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

    Gene ID: 10179, updated on 2-Nov-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, Nov 2024]
    Expression
    Ubiquitous expression in bone marrow (RPKM 12.9), urinary bladder (RPKM 8.3) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See RBM7 in Genome Data Viewer
    Location:
    11q23.2
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (114400666..114410607)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (114411085..114421025)
    RS_2024_09 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 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. 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
    4. 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
    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 (85) 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_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
      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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