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    SNAPC5 small nuclear RNA activating complex polypeptide 5 [ Homo sapiens (human) ]

    Gene ID: 10302, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SNAPC5provided by HGNC
    Official Full Name
    small nuclear RNA activating complex polypeptide 5provided by HGNC
    Primary source
    HGNC:HGNC:15484
    See related
    Ensembl:ENSG00000174446 MIM:605979; AllianceGenome:HGNC:15484
    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
    SNAP19
    Summary
    This gene encodes a subunit of the small nuclear RNA (snRNA)-activating protein complex that plays a role in the transcription of snRNA genes. This complex binds to the promoters of snRNA genes transcribed by either RNA polymerase II or III and recruits other regulatory factors to activate snRNA gene transcription. The encoded protein may play a role in stabilizing this complex. A pseudogene of this gene has been identified on chromosome 6. [provided by RefSeq, Jul 2016]
    Expression
    Ubiquitous expression in brain (RPKM 30.5), fat (RPKM 21.0) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SNAPC5 in Genome Data Viewer
    Location:
    15q22.31
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (66489748..66497762, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (64311223..64319236, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (66782086..66790100, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene mitogen-activated protein kinase kinase 1 Neighboring gene ATP synthase membrane subunit f pseudogene 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:66720755-66721254 Neighboring gene ribosomal protein L35a pseudogene 32 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:66763159-66763836 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9613 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9614 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:66767223-66767899 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:66768557-66769080 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:66769081-66769604 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:66788751-66789486 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:66789487-66790222 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr15:66792902-66794101 Neighboring gene microRNA 4512 Neighboring gene small nucleolar RNA, C/D box 18C Neighboring gene small nucleolar RNA, C/D box 18B Neighboring gene ribosomal protein L4

    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. COL3A1 and SNAP91: novel glioblastoma markers with diagnostic and prognostic value. Gao YF, et al. Oncotarget, 2016 Oct 25. PMID 27655637, Free PMC Article
    2. SNAP19 mediates the assembly of a functional core promoter complex (SNAPc) shared by RNA polymerases II and III. Henry RW, et al. Genes Dev, 1998 Sep 1. PMID 9732265, Free PMC Article
    3. A map of protein-protein contacts within the small nuclear RNA-activating protein complex SNAPc. Ma B, et al. J Biol Chem, 2001 Feb 16. PMID 11056176
    4. Cell-free cotranslation and selection using in vitro virus for high-throughput analysis of protein-protein interactions and complexes. Miyamoto-Sato E, et al. Genome Res, 2005 May. PMID 15867431, Free PMC Article
    5. Interaction between the scaffold proteins CBP by IQGAP1 provides an interface between gene expression and cytoskeletal activity. Kosol S, et al. Sci Rep, 2020 Apr 1. PMID 32238831, Free PMC Article

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Kaplan-Meir analysis of GSE7696 indicate that COL3A1 and SNAP91 correlated with survival.
      Title: COL3A1 and SNAP91: novel glioblastoma markers with diagnostic and prognostic value.
    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

    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 polymerase II general transcription initiation factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA polymerase III general transcription initiation factor activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in snRNA transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in snRNA transcription by RNA polymerase III IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in transcription initiation at RNA polymerase III promoter IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nuclear body IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleolus 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 TAS
    Traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    snRNA-activating protein complex subunit 5
    Names
    SNAPc 19 kDa subunit
    SNAPc subunit 5
    snRNA-activating protein complex 19 kDa subunit

    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.

    Genomic

    1. NG_051234.1 RefSeqGene

      Range
      5054..9348
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001329613.2 → NP_001316542.1  snRNA-activating protein complex subunit 5 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in its 5' coding region and differs in the 3' UTR compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AC116913, AK024763, BC014315
      Consensus CDS
      CCDS86469.1
      UniProtKB/Swiss-Prot
      O75971
      Related
      ENSP00000308439.7, ENST00000307979.7
      Conserved Domains (1) summary
      pfam15497
      Location:8 → 50
      SNAPc19; snRNA-activating protein complex subunit 19, SNAPc subunit 19

    2. NM_001329614.2 → NP_001316543.1  snRNA-activating protein complex subunit 5 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' and 3' UTRs, and uses a downstream translation start site compared to variant 1. The encoded isoform (3) has a shorter N-terminus than isoform 1.
      Source sequence(s)
      AC116913, AK024763

    3. NM_001329615.2 → NP_001316544.1  snRNA-activating protein complex subunit 5 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 3' UTR compared to variant 1. Both variants 1 and 4 encode the same isoform (1).
      Source sequence(s)
      AC116913, AK024763, BG764762
      Consensus CDS
      CCDS10217.1
      UniProtKB/Swiss-Prot
      A8K7N6, O75971, Q96CF3
      Related
      ENSP00000319597.5, ENST00000316634.6
      Conserved Domains (1) summary
      pfam15497
      Location:8 → 80
      SNAPc19; snRNA-activating protein complex subunit 19, SNAPc subunit 19

    4. NM_006049.4 → NP_006040.1  snRNA-activating protein complex subunit 5 isoform 1

      See identical proteins and their annotated locations for NP_006040.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1). Both variants 1 and 4 encode the same isoform (1).
      Source sequence(s)
      BU679510, CN347010, DB037177, HY005747
      Consensus CDS
      CCDS10217.1
      UniProtKB/Swiss-Prot
      A8K7N6, O75971, Q96CF3
      Related
      ENSP00000457892.1, ENST00000563480.6
      Conserved Domains (1) summary
      pfam15497
      Location:8 → 80
      SNAPc19; snRNA-activating protein complex subunit 19, SNAPc subunit 19

    RNA

    1. NR_138061.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) uses an alternate splice site in an internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      BC066984, BP211241, BU679510, HY005747

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      66489748..66497762 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_007064417.1 RNA Sequence

    2. XR_007064416.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      64311223..64319236 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_008488910.1 RNA Sequence

    2. XR_008488909.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O75971.1 GenPept UniProtKB/Swiss-Prot:O75971

    Gene LinkOut

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

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