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Aliases for RNPC3 Gene

Aliases for RNPC3 Gene

  • RNA Binding Region (RNP1, RRM) Containing 3 2 3 5
  • U11/U12 Small Nuclear Ribonucleoprotein 65 KDa Protein 3 4
  • RNA-Binding Region-Containing Protein 3 3 4
  • RNA-Binding Motif Protein 40 3 4
  • U11/U12 SnRNP 65 KDa Protein 3 4
  • U11/U12 SnRNP 65K 2 3
  • U11/U12-65K 3 4
  • RBM40 3 4
  • RNP 3 4
  • RNA-Binding Protein 40 3
  • KIAA1839 4
  • SNRNP65 3

External Ids for RNPC3 Gene

Previous GeneCards Identifiers for RNPC3 Gene

  • GC00U991276
  • GC01P103782
  • GC01P103893
  • GC01P104068
  • GC01P102123

Summaries for RNPC3 Gene

Entrez Gene Summary for RNPC3 Gene

  • Two types of spliceosomes catalyze splicing of pre-mRNAs. The major U2-type spliceosome is found in all eukaryotes and removes U2-type introns, which represent more than 99% of pre-mRNA introns. The minor U12-type spliceosome is found in some eukaryotes and removes U12-type introns, which are rare and have distinct splice consensus signals. The U12-type spliceosome consists of several small nuclear RNAs and associated proteins. This gene encodes a 65K protein that is a component of the U12-type spliceosome. This protein contains two RNA recognition motifs (RRMs), suggesting that it may contact one of the small nuclear RNAs of the minor spliceosome. [provided by RefSeq, Jul 2008]

GeneCards Summary for RNPC3 Gene

RNPC3 (RNA Binding Region (RNP1, RRM) Containing 3) is a Protein Coding gene. Diseases associated with RNPC3 include Isolated Growth Hormone Deficiency, Type Ia and Mixed Connective Tissue Disease. Among its related pathways are mRNA Splicing - Major Pathway and mRNA Splicing - Minor Pathway. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and nucleotide binding. An important paralog of this gene is RBM41.

UniProtKB/Swiss-Prot for RNPC3 Gene

  • Participates in pre-mRNA U12-dependent splicing, performed by the minor spliceosome which removes U12-type introns. U12-type introns comprises less than 1% of all non-coding sequences. Binds to the 3-stem-loop of m(7)G-capped U12 snRNA.

Additional gene information for RNPC3 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RNPC3 Gene

Genomics for RNPC3 Gene

GeneHancer (GH) Regulatory Elements for RNPC3 Gene

Promoters and enhancers for RNPC3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J103524 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.7 +0.4 366 3.1 PKNOX1 ATF1 SMAD1 ARID4B SIN3A DMAP1 BRCA1 YY1 POLR2B ZNF143 LOC101928436 RNPC3 AMY2B GC01M103512
GH01J103561 Enhancer 0.8 Ensembl ENCODE 12.3 +36.2 36210 1.4 FOXA2 RXRA RBBP5 MEF2B FOXA1 SP1 HNF4A ZBTB33 RUNX3 AMY2B RNPC3 LOC101928436 RN7SKP285 ACTG1P4
GH01J103562 Enhancer 0.2 Ensembl 12.3 +37.2 37210 0.2 RNPC3 LOC101928436 RN7SKP285 ACTG1P4 AMY2B
GH01J103529 Enhancer 0.4 ENCODE 0.7 +4.3 4283 0.2 PKNOX1 SCRT2 ZKSCAN1 RNPC3 GC01M103512
GH01J103554 Promoter 0.5 EPDnew 0.3 +29.3 29307 0.1 AMY2B ACTG1P4 RNPC3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RNPC3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RNPC3 gene promoter:
  • E47
  • GATA-3
  • GATA-2
  • GATA-1
  • FOXJ2
  • FOXJ2 (long isoform)
  • AP-2gamma
  • AP-2beta
  • AP-2alphaA
  • AP-2alpha

Genomic Locations for RNPC3 Gene

Genomic Locations for RNPC3 Gene
29,549 bases
Plus strand
29,549 bases
Plus strand

Genomic View for RNPC3 Gene

Genes around RNPC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RNPC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RNPC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RNPC3 Gene

Proteins for RNPC3 Gene

  • Protein details for RNPC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    RNA-binding protein 40
    Protein Accession:
    Secondary Accessions:
    • A8K1C9
    • D3DT74
    • Q5TZ87
    • Q96FK7
    • Q96JI8
    • Q9NSU7
    • Q9NXX2

