360, BY261809

Consensus CDS

CCDS79671.1

UniProtKB/TrEMBL

A0A494BAP6, Q5CZX8

Related

ENSMUSP00000136254.2, ENSMUST00000178615.8

Conserved Domains (1) summary

cl17169
Location:78 → 138

RRM_SF; RNA recognition motif (RRM) superfamily
NM_009032.3 → NP_033058.2 RNA-binding protein 4 isoform a

See identical proteins and their annotated locations for NP_033058.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1, 2 and 3 all encode isoform a.

Source sequence(s)

AK049659, BM932360, BY261809

Consensus CDS

CCDS29436.1

UniProtKB/Swiss-Prot

O08752, Q8BN66, Q8C7Q4

UniProtKB/TrEMBL

A1L3S3, B7ZN14

Related

ENSMUSP00000137345.2, ENSMUST00000180248.8

Conserved Domains (3) summary

smart00343
Location:161 → 176

ZnF_C2HC; zinc finger

cd12606
Location:2 → 68

RRM1_RBM4; RNA recognition motif 1 in vertebrate RNA-binding protein 4 (RBM4)

cd12607
Location:78 → 144

RRM2_RBM4; RNA recognition motif 2 in vertebrate RNA-binding protein 4 (RBM4)