Human Gene SNRNP48 (ENST00000342415.6_4) from GENCODE V47lift37
  Description: small nuclear ribonucleoprotein U11/U12 subunit 48 (from RefSeq NM_152551.4)
Gencode Transcript: ENST00000342415.6_4
Gencode Gene: ENSG00000168566.13_7
Transcript (Including UTRs)
   Position: hg19 chr6:7,590,431-7,612,200 Size: 21,770 Total Exon Count: 9 Strand: +
Coding Region
   Position: hg19 chr6:7,590,491-7,609,106 Size: 18,616 Coding Exon Count: 9 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:7,590,431-7,612,200)mRNA (may differ from genome)Protein (339 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMGIPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SNR48_HUMAN
DESCRIPTION: RecName: Full=U11/U12 small nuclear ribonucleoprotein 48 kDa protein; Short=U11/U12 snRNP 48 kDa protein; Short=U11/U12-48K;
FUNCTION: Likely involved in U12-type 5' splice site recognition.
SUBUNIT: Component of the U11/U12 snRNPs that are part of the U12- type spliceosome. Not found in the major spliceosome.
SUBCELLULAR LOCATION: Nucleus.
DOMAIN: The CHHC region interacts with the 5' splice site of the U12-type intron.
SIMILARITY: Contains 1 CHHC-type zinc finger.

-  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: 10.95 RPKM in Brain - Cerebellar Hemisphere
Total median expression: 228.76 RPKM



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

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -30.5060-0.508 Picture PostScript Text
3' UTR -773.603094-0.250 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
IPR022776 - TRM13/UPF0224_CHHC_Znf_dom
IPR007917 - UPF0224

Pfam Domains:
PF05253 - U11-48K-like CHHC zinc finger

SCOP Domains:
57667 - beta-beta-alpha zinc fingers

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2VY4 - NMR MuPIT 2VY5 - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q6IEG0
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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:0046872 metal ion binding

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

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex
GO:0005689 U12-type spliceosomal complex
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  AL832462 - Homo sapiens mRNA; cDNA DKFZp313D031 (from clone DKFZp313D031).
AK292409 - Homo sapiens cDNA FLJ77380 complete cds.
AK056796 - Homo sapiens cDNA FLJ32234 fis, clone PLACE6004687.
BC114631 - Homo sapiens small nuclear ribonucleoprotein 48kDa (U11/U12), mRNA (cDNA clone MGC:138905 IMAGE:40084903), complete cds.
BC114630 - Homo sapiens small nuclear ribonucleoprotein 48kDa (U11/U12), mRNA (cDNA clone MGC:138904 IMAGE:40084896), complete cds.
BC062458 - Homo sapiens chromosome 6 open reading frame 151, mRNA (cDNA clone IMAGE:6471427).
KJ900310 - Synthetic construct Homo sapiens clone ccsbBroadEn_09704 SNRNP48 gene, encodes complete protein.
BC054008 - Homo sapiens chromosome 6 open reading frame 151, mRNA (cDNA clone IMAGE:6606658).
JD352160 - Sequence 333184 from Patent EP1572962.
AK027220 - Homo sapiens cDNA: FLJ23567 fis, clone LNG10928.
AK092158 - Homo sapiens cDNA FLJ34839 fis, clone NT2NE2010688.
JD042563 - Sequence 23587 from Patent EP1572962.
JD039030 - Sequence 20054 from Patent EP1572962.
JD082140 - Sequence 63164 from Patent EP1572962.
JD162234 - Sequence 143258 from Patent EP1572962.
JD062151 - Sequence 43175 from Patent EP1572962.
JD448814 - Sequence 429838 from Patent EP1572962.
JD304661 - Sequence 285685 from Patent EP1572962.
JD429672 - Sequence 410696 from Patent EP1572962.
JD093549 - Sequence 74573 from Patent EP1572962.
AJ420586 - Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 1998777.
BC001558 - Homo sapiens small nuclear ribonucleoprotein 48kDa (U11/U12), mRNA (cDNA clone IMAGE:3459352).
JD258582 - Sequence 239606 from Patent EP1572962.
JD245732 - Sequence 226756 from Patent EP1572962.
JD308298 - Sequence 289322 from Patent EP1572962.
JD441156 - Sequence 422180 from Patent EP1572962.
JD441157 - Sequence 422181 from Patent EP1572962.
JD064001 - Sequence 45025 from Patent EP1572962.
JD064002 - Sequence 45026 from Patent EP1572962.
JD535137 - Sequence 516161 from Patent EP1572962.

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

Protein Q6IEG0 (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: A8K8P4, C6orf151, ENST00000342415.1, ENST00000342415.2, ENST00000342415.3, ENST00000342415.4, ENST00000342415.5, NM_152551, Q14C91, Q5T339, Q5THM1, Q5THM2, Q6IEG0, Q96MK1, SNR48_HUMAN, uc317wim.1, uc317wim.2
UCSC ID: ENST00000342415.6_4
RefSeq Accession: NM_152551.4
Protein: Q6IEG0 (aka SNR48_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.