Human Gene RNPC3 (ENST00000423855.7_11) from GENCODE V47lift37
  Description: RNA binding region (RNP1, RRM) containing 3 (from RefSeq NM_017619.4)
Gencode Transcript: ENST00000423855.7_11
Gencode Gene: ENSG00000185946.16_13
Transcript (Including UTRs)
   Position: hg19 chr1:104,068,321-104,097,861 Size: 29,541 Total Exon Count: 15 Strand: +
Coding Region
   Position: hg19 chr1:104,068,693-104,094,402 Size: 25,710 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:104,068,321-104,097,861)mRNA (may differ from genome)Protein (517 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RBM40_HUMAN
DESCRIPTION: RecName: Full=RNA-binding protein 40; AltName: Full=RNA-binding motif protein 40; AltName: Full=RNA-binding region-containing protein 3; AltName: Full=U11/U12 small nuclear ribonucleoprotein 65 kDa protein; Short=U11/U12 snRNP 65 kDa protein; Short=U11/U12-65K;
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.
SUBUNIT: 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.
SUBCELLULAR LOCATION: Nucleus.
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.
SIMILARITY: Contains 2 RRM (RNA recognition motif) domains.
SEQUENCE CAUTION: Sequence=BAA90885.1; Type=Erroneous initiation; Note=Translation N-terminally extended; Sequence=BAA90885.1; Type=Miscellaneous discrepancy; Note=Potential poly-A sequence; Sequence=BAB47468.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: RNPC3
Diseases sorted by gene-association score: growth hormone deficiency, isolated, type ia* (145), mixed connective tissue disease (28), rheumatic disease (15), microcephalic osteodysplastic primordial dwarfism, type i (12), connective tissue disease (7), rabies (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 30.59 RPKM in Thyroid
Total median expression: 683.28 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -100.90372-0.271 Picture PostScript Text
3' UTR -34.40218-0.158 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR012677 - Nucleotide-bd_a/b_plait
IPR000504 - RRM_dom

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)

SCOP Domains:
54928 - RNA-binding domain, RBD

Protein Data Bank (PDB) 3-D Structure
MuPIT help
3EGN - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q96LT9
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0030626 U12 snRNA binding
GO:0097157 pre-mRNA intronic binding

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:0032502 developmental process

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005689 U12-type spliceosomal complex


-  Descriptions from all associated GenBank mRNAs
  AK289844 - Homo sapiens cDNA FLJ77710 complete cds.
AB058742 - Homo sapiens KIAA1839 mRNA for KIAA1839 protein.
AY099329 - Homo sapiens RNA recognition protein (RNP) mRNA, complete cds.
AK057799 - Homo sapiens cDNA FLJ25070 fis, clone CBL05164.
BC010697 - Homo sapiens RNA-binding region (RNP1, RRM) containing 3, mRNA (cDNA clone MGC:9935 IMAGE:3873751), complete cds.
AB463239 - Synthetic construct DNA, clone: pF1KA1839, Homo sapiens RNPC3 gene for RNA-binding region (RNP1, RRM) containing 3, without stop codon, in Flexi system.
AL832291 - Homo sapiens mRNA; cDNA DKFZp667O0118 (from clone DKFZp667O0118).
AL137730 - Homo sapiens mRNA; cDNA DKFZp434I1820 (from clone DKFZp434I1820).
AK000015 - Homo sapiens cDNA FLJ20008 fis, clone ADKA03052.
CU679795 - Synthetic construct Homo sapiens gateway clone IMAGE:100018657 5' read RNPC3 mRNA.
KJ902835 - Synthetic construct Homo sapiens clone ccsbBroadEn_12229 RNPC3 gene, encodes complete protein.
AK095605 - Homo sapiens cDNA FLJ38286 fis, clone FCBBF3008153, highly similar to ALPHA-AMYLASE 2B PRECURSOR (EC 3.2.1.1).
BC011179 - Homo sapiens amylase, alpha 2B (pancreatic), mRNA (cDNA clone MGC:17195 IMAGE:4150646), complete cds.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q96LT9 (Reactome details) participates in the following event(s):

R-HSA-75080 Formation of AT-AC A complex
R-HSA-75083 ATAC spliceosome mediated 3' splice site cleavage, exon ligation
R-HSA-75081 Formation of AT-AC B Complex
R-HSA-75082 ATAC spliceosome mediated Lariat formation,5' splice site cleavage
R-HSA-75079 Formation of AT-AC C complex
R-HSA-72165 mRNA Splicing - Minor Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: A8K1C9, D3DT74, ENST00000423855.1, ENST00000423855.2, ENST00000423855.3, ENST00000423855.4, ENST00000423855.5, ENST00000423855.6, KIAA1839, NM_017619, Q5TZ87, Q96FK7, Q96JI8, Q96LT9, Q9NSU7, Q9NXX2, RBM40, RNP, RNPC3_HUMAN, SNRNP65, uc319tdf.1, uc319tdf.2
UCSC ID: ENST00000423855.7_11
RefSeq Accession: NM_017619.4
Protein: Q96LT9 (aka RBM40_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.