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SNRPD2 small nuclear ribonucleoprotein D2 polypeptide [ Homo sapiens (human) ]

Gene ID: 6633, updated on 9-Aug-2020

Summary

Official Symbol
SNRPD2provided by HGNC
Official Full Name
small nuclear ribonucleoprotein D2 polypeptideprovided by HGNC
Primary source
HGNC:HGNC:11159
See related
Ensembl:ENSG00000125743 MIM:601061
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SMD2; Sm-D2; SNRPD1
Summary
The protein encoded by this gene belongs to the small nuclear ribonucleoprotein core protein family. It is required for pre-mRNA splicing and small nuclear ribonucleoprotein biogenesis. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]
Expression
Ubiquitous expression in ovary (RPKM 85.9), lymph node (RPKM 73.9) and 25 other tissues See more
Orthologs

Genomic context

See SNRPD2 in Genome Data Viewer
Location:
19q13.32
Exon count:
6
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (45687454..45692316, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (46190712..46195569, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 836, pseudogene Neighboring gene gastric inhibitory polypeptide receptor Neighboring gene microRNA 642a Neighboring gene microRNA 642b Neighboring gene glutaminyl-peptide cyclotransferase like Neighboring gene F-box protein 46

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Tat tat U2 snRNPs interact with the HIV-1 Tat cofactor TAT-SF1 and stimulate transcription from the HIV-1 LTR promoter PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding HDA PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
RNA splicing TAS
Traceable Author Statement
more info
PubMed 
import into nucleus TAS
Traceable Author Statement
more info
 
mRNA splicing, via spliceosome IC
Inferred by Curator
more info
PubMed 
mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
spliceosomal complex assembly TAS
Traceable Author Statement
more info
PubMed 
spliceosomal snRNP assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
spliceosomal snRNP assembly IDA
Inferred from Direct Assay
more info
PubMed 
spliceosomal snRNP assembly TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
SMN-Sm protein complex IDA
Inferred from Direct Assay
more info
PubMed 
U1 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U1 snRNP IDA
Inferred from Direct Assay
more info
PubMed 
U12-type spliceosomal complex IDA
Inferred from Direct Assay
more info
PubMed 
U2 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U2-type catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
U2-type precatalytic spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
U4 snRNP IDA
Inferred from Direct Assay
more info
PubMed 
U4/U6 x U5 tri-snRNP complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U4/U6 x U5 tri-snRNP complex IDA
Inferred from Direct Assay
more info
PubMed 
U5 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
catalytic step 2 spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 
methylosome IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
pICln-Sm protein complex IDA
Inferred from Direct Assay
more info
PubMed 
precatalytic spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
small nuclear ribonucleoprotein complex TAS
Traceable Author Statement
more info
PubMed 
spliceosomal complex TAS
Traceable Author Statement
more info
PubMed 

General protein information

Preferred Names
small nuclear ribonucleoprotein Sm D2
Names
small nuclear ribonucleoprotein D2 polypeptide 16.5kDa
snRNP core protein D2

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001369751.1NP_001356680.1  small nuclear ribonucleoprotein Sm D2 isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3), as well as variant 2, encodes isoform 2.
    Source sequence(s)
    AC007191
    Related
    ENSP00000465952.1, ENST00000587367.5
    Conserved Domains (1) summary
    cd01720
    Location:14103
    Sm_D2; Sm protein D2
  2. NM_001369752.1NP_001356681.1  small nuclear ribonucleoprotein Sm D2 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC007191, DW433845
    Related
    ENSP00000468247.1, ENST00000590212.1
    Conserved Domains (1) summary
    cl00259
    Location:2460
    Sm_like; Sm and related proteins
  3. NM_004597.6NP_004588.1  small nuclear ribonucleoprotein Sm D2 isoform 1

    See identical proteins and their annotated locations for NP_004588.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the shorter transcript, but encodes the longer isoform (1).
    Source sequence(s)
    AC007191, AJ707552, CF130080
    Consensus CDS
    CCDS33053.1
    UniProtKB/Swiss-Prot
    P62316
    Related
    ENSP00000465216.1, ENST00000588301.5
    Conserved Domains (1) summary
    cd01720
    Location:24113
    Sm_D2; Sm protein D2
  4. NM_177542.3NP_808210.2  small nuclear ribonucleoprotein Sm D2 isoform 2

    See identical proteins and their annotated locations for NP_808210.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) includes an alternate exon and uses a downstream start codon compared to variant 1. Isoform 2 has a shorter N-terminus compared to isoform 1. Variants 2 and 3 both encode isoform 2.
    Source sequence(s)
    AC007191, AJ707552, BU531743
    Consensus CDS
    CCDS54281.1
    UniProtKB/Swiss-Prot
    P62316
    Related
    ENSP00000375798.2, ENST00000391932.7
    Conserved Domains (1) summary
    cd01720
    Location:14103
    Sm_D2; Sm protein D2

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20200522

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

    Range
    45687454..45692316 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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