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    scfd1 sec1 family domain containing 1 [ Danio rerio (zebrafish) ]

    Gene ID: 317732, updated on 9-Dec-2024

    Summary

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    Official Symbol
    scfd1provided by ZNC
    Official Full Name
    sec1 family domain containing 1provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030116-3
    See related
    Ensembl:ENSDARG00000000779 AllianceGenome:ZFIN:ZDB-GENE-030116-3
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    sly1; dZ234G15.2; SI:dZ115O7.1; SI:dZ234G15.3; SI:dZ234G15.4; SI:dZ234G15.5; SI:dZ234G15.7; si:dz234g15.2; si:busm1-234g15.2
    Summary
    Predicted to enable syntaxin binding activity. Acts upstream of or within several processes, including fin regeneration; glycoprotein transport; and skeletal system development. Predicted to be active in Golgi membrane. Is expressed in digestive system; head; myotome; notochord; and pharyngeal arch. Orthologous to human SCFD1 (sec1 family domain containing 1). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See scfd1 in Genome Data Viewer
    Location:
    chromosome: 17
    Exon count:
    25
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 17 NC_007128.7 (28771027..28797395, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 17 NC_007128.6 (28754064..28780432, complement)

    Chromosome 17 - NC_007128.7Genomic Context describing neighboring genes Neighboring gene coagulation factor C homolog, cochlin (Limulus polyphemus) Neighboring gene opsin 6, group member b Neighboring gene si:dkey-28g23.3 Neighboring gene uncharacterized LOC108179771 Neighboring gene G2/M-phase specific E3 ubiquitin protein ligase

    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
    • 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. Positional cloning of a temperature-sensitive mutant emmental reveals a role for sly1 during cell proliferation in zebrafish fin regeneration. Nechiporuk A, et al. Dev Biol, 2003 Jun 15. PMID 12798289
    2. The Sec domain protein Scfd1 facilitates trafficking of ECM components during chondrogenesis. Hou N, et al. Dev Biol, 2017 Jan 1. PMID 27851892
    3. Loss of Sec-1 Family Domain-Containing 1 (scfd1) Causes Severe Cardiac Defects and Endoplasmic Reticulum Stress in Zebrafish. Huttner IG, et al. J Cardiovasc Dev Dis, 2023 Sep 22. PMID 37887855, Free PMC Article
    4. Simplet controls cell proliferation and gene transcription during zebrafish caudal fin regeneration. Kizil C, et al. Dev Biol, 2009 Jan 15. PMID 19014929
    5. The BH3-only SNARE BNip1 mediates photoreceptor apoptosis in response to vesicular fusion defects. Nishiwaki Y, et al. Dev Cell, 2013 May 28. PMID 23725763

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. the existence of a specific export pathway, mediated by a complex containing SCFD1 and STX18 that plays an essential role in secretion of large extracellular matrix proteins during chondrogenesis.
      Title: The Sec domain protein Scfd1 facilitates trafficking of ECM components during chondrogenesis.
    2. sly1 is essential for blastemal organization and proliferation during two stages of fin regeneration
      Title: Positional cloning of a temperature-sensitive mutant emmental reveals a role for sly1 during cell proliferation in zebrafish fin regeneration.
    Submit: New GeneRIF Correction

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables syntaxin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within cartilage development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within embryonic neurocranium morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within endoplasmic reticulum to Golgi vesicle-mediated transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within fin regeneration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within glycoprotein transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within heart contraction IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in intracellular protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within regulation of cardiac muscle fiber development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within regulation of response to endoplasmic reticulum stress IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in Golgi membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    sec1 family domain-containing protein 1
    Names
    emm
    emmental
    suppressor of ypt1
    vesicle-transport

    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_182861.2 → NP_878281.2  sec1 family domain-containing protein 1

      Status: VALIDATED

      Source sequence(s)
      BX324186
      UniProtKB/TrEMBL
      Q8AUT3
      Related
      ENSDARP00000121390.2, ENSDART00000134735.4

    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_007128.7 Reference GRCz11 Primary Assembly

      Range
      28771027..28797395 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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