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SNAPC3 small nuclear RNA activating complex polypeptide 3 [ Homo sapiens (human) ]

Gene ID: 6619, updated on 2-Nov-2024

Summary

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Official Symbol
SNAPC3provided by HGNC
Official Full Name
small nuclear RNA activating complex polypeptide 3provided by HGNC
Primary source
HGNC:HGNC:11136
See related
Ensembl:ENSG00000164975 MIM:602348; AllianceGenome:HGNC:11136
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SNAP50; PTFbeta
Summary
Predicted to enable RNA polymerase III type 3 promoter sequence-specific DNA binding activity and bent DNA binding activity. Predicted to contribute to RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and core promoter sequence-specific DNA binding activity. Predicted to be involved in snRNA transcription by RNA polymerase II and snRNA transcription by RNA polymerase III. Located in nuclear body and nucleolus. [provided by Alliance of Genome Resources, Nov 2024]
Expression
Broad expression in testis (RPKM 18.8), brain (RPKM 8.0) and 24 other tissues See more
Orthologs
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Genomic context

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See SNAPC3 in Genome Data Viewer
Location:
9p22.3
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (15422876..15466735)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (15434805..15478667)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (15422874..15466733)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene NANOG hESC enhancer GRCh37_chr9:15175934-15176435 Neighboring gene tetratricopeptide repeat domain 39B Neighboring gene Sharpr-MPRA regulatory region 7105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19777 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:15305852-15306415 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:15306979-15307541 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:15354881-15355722 Neighboring gene ribosomal protein L7 pseudogene 33 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:15418920-15419420 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19780 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28214 Neighboring gene RNA, U6 small nuclear 319, pseudogene Neighboring gene PC4 and SRSF1 interacting protein 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:15510081-15511034 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:15511035-15511987 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr9:15512640-15513258 Neighboring gene thymosin beta-11-like Neighboring gene RNA, 7SL, cytoplasmic 98, pseudogene

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. [Diagnostic importance of determining 17-ketosteroids in gynecology]. Bagramian ER, et al. Akush Ginekol (Mosk), 1977 Feb. PMID 900378
  2. The unorthodox SNAP50 zinc finger domain contributes to cooperative promoter recognition by human SNAPC. Jawdekar GW, et al. J Biol Chem, 2006 Oct 13. PMID 16901896
  3. Cloning and characterization of the beta subunit of human proximal sequence element-binding transcription factor and its involvement in transcription of small nuclear RNA genes by RNA polymerases II and III. Bai L, et al. Mol Cell Biol, 1996 Oct. PMID 8816454, Free PMC Article
  4. Structural basis of human SNAPc recognizing proximal sequence element of snRNA promoter. Sun J, et al. Nat Commun, 2022 Nov 11. PMID 36369505, Free PMC Article
  5. Cloning and characterization of SNAP50, a subunit of the snRNA-activating protein complex SNAPc. Henry RW, et al. EMBO J, 1996 Dec 16. PMID 9003788, Free PMC Article

See all (27) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SNAP50 zinc finger domain contributes to cooperative promoter recognition by human SNAPC
    Title: The unorthodox SNAP50 zinc finger domain contributes to cooperative promoter recognition by human SNAPC.
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

Clone Names

  • MGC33124, MGC132011

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding TAS
Traceable Author Statement
more info
 PubMed 
contributes_to RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase III general transcription initiation factor activity NAS
Non-traceable Author Statement
more info
 PubMed 
enables RNA polymerase III type 3 promoter sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables bent DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
contributes_to core promoter sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in snRNA transcription TAS
Traceable Author Statement
more info
 PubMed 
involved_in snRNA transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in snRNA transcription by RNA polymerase III IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 PubMed 
involved_in transcription by RNA polymerase III TAS
Traceable Author Statement
more info
 PubMed 
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 
part_of snRNA-activating protein complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
snRNA-activating protein complex subunit 3
Names
PSE-binding factor subunit beta
PTF subunit beta
SNAPc 50 kDa subunit
SNAPc subunit 3
proximal sequence element-binding transcription factor subunit beta
small nuclear RNA activating complex, polypeptide 3, 50kD
small nuclear RNA activating complex, polypeptide 3, 50kDa
snRNA-activating protein complex 50 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.

