RBM7 Gene (Protein Coding)

RNA Binding Motif Protein 7

GC11P114401
GIFtS:
38
See more...

Aliases for RBM7 Gene

Aliases for RBM7 Gene

  • RNA Binding Motif Protein 7 2 3 5
  • RNA-Binding Protein 7 3 4
  • RNA-Binding Motif Protein 7 4
  • RBM7 5

External Ids for RBM7 Gene

Previous GeneCards Identifiers for RBM7 Gene

  • GC11P116624
  • GC11P115783
  • GC11P114305
  • GC11P113808
  • GC11P113776
  • GC11P110199
  • GC11P114270

Summaries for RBM7 Gene

GeneCards Summary for RBM7 Gene

RBM7 (RNA Binding Motif Protein 7) is a Protein Coding gene. Diseases associated with RBM7 include Pontocerebellar Hypoplasia. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and nucleotide binding. An important paralog of this gene is ENSG00000255663.

UniProtKB/Swiss-Prot Summary for RBM7 Gene

  • RNA-binding subunit of the trimeric nuclear exosome targeting (NEXT) complex, a complex that functions as an RNA exosome cofactor that directs a subset of non-coding short-lived RNAs for exosomal degradation (PubMed:25189701, PubMed:25578728, PubMed:25525152, PubMed:25852104, PubMed:27871484). NEXT is involved in surveillance and turnover of aberrant transcripts and non-coding RNAs (PubMed:25189701, PubMed:27871484, PubMed:25852104). Binds preferentially polyuridine sequences and associates with newly synthesized RNAs, including pre-mRNAs and short-lived exosome substrates such as promoter upstream transcripts (PROMPTs), enhancer RNAs (eRNAs), and 3'-extended products from small nuclear RNAs (snRNAs) (PubMed:25189701, PubMed:25578728, PubMed:25525152, PubMed:25852104). Participates in several biological processes including DNA damage response (DDR) and stress response (PubMed:25525152, PubMed:30824372). During stress response, activation of the p38MAPK-MK2 pathway decreases RBM7-RNA-binding and subsequently the RNA exosome degradation activities, thereby modulating the turnover of non-coding transcriptome (PubMed:25525152). Participates in DNA damage response (DDR), through its interaction with MEPCE and LARP7, the core subunits of 7SK snRNP complex, that release the positive transcription elongation factor b (P-TEFb) complex from the 7SK snRNP. In turn, activation of P-TEFb complex induces the transcription of P-TEFb-dependent DDR genes to promote cell viability (PubMed:30824372).

Gene Wiki entry for RBM7 Gene

Additional gene information for RBM7 Gene

No data available for Entrez Gene Summary , CIViC Summary , Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RBM7 Gene

Genomics for RBM7 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for RBM7 Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RBM7 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RBM7

Top Transcription factor binding sites by QIAGEN in the RBM7 gene promoter:
  • aMEF-2
  • ATF-2
  • c-Jun
  • CUTL1
  • GATA-1
  • GCNF
  • GCNF-1
  • MEF-2A
  • POU2F1
  • POU2F1a

Genomic Locations for RBM7 Gene

Latest Assembly
chr11:114,400,030-114,414,203
(GRCh38/hg38)
Size:
14,174 bases
Orientation:
Plus strand

Previous Assembly
chr11:114,271,388-114,281,329
(GRCh37/hg19 by Entrez Gene)
Size:
9,942 bases
Orientation:
Plus strand

chr11:114,270,752-114,284,925
(GRCh37/hg19 by Ensembl)
Size:
14,174 bases
Orientation:
Plus strand

Genomic View for RBM7 Gene

Genes around RBM7 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RBM7 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RBM7 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for RBM7 Gene

Proteins for RBM7 Gene

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  • Protein details for RBM7 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y580-RBM7_HUMAN
    Recommended name:
    RNA-binding protein 7
    Protein Accession:
    Q9Y580
    Secondary Accessions:
    • B2R6K8
    • Q9NUT4

