Human Gene SNRPA (ENST00000243563.8_4) from GENCODE V47lift37
  Description: small nuclear ribonucleoprotein polypeptide A (from RefSeq NM_004596.5)
Gencode Transcript: ENST00000243563.8_4
Gencode Gene: ENSG00000077312.9_12
Transcript (Including UTRs)
   Position: hg19 chr19:41,257,108-41,271,294 Size: 14,187 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr19:41,257,314-41,271,072 Size: 13,759 Coding Exon Count: 6 

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 (chr19:41,257,108-41,271,294)mRNA (may differ from genome)Protein (282 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SNRPA_HUMAN
DESCRIPTION: RecName: Full=U1 small nuclear ribonucleoprotein A; Short=U1 snRNP A; Short=U1-A; Short=U1A;
FUNCTION: Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.
SUBUNIT: Belongs to the spliceosome where it is associated with snRNP U1. Interacts with SFPQ. Also component of a snRNP-free complex with SFPQ.
INTERACTION: P23246:SFPQ; NbExp=4; IntAct=EBI-607085, EBI-355453;
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Belongs to the RRM U1 A/B'' family.
SIMILARITY: Contains 2 RRM (RNA recognition motif) domains.

-  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: SNRPA
Diseases sorted by gene-association score: connective tissue disease (2), suppression amblyopia (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 94.31 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 2003.48 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 -53.80206-0.261 Picture PostScript Text
3' UTR -71.30222-0.321 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
IPR024888 - U1_snRNP_A/U2_snRNP_B''

Pfam Domains:
PF00076 - RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
PF13893 - 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
1AUD - NMR MuPIT 1CX0 - X-ray 1DRZ - X-ray 1DZ5 - NMR MuPIT 1FHT - NMR MuPIT 1M5K - X-ray MuPIT 1M5O - X-ray MuPIT 1M5P - X-ray MuPIT 1M5V - X-ray MuPIT 1NU4 - X-ray MuPIT 1OIA - X-ray MuPIT 1SJ3 - X-ray MuPIT 1SJ4 - X-ray MuPIT 1SJF - X-ray MuPIT 1U6B - X-ray MuPIT 1URN - X-ray MuPIT 1VBX - X-ray MuPIT 1VBY - X-ray MuPIT 1VBZ - X-ray MuPIT 1VC0 - X-ray MuPIT 1VC5 - X-ray MuPIT 1VC6 - X-ray MuPIT 1VC7 - X-ray 1ZZN - X-ray MuPIT 2A3J - NMR 2NZ4 - X-ray MuPIT 2OIH - X-ray MuPIT 2OJ3 - X-ray MuPIT 2U1A - NMR MuPIT 3BO2 - X-ray MuPIT 3BO3 - X-ray MuPIT 3BO4 - X-ray MuPIT 3CUL - X-ray MuPIT 3CUN - X-ray MuPIT 3EGZ - X-ray MuPIT 3G8S - X-ray MuPIT 3G8T - X-ray MuPIT 3G96 - X-ray MuPIT 3G9C - X-ray MuPIT 3HHN - X-ray MuPIT 3IIN - X-ray MuPIT 3IRW - X-ray MuPIT 3IWN - X-ray MuPIT 3K0J - X-ray MuPIT 3L3C - X-ray MuPIT 3MUM - X-ray MuPIT 3MUR - X-ray MuPIT 3MUT - X-ray MuPIT 3MUV - X-ray MuPIT 3MXH - X-ray MuPIT 3P49 - X-ray 3PGW - X-ray 3R1H - X-ray MuPIT 3R1L - X-ray MuPIT 3UCU - X-ray MuPIT 3UCZ - X-ray MuPIT 3UD3 - X-ray MuPIT 3UD4 - X-ray MuPIT 3UTR - Model


ModBase Predicted Comparative 3D Structure on P09012
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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    
Gene SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0030619 U1 snRNA binding
GO:0035614 snRNA stem-loop binding
GO:0042802 identical protein binding
GO:1990446 U1 snRNP binding

