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    Snx12 sorting nexin 12 [ Mus musculus (house mouse) ]

    Gene ID: 55988, updated on 27-Nov-2024

    Summary

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    Official Symbol
    Snx12provided by MGI
    Official Full Name
    sorting nexin 12provided by MGI
    Primary source
    MGI:MGI:1919331
    See related
    Ensembl:ENSMUSG00000046032 AllianceGenome:MGI:1919331
    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
    SDP8; 2610001F05Rik
    Summary
    Predicted to enable enzyme binding activity and phosphatidylinositol-3-phosphate binding activity. Predicted to be involved in several processes, including endosomal transport; negative regulation of protein metabolic process; and regulation of vesicle-mediated transport. Predicted to be located in early endosome. Predicted to be part of retromer complex. Predicted to be active in early endosome membrane. Is expressed in central nervous system; lung; and spleen. Orthologous to human SNX12 (sorting nexin 12). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in placenta adult (RPKM 5.4), CNS E14 (RPKM 4.4) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Snx12 in Genome Data Viewer
    Location:
    X D; X 43.72 cM
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) X NC_000086.8 (100132973..100266185, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) X NC_000086.7 (101089367..101222583, complement)

    Chromosome X - NC_000086.8Genomic Context describing neighboring genes Neighboring gene high mobility group protein B1-like Neighboring gene STARR-seq mESC enhancer starr_47640 Neighboring gene predicted gene 3820 Neighboring gene solute carrier family 7 (cationic amino acid transporter, y+ system), member 3 Neighboring gene predicted gene, 24061 Neighboring gene STARR-seq mESC enhancer starr_47642 Neighboring gene predicted gene, 22472 Neighboring gene STARR-seq mESC enhancer starr_47643 Neighboring gene forkhead box O4

    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
    • 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. Expression of sorting nexin 12 is regulated in developing cerebral cortical neurons. Mizutani R, et al. J Neurosci Res, 2012 Apr. PMID 22109349
    2. Phenotypic annotation of the mouse X chromosome. Cox BJ, et al. Genome Res, 2010 Aug. PMID 20548051, Free PMC Article
    3. Mutagenesis of diploid mammalian genes by gene entrapment. Lin Q, et al. Nucleic Acids Res, 2006. PMID 17062627, Free PMC Article
    4. Identification of new ciliary signaling pathways in the brain and insights into neurological disorders. Loukil A, et al. bioRxiv, 2023 Dec 