    Protein attributes for RBM7 Gene

    Size:
    266 amino acids
    Molecular mass:
    30504 Da
    Quaternary structure:
    • Component of the nuclear exosome targeting (NEXT) complex composed of MTREX, ZCCHC8, and RBM7 that directs a subset of non-coding short-lived RNAs for exosomal degradation (PubMed:27905398, PubMed:27871484, PubMed:25189701). Interacts with ZCCHC8 and SF3B2/SAP145 (PubMed:27905398, PubMed:27871484, PubMed:16263084). Binds to MTREX through ZCCHC8 (PubMed:27871484). Interacts with YWHAE and YWHAZ; these interactions are stress-dependent and RBM7 phosphorylation dependent; release RNA from the NEXT complex and may affect RNA targeting to the nuclear RNA exosomome for degradation (PubMed:25189701). Interacts with MEPCE and LARP7, the core subunits of 7SK snRNP; upon genotoxic stress this interaction is enhanced, triggering the release of inactive P-TEFb complex from the core and P-TEFb complex activation (PubMed:30824372).

    Three dimensional structures from OCA and Proteopedia for RBM7 Gene

neXtProt entry for RBM7 Gene

Protein Expression for RBM7 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for RBM7 Gene

  • Phosphorylated at Ser-136 by MAPK14/p38-alpha-activated MAPKAPK2/MK2; this phosphorylation is stress-dependent; this phosphorylation decreases its RNA-binding capacity therefore affecting RNA nuclear exosome-mediated degradation (PubMed:25525152, PubMed:25189701). This phosphorylation mediates YWHAE and YWHAZ interactions (PubMed:25189701).
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RBM7 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RBM7 Gene

Domains & Families for RBM7 Gene

Gene Families for RBM7 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for RBM7 Gene

InterPro:
Blocks:
  • RNA-binding region RNP-1 (RNA recognition motif)
ProtoNet:

Suggested Antigen Peptide Sequences for RBM7 Gene

GenScript: Design optimal peptide antigens:
  • RNA binding motif protein 7 (Q6IRX3_HUMAN)
  • RNA-binding motif protein 7 (RBM7_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9Y580

UniProtKB/Swiss-Prot:

RBM7_HUMAN :
  • The RRM domain mediates RNA binding; the RNA must have four nucleotides for efficient binding (PubMed:25852104). Mediates the interaction of NEXT complex with promoter upstream transcripts (PROMPTs) and potentially aberrant forms of other non coding RNAs, such as snRNAs (PubMed:25852104). The RRM domain exhibits specificity for polyuridine sequences (PubMed:25852104).
Domain:
  • The RRM domain mediates RNA binding; the RNA must have four nucleotides for efficient binding (PubMed:25852104). Mediates the interaction of NEXT complex with promoter upstream transcripts (PROMPTs) and potentially aberrant forms of other non coding RNAs, such as snRNAs (PubMed:25852104). The RRM domain exhibits specificity for polyuridine sequences (PubMed:25852104).
genes like me logo Genes that share domains with RBM7: view

Function for RBM7 Gene

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  6. Cell Lines for research

Molecular function for RBM7 Gene

UniProtKB/Swiss-Prot Function:
RNA-binding subunit of the trimeric nuclear exosome targeting (NEXT) complex, a complex that functions as an RNA exosome cofactor that directs a subset of non-coding short-lived RNAs for exosomal degradation (PubMed:25189701, PubMed:25578728, PubMed:25525152, PubMed:25852104, PubMed:27871484). NEXT is involved in surveillance and turnover of aberrant transcripts and non-coding RNAs (PubMed:25189701, PubMed:27871484, PubMed:25852104). Binds preferentially polyuridine sequences and associates with newly synthesized RNAs, including pre-mRNAs and short-lived exosome substrates such as promoter upstream transcripts (PROMPTs), enhancer RNAs (eRNAs), and 3'-extended products from small nuclear RNAs (snRNAs) (PubMed:25189701, PubMed:25578728, PubMed:25525152, PubMed:25852104). Participates in several biological processes including DNA damage response (DDR) and stress response (PubMed:25525152, PubMed:30824372). During stress response, activation of the p38MAPK-MK2 pathway decreases RBM7-RNA-binding and subsequently the RNA exosome degradation activities, thereby modulating the turnover of non-coding transcriptome (PubMed:25525152). Participates in DNA damage response (DDR), through its interaction with MEPCE and LARP7, the core subunits of 7SK snRNP complex, that release the positive transcription elongation factor b (P-TEFb) complex from the 7SK snRNP. In turn, activation of P-TEFb complex induces the transcription of P-TEFb-dependent DDR genes to promote cell viability (PubMed:30824372).

