U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination
    • Showing Current items.

    Scfd1 Sec1 family domain containing 1 [ Mus musculus (house mouse) ]

    Gene ID: 76983, updated on 5-Mar-2024

    Summary

    Go to the top of the page Help
    Official Symbol
    Scfd1provided by MGI
    Official Full Name
    Sec1 family domain containing 1provided by MGI
    Primary source
    MGI:MGI:1924233
    See related
    Ensembl:ENSMUSG00000020952 AllianceGenome:MGI:1924233
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    RA410; STXBP1L2; 3110021P21Rik
    Summary
    Predicted to enable protein N-terminus binding activity and syntaxin binding activity. Acts upstream of or within toxin transport. Predicted to be located in Golgi-associated vesicle; cis-Golgi network; and plasma membrane. Predicted to be active in Golgi membrane. Is expressed in vertebral axis musculature. Orthologous to human SCFD1 (sec1 family domain containing 1). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in placenta adult (RPKM 10.2), limb E14.5 (RPKM 6.3) and 24 other tissues See more
    Orthologs
    human all
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    Go to the top of the page Help
    Location:
    12 B3; 12 22.11 cM
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 12 NC_000078.7 (51424296..51496887)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 12 NC_000078.6 (51377513..51450104)

    Chromosome 12 - NC_000078.7Genomic Context describing neighboring genes Neighboring gene ribosomal protein S11, pseudogene 4 Neighboring gene STARR-seq mESC enhancer starr_32102 Neighboring gene STARR-seq mESC enhancer starr_32103 Neighboring gene G2/M-phase specific E3 ubiquitin ligase Neighboring gene predicted gene, 40422 Neighboring gene high mobility group protein 1 pseudogene Neighboring gene STARR-seq mESC enhancer starr_32104 Neighboring gene zyg-11 homolog A pseudogene Neighboring gene cochlin

    Genomic regions, transcripts, and products

    Go to the top of the page Help

    Go to nucleotide: Graphics FASTA GenBank

    Expression

    Go to the top of the page Help
    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

    Go to the top of the pageHelp

    Related articles in PubMed

    1. CCT chaperonin complex is required for efficient delivery of anthrax toxin into the cytosol of host cells. Slater LH, et al. Proc Natl Acad Sci U S A, 2013 Jun 11. PMID 23716698, Free PMC Article
    2. Prediction of the coding sequences of mouse homologues of KIAA gene: III. the complete nucleotide sequences of 500 mouse KIAA-homologous cDNAs identified by screening of terminal sequences of cDNA clones randomly sampled from size-fractionated libraries. Okazaki N, et al. DNA Res, 2003 Aug 31. PMID 14621295
    3. Complementary proteomics strategies capture an ataxin-1 interactome in Neuro-2a cells. Zhang S, et al. Sci Data, 2018 Nov 20. PMID 30457570, Free PMC Article
    4. Irisin Mediates Effects on Bone and Fat via αV Integrin Receptors. Kim H, et al. Cell, 2018 Dec 13. PMID 30550785, Free PMC Article
    5. Database resources of the National Center for Biotechnology Information. Wheeler DL, et al. Nucleic Acids Res, 2001 Jan 1. PMID 11125038, Free PMC Article

    See all (22) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

    Go to the top of the page Help

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 

    Pathways from PubChem

    Go to the top of the page

    Interactions

    Go to the top of the page Help
    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Go to the top of the page Help

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    enables protein-containing complex binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables syntaxin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables syntaxin binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in endoplasmic reticulum to Golgi vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in intracellular protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of autophagosome assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in post-Golgi vesicle-mediated transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of ER to Golgi vesicle-mediated transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of protein transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in Golgi apparatus IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in Golgi membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in Golgi-associated vesicle ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cis-Golgi network ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in endoplasmic reticulum IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

    Go to the top of the page Help
    Preferred Names
    sec1 family domain-containing protein 1
    Names
    syntaxin-binding protein 1-like 2

    NCBI Reference Sequences (RefSeq)

    Go to the top of the page Help

    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.

    mRNA and Protein(s)

    1. NM_001306178.1 → NP_001293107.1  sec1 family domain-containing protein 1 isoform 2

      See identical proteins and their annotated locations for NP_001293107.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks many exons and uses an alternate 3' terminal exon, compared to variant 1. This results in a novel 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AC161116, AK041028, BY210008
      Consensus CDS
      CCDS88336.1
      UniProtKB/Swiss-Prot
      Q8BRF7
      Related
      ENSMUSP00000151347.2, ENSMUST00000219434.2
      Conserved Domains (1) summary
      pfam00995
      Location:41 → 386
      Sec1; Sec1 family

    2. NM_029825.3 → NP_084101.1  sec1 family domain-containing protein 1 isoform 1

      See identical proteins and their annotated locations for NP_084101.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC161116, AK044943, BY210008, CO044480
      Consensus CDS
      CCDS36439.1
      UniProtKB/Swiss-Prot
      Q8BRF7, Q8BRZ2, Q8K179, Q9CXR8
      Related
      ENSMUSP00000021335.6, ENSMUST00000021335.7
      Conserved Domains (1) summary
      pfam00995
      Location:41 → 626
      Sec1; Sec1 family

    RNA

    1. NR_157117.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC161116, AC163670

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000078.7 Reference GRCm39 C57BL/6J

      Range
      51424296..51496887
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_003950090.1 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BRF7.1 GenPept UniProtKB/Swiss-Prot:Q8BRF7

    Gene LinkOut

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

    Chemical Information
    Molecular Biology Databases
    Research Materials
    Tools
    Miscellaneous