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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
    mouse all
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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.

    Chemical Information
    Molecular Biology Databases
    Research Materials
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