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    Scfd2 Sec1 family domain containing 2 [ Mus musculus (house mouse) ]

    Gene ID: 212986, updated on 2-Nov-2024

    Summary

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    Official Symbol
    Scfd2provided by MGI
    Official Full Name
    Sec1 family domain containing 2provided by MGI
    Primary source
    MGI:MGI:2443446
    See related
    Ensembl:ENSMUSG00000062110 AllianceGenome:MGI:2443446
    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
    STXBP1L1; E430013M20Rik
    Summary
    Predicted to be involved in intracellular protein transport and vesicle-mediated transport. Orthologous to human SCFD2 (sec1 family domain containing 2). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in adrenal adult (RPKM 2.3), genital fat pad adult (RPKM 2.1) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Scfd2 in Genome Data Viewer
    Location:
    5 C3.3; 5 39.44 cM
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 5 NC_000071.7 (74365477..74692436, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 5 NC_000071.6 (74204816..74531742, complement)

    Chromosome 5 - NC_000071.7Genomic Context describing neighboring genes Neighboring gene predicted gene, 32002 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:74596657-74596859 Neighboring gene RAS-like, family 11, member B Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:74656347-74656530 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:74656616-74656725 Neighboring gene STARR-seq mESC enhancer starr_13406 Neighboring gene predicted gene, 32064 Neighboring gene VISTA enhancer mm139 Neighboring gene CapStarr-seq enhancer MGSCv37_chr5:74762842-74763025 Neighboring gene STARR-seq mESC enhancer starr_13407 Neighboring gene STARR-positive B cell enhancer ABC_E2746 Neighboring gene STARR-positive B cell enhancer ABC_E6339 Neighboring gene factor interacting with PAPOLA and CPSF1 Neighboring gene ligand of numb-protein X 1 Neighboring gene predicted gene, 32304

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data 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

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    Related articles in PubMed

    1. Database resources of the National Center for Biotechnology Information. Wheeler DL, et al. Nucleic Acids Res, 2001 Jan 1. PMID 11125038, Free PMC Article
    2. BayGenomics: a resource of insertional mutations in mouse embryonic stem cells. Stryke D, et al. Nucleic Acids Res, 2003 Jan 1. PMID 12520002, Free PMC Article
    3. Genetic determinants of micronucleus formation in vivo. Adams DJ, et al. Nature, 2024 Mar. PMID 38355793, Free PMC Article
    4. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, et al. Genome Res, 1996 Sep. PMID 8889548
    5. Wnk1 kinase deficiency lowers blood pressure in mice: a gene-trap screen to identify potential targets for therapeutic intervention. Zambrowicz BP, et al. Proc Natl Acad Sci U S A, 2003 Nov 25. PMID 14610273, Free PMC Article

    See all (16) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

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

    General gene information

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    Markers

    Homology

    Clone Names

    • 9330137G15

    Gene Ontology Provided by MGI

    Process Evidence Code Pubs
    involved_in intracellular protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in vesicle-mediated transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in vesicle-mediated transport IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    sec1 family domain-containing protein 2
    Names
    neuronal Sec1
    syntaxin-binding protein 1-like 1

    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_001114660.2 → NP_001108132.1  sec1 family domain-containing protein 2 isoform a

      See identical proteins and their annotated locations for NP_001108132.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (a) encodes the longest isoform (a).
      Source sequence(s)
      AC115823, AI850693, AK140246
      Consensus CDS
      CCDS51519.1
      UniProtKB/Swiss-Prot
      Q3USN5, Q8BFV9, Q8BKU5, Q8BKZ0, Q8BTP6, Q8BTQ9, Q8BTY8, Q8BXI1, Q8BXS0, Q8BZ58
      UniProtKB/TrEMBL
      Q3UPD0
      Related
      ENSMUSP00000072636.7, ENSMUST00000072857.13
      Conserved Domains (1) summary
      cl15415
      Location:625 → 665
      Sec1; Sec1 family

    2. NM_001286437.1 → NP_001273366.1  sec1 family domain-containing protein 2 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (c) lacks an alternate in-frame exon in the 3' coding region, compared to variant a. It encodes isoform c, which is shorter than isoform a.
      Source sequence(s)
      AC115823, AI850693, AK135666, AK140246
      Consensus CDS
      CCDS71603.1
      UniProtKB/TrEMBL
      Q3UPD0
      Related
      ENSMUSP00000109170.3, ENSMUST00000113542.9

    3. NM_178672.7 → NP_848787.2  sec1 family domain-containing protein 2 isoform b

      See identical proteins and their annotated locations for NP_848787.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (b) lacks several exons and includes an alternate 3' terminal exon, compared to variant a. It encodes isoform b which is shorter and has a distinct C-terminus, compared to isoform a.
      Source sequence(s)
      AK034000, AK140246, AK163028
      Consensus CDS
      CCDS19345.1
      UniProtKB/TrEMBL
      Q3TR67
      Related
      ENSMUSP00000121098.2, ENSMUST00000151474.3

    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_000071.7 Reference GRCm39 C57BL/6J

      Range
      74365477..74692436 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036164982.1 → XP_036020875.1  sec1 family domain-containing protein 2 isoform X1

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BTY8.1 GenPept UniProtKB/Swiss-Prot:Q8BTY8

    Gene LinkOut

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

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