Human Gene SNRNP35 (ENST00000526639.3_4) from GENCODE V47lift37
  Description: small nuclear ribonucleoprotein U11/U12 subunit 35, transcript variant 2 (from RefSeq NM_022717.4)
Gencode Transcript: ENST00000526639.3_4
Gencode Gene: ENSG00000184209.15_8
Transcript (Including UTRs)
   Position: hg19 chr12:123,942,686-123,951,483 Size: 8,798 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg19 chr12:123,950,088-123,950,828 Size: 741 Coding Exon Count: 1 

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 (chr12:123,942,686-123,951,483)mRNA (may differ from genome)Protein (246 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: U1SBP_HUMAN
DESCRIPTION: RecName: Full=U11/U12 small nuclear ribonucleoprotein 35 kDa protein; Short=U11/U12 snRNP 35 kDa protein; Short=U11/U12-35K; AltName: Full=Protein HM-1; AltName: Full=U1 snRNP-binding protein homolog;
SUBUNIT: Component of the U11/U12 snRNPs that are part of the U12- type spliceosome.
SUBCELLULAR LOCATION: Nucleus.
TISSUE SPECIFICITY: Expressed in heart, liver, skeletal muscle and pancreas.
SIMILARITY: Contains 1 RRM (RNA recognition motif) domain.

-  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           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: 8.24 RPKM in Spleen
Total median expression: 282.34 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 -28.5081-0.352 Picture PostScript Text
3' UTR -201.90655-0.308 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

ModBase Predicted Comparative 3D Structure on Q16560
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 SorterGene Sorter    
 RGD    
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0017069 snRNA binding

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

Cellular Component:
GO:0000243 commitment complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005689 U12-type spliceosomal complex
GO:0005730 nucleolus
GO:0071011 precatalytic spliceosome


-  Descriptions from all associated GenBank mRNAs
  BC028485 - Homo sapiens small nuclear ribonucleoprotein 35kDa (U11/U12), mRNA (cDNA clone IMAGE:3536581).
LF384024 - JP 2014500723-A/191527: Polycomb-Associated Non-Coding RNAs.
AK290127 - Homo sapiens cDNA FLJ76349 complete cds, highly similar to Homo sapiens U11/U12 snRNP 35K (U1SNRNPBP), transcript variant 1, mRNA.
BC047678 - Homo sapiens small nuclear ribonucleoprotein 35kDa (U11/U12), mRNA (cDNA clone MGC:51824 IMAGE:5767646), complete cds.
BC020829 - Homo sapiens mRNA similar to hypothetical protein FLJ21394 (cDNA clone IMAGE:4770900).
JD440815 - Sequence 421839 from Patent EP1572962.
JD161695 - Sequence 142719 from Patent EP1572962.
U44799 - Human U1-snRNP binding protein homolog mRNA, complete cds.
JD547712 - Sequence 528736 from Patent EP1572962.
LF359685 - JP 2014500723-A/167188: Polycomb-Associated Non-Coding RNAs.
JD150028 - Sequence 131052 from Patent EP1572962.
BC054034 - Homo sapiens small nuclear ribonucleoprotein 35kDa (U11/U12), mRNA (cDNA clone MGC:64961 IMAGE:3901191), complete cds.
BC009622 - Homo sapiens small nuclear ribonucleoprotein 35kDa (U11/U12), mRNA (cDNA clone MGC:17036 IMAGE:3893396), complete cds.
U44798 - Human U1-snRNP binding protein homolog mRNA, complete cds.
BC093671 - Homo sapiens small nuclear ribonucleoprotein 35kDa (U11/U12), mRNA (cDNA clone MGC:120706 IMAGE:7939516), complete cds.
BC111955 - Homo sapiens small nuclear ribonucleoprotein 35kDa (U11/U12), mRNA (cDNA clone MGC:138160 IMAGE:8327423), complete cds.
HQ447429 - Synthetic construct Homo sapiens clone IMAGE:100070755; CCSB015057_01 U11/U12 snRNP 35K (U1SNRNPBP) gene, encodes complete protein.
KJ893215 - Synthetic construct Homo sapiens clone ccsbBroadEn_02609 SNRNP35 gene, encodes complete protein.
LF359686 - JP 2014500723-A/167189: Polycomb-Associated Non-Coding RNAs.
JD215526 - Sequence 196550 from Patent EP1572962.
MA619601 - JP 2018138019-A/191527: Polycomb-Associated Non-Coding RNAs.
MA595262 - JP 2018138019-A/167188: Polycomb-Associated Non-Coding RNAs.
MA595263 - JP 2018138019-A/167189: Polycomb-Associated Non-Coding RNAs.

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

Protein Q16560 (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: A8K262, ENST00000526639.1, ENST00000526639.2, HM1, NM_022717, Q16560, Q5XKN9, U1SBP_HUMAN, U1SNRNPBP, uc324cfc.1, uc324cfc.2
UCSC ID: ENST00000526639.3_4
RefSeq Accession: NM_022717.4
Protein: Q16560 (aka U1SBP_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.