mRNA and Protein(s)

  1. NM_001039697.2 → NP_001034786.1  snRNA-activating protein complex subunit 3 isoform 1

    See identical proteins and their annotated locations for NP_001034786.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AL441925
    Consensus CDS
    CCDS6478.1
    UniProtKB/Swiss-Prot
    D3DRI8, Q2VPI6, Q5T285, Q92966
    Related
    ENSP00000370200.3, ENST00000380821.8
    Conserved Domains (1) summary
    pfam12251
    Location:202 → 403
    zf-SNAP50_C; snRNA-activating protein of 50kDa MW C terminal

  2. NM_001369647.3 → NP_001356576.1  snRNA-activating protein complex subunit 3 isoform 2

    Status: VALIDATED

    Source sequence(s)
    AL441925
    Conserved Domains (1) summary
    pfam12251
    Location:202 → 377
    zf-SNAP50_C; snRNA-activating protein of 50kDa MW C terminal

  3. NM_001369648.2 → NP_001356577.1  snRNA-activating protein complex subunit 3 isoform 3

    Status: VALIDATED

    Source sequence(s)
    AL359998, AL441925
    Conserved Domains (1) summary
    pfam12251
    Location:202 → 363
    zf-SNAP50_C; snRNA-activating protein of 50kDa MW C terminal

  4. NM_001369649.3 → NP_001356578.1  snRNA-activating protein complex subunit 3 isoform 4

    Status: VALIDATED

    Source sequence(s)
    AL441925
    Conserved Domains (1) summary
    pfam12251
    Location:194 → 353
    zf-SNAP50_C; snRNA-activating protein of 50kDa MW C terminal

  5. NM_001369650.3 → NP_001356579.1  snRNA-activating protein complex subunit 3 isoform 5

    Status: VALIDATED

    Source sequence(s)
    AL441925
    Conserved Domains (1) summary
    pfam12251
    Location:202 → 348
    zf-SNAP50_C; snRNA-activating protein of 50kDa MW C terminal

  6. NM_001369651.2 → NP_001356580.1  snRNA-activating protein complex subunit 3 isoform 6

    Status: VALIDATED

    Source sequence(s)
    AL359998, AL441925
    Conserved Domains (1) summary
    pfam12251
    Location:202 → 335
    zf-SNAP50_C; snRNA-activating protein of 50kDa MW C terminal

RNA

  1. NR_161433.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL359998, AL441925

  2. NR_161434.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL359998, AL441925

  3. NR_161435.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL359998, AL441925

  4. NR_161436.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL441925

  5. NR_161437.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL359998, AL441925

  6. NR_161438.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL359998, AL441925

  7. NR_161439.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL359998, AL441925

  8. NR_161440.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL359998, AL441925

  9. NR_161441.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL441925

  10. NR_161442.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL441925

  11. NR_161443.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL359998, AL441925

  12. NR_161444.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL359998, AL441925

  13. NR_161445.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL441925

  14. NR_161446.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL441925

  15. NR_161447.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL359998, AL441925

  16. NR_161448.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL441925

  17. NR_161449.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL441925

  18. NR_161450.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AL359998, AL441925

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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    15422876..15466735
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017015056.3 → XP_016870545.1  snRNA-activating protein complex subunit 3 isoform X1

    UniProtKB/Swiss-Prot
    D3DRI8, Q2VPI6, Q5T285, Q92966
    Related
    ENSP00000432393.1, ENST00000490969.5
    Conserved Domains (1) summary
    pfam12251
    Location:202 → 403
    zf-SNAP50_C; snRNA-activating protein of 50kDa MW C terminal

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    15434805..15478667
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054363622.1 → XP_054219597.1  snRNA-activating protein complex subunit 3 isoform X1

    UniProtKB/Swiss-Prot
    D3DRI8, Q2VPI6, Q5T285, Q92966

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_003084.1: Suppressed sequence

    Description
    NM_003084.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q92966.1 GenPept UniProtKB/Swiss-Prot:Q92966

Gene LinkOut

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

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