    Protein attributes for RNPC3 Gene

    517 amino acids
    Molecular mass:
    58575 Da
    Quaternary structure:
    • Component of the U11/U12 snRNPs that are part of the U12-type spliceosome. Found in a complex with m(7)G-capped U12 snRNA. Interacts with PDCD7.
    • Sequence=BAA90885.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAA90885.1; Type=Miscellaneous discrepancy; Note=Potential poly-A sequence.; Evidence={ECO:0000305}; Sequence=BAB47468.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for RNPC3 Gene

    Alternative splice isoforms for RNPC3 Gene


neXtProt entry for RNPC3 Gene

Post-translational modifications for RNPC3 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for RNPC3 Gene

No data available for DME Specific Peptides for RNPC3 Gene

Domains & Families for RNPC3 Gene

Gene Families for RNPC3 Gene

Suggested Antigen Peptide Sequences for RNPC3 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with RNPC3: view

No data available for UniProtKB/Swiss-Prot for RNPC3 Gene

Function for RNPC3 Gene

Molecular function for RNPC3 Gene

UniProtKB/Swiss-Prot Function:
Participates in pre-mRNA U12-dependent splicing, performed by the minor spliceosome which removes U12-type introns. U12-type introns comprises less than 1% of all non-coding sequences. Binds to the 3-stem-loop of m(7)G-capped U12 snRNA.

Gene Ontology (GO) - Molecular Function for RNPC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0003723 RNA binding IEA --
GO:0005515 protein binding IEA --
GO:0030626 U12 snRNA binding IBA --
GO:0097157 pre-mRNA intronic binding IBA --
genes like me logo Genes that share ontologies with RNPC3: view
genes like me logo Genes that share phenotypes with RNPC3: view

Animal Model Products

miRNA for RNPC3 Gene

miRTarBase miRNAs that target RNPC3

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for RNPC3 Gene

Localization for RNPC3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for RNPC3 Gene

Subcellular locations from

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 RNPC3 gene
Compartment Confidence
nucleus 5
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for RNPC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 18559850
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
GO:0005689 U12-type spliceosomal complex IDA 15146077
genes like me logo Genes that share ontologies with RNPC3: view

Pathways & Interactions for RNPC3 Gene

genes like me logo Genes that share pathways with RNPC3: view

Pathways by source for RNPC3 Gene

Gene Ontology (GO) - Biological Process for RNPC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006397 mRNA processing IEA --
GO:0008380 RNA splicing IEA,IC 15146077
GO:0032502 developmental process IBA --
genes like me logo Genes that share ontologies with RNPC3: view

No data available for SIGNOR curated interactions for RNPC3 Gene

Drugs & Compounds for RNPC3 Gene

(25) Drugs for RNPC3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(13) Additional Compounds for RNPC3 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with RNPC3: view

Transcripts for RNPC3 Gene

mRNA/cDNA for RNPC3 Gene

(1) REFSEQ mRNAs :
(5) Additional mRNA sequences :
(222) Selected AceView cDNA sequences:
(9) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for RNPC3 Gene

RNA-binding region (RNP1, RRM) containing 3:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RNPC3 Gene

No ASD Table

Relevant External Links for RNPC3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for RNPC3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RNPC3 Gene

Protein differential expression in normal tissues from HIPED for RNPC3 Gene

This gene is overexpressed in Salivary gland (64.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RNPC3 Gene

Protein tissue co-expression partners for RNPC3 Gene

NURSA nuclear receptor signaling pathways regulating expression of RNPC3 Gene:


SOURCE GeneReport for Unigene cluster for RNPC3 Gene:


mRNA Expression by UniProt/SwissProt for RNPC3 Gene:

Tissue specificity: Highly expressed in pancreas and kidney. Detected at lower levels in heart, brain, placenta, lung, liver, spleen, thymus, prostate, testis, ovary, small intestine, colon and leukocytes.

Evidence on tissue expression from TISSUES for RNPC3 Gene

  • Nervous system(4.6)
  • Eye(4.1)
  • Liver(4.1)
genes like me logo Genes that share expression patterns with RNPC3: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for RNPC3 Gene

Orthologs for RNPC3 Gene

This gene was present in the common ancestor of animals.

