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

Gene ID: 76983, updated on 2-Nov-2024

Summary

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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 syntaxin binding activity. Predicted to be involved in several processes, including Golgi vesicle transport; negative regulation of autophagosome assembly; and regulation of ER to Golgi vesicle-mediated transport. Predicted to be located in Golgi-associated vesicle and cis-Golgi network. 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, Nov 2024]
Expression
Broad expression in placenta adult (RPKM 10.2), limb E14.5 (RPKM 6.3) and 24 other tissues See more
Orthologs
human all
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Genomic context

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See Scfd1 in Genome Data Viewer
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

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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. 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 (23) 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) 

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
  
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 IEA
Inferred from Electronic Annotation
more info
  
enables syntaxin binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
involved_in cell morphogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
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 IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of autophagosome assembly ISO
Inferred from Sequence Orthology
more info
  
involved_in post-Golgi vesicle-mediated transport IEA
Inferred from Electronic Annotation
more info
  
involved_in post-Golgi vesicle-mediated transport ISO
Inferred from Sequence Orthology
more info
  
involved_in protein transport IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of ER to Golgi vesicle-mediated 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 IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of protein transport ISO
Inferred from Sequence Orthology
more info
  
involved_in response to hypoxia IEA
Inferred from Electronic Annotation
more info
  
involved_in response to toxic substance IEA
Inferred from Electronic Annotation
more info
  
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
  
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in Golgi cisterna membrane 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 IEA
Inferred from Electronic Annotation
more info
  
located_in Golgi-associated vesicle ISO
Inferred from Sequence Orthology
more info
  
located_in cis-Golgi network IEA
Inferred from Electronic Annotation
more info
  
located_in cis-Golgi network ISO
Inferred from Sequence Orthology
more info
  
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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

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_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

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