Aliases for RBM47 Gene

Aliases for RBM47 Gene

  • RNA Binding Motif Protein 47 2 3 5
  • RNA-Binding Protein 47 3 4
  • NET18 2 3
  • RNA-Binding Motif Protein 47 4
  • FLJ20273 2
  • RBM47 5

External Ids for RBM47 Gene

Previous GeneCards Identifiers for RBM47 Gene

  • GC04M040121
  • GC04M039747

Summaries for RBM47 Gene

GeneCards Summary for RBM47 Gene

RBM47 (RNA Binding Motif Protein 47) is a Protein Coding gene. Diseases associated with RBM47 include Lung Acinar Adenocarcinoma. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and nucleotide binding. An important paralog of this gene is A1CF.

Additional gene information for RBM47 Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RBM47 Gene

Genomics for RBM47 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RBM47 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH04J040625 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas dbSUPER 600.7 +1.9 1917 7.2 PRDM10 POLR2A BACH1 TARDBP ZHX2 FOXA1 LARP7 PRDM1 ZIC2 PATZ1 RBM47 lnc-APBB2-3 UCHL1 MN298107 CHRNA9
GH04J040510 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 600.1 +116.9 116894 7.2 HNRNPL REST LEF1 NFKBIZ ZNF692 JUND PRDM1 ZNF143 RELA PKNOX1 RBM47 PDS5A RNU7-74P FJ601666-055 piR-57460-518 CHRNA9
GH04J040572 Enhancer 1.4 FANTOM5 ENCODE dbSUPER 24.8 +55.3 55265 6.8 RNF2 GATAD2A REST TFE3 ZNF512 RFX1 LEF1 SOX13 IKZF1 KDM1A RBM47 PDS5A N4BP2 CHRNA9 ENSG00000250906 RNU7-74P NSUN7 piR-43105-488 piR-55985-141 lnc-APBB2-3
GH04J040584 Enhancer 1.3 FANTOM5 Ensembl ENCODE dbSUPER 23.7 +42.8 42810 8.6 FOXA1 SP1 TOE1 SCRT2 CEBPB FOXA2 RAD51 ZBTB40 FOS YY1 RBM47 RNU7-74P CHRNA9 MN298107 piR-43105-488 piR-43107-235 lnc-APBB2-3
GH04J040721 Enhancer 1.2 FANTOM5 ENCODE dbSUPER 25.2 -91.9 -91850 3 POLR2A ETV6 PKNOX1 EP300 HMBOX1 RUNX3 CTBP1 FOXA2 ZBTB40 NR2C2 RBM47 ENSG00000250906 CHRNA9 RNU7-74P NSUN7 lnc-RBM47-1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RBM47 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RBM47

Top Transcription factor binding sites by QIAGEN in the RBM47 gene promoter:
  • C/EBPalpha
  • GATA-3
  • HOXA3
  • Ik-2
  • IRF-1
  • NF-kappaB
  • NF-kappaB1
  • NF-kappaB2
  • S8
  • STAT5B

Genomic Locations for RBM47 Gene

Genomic Locations for RBM47 Gene
chr4:40,423,267-40,630,911
(GRCh38/hg38)
Size:
207,645 bases
Orientation:
Minus strand
chr4:40,425,272-40,632,892
(GRCh37/hg19)
Size:
207,621 bases
Orientation:
Minus strand

Genomic View for RBM47 Gene

Genes around RBM47 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RBM47 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RBM47 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RBM47 Gene

Proteins for RBM47 Gene

  • Protein details for RBM47 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    A0AV96-RBM47_HUMAN
    Recommended name:
    RNA-binding protein 47
    Protein Accession:
    A0AV96
    Secondary Accessions:
    • A0PJK2
    • B5MED4
    • Q8NI52
    • Q8NI53
    • Q9NXG3

    Protein attributes for RBM47 Gene

    Size:
    593 amino acids
    Molecular mass:
    64099 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=AAM21973.1; Type=Frameshift; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RBM47 Gene

    Alternative splice isoforms for RBM47 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RBM47 Gene

Post-translational modifications for RBM47 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for RBM47 Gene