Orthologs for RNPC3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia RNPC3 34 33
  • 99.68 (n)
(Canis familiaris)
Mammalia RNPC3 34 33
  • 92.05 (n)
(Bos Taurus)
Mammalia RNPC3 34 33
  • 91.73 (n)
(Mus musculus)
Mammalia Rnpc3 16 34 33
  • 87.29 (n)
(Rattus norvegicus)
Mammalia Rnpc3 33
  • 85.37 (n)
(Ornithorhynchus anatinus)
Mammalia RNPC3 34
  • 79 (a)
(Monodelphis domestica)
Mammalia RNPC3 34
  • 79 (a)
(Gallus gallus)
Aves RNPC3 34 33
  • 74.33 (n)
(Anolis carolinensis)
Reptilia RNPC3 34
  • 70 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia rnpc3 33
  • 63.5 (n)
Str.10852 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.33695 33
(Danio rerio)
Actinopterygii rnpc3 34 33
  • 62.31 (n)
fruit fly
(Drosophila melanogaster)
Insecta Snp 34
  • 24 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 39 (a)
Species where no ortholog for RNPC3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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 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)
  • worm (Caenorhabditis elegans)

Evolution for RNPC3 Gene

Gene Tree for RNPC3 (if available)
Gene Tree for RNPC3 (if available)
Evolutionary constrained regions (ECRs) for RNPC3: view image

Paralogs for RNPC3 Gene

Paralogs for RNPC3 Gene Pseudogenes for RNPC3 Gene

genes like me logo Genes that share paralogs with RNPC3: view

Variants for RNPC3 Gene

Sequence variations from dbSNP and Humsavar for RNPC3 Gene

SNP ID Clin Chr 01 pos Variation AA Info Type
rs1000236203 -- 103,545,753(+) A/T intron_variant
rs1000245960 -- 103,546,154(+) C/G intron_variant
rs1000284333 -- 103,525,216(+) G/A upstream_transcript_variant
rs1000329519 -- 103,531,550(+) A/G intron_variant
rs1000334564 -- 103,527,483(+) G/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for RNPC3 Gene

Variant ID Type Subtype PubMed ID
dgv14n21 CNV gain 19592680
dgv213n100 CNV gain 25217958
dgv390n54 CNV loss 21841781
dgv391n54 CNV loss 21841781
dgv392n54 CNV gain 21841781
esv27438 CNV gain 19812545
esv2758954 CNV gain+loss 17122850
esv3583026 CNV gain 25503493
esv3893856 CNV gain+loss 25118596
nsv428157 CNV gain+loss 18775914
nsv523177 CNV gain 19592680
nsv526367 CNV gain 19592680
nsv546939 CNV loss 21841781
nsv546940 CNV loss 21841781
nsv546944 CNV loss 21841781
nsv830904 CNV loss 17160897
nsv830915 CNV gain+loss 17160897
nsv946105 CNV duplication 23825009

Variation tolerance for RNPC3 Gene

Gene Damage Index Score: 1.13; 22.97% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RNPC3 Gene

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

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RNPC3 Gene

Disorders for RNPC3 Gene

MalaCards: The human disease database

(8) MalaCards diseases for RNPC3 Gene - From: HGMD, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
isolated growth hormone deficiency, type ia
  • ighd1a
mixed connective tissue disease
  • connective tissue disease overlap syndrome
rheumatic disease
  • collagen diseases
microcephalic osteodysplastic primordial dwarfism, type i
  • mopd1
primary sjögren syndrome
  • primary sjögren-gougerot syndrome
- elite association - COSMIC cancer census association via MalaCards
Search RNPC3 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for RNPC3

genes like me logo Genes that share disorders with RNPC3: view

No data available for UniProtKB/Swiss-Prot and Genatlas for RNPC3 Gene

Publications for RNPC3 Gene

  1. The human 18S U11/U12 snRNP contains a set of novel proteins not found in the U2-dependent spliceosome. (PMID: 15146077) Will CL … Lührmann R (RNA (New York, N.Y.) 2004) 2 3 4 58
  2. Cloning and identification of a novel human RNPC3 gene that encodes a protein with two RRM domains and is expressed in the cell nucleus. (PMID: 14974681) Zhao E … Mao Y (Biochemical genetics 2003) 2 3 4 58
  3. The U11/U12 snRNP 65K protein acts as a molecular bridge, binding the U12 snRNA and U11-59K protein. (PMID: 16096647) Benecke H … Will CL (The EMBO journal 2005) 3 4 58
  4. Prediction of the coding sequences of unidentified human genes. XX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 11347906) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2001) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for RNPC3 Gene

Sources for RNPC3 Gene

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