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008380 RNA splicing
GO:1900363 regulation of mRNA polyadenylation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005685 U1 snRNP


-  Descriptions from all associated GenBank mRNAs
  BC000405 - Homo sapiens small nuclear ribonucleoprotein polypeptide A, mRNA (cDNA clone MGC:8567 IMAGE:2822987), complete cds.
AK293140 - Homo sapiens cDNA FLJ52249 complete cds, highly similar to U1 small nuclear ribonucleoprotein A.
LF209619 - JP 2014500723-A/17122: Polycomb-Associated Non-Coding RNAs.
AK313182 - Homo sapiens cDNA, FLJ93681, highly similar to Homo sapiens small nuclear ribonucleoprotein polypeptide A (SNRPA), mRNA.
X06347 - Human mRNA for U1 small nuclear RNP-specific A protein.
BC008290 - Homo sapiens small nuclear ribonucleoprotein polypeptide A, mRNA (cDNA clone MGC:12696 IMAGE:3677365), complete cds.
JD501705 - Sequence 482729 from Patent EP1572962.
JD240011 - Sequence 221035 from Patent EP1572962.
AB464219 - Synthetic construct DNA, clone: pF1KB6320, Homo sapiens SNRPA gene for small nuclear ribonucleoprotein polypeptide A, without stop codon, in Flexi system.
CU674198 - Synthetic construct Homo sapiens gateway clone IMAGE:100018071 5' read SNRPA mRNA.
KJ892172 - Synthetic construct Homo sapiens clone ccsbBroadEn_01566 SNRPA gene, encodes complete protein.
LF208596 - JP 2014500723-A/16099: Polycomb-Associated Non-Coding RNAs.
LF330176 - JP 2014500723-A/137679: Polycomb-Associated Non-Coding RNAs.
LF330177 - JP 2014500723-A/137680: Polycomb-Associated Non-Coding RNAs.
LF378336 - JP 2014500723-A/185839: Polycomb-Associated Non-Coding RNAs.
LF330178 - JP 2014500723-A/137681: Polycomb-Associated Non-Coding RNAs.
LF378335 - JP 2014500723-A/185838: Polycomb-Associated Non-Coding RNAs.
JD389213 - Sequence 370237 from Patent EP1572962.
LF330179 - JP 2014500723-A/137682: Polycomb-Associated Non-Coding RNAs.
LF378334 - JP 2014500723-A/185837: Polycomb-Associated Non-Coding RNAs.
MA565753 - JP 2018138019-A/137679: Polycomb-Associated Non-Coding RNAs.
MA565754 - JP 2018138019-A/137680: Polycomb-Associated Non-Coding RNAs.
MA565755 - JP 2018138019-A/137681: Polycomb-Associated Non-Coding RNAs.
MA565756 - JP 2018138019-A/137682: Polycomb-Associated Non-Coding RNAs.
MA445196 - JP 2018138019-A/17122: Polycomb-Associated Non-Coding RNAs.
MA444173 - JP 2018138019-A/16099: Polycomb-Associated Non-Coding RNAs.
MA613913 - JP 2018138019-A/185839: Polycomb-Associated Non-Coding RNAs.
MA613912 - JP 2018138019-A/185838: Polycomb-Associated Non-Coding RNAs.
MA613911 - JP 2018138019-A/185837: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_smPathway - Spliceosomal Assembly

Reactome (by CSHL, EBI, and GO)

Protein P09012 (Reactome details) participates in the following event(s):

R-HSA-72107 Formation of the Spliceosomal E complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72163 mRNA Splicing - Major 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: ENST00000243563.1, ENST00000243563.2, ENST00000243563.3, ENST00000243563.4, ENST00000243563.5, ENST00000243563.6, ENST00000243563.7, NM_004596, P09012, SNRPA_HUMAN, uc317emm.1, uc317emm.2
UCSC ID: ENST00000243563.8_4
RefSeq Accession: NM_004596.5
Protein: P09012 (aka SNRPA_HUMAN or RU1A_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.