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snapc4 small nuclear RNA activating complex, polypeptide 4 [ Danio rerio (zebrafish) ]

Gene ID: 561241, updated on 2-Nov-2024

Summary

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Official Symbol
snapc4provided by ZNC
Official Full Name
small nuclear RNA activating complex, polypeptide 4provided by ZNC
Primary source
ZFIN:ZDB-GENE-030131-5794
See related
Ensembl:ENSDARG00000067673 AllianceGenome:ZFIN:ZDB-GENE-030131-5794
Gene type
protein coding
RefSeq status
PROVISIONAL
Organism
Danio rerio
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as
fi18h02; wu:fi18h02; si:dkey-1o2.4; si:dkey-1o2.5
Summary
Predicted to enable RNA polymerase III type 3 promoter sequence-specific DNA binding activity. Predicted to contribute to RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Acts upstream of or within intrahepatic bile duct development and pancreas development. Predicted to be located in nucleus. Predicted to be part of snRNA-activating protein complex. Is expressed in brain; digestive system; and head. Orthologous to human SNAPC4 (small nuclear RNA activating complex polypeptide 4). [provided by Alliance of Genome Resources, Nov 2024]
Orthologs
human mouse all
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Genomic context

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See snapc4 in Genome Data Viewer
Location:
chromosome: 5
Exon count:
27
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCz11 (GCF_000002035.6) 5 NC_007116.7 (51168832..51198464, complement)
105 previous assembly GRCz10 (GCF_000002035.5) 5 NC_007116.6 (50522239..50551951, complement)

Chromosome 5 - NC_007116.7Genomic Context describing neighboring genes Neighboring gene protein-O-mannosyltransferase 1 Neighboring gene coiled-coil domain containing 180 Neighboring gene caspase recruitment domain family, member 9 Neighboring gene endosome associated trafficking regulator 1 Neighboring gene UBA domain containing 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
  • BioProject: PRJEB1986
  • Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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Related articles in PubMed

  1. Mutation of zebrafish Snapc4 is associated with loss of the intrahepatic biliary network. Schaub M, et al. Dev Biol, 2012 Mar 1. PMID 22222761, Free PMC Article
  2. Fast homozygosity mapping and identification of a zebrafish ENU-induced mutation by whole-genome sequencing. Voz ML, et al. PLoS One, 2012. PMID 22496837, Free PMC Article
  3. Structure and expression pattern of teleost caspase recruitment domain (CARD) containing proteins that are potentially involved in NF-kappaB signalling. Chang MX, et al. Dev Comp Immunol, 2010 Jan. PMID 19699229
  4. Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy. Lee YR, et al. Nat Commun, 2020 Jul 23. PMID 32703943, Free PMC Article
  5. Zebrafish models of human liver development and disease. Wilkins BJ, et al. Compr Physiol, 2013 Jul. PMID 23897685, Free PMC Article

See all (8) citations in PubMed

GeneRIFs: Gene References Into Functions

General gene information

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Markers

Homology

Gene Ontology Provided by ZFIN

Function Evidence Code Pubs
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 type 3 promoter sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within intrahepatic bile duct development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within pancreas development IMP
Inferred from Mutant Phenotype
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
  
Component Evidence Code Pubs
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
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 4

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_001258410.1 → NP_001245339.1  snRNA-activating protein complex subunit 4

    See identical proteins and their annotated locations for NP_001245339.1

    Status: PROVISIONAL

    Source sequence(s)
    JQ434101
    UniProtKB/TrEMBL
    I1V1W6
    Conserved Domains (4) summary
    smart00717
    Location:373 → 424
    SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains
    pfam00249
    Location:428 → 474
    Myb_DNA-binding; Myb-like DNA-binding domain
    pfam13921
    Location:376 → 439
    Myb_DNA-bind_6; Myb-like DNA-binding domain
    cl21498
    Location:316 → 369
    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_000002035.6-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCz11 Primary Assembly

Genomic

  1. NC_007116.7 Reference GRCz11 Primary Assembly

    Range
    51168832..51198464 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_009301777.4 → XP_009300052.2  snRNA-activating protein complex subunit 4 isoform X1

  2. XM_021476210.2 → XP_021331885.1  snRNA-activating protein complex subunit 4 isoform X2

    UniProtKB/TrEMBL
    A0A0R4IFN5, A0A8M6Z6X7, F1QVS5
    Related
    ENSDARP00000088244.5, ENSDART00000097473.5
    Conserved Domains (5) summary
    pfam00249
    Location:428 → 474
    Myb_DNA-binding; Myb-like DNA-binding domain
    pfam13921
    Location:376 → 439
    Myb_DNA-bind_6; Myb-like DNA-binding domain
    cl21498
    Location:316 → 369
    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 ...
    cl25732
    Location:5 → 150
    SMC_N; RecF/RecN/SMC N terminal domain
    cl28544
    Location:426 → 539
    SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains

  3. XM_021476209.2 → XP_021331884.1  snRNA-activating protein complex subunit 4 isoform X2

    UniProtKB/TrEMBL
    A0A0R4IFN5, A0A8M6Z6X7, F1QVS5
    Conserved Domains (5) summary
    pfam00249
    Location:428 → 474
    Myb_DNA-binding; Myb-like DNA-binding domain
    pfam13921
    Location:376 → 439
    Myb_DNA-bind_6; Myb-like DNA-binding domain
    cl21498
    Location:316 → 369
    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 ...
    cl25732
    Location:5 → 150
    SMC_N; RecF/RecN/SMC N terminal domain
    cl28544
    Location:426 → 539
    SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains

  4. XM_017356122.3 → XP_017211611.2  snRNA-activating protein complex subunit 4 isoform X2

    UniProtKB/TrEMBL
    A0A0R4IFN5, A0A8M6Z6X7, F1QVS5
    Related
    ENSDARP00000132199.1, ENSDART00000165870.2
    Conserved Domains (5) summary
    pfam00249
    Location:428 → 474
    Myb_DNA-binding; Myb-like DNA-binding domain
    pfam13921
    Location:376 → 439
    Myb_DNA-bind_6; Myb-like DNA-binding domain
    cl21498
    Location:316 → 369
    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 ...
    cl25732
    Location:5 → 150
    SMC_N; RecF/RecN/SMC N terminal domain
    cl28544
    Location:426 → 539
    SANT; SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains

Reference GRCz11 ALT_DRER_TU_1

Genomic

  1. NW_018394610.1 Reference GRCz11 ALT_DRER_TU_1

    Range
    299752..315471 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCz11 ALT_DRER_TU_1

Genomic

  1. NW_018394611.1 Reference GRCz11 ALT_DRER_TU_1

    Range
    3202..12583 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein Strain
Heading Accession and Version

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