Domains & Families for RBM47 Gene

Gene Families for RBM47 Gene

Suggested Antigen Peptide Sequences for RBM47 Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ51456, moderately similar to APOBEC1 complementation factor (B7Z8Z7_HUMAN)
  • RNA binding motif protein 47 (B7ZLP7_HUMAN)
  • RNA-binding motif protein 47 (RBM47_HUMAN)

Graphical View of Domain Structure for InterPro Entry

A0AV96

UniProtKB/Swiss-Prot:

RBM47_HUMAN :
  • Belongs to the RRM RBM47 family.
Family:
  • Belongs to the RRM RBM47 family.
genes like me logo Genes that share domains with RBM47: view

Function for RBM47 Gene

Phenotypes From GWAS Catalog for RBM47 Gene

Gene Ontology (GO) - Molecular Function for RBM47 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA,IBA 21873635
GO:0003729 mRNA binding IBA 21873635
genes like me logo Genes that share ontologies with RBM47: view
genes like me logo Genes that share phenotypes with RBM47: view

Animal Model Products

CRISPR Products

miRNA for RBM47 Gene

miRTarBase miRNAs that target RBM47

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RBM47

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RBM47 Gene

Localization for RBM47 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RBM47 Gene

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 RBM47 gene
Compartment Confidence
nucleus 5
cytosol 2
plasma membrane 1
extracellular 1
cytoskeleton 1
mitochondrion 1
peroxisome 1
lysosome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RBM47 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IBA 21873635
genes like me logo Genes that share ontologies with RBM47: view

Pathways & Interactions for RBM47 Gene

PathCards logo

SuperPathways for RBM47 Gene

No Data Available

Gene Ontology (GO) - Biological Process for RBM47 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002244 hematopoietic progenitor cell differentiation IEA --
GO:0016554 cytidine to uridine editing IEA --
genes like me logo Genes that share ontologies with RBM47: view

No data available for Pathways by source and SIGNOR curated interactions for RBM47 Gene

Drugs & Compounds for RBM47 Gene

No Compound Related Data Available

Transcripts for RBM47 Gene

mRNA/cDNA for RBM47 Gene

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

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RBM47

Alternative Splicing Database (ASD) splice patterns (SP) for RBM47 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7 ^ 8a · 8b ^ 9
SP1: - - - - -
SP2: -
SP3: - -
SP4: -
SP5:
SP6: -

Relevant External Links for RBM47 Gene

GeneLoc Exon Structure for
RBM47

Expression for RBM47 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RBM47 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RBM47 Gene

This gene is overexpressed in Colon - Transverse (x4.9), Adrenal Gland (x4.5), and Whole Blood (x4.0).

Protein differential expression in normal tissues from HIPED for RBM47 Gene

This gene is overexpressed in Cervix (17.2) and Salivary gland (10.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RBM47 Gene



Protein tissue co-expression partners for RBM47 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RBM47

SOURCE GeneReport for Unigene cluster for RBM47 Gene:

Hs.518727

Evidence on tissue expression from TISSUES for RBM47 Gene

  • Lung(4.4)
  • Nervous system(4.3)
  • Kidney(3.2)
  • Intestine(2.7)
  • Liver(2.1)
  • Blood(2.1)
  • Thyroid gland(2)
genes like me logo Genes that share expression patterns with RBM47: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for RBM47 Gene

Orthologs for RBM47 Gene

This gene was present in the common ancestor of animals.

Orthologs for RBM47 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia RBM47 30 31
  • 99.44 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia DKFZP686F02235 31
  • 98 (a)
OneToOne
RBM47 30
  • 92.02 (n)
Oppossum
(Monodelphis domestica)
Mammalia -- 31
  • 92 (a)
OneToMany
-- 31
  • 82 (a)
OneToMany
-- 31
  • 82 (a)
OneToMany
Dog
(Canis familiaris)
Mammalia RBM47 30 31
  • 91.65 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia RBM47 31
  • 89 (a)
OneToOne
Mouse
(Mus musculus)
Mammalia Rbm47 30 17 31
  • 87.41 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Rbm47 30
  • 86.62 (n)
Chicken
(Gallus gallus)
Aves RBM47 30 31
  • 80.17 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RBM47 31
  • 87 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia rbm47 30
  • 70.63 (n)
Zebrafish
(Danio rerio)
Actinopterygii RBM47 31
  • 78 (a)
OneToOne
rbm47 30
  • 73.08 (n)
Fruit Fly
(Drosophila melanogaster)
Insecta CG17838 31
  • 28 (a)
OneToMany
Worm
(Caenorhabditis elegans)
Secernentea hrp-2 31
  • 29 (a)
OneToMany
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 50 (a)
OneToOne
Species where no ortholog for RBM47 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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 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 RBM47 Gene

