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

Gene ID: 6633, updated on 10-Oct-2019

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
109.20190905 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

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 BioSystems

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Metabolism of non-coding RNA, organism-specific biosystem (from REACTOME)
    Metabolism of non-coding RNA, organism-specific biosystemThe term non-coding is commonly employed for RNA that does not encode a protein, but this does not mean that such RNAs do not contain information nor have function. There is considerable evidence tha...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • Sm core complex, organism-specific biosystem (from KEGG)
    Sm core complex, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
  • Sm core complex, conserved biosystem (from KEGG)
    Sm core complex, conserved biosystemStructural complex; Genetic information processing; Spliceosome
  • Spliceosome, organism-specific biosystem (from KEGG)
    Spliceosome, organism-specific biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, conserved biosystem (from KEGG)
    Spliceosome, conserved biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, 35S U5-snRNP, organism-specific biosystem (from KEGG)
    Spliceosome, 35S U5-snRNP, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
  • Spliceosome, 35S U5-snRNP, conserved biosystem (from KEGG)
    Spliceosome, 35S U5-snRNP, conserved biosystemStructural complex; Genetic information processing; Spliceosome
  • Spliceosome, U1-snRNP, organism-specific biosystem (from KEGG)
    Spliceosome, U1-snRNP, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
  • Spliceosome, U1-snRNP, conserved biosystem (from KEGG)
    Spliceosome, U1-snRNP, conserved biosystemStructural complex; Genetic information processing; Spliceosome
  • Spliceosome, U2-snRNP, organism-specific biosystem (from KEGG)
    Spliceosome, U2-snRNP, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
  • Spliceosome, U2-snRNP, conserved biosystem (from KEGG)
    Spliceosome, U2-snRNP, conserved biosystemStructural complex; Genetic information processing; Spliceosome
  • Spliceosome, U4/U6.U5 tri-snRNP, organism-specific biosystem (from KEGG)
    Spliceosome, U4/U6.U5 tri-snRNP, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
  • Spliceosome, U4/U6.U5 tri-snRNP, conserved biosystem (from KEGG)
    Spliceosome, U4/U6.U5 tri-snRNP, conserved biosystemStructural complex; Genetic information processing; Spliceosome
  • mRNA Processing, organism-specific biosystem (from WikiPathways)
    mRNA Processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...
  • mRNA Splicing - Minor Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Minor Pathway, organism-specific biosystemThe splicing of a subset of pre-mRNA introns occurs by a second pathway, designated the AT-AC or U12-dependent splicing pathway. AT-AC introns have highly conserved, non-canonical splice sites that ...
  • snRNP Assembly, organism-specific biosystem (from REACTOME)
    snRNP Assembly, organism-specific biosystemSmall nuclear ribonucleoproteins (snRNPs) are crucial for pre-mRNA processing to mRNAs. Each snRNP contains a small nuclear RNA (snRNA) and an extremely stable core of seven Sm proteins. The U6 snRNA...

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 
U1 snRNP binding IEA
Inferred from Electronic Annotation
more info
 
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 
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 109.20190905

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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