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

Gene ID: 6633, updated on 3-Nov-2024

Summary

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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; AllianceGenome:HGNC:11159
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
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Genomic context

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See SNRPD2 in Genome Data Viewer
Location:
19q13.32
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (45687454..45692316, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (48514991..48519856, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (46190712..46195574, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene RNA, 7SL, cytoplasmic 836, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10787 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14810 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46173596-46174114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:46174115-46174633 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10790 Neighboring gene gastric inhibitory polypeptide receptor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10791 Neighboring gene microRNA 642a Neighboring gene microRNA 642b Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14811 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10792 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46194747-46195467 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:46196081-46196631 Neighboring gene glutaminyl-peptide cyclotransferase like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14814 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46220214-46220884 Neighboring gene F-box protein 46 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:46220885-46221555 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:46223908-46224408 Neighboring gene Sharpr-MPRA regulatory regions 3721 and 14243 Neighboring gene Sharpr-MPRA regulatory region 6016 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14816 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14817

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 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. USP9X deubiquitinates and stabilizes CDC123 to promote breast carcinogenesis through regulating cell cycle. Song N, et al. Mol Carcinog, 2023 Oct. PMID 37314216
  2. Molecular cloning of a cDNA encoding the human Sm-D autoantigen. Rokeach LA, et al. Proc Natl Acad Sci U S A, 1988 Jul. PMID 3260384, Free PMC Article
  3. Evidence for three distinct D proteins, which react differentially with anti-Sm autoantibodies, in the cores of the major snRNPs U1, U2, U4/U6 and U5. Lehmeier T, et al. Nucleic Acids Res, 1990 Nov 25. PMID 1701240, Free PMC Article
  4. Nuclear retention element recruits U1 snRNP components to restrain spliced lncRNAs in the nucleus. Azam S, et al. RNA Biol, 2019 Aug. PMID 31107149, Free PMC Article
  5. cDNA cloning of the Sm proteins D2 and D3 from human small nuclear ribonucleoproteins: evidence for a direct D1-D2 interaction. Lehmeier T, et al. Proc Natl Acad Sci U S A, 1994 Dec 6. PMID 7527560, Free PMC Article

See all (228) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Intron Retention of DDX39A Driven by SNRPD2 is a Crucial Splicing Axis for Oncogenic MYC/Spliceosome Program in Hepatocellular Carcinoma.
    Title: Intron Retention of DDX39A Driven by SNRPD2 is a Crucial Splicing Axis for Oncogenic MYC/Spliceosome Program in Hepatocellular Carcinoma.
  2. Screen using siRNA revealed depletion of U1 snRNP components SNRPA, SNRNP70 or SNRPD2 caused significant cytoplasmic localization of MEG3 reporter transcripts.
    Title: Nuclear retention element recruits U1 snRNP components to restrain spliced lncRNAs in the nucleus.
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 for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.
EBI GWAS Catalog

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 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 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 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 IBA
Inferred from Biological aspect of Ancestor
more info
  
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 
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 
part_of methylosome IDA
Inferred from Direct Assay
more info
 PubMed 
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 

General protein information

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Preferred Names
small nuclear ribonucleoprotein Sm D2
Names
small nuclear ribonucleoprotein D2 polypeptide 16.5kDa
snRNP core protein D2

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_001369751.1 → NP_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
    Consensus CDS
    CCDS54281.1
    Related
    ENSP00000465952.1, ENST00000587367.5
    Conserved Domains (1) summary
    cd01720
    Location:14 → 103
    Sm_D2; Sm protein D2

  2. NM_001369752.1 → NP_001356681.1  small nuclear ribonucleoprotein Sm D2 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC007191, DW433845
    Consensus CDS
    CCDS92646.1
    UniProtKB/TrEMBL
    K7ERG4
    Related
    ENSP00000468247.1, ENST00000590212.1
    Conserved Domains (1) summary
    cl00259
    Location:24 → 60
    Sm_like; Sm and related proteins

  3. NM_001384647.1 → NP_001371576.1  small nuclear ribonucleoprotein Sm D2 isoform 1

    Status: REVIEWED

    Source sequence(s)
    CD175580
    Consensus CDS
    CCDS33053.1
    UniProtKB/Swiss-Prot
    A8K797, J3KPM5, P43330, P62316
    Related
    ENSP00000342374.2, ENST00000342669.8
    Conserved Domains (1) summary
    cd01720
    Location:24 → 113
    Sm_D2; Sm protein D2

  4. NM_004597.6 → NP_004588.1  small nuclear ribonucleoprotein Sm D2 isoform 1

    See identical proteins and their annotated locations for NP_004588.1

    Status: REVIEWED

    Source sequence(s)
    AC007191, AJ707552, CF130080
    Consensus CDS
    CCDS33053.1
    UniProtKB/Swiss-Prot
    A8K797, J3KPM5, P43330, P62316
    Related
    ENSP00000465216.1, ENST00000588301.5
    Conserved Domains (1) summary
    cd01720
    Location:24 → 113
    Sm_D2; Sm protein D2

  5. NM_177542.3 → NP_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:14 → 103
    Sm_D2; Sm protein D2

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    45687454..45692316 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    48514991..48519856 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P62316.1 GenPept UniProtKB/Swiss-Prot:P62316

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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