SNRPD3 small nuclear ribonucleoprotein D3 polypeptide [Homo sapiens (human)] - Gene

Summary

Official Symbol: SNRPD3provided by HGNC
Official Full Name: small nuclear ribonucleoprotein D3 polypeptideprovided by HGNC
Primary source: HGNC:HGNC:11160
See related: Ensembl:ENSG00000100028 MIM:601062; AllianceGenome:HGNC:11160
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: SMD3; Sm-D3
Summary: This gene encodes a core component of the spliceosome, which is a nuclear ribonucleoprotein complex that functions in pre-mRNA splicing. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
Expression: Ubiquitous expression in thyroid (RPKM 22.3), prostate (RPKM 19.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 22q11.23

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	22	NC_000022.11 (24555650..24574971)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	22	NC_060946.1 (25017257..25036577)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	22	NC_000022.10 (24951618..24970939)

Chromosome 22 - NC_000022.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

MYCN and SNRPD3 cooperate to maintain a balance of alternative splicing events that drives neuroblastoma progression.
Title: MYCN and SNRPD3 cooperate to maintain a balance of alternative splicing events that drives neuroblastoma progression.
Silencing Core Spliceosome Sm Gene Expression Induces a Cytotoxic Splicing Switch in the Proteasome Subunit Beta 3 mRNA in Non-Small Cell Lung Cancer Cells.
Title: Silencing Core Spliceosome Sm Gene Expression Induces a Cytotoxic Splicing Switch in the Proteasome Subunit Beta 3 mRNA in Non-Small Cell Lung Cancer Cells.
The dimethylated arginine residues play an essential role in the formation of major SmD3 autoepitopes. 1 particular peptide of SmD3 represents a more sensitive and more reliable substrate for the detection of a subclass of anti-Sm antibodies.
Title: Identification of a SmD3 epitope with a single symmetrical dimethylation of an arginine residue as a specific target of a subpopulation of anti-Sm antibodies.

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

EBI GWAS Catalog

Description
Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of small nuclear ribonucleoprotein D3 polypeptide (SNRPD3, 18kDa) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH121336 (e-PCR)
- UniSTS:138600

STS-W80851 (e-PCR)
- UniSTS:66958

SHGC-12625 (e-PCR)
- UniSTS:78737

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables RNA binding	HDA more info	PubMed
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IPI Inferred from Physical Interaction more info	PubMed
enables U1 snRNP binding	IEA Inferred from Electronic Annotation more info
enables U7 snRNA binding	IPI Inferred from Physical Interaction more info	PubMed
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables histone pre-mRNA DCP binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables telomerase RNA 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
acts_upstream_of_or_within protein methylation	IDA Inferred from Direct Assay 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 U7 snRNP	IDA Inferred from Direct Assay 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 nuclear body	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay 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
part_of telomerase holoenzyme complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: small nuclear ribonucleoprotein Sm D3

Names: small nuclear ribonucleoprotein D3 polypeptide 18kDa; snRNP core protein D3

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)

NM_001278656.2 → NP_001265585.1 small nuclear ribonucleoprotein Sm D3

See identical proteins and their annotated locations for NP_001265585.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate splice site in the 5' UTR, compared to variant 1. Variants 1 and 2 encode the same protein.

Source sequence(s)

AP000356, BY993733, CN286602

Consensus CDS

CCDS13828.1

UniProtKB/Swiss-Prot

B4DJP7, B5BU13, P43331, P62318

Conserved Domains (1) summary

cd01721
Location:6 → 75

Sm_D3; Sm protein D3
NM_004175.5 → NP_004166.1 small nuclear ribonucleoprotein Sm D3

See identical proteins and their annotated locations for NP_004166.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 2 encode the same protein.

Source sequence(s)

AP000356, BC000457, CN286602

Consensus CDS

CCDS13828.1

UniProtKB/Swiss-Prot

B4DJP7, B5BU13, P43331, P62318

Related

ENSP00000215829.3, ENST00000215829.8

Conserved Domains (1) summary

cd01721
Location:6 → 75

Sm_D3; Sm protein D3