Phenotypes From GWAS Catalog for RBM7 Gene

Gene Ontology (GO) - Molecular Function for RBM7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA,IMP 25189701
GO:0003727 single-stranded RNA binding IBA 21873635
GO:0005515 protein binding IPI 16263084
GO:0017069 snRNA binding IDA 25852104
genes like me logo Genes that share ontologies with RBM7: view
genes like me logo Genes that share phenotypes with RBM7: view

Animal Models for research

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RBM7

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RBM7 Gene

Localization for RBM7 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RBM7 Gene

Nucleus, nucleoplasm. Nucleus. Note=Excluded from the nucleolus. {ECO:0000269 PubMed:21855801}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RBM7 gene
Compartment Confidence
nucleus 5
extracellular 2
cytoskeleton 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoplasm (4)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RBM7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA,IDA 21855801
GO:0005654 nucleoplasm IDA 16263084
GO:0005730 NOT nucleolus IDA 21855801
genes like me logo Genes that share ontologies with RBM7: view

Pathways & Interactions for RBM7 Gene

PathCards logo

SuperPathways for RBM7 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RBM7 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000381 regulation of alternative mRNA splicing, via spliceosome IBA 21873635
GO:0016076 snRNA catabolic process IMP 25852104
GO:0051321 meiotic cell cycle IEA --
genes like me logo Genes that share ontologies with RBM7: view

No data available for Pathways by source and SIGNOR curated interactions for RBM7 Gene

Drugs & Compounds for RBM7 Gene

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No Compound Related Data Available

Transcripts for RBM7 Gene

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mRNA/cDNA for RBM7 Gene

5 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
8 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RBM7

Alternative Splicing Database (ASD) splice patterns (SP) for RBM7 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5
SP1: -
SP2: -
SP3: -
SP4: -
SP5:

Relevant External Links for RBM7 Gene

GeneLoc Exon Structure for
RBM7

Expression for RBM7 Gene

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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RBM7 Gene

mRNA expression in normal human tissues for RBM7 Gene
mRNA expression by BioGPS for RBM7 GenemRNA expression by GTEx for RBM7 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for RBM7 Gene

This gene is overexpressed in Lung (39.4) and Peripheral blood mononuclear cells (8.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RBM7 Gene



Protein tissue co-expression partners for RBM7 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RBM7

SOURCE GeneReport for Unigene cluster for RBM7 Gene:

Hs.7527

mRNA Expression by UniProt/SwissProt for RBM7 Gene:

Q9Y580-RBM7_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for RBM7 Gene

  • Nervous system(4.6)
  • Lung(4.3)
  • Liver(4.2)
genes like me logo Genes that share expression patterns with RBM7: view

Primer products for research

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for RBM7 Gene

Orthologs for RBM7 Gene

This gene was present in the common ancestor of animals.

