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

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; 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: mouse all
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Genomic context

Location:: 18q11.2

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	18	NC_000018.10 (21612314..21633520)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	18	NC_060942.1 (21797409..21818615)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	18	NC_000018.9 (19192275..19213481)

Chromosome 18 - NC_000018.10 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 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?

Effect of E134K pathogenic mutation of SMN protein on SMN-SmD1 interaction, with implication in spinal muscular atrophy: A molecular dynamics study.
Title: Effect of E134K pathogenic mutation of SMN protein on SMN-SmD1 interaction, with implication in spinal muscular atrophy: A molecular dynamics study.
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.
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.
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.
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.
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.
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.

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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)

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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AW464517 (e-PCR)
- UniSTS:278079

RH124565 (e-PCR)
- UniSTS:161387

STS-J03798 (e-PCR)
- UniSTS:20977

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 U1 snRNP binding	IEA Inferred from Electronic Annotation 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	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 more info	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)

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
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