Human Gene SNRPB2 (ENST00000246071.8_4) from GENCODE V47lift37
  Description: small nuclear ribonucleoprotein polypeptide B2, transcript variant 2 (from RefSeq NM_198220.3)
Gencode Transcript: ENST00000246071.8_4
Gencode Gene: ENSG00000125870.11_7
Transcript (Including UTRs)
   Position: hg19 chr20:16,710,671-16,723,209 Size: 12,539 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr20:16,712,348-16,721,650 Size: 9,303 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 (chr20:16,710,671-16,723,209)mRNA (may differ from genome)Protein (225 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: RU2B_HUMAN
DESCRIPTION: RecName: Full=U2 small nuclear ribonucleoprotein B''; Short=U2 snRNP B'';
FUNCTION: Involved in pre-mRNA splicing. This protein is associated with snRNP U2. It binds stem loop IV of U2 snRNA only in presence of the U2A' protein.
SUBUNIT: Identified in the spliceosome C complex. Present in a spliceosome complex assembled in vitro, and composed of SNRPB2, HPRP8BP and CRNKL1.
SUBCELLULAR LOCATION: Nucleus.
MISCELLANEOUS: Patients with systemic lupus erythematosus produce antibodies which interact with snRNP proteins.
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


-  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: 41.03 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 853.42 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 -52.50174-0.302 Picture PostScript Text
3' UTR -369.301559-0.237 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
1A9N - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P08579
FrontTopSide
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 DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
      
      

-  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:0070990 snRNP binding

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

Cellular Component:
GO:0001650 fibrillar center
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005685 U1 snRNP
GO:0005686 U2 snRNP
GO:0016607 nuclear speck
GO:0030532 small nuclear ribonucleoprotein complex
GO:0071005 U2-type precatalytic spliceosome
GO:0071007 U2-type catalytic step 2 spliceosome
GO:0071013 catalytic step 2 spliceosome


-  Descriptions from all associated GenBank mRNAs
  BC018022 - Homo sapiens small nuclear ribonucleoprotein polypeptide B'', mRNA (cDNA clone MGC:24807 IMAGE:4286926), complete cds.
BC036737 - Homo sapiens small nuclear ribonucleoprotein polypeptide B'', mRNA (cDNA clone MGC:45309 IMAGE:5533477), complete cds.
AK313004 - Homo sapiens cDNA, FLJ93469, Homo sapiens small nuclear ribonucleoprotein polypeptide B''(SNRPB2), mRNA.
BC022311 - Homo sapiens cDNA clone IMAGE:4807240, containing frame-shift errors.
BC008311 - Homo sapiens, Similar to small nuclear ribonucleoprotein polypeptide B'', clone IMAGE:3503191, mRNA, partial cds.
JD242408 - Sequence 223432 from Patent EP1572962.
M15841 - Human U2 small nuclear RNA-associated B'' antigen mRNA, complete cds.
AB529189 - Synthetic construct DNA, clone: pF1KB6918, Homo sapiens SNRPB2 gene for small nuclear ribonucleoprotein polypeptide B'', without stop codon, in Flexi system.
DQ894019 - Synthetic construct Homo sapiens clone IMAGE:100008479; FLH166597.01L; RZPDo839B0287D small nuclear ribonucleoprotein polypeptide B'' (SNRPB2) gene, encodes complete protein.
DQ890864 - Synthetic construct clone IMAGE:100003494; FLH166601.01X; RZPDo839B0288D small nuclear ribonucleoprotein polypeptide B'' (SNRPB2) gene, encodes complete protein.
KJ892175 - Synthetic construct Homo sapiens clone ccsbBroadEn_01569 SNRPB2 gene, encodes complete protein.
AB451359 - Homo sapiens SNRPB2 mRNA for small nuclear ribonucleoprotein polypeptide B'', partial cds, clone: FLJ08031AAAF.
AB451234 - Homo sapiens SNRPB2 mRNA for small nuclear ribonucleoprotein polypeptide B'', complete cds, clone: FLJ08031AAAN.
AK095316 - Homo sapiens cDNA FLJ37997 fis, clone CTONG2011985.

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

Reactome (by CSHL, EBI, and GO)

Protein P08579 (Reactome details) participates in the following event(s):

R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-156661 Formation of Exon Junction 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: B2R7J3, D3DW21, ENST00000246071.1, ENST00000246071.2, ENST00000246071.3, ENST00000246071.4, ENST00000246071.5, ENST00000246071.6, ENST00000246071.7, NM_198220, P08579, Q9UJD4, RU2B_HUMAN, uc317esl.1, uc317esl.2
UCSC ID: ENST00000246071.8_4
RefSeq Accession: NM_003092.5
Protein: P08579 (aka RU2B_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.