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

Gene ID: 6632, updated on 7-Apr-2024

Summary

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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; AllianceGenome:HGNC:11158
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
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Genomic context

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Location:
18q11.2
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (21612314..21633520)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (21797409..21818615)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (19192275..19213481)

Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene GREB1 like retinoic acid receptor coactivator Neighboring gene uncharacterized LOC101927521 Neighboring gene small nucleolar RNA SNORD23 Neighboring gene establishment of sister chromatid cohesion N-acetyltransferase 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr18:19171613-19172342 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:19173073-19173800 Neighboring gene Sharpr-MPRA regulatory region 3945 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13133 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13134 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13135 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9341 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13136 Neighboring gene MPRA-validated peak3065 silencer Neighboring gene MPRA-validated peak3066 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13137 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9342 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13138 Neighboring gene MPRA-validated peak3067 silencer Neighboring gene abhydrolase domain containing 3, phospholipase Neighboring gene small nucleolar RNA SNORA81 Neighboring gene microRNA 320c-1 Neighboring gene MIB E3 ubiquitin protein ligase 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. SNRPD1 inhibition suppresses the proliferation of hepatocellular carcinoma and promotes autophagy through the PI3K/AKT/mTOR/4EBP1 pathway. Wang H, et al. Arch Biochem Biophys, 2023 Jul 15. PMID 37268273
  2. Anti-SmD1 antibodies are associated with renal disorder, seizures, and pulmonary arterial hypertension in Chinese patients with active SLE. Hu C, et al. Sci Rep, 2017 Aug 8. PMID 28790444, Free PMC Article
  3. Association of cerebrospinal fluid anti-Sm antibodies with acute confusional state in systemic lupus erythematosus. Hirohata S, et al. Arthritis Res Ther, 2014 Oct 2. PMID 25273532, Free PMC Article
  4. Analysis of genes for human snRNP Sm-D1 protein and identification of the promoter sequence which shows segmental homology to the promoters of Sm-E and U1 snRNA genes. Sun D, et al. Gene, 1997 Apr 21. PMID 9168134
  5. Targeting the deregulated spliceosome core machinery in cancer cells triggers mTOR blockade and autophagy. Quidville V, et al. Cancer Res, 2013 Apr 1. PMID 23358685

See all (208) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SNRPD1 inhibition suppresses the proliferation of hepatocellular carcinoma and promotes autophagy through the PI3K/AKT/mTOR/4EBP1 pathway.
    Title: SNRPD1 inhibition suppresses the proliferation of hepatocellular carcinoma and promotes autophagy through the PI3K/AKT/mTOR/4EBP1 pathway.
  2. Anti-SmD1 antibodies are associated with renal disorder, seizures, and pulmonary arterial hypertension in Chinese patients with active systemic lupus erythematosus.
    Title: Anti-SmD1 antibodies are associated with renal disorder, seizures, and pulmonary arterial hypertension in Chinese patients with active SLE.
  3. Data suggest that SNRPA1, SNRPD1, and PNN are key players in the regulation of pluripotency-specific spliceosome assembly and the acquisition and maintenance of pluripotency.
    Title: The unique spliceosome signature of human pluripotent stem cells is mediated by SNRPA1, SNRPD1, and PNN.
  4. Data show that the elevation of cerebrospinal fluid anti-Sm antibodies through transudation from systemic circulation due to damaged blood-brain barrier (BBB) plays a critical role in the pathogenesis of acute confusional state (ACS).
    Title: Association of cerebrospinal fluid anti-Sm antibodies with acute confusional state in systemic lupus erythematosus.
  5. The interaction of SMN with the spliceosomal SmD1 (also known as SNRPD1), severely decreases SMN-coilin interaction and prevents Cajal body assembly.
    Title: The SMN Tudor SIM-like domain is key to SmD1 and coilin interactions and to Cajal body biogenesis.
  6. Overexpression of SNRPD1 is associated with highly aggressive breast cancers.
    Title: Targeting the deregulated spliceosome core machinery in cancer cells triggers mTOR blockade and autophagy.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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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

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding HDA PubMed 
enables RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in 7-methylguanosine cap hypermethylation NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in RNA splicing TAS
Traceable Author Statement
more info
 PubMed 
involved_in U2-type prespliceosome assembly NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IC
Inferred by Curator
more info
 PubMed 
involved_in mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in mRNA splicing, via spliceosome NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in spliceosomal complex assembly TAS
Traceable Author Statement
more info
 PubMed 
involved_in spliceosomal snRNP assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in spliceosomal snRNP assembly IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
part_of SMN-Sm protein complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of SMN-Sm protein complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U1 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U1 snRNP IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U1 snRNP IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of U1 snRNP NAS
Non-traceable Author Statement
more info
 PubMed 
part_of U12-type spliceosomal complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U12-type spliceosomal complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U2 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U2 snRNP NAS
Non-traceable Author Statement
more info
 PubMed 
part_of U2-type catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U2-type precatalytic spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U2-type spliceosomal complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U4 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U4 snRNP IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U4 snRNP NAS
Non-traceable Author Statement
more info
 PubMed 
part_of U4/U6 x U5 tri-snRNP complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of U4/U6 x U5 tri-snRNP complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of U5 snRNP IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of U5 snRNP NAS
Non-traceable Author Statement
more info
 PubMed 
part_of catalytic step 2 spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of catalytic step 2 spliceosome IDA
Inferred from Direct Assay
more info
 PubMed 
part_of commitment complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
part_of methylosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
located_in nucleus HDA PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IMP
Inferred from Mutant Phenotype
more info
 PubMed 
located_in nucleus NAS
Non-traceable Author Statement
more info
 PubMed 
part_of pICln-Sm protein complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of pICln-Sm protein complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of precatalytic spliceosome IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of small nuclear ribonucleoprotein complex TAS
Traceable Author Statement
more info
 PubMed 
part_of spliceosomal complex IPI
Inferred from Physical Interaction
more info
 PubMed 
part_of spliceosomal complex NAS
Non-traceable Author Statement
more info
 PubMed 
part_of spliceosomal tri-snRNP complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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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)

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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_001291916.2 → NP_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, CN354758, HY043971, J03798
    UniProtKB/Swiss-Prot
    P62314
    Conserved Domains (1) summary
    cl00259
    Location:2 → 52
    Sm_like; Sm and related proteins

  2. NM_006938.4 → NP_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
    B5BTZ1, P13641, P62314
    Related
    ENSP00000300413.4, ENST00000300413.10
    Conserved Domains (1) summary
    cd01724
    Location:2 → 93
    Sm_D1; Sm protein D1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000018.10 Reference GRCh38.p14 Primary Assembly

    Range
    21612314..21633520
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060942.1 Alternate T2T-CHM13v2.0

    Range
    21797409..21818615
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P62314.1 GenPept UniProtKB/Swiss-Prot:P62314

Gene LinkOut

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