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    SNAPC4 small nuclear RNA activating complex polypeptide 4 [ Homo sapiens (human) ]

    Gene ID: 6621, updated on 27-Nov-2024

    Summary

    Official Symbol
    SNAPC4provided by HGNC
    Official Full Name
    small nuclear RNA activating complex polypeptide 4provided by HGNC
    Primary source
    HGNC:HGNC:11137
    See related
    Ensembl:ENSG00000165684 MIM:602777; AllianceGenome:HGNC:11137
    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
    NEDRSO; SNAP190; PTFalpha
    Summary
    This gene encodes the largest subunit of the small nuclear RNA-activating protein (SNAP) complex. The encoded protein contains a Myb DNA-binding domain, and is essential for RNA polymerase II and III polymerase transcription from small nuclear RNA promoters. A mutation in this gene is associated with ankylosing spondylitis. [provided by RefSeq, Jul 2016]
    Expression
    Broad expression in testis (RPKM 5.9), spleen (RPKM 2.6) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SNAPC4 in Genome Data Viewer
    Location:
    9q34.3
    Exon count:
    24
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (136375571..136400170, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (148604905..148629504, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (139270023..139294622, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene G protein signaling modulator 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20508 Neighboring gene uncharacterized LOC124902309 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20509 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20510 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139258773-139259663 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139259664-139260553 Neighboring gene DNL-type zinc finger Neighboring gene caspase recruitment domain family member 9 Neighboring gene Sharpr-MPRA regulatory region 3996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139268303-139269016 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:139291906-139293105 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20511 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20512 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20513 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:139294835-139295771 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29306 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:139301375-139301963 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29307 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20515 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20516 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29308 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29309 Neighboring gene endosome associated trafficking regulator 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:139310410-139311609 Neighboring gene peptidase, mitochondrial processing subunit alpha

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Neurodevelopmental disorder with motor regression, progressive spastic paraplegia, and oromotor dysfunction
    MedGen: C5882695 OMIM: 620515 GeneReviews: Not available
    not available

    EBI GWAS Catalog

    Description
    A genome-wide association study on a southern European population identifies a new Crohn's disease susceptibility locus at RBX1-EP300.
    EBI GWAS Catalog
    Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
    EBI GWAS Catalog
    Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ13451

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in snRNA transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in snRNA transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in snRNA transcription by RNA polymerase III IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in snRNA transcription by RNA polymerase III IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IC
    Inferred by Curator
    more info
    PubMed 
    part_of snRNA-activating protein complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of snRNA-activating protein complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    snRNA-activating protein complex subunit 4
    Names
    PSE-binding factor subunit alpha
    PTF subunit alpha
    SNAPc 190 kDa subunit
    SNAPc subunit 4
    proximal sequence element-binding transcription factor subunit alpha
    snRNA-activating protein complex 190 kDa subunit

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_051233.1 RefSeqGene

      Range
      5051..29650
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001394201.1NP_001381130.1  snRNA-activating protein complex subunit 4 isoform a

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (a). Variants 1 and 2 both encode the same isoform (a).
      Source sequence(s)
      AL592301
      Consensus CDS
      CCDS6998.1
      UniProtKB/Swiss-Prot
      Q5SXM2, Q9Y6P7
      Related
      ENSP00000490037.2, ENST00000637388.2
      Conserved Domains (5) summary
      smart00717
      Location:401448
      SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
      PLN03091
      Location:399502
      PLN03091; hypothetical protein; Provisional
      PHA03247
      Location:8171215
      PHA03247; large tegument protein UL36; Provisional
      pfam13921
      Location:297357
      Myb_DNA-bind_6; Myb-like DNA-binding domain
      cl21498
      Location:262305
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...
    2. NM_001394202.1NP_001381131.1  snRNA-activating protein complex subunit 4 isoform b

      Status: REVIEWED

      Source sequence(s)
      AL592301
      Conserved Domains (5) summary
      smart00717
      Location:401448
      SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
      PLN03091
      Location:399502
      PLN03091; hypothetical protein; Provisional
      PHA03247
      Location:7891187
      PHA03247; large tegument protein UL36; Provisional
      pfam13921
      Location:297357
      Myb_DNA-bind_6; Myb-like DNA-binding domain
      cl21498
      Location:262305
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...
    3. NM_001394203.1NP_001381132.1  snRNA-activating protein complex subunit 4 isoform b

      Status: REVIEWED

      Source sequence(s)
      AL592301
      Conserved Domains (5) summary
      smart00717
      Location:401448
      SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
      PLN03091
      Location:399502
      PLN03091; hypothetical protein; Provisional
      PHA03247
      Location:7891187
      PHA03247; large tegument protein UL36; Provisional
      pfam13921
      Location:297357
      Myb_DNA-bind_6; Myb-like DNA-binding domain
      cl21498
      Location:262305
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...
    4. NM_003086.4NP_003077.2  snRNA-activating protein complex subunit 4 isoform a

      See identical proteins and their annotated locations for NP_003077.2

      Status: REVIEWED

      Source sequence(s)
      AL592301
      Consensus CDS
      CCDS6998.1
      UniProtKB/Swiss-Prot
      Q5SXM2, Q9Y6P7
      Related
      ENSP00000510559.1, ENST00000684778.1
      Conserved Domains (5) summary
      smart00717
      Location:401448
      SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
      PLN03091
      Location:399502
      PLN03091; hypothetical protein; Provisional
      PHA03247
      Location:8171215
      PHA03247; large tegument protein UL36; Provisional
      pfam13921
      Location:297357
      Myb_DNA-bind_6; Myb-like DNA-binding domain
      cl21498
      Location:262305
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...

    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
      136375571..136400170 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047423780.1XP_047279736.1  snRNA-activating protein complex subunit 4 isoform X2

    2. XM_006717242.5XP_006717305.1  snRNA-activating protein complex subunit 4 isoform X1

      See identical proteins and their annotated locations for XP_006717305.1

      UniProtKB/Swiss-Prot
      Q5SXM2, Q9Y6P7
      Conserved Domains (5) summary
      smart00717
      Location:401448
      SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
      PLN03091
      Location:399502
      PLN03091; hypothetical protein; Provisional
      PHA03247
      Location:8171215
      PHA03247; large tegument protein UL36; Provisional
      pfam13921
      Location:297357
      Myb_DNA-bind_6; Myb-like DNA-binding domain
      cl21498
      Location:262305
      SANT; 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is ...
    3. XM_006717244.3XP_006717307.1  snRNA-activating protein complex subunit 4 isoform X4

      Conserved Domains (1) summary
      PHA03247
      Location:221619
      PHA03247; large tegument protein UL36; Provisional
    4. XM_047423781.1XP_047279737.1  snRNA-activating protein complex subunit 4 isoform X3

    5. XM_047423782.1XP_047279738.1  snRNA-activating protein complex subunit 4 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      148604905..148629504 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054363624.1XP_054219599.1  snRNA-activating protein complex subunit 4 isoform X2

    2. XM_054363623.1XP_054219598.1  snRNA-activating protein complex subunit 4 isoform X1

    3. XM_054363626.1XP_054219601.1  snRNA-activating protein complex subunit 4 isoform X4

    4. XM_054363625.1XP_054219600.1  snRNA-activating protein complex subunit 4 isoform X3

    5. XM_054363627.1XP_054219602.1  snRNA-activating protein complex subunit 4 isoform X5