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RBM7 RNA binding motif protein 7 [ Homo sapiens (human) ]

Gene ID: 10179, updated on 7-Apr-2024

Summary

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Official Symbol
RBM7provided by HGNC
Official Full Name
RNA binding motif protein 7provided by HGNC
Primary source
HGNC:HGNC:9904
See related
Ensembl:ENSG00000076053 MIM:612413; AllianceGenome:HGNC:9904
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 14-3-3 protein binding activity; pre-mRNA intronic binding activity; and snRNA binding activity. Involved in snRNA catabolic process. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bone marrow (RPKM 12.9), urinary bladder (RPKM 8.3) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
11q23.2
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (114400666..114410607)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (114411085..114421025)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (114271388..114281329)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928940 Neighboring gene uncharacterized LOC107984391 Neighboring gene chromosome 11 open reading frame 71 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancers GRCh37_chr11:114270475-114271017 and GRCh37_chr11:114271018-114271560 Neighboring gene RNA exonuclease 2 Neighboring gene nocturnin pseudogene

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. RRM domain of human RBM7: purification, crystallization and structure determination. Sofos N, et al. Acta Crystallogr F Struct Biol Commun, 2016 May. PMID 27139832, Free PMC Article
  2. RBM7 subunit of the NEXT complex binds U-rich sequences and targets 3'-end extended forms of snRNAs. Hrossova D, et al. Nucleic Acids Res, 2015 Apr 30. PMID 25852104, Free PMC Article
  3. Novel insights into the pathogenesis of lung fibrosis: the RBM7-NEAT1-CXCL12-SatM axis at fibrosis onset. Fukushima K, et al. Int Immunol, 2021 Nov 25. PMID 34165514
  4. Spermatogenetic expression of RNA-binding motif protein 7, a protein that interacts with splicing factors. Guo TB, et al. J Androl, 2003 Mar-Apr. PMID 12634307
  5. Structural basis for MTR4-ZCCHC8 interactions that stimulate the MTR4 helicase in the nuclear exosome-targeting complex. Puno MR, et al. Proc Natl Acad Sci U S A, 2018 Jun 12. PMID 29844170, Free PMC Article

See all (77) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Novel insights into the pathogenesis of lung fibrosis: the RBM7-NEAT1-CXCL12-SatM axis at fibrosis onset.
    Title: Novel insights into the pathogenesis of lung fibrosis: the RBM7-NEAT1-CXCL12-SatM axis at fibrosis onset.
  2. interfering with the axis of RBM7 and P-TEFb provokes cellular hypersensitivity to DNA-damage-inducing agents due to activation of apoptosis. Our work uncovers the importance of stress-dependent stimulation of Pol II pause release, which enables a pro-survival transcriptional response that is crucial for cell fate upon genotoxic insult.
    Title: P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress.
  3. a proline-rich segment of ZCCHC8 as the interaction site for the RNA-recognition motif (RRM) of RBM7 and present the crystal structure of the corresponding complex at 2.0 A resolution.
    Title: Structure of the RBM7-ZCCHC8 core of the NEXT complex reveals connections to splicing factors.
  4. Knock-down of rbm7, exosc8 and exosc3 in zebrafish showed a common pattern of defects in motor neurons and cerebellum. Our data indicate that impaired RNA metabolism may underlie the clinical phenotype by fine tuning gene expression which is essential for correct neuronal differentiation
    Title: Altered RNA metabolism due to a homozygous RBM7 mutation in a patient with spinal motor neuropathy.
  5. RBM8 and CBP20 RRM-domain crystal structures were used to successfully determine the RBM7 structure by molecular replacement. The structure reveals a ring-shaped pentameric assembly, which is most likely a consequence of crystal packing
    Title: RRM domain of human RBM7: purification, crystallization and structure determination.
  6. Phosphorylation of RBM7 by the p38(MAPK)/MK2 axis increases nuclear ncRNA stability by blocking their RBM7-binding and subsequent RNA exosome targeting to allow stress-dependent modulations of the noncoding transcriptome.
    Title: p38MAPK/MK2-mediated phosphorylation of RBM7 regulates the human nuclear exosome targeting complex.
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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Replication interactions

Interaction Pubs
Knockdown of RNA binding motif protein 7 (RBM7) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 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

  • FLJ11153

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 14-3-3 protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables 14-3-3 protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables RNA binding HDA PubMed 
enables RNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA binding IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables pre-mRNA intronic binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables single-stranded RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables snRNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in meiotic cell cycle IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of alternative mRNA splicing, via spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in snRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
NOT located_in nucleolus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
RNA-binding protein 7

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_001286045.2 → NP_001272974.1  RNA-binding protein 7 isoform a

    See identical proteins and their annotated locations for NP_001272974.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
    Source sequence(s)
    AK002015, AK225615, AP002373
    Consensus CDS
    CCDS66233.1
    UniProtKB/TrEMBL
    J3KPD3, Q6IRX3
    Related
    ENSP00000364639.5, ENST00000375490.10
    Conserved Domains (2) summary
    COG0724
    Location:9 → 84
    RRM; RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis]
    cd12592
    Location:9 → 83
    RRM_RBM7; RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)

  2. NM_001286046.2 → NP_001272975.1  RNA-binding protein 7 isoform c

    See identical proteins and their annotated locations for NP_001272975.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate splice site in the 5' region and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus than isoform a. Variants 3, 4, and 5 encode the same isoform (c).
    Source sequence(s)
    AP002373, BC013320, BC034381, DA027521
    Consensus CDS
    CCDS73395.1
    UniProtKB/TrEMBL
    G3V1T9

  3. NM_001286047.2 → NP_001272976.1  RNA-binding protein 7 isoform c

    See identical proteins and their annotated locations for NP_001272976.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate exon in the 5' region and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus than isoform a. Variants 3, 4, and 5 encode the same isoform (c).
    Source sequence(s)
    AP002373, BC034381, CN308273
    Consensus CDS
    CCDS73395.1
    UniProtKB/TrEMBL
    G3V1T9

  4. NM_001286048.2 → NP_001272977.1  RNA-binding protein 7 isoform c

    See identical proteins and their annotated locations for NP_001272977.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) lacks two alternate exons in the 5' region and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (c) has a shorter N-terminus than isoform a. Variants 3, 4, and 5 encode the same isoform (c).
    Source sequence(s)
    AP002373, BC034381, BQ067937, DA027521
    Consensus CDS
    CCDS73395.1
    UniProtKB/TrEMBL
    G3V1T9
    Related
    ENSP00000445848.1, ENST00000545678.1

  5. NM_016090.4 → NP_057174.1  RNA-binding protein 7 isoform b

    See identical proteins and their annotated locations for NP_057174.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site, compared to variant 1. The encoded isoform (b) is shorter than isoform a.
    Source sequence(s)
    AP002373, BC034381
    Consensus CDS
    CCDS8370.1
    UniProtKB/Swiss-Prot
    B2R6K8, Q9NUT4, Q9Y580
    UniProtKB/TrEMBL
    Q6IRX3
    Related
    ENSP00000439918.1, ENST00000540163.5
    Conserved Domains (2) summary
    cd12592
    Location:9 → 83
    RRM_RBM7; RNA recognition motif in vertebrate RNA-binding protein 7 (RBM7)
    cl25617
    Location:10 → 238
    LSM_int_assoc; LSM-interacting associated unstructured

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_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    114400666..114410607
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    114411085..114421025
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y580.1 GenPept UniProtKB/Swiss-Prot:Q9Y580

Gene LinkOut

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