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

    Gene ID: 6619, updated on 27-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
    mouse all
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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
    • 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)

    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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