Human Gene SNRNP27 (ENST00000244227.8_4) from GENCODE V47lift37
  Description: small nuclear ribonucleoprotein U4/U6.U5 subunit 27, transcript variant 2 (from RefSeq NR_037862.2)
Gencode Transcript: ENST00000244227.8_4
Gencode Gene: ENSG00000124380.11_8
Transcript (Including UTRs)
   Position: hg19 chr2:70,121,088-70,132,368 Size: 11,281 Total Exon Count: 6 Strand: +
Coding Region
   Position: hg19 chr2:70,121,117-70,131,440 Size: 10,324 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:70,121,088-70,132,368)mRNA (may differ from genome)Protein (155 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SNR27_HUMAN
DESCRIPTION: RecName: Full=U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein; Short=U4/U6.U5 snRNP 27 kDa protein; Short=U4/U6.U5-27K; AltName: Full=Nucleic acid-binding protein RY-1; AltName: Full=U4/U6.U5 tri-snRNP-associated 27 kDa protein; Short=27K; AltName: Full=U4/U6.U5 tri-snRNP-associated protein 3;
FUNCTION: May play a role in mRNA splicing.
SUBUNIT: Part of a tri-snRNP complex.
SUBCELLULAR LOCATION: Nucleus (Potential).
PTM: Phosphorylated upon DNA damage, probably by ATM or ATR. Phosphorylated in vitro by snRNP-associated protein kinase.
SIMILARITY: Belongs to the SNUT3 family.
SEQUENCE CAUTION: Sequence=CAA53949.1; 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


-  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: 12.09 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 364.44 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -5.2029-0.179 Picture PostScript Text
3' UTR -167.70928-0.181 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
IPR013957 - DUF1777

Pfam Domains:
PF08648 - U4/U6.U5 small nuclear ribonucleoproteins

ModBase Predicted Comparative 3D Structure on Q8WVK2
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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:0005515 protein binding

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0008150 biological_process
GO:0008380 RNA splicing

Cellular Component:
GO:0005575 cellular_component
GO:0005634 nucleus
GO:0005654 nucleoplasm


-  Descriptions from all associated GenBank mRNAs
  BC017890 - Homo sapiens small nuclear ribonucleoprotein 27kDa (U4/U6.U5), mRNA (cDNA clone MGC:22775 IMAGE:4699198), complete cds.
X76302 - H.sapiens RY-1 mRNA for putative nucleic acid binding protein.
AK291128 - Homo sapiens cDNA FLJ78125 complete cds, highly similar to Homo sapiens putative nucleic acid binding protein RY-1 (RY1), mRNA.
AK312041 - Homo sapiens cDNA, FLJ92318, Homo sapiens putative nucleic acid binding protein RY-1 (RY1),mRNA.
CU676102 - Synthetic construct Homo sapiens gateway clone IMAGE:100022072 5' read RY1 mRNA.
HQ447740 - Synthetic construct Homo sapiens clone IMAGE:100071071; CCSB012970_01 putative nucleic acid binding protein RY-1 (RY1) gene, encodes complete protein.
KJ893203 - Synthetic construct Homo sapiens clone ccsbBroadEn_02597 SNRNP27 gene, encodes complete protein.
JD227338 - Sequence 208362 from Patent EP1572962.

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

Protein Q8WVK2 (Reactome details) participates in the following event(s):

R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) 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: ENST00000244227.1, ENST00000244227.2, ENST00000244227.3, ENST00000244227.4, ENST00000244227.5, ENST00000244227.6, ENST00000244227.7, NR_037862, Q15410, Q8WVK2, SNR27_HUMAN, uc317eoc.1, uc317eoc.2
UCSC ID: ENST00000244227.8_4
RefSeq Accession: NM_006857.3
Protein: Q8WVK2 (aka SNR27_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.