Orthologs for RBM7 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia RBM7 30 31
  • 99.25 (n)
 OneToMany
Cow
(Bos Taurus)
 Mammalia RBM7 30 31
  • 90.46 (n)
 OneToMany
Dog
(Canis familiaris)
 Mammalia -- 31
  • 90 (a)
 OneToMany
RBM7 30
  • 89.06 (n)
Mouse
(Mus musculus)
 Mammalia Rbm7 30 17 31
  • 85.16 (n)
 OneToMany
Rat
(Rattus norvegicus)
 Mammalia Rbm7 30
  • 83.42 (n)
Oppossum
(Monodelphis domestica)
 Mammalia -- 31
  • 75 (a)
 OneToMany
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 31
  • 66 (a)
 OneToMany
Chicken
(Gallus gallus)
 Aves RBM7 30 31
  • 64.57 (n)
 OneToMany
Lizard
(Anolis carolinensis)
 Reptilia -- 31
  • 49 (a)
 OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia LOC101735152 30
  • 69.86 (n)
Str.10735 30
African clawed frog
(Xenopus laevis)
 Amphibia rbm7-prov 30
Zebrafish
(Danio rerio)
 Actinopterygii zgc:77304 30
  • 55.04 (n)
RBM7 31
  • 43 (a)
 OneToMany
wufa03f03 30
Fruit Fly
(Drosophila melanogaster)
 Insecta CG11454 31
  • 22 (a)
 OneToMany
Worm
(Caenorhabditis elegans)
 Secernentea Y37D8A.21 31
  • 23 (a)
 OneToMany
Species where no ortholog for RBM7 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)

Evolution for RBM7 Gene

ENSEMBL:
Gene Tree for RBM7 (if available)
TreeFam:
Gene Tree for RBM7 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RBM7: view image

Paralogs for RBM7 Gene

Paralogs for RBM7 Gene

(6) SIMAP similar genes for RBM7 Gene using alignment to 8 proteins:

  • RBM7_HUMAN
  • F5GXV8_HUMAN
  • F5GY08_HUMAN
  • F5H606_HUMAN
  • F5H674_HUMAN
  • G3V1T9_HUMAN
  • J3KPD3_HUMAN
  • Q6IRX3_HUMAN

Pseudogenes.org Pseudogenes for RBM7 Gene

genes like me logo Genes that share paralogs with RBM7: view

Variants for RBM7 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RBM7 Gene

SNP ID Clinical significance and condition Chr 11 pos Variation AA Info Type
871214 Uncertain Significance: not provided 114,407,683(+) A/G
NM_016090.3(RBM7):c.677A>G (p.His226Arg) 		MISSENSE
VAR_082580 - p.Pro79Arg

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RBM7 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for RBM7 Gene

Variant ID Type Subtype PubMed ID
nsv983063 CNV duplication 23825009

Variation tolerance for RBM7 Gene

Residual Variation Intolerance Score: 29% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.48; 10.42% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RBM7 Gene

Human Gene Mutation Database (HGMD)
RBM7
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RBM7

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RBM7 Gene

Disorders for RBM7 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RBM7 Gene - From: COP

Disorder Aliases PubMed IDs
pontocerebellar hypoplasia
  • pch
- elite association - COSMIC cancer census association via MalaCards
Search RBM7 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RBM7

Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with RBM7: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RBM7 Gene

Publications for RBM7 Gene

  1. RBM7 subunit of the NEXT complex binds U-rich sequences and targets 3'-end extended forms of snRNAs. (PMID: 25852104) Hrossova D … Vanacova S (Nucleic acids research 2015) 2 3 4
  2. P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress. (PMID: 30824372) Bugai A … Barborič M (Molecular cell 2019) 3 4
  3. Identification of a Nuclear Exosome Decay Pathway for Processed Transcripts. (PMID: 27871484) Meola N … Jensen TH (Molecular cell 2016) 3 4
  4. Structure of the RBM7-ZCCHC8 core of the NEXT complex reveals connections to splicing factors. (PMID: 27905398) Falk S … Conti E (Nature communications 2016) 3 4
  5. Altered RNA metabolism due to a homozygous RBM7 mutation in a patient with spinal motor neuropathy. (PMID: 27193168) Giunta M … Horvath R (Human molecular genetics 2016) 3 4

ExternalLinks

View latest publications for RBM7 gene in Mastermind

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