Free for academic non-profit institutions. Other users need a Commercial license

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 Growth Hormone Deficiency, Isolated, Type Ia and Mixed Connective Tissue Disease. Among its related pathways are Gene Expression and mRNA Splicing - Major Pathway. 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.

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

Regulatory Elements for RNPC3 Gene

Enhancers for RNPC3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01G103561 0.8 Ensembl ENCODE 12.3 +36.2 36211 1.4 ZNF316 RAD51 RBBP5 HNF4A ZBTB33 RELB FOXA1 AMY2B RN7SKP285 RNPC3 LOC101928436 ACTG1P4
GH01G103562 0.2 Ensembl 12.3 +37.2 37210 0.2 LOC101928436 RN7SKP285 RNPC3 AMY2B ACTG1P4
GH01G103524 1 ENCODE 0.7 +0.1 73 2.5 PKNOX1 ATF1 CREB3L1 ARID4B SIN3A DMAP1 BRCA1 YY1 ZNF143 ZNF263 AMY2B RNPC3 GC01M103512
GH01G103529 0.5 ENCODE 0.7 +4.3 4283 0.2 PKNOX1 BHLHE40 SCRT2 ZKSCAN1 RNPC3 GC01M103512
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around RNPC3 on UCSC Golden Path with GeneCards custom track

Promoters for RNPC3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000010814 609 2601 PKNOX1 ATF1 CREB3L1 ARID4B SIN3A DMAP1 BRCA1 YY1 ZNF143 FOS

Genomic Location for RNPC3 Gene

Chromosome:
1
Start:
103,525,691 bp from pter
End:
103,555,239 bp from pter
Size:
29,549 bases
Orientation:
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:
    Q96LT9-RBM40_HUMAN
    Recommended name:
    RNA-binding protein 40
    Protein Accession:
    Q96LT9
    Secondary Accessions:
    • A8K1C9
    • D3DT74
    • Q5TZ87
    • Q96FK7
    • Q96JI8
    • Q9NSU7
    • Q9NXX2

    Protein attributes for RNPC3 Gene

    Size:
    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.
    SequenceCaution:
    • 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

    UniProtKB/Swiss-Prot:

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: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

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , 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

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 RNPC3 gene
Compartment Confidence
nucleus 5
cytosol 2

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 IC,IEA 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

(24) Drugs for RNPC3 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(14) 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

Unigene Clusters for RNPC3 Gene

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

Inhibitory RNA Products

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
RNPC3
ECgene alternative splicing isoforms for
RNPC3

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, PaxDb, MaxQB, and MOPED for RNPC3 Gene



Protein tissue co-expression partners for RNPC3 Gene

NURSA nuclear receptor signaling pathways regulating expression of RNPC3 Gene:

RNPC3

SOURCE GeneReport for Unigene cluster for RNPC3 Gene:

Hs.632423

mRNA Expression by UniProt/SwissProt for RNPC3 Gene:

Q96LT9-RBM40_HUMAN
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

Primer Products

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
chimpanzee
(Pan troglodytes)
Mammalia RNPC3 34 35
  • 99.68 (n)
dog
(Canis familiaris)
Mammalia RNPC3 34 35
  • 92.05 (n)
cow
(Bos Taurus)
Mammalia RNPC3 34 35
  • 91.73 (n)
mouse
(Mus musculus)
Mammalia Rnpc3 34 16 35
  • 87.29 (n)
rat
(Rattus norvegicus)
Mammalia Rnpc3 34
  • 85.37 (n)
oppossum
(Monodelphis domestica)
Mammalia RNPC3 35
  • 79 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia RNPC3 35
  • 79 (a)
OneToOne
chicken
(Gallus gallus)
Aves RNPC3 34 35
  • 74.33 (n)
lizard
(Anolis carolinensis)
Reptilia RNPC3 35
  • 70 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia rnpc3 34
  • 63.5 (n)
Str.10852 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.33695 34
zebrafish
(Danio rerio)
Actinopterygii rnpc3 34 35
  • 62.31 (n)
fruit fly
(Drosophila melanogaster)
Insecta Snp 35
  • 24 (a)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 35
  • 39 (a)
OneToOne
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

ENSEMBL:
Gene Tree for RNPC3 (if available)
TreeFam:
Gene Tree for RNPC3 (if available)

Paralogs for RNPC3 Gene

Paralogs for RNPC3 Gene

Pseudogenes.org 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 Sequence Context AA Info Type
rs1000236203 -- 103,545,753(+) CTGAT(A/T)CTGTG intron-variant
rs1000245960 -- 103,546,154(+) TTTGT(C/G)TATTT intron-variant
rs1000284333 -- 103,525,216(+) TCTGC(A/G)AAATG intron-variant, upstream-variant-2KB
rs1000329519 -- 103,531,550(+) GGAGT(A/G)AGGAG intron-variant
rs1000334564 -- 103,527,483(+) TATAT(C/G)ATAGA intron-variant, upstream-variant-2KB

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)

Relevant External Links for RNPC3 Gene

Human Gene Mutation Database (HGMD)
RNPC3
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RNPC3

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

Disorders for RNPC3 Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
growth hormone deficiency, isolated, type ia
  • isolated growth hormone deficiency, type ia
mixed connective tissue disease
  • connective tissue disease overlap syndrome
rheumatic disease
  • collagen diseases
parainfluenza virus type 3
  • human parainfluenza virus type 3
microcephalic osteodysplastic primordial dwarfism, type i
  • microcephalic osteodysplastic primordial dwarfism type i
- elite association - COSMIC cancer census association via MalaCards
Search RNPC3 in MalaCards View complete list of genes associated with diseases

Relevant External Links for RNPC3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
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 C.L. … Luehrmann R. (RNA 2004) 2 3 4 64
  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. (Biochem. Genet. 2003) 2 3 4 64
  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 C.L. (EMBO J. 2005) 3 4 64
  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 Res. 2001) 3 4 64
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3 64

Products for RNPC3 Gene

Sources for RNPC3 Gene

Content
Loading form....