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SNRPD1 small nuclear ribonucleoprotein D1 polypeptide [ Homo sapiens (human) ]

Gene ID: 6632, updated on 12-Jan-2019

Summary

Official Symbol
SNRPD1provided by HGNC
Official Full Name
small nuclear ribonucleoprotein D1 polypeptideprovided by HGNC
Primary source
HGNC:HGNC:11158
See related
Ensembl:ENSG00000167088 MIM:601063
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
SMD1; SNRPD; Sm-D1; HsT2456
Summary
This gene encodes a small nuclear ribonucleoprotein that belongs to the SNRNP core protein family. The protein may act as a charged protein scaffold to promote SNRNP assembly or strengthen SNRNP-SNRNP interactions through nonspecific electrostatic contacts with RNA. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2014]
Expression
Ubiquitous expression in lymph node (RPKM 17.9), bone marrow (RPKM 15.5) and 25 other tissues See more
Orthologs

Genomic context

See SNRPD1 in Genome Data Viewer
Location:
18q11.2
Exon count:
4
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 18 NC_000018.10 (21612269..21630247)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (19192260..19210208)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene GREB1 like retinoic acid receptor coactivator Neighboring gene uncharacterized LOC101927521 Neighboring gene establishment of sister chromatid cohesion N-acetyltransferase 1 Neighboring gene abhydrolase domain containing 3 Neighboring gene uncharacterized LOC105376866 Neighboring gene microRNA 320c-1

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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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
  • Systemic lupus erythematosus, organism-specific biosystem (from KEGG)
    Systemic lupus erythematosus, organism-specific biosystemSystemic lupus erythematosus (SLE) is a prototypic autoimmune disease characterised by the production of IgG autoantibodies that are specific for self-antigens, such as DNA, nuclear proteins and cert...
  • Systemic lupus erythematosus, conserved biosystem (from KEGG)
    Systemic lupus erythematosus, conserved biosystemSystemic lupus erythematosus (SLE) is a prototypic autoimmune disease characterised by the production of IgG autoantibodies that are specific for self-antigens, such as DNA, nuclear proteins and cert...
  • 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 
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 IBA
Inferred from Biological aspect of Ancestor
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 IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U4 snRNP IDA
Inferred from Direct Assay
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 
commitment complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
methylosome IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus HDA PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IMP
Inferred from Mutant Phenotype
more info
PubMed 
pICln-Sm protein complex IBA
Inferred from Biological aspect of Ancestor
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 

General protein information

Preferred Names
small nuclear ribonucleoprotein Sm D1
Names
Sm-D autoantigen
small nuclear ribonucleoprotein D1 polypeptide 16kDa pseudogene
snRNP core protein D1

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_001291916.1NP_001278845.1  small nuclear ribonucleoprotein Sm D1 isoform 2

    See identical proteins and their annotated locations for NP_001278845.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC106037, BU565530, CN354758, HY043971, J03798
    UniProtKB/Swiss-Prot
    P62314
    Conserved Domains (1) summary
    cl00259
    Location:252
    Sm_like; Sm and related proteins
  2. NM_006938.4NP_008869.1  small nuclear ribonucleoprotein Sm D1 isoform 1

    See identical proteins and their annotated locations for NP_008869.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC106037, J03798
    Consensus CDS
    CCDS32801.1
    UniProtKB/Swiss-Prot
    P62314
    Related
    ENSP00000300413.4, ENST00000300413.9
    Conserved Domains (1) summary
    cd01724
    Location:293
    Sm_D1; Sm protein D1

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000018.10 Reference GRCh38.p12 Primary Assembly

    Range
    21612269..21630247
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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