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

Gene ID: 10302, updated on 7-Apr-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
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Genomic context

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Location:
15q22.31
Exon count:
4
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (66489748..66497762, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (64311223..64319236, complement)
105.20220307 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
  • 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 (22) 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_2023_10

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

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