ENSEMBL:
Gene Tree for RBM47 (if available)
TreeFam:
Gene Tree for RBM47 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RBM47: view image

Paralogs for RBM47 Gene

(10) SIMAP similar genes for RBM47 Gene using alignment to 11 proteins:

  • RBM47_HUMAN
  • B7Z8Z7_HUMAN
  • B7ZLP7_HUMAN
  • D6R9D6_HUMAN
  • D6R9M7_HUMAN
  • D6RA49_HUMAN
  • D6RBP6_HUMAN
  • D6RBS9_HUMAN
  • D6RCT1_HUMAN
  • D6REZ6_HUMAN
  • D6RFL5_HUMAN
genes like me logo Genes that share paralogs with RBM47: view

Variants for RBM47 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RBM47 Gene

SNP ID Clinical significance and condition Chr 04 pos Variation AA Info Type
769204 Benign: not provided 40,436,559(-) A/. NO_SEQUENCE_ALTERATION,INTRON_VARIANT
780461 Benign: not provided 40,432,846(-) A/G SYNONYMOUS_VARIANT
rs278981 - p.Met565Val
rs35529250 - p.Gly538Arg

Additional dbSNP identifiers (rs#s) for RBM47 Gene

Structural Variations from Database of Genomic Variants (DGV) for RBM47 Gene

Variant ID Type Subtype PubMed ID
dgv935e199 CNV deletion 23128226
dgv936e199 CNV deletion 23128226
esv2661897 CNV deletion 23128226
esv2759248 CNV loss 17122850
esv3563750 CNV deletion 23714750
esv3569394 CNV loss 25503493
esv3600305 CNV loss 21293372
esv3600306 CNV loss 21293372
esv3600307 CNV loss 21293372
esv3600309 CNV loss 21293372
esv3600310 CNV loss 21293372
esv3600311 CNV loss 21293372
esv3600312 CNV loss 21293372
esv3600313 CNV loss 21293372
nsv10482 CNV loss 18304495
nsv10484 CNV loss 18304495
nsv1071974 CNV deletion 25765185
nsv1117074 CNV deletion 24896259
nsv829910 CNV loss 17160897
nsv997983 CNV gain 25217958

Variation tolerance for RBM47 Gene

Residual Variation Intolerance Score: 15.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.12; 38.58% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RBM47 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
RBM47

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RBM47 Gene

Disorders for RBM47 Gene

MalaCards: The human disease database

(1) MalaCards diseases for RBM47 Gene - From: DISEASES

Disorder Aliases PubMed IDs
lung acinar adenocarcinoma
  • acinar adenocarcinoma of the lung
- elite association - COSMIC cancer census association via MalaCards
Search RBM47 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RBM47

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with RBM47: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RBM47 Gene

Publications for RBM47 Gene

  1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 41
  2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  3. A reference map of the human binary protein interactome. (PMID: 32296183) Luck K … Calderwood MA (Nature 2020) 3
  4. Distinct genome-wide methylation patterns in sporadic and hereditary nonfunctioning pancreatic neuroendocrine tumors. (PMID: 30620390) Tirosh A … Kebebew E (Cancer 2019) 3
  5. RBM47-regulated alternative splicing of TJP1 promotes actin stress fiber assembly during epithelial-to-mesenchymal transition. (PMID: 31358901) Kim YE … Kim KK (Oncogene 2019) 3

Products for RBM47 Gene

Sources for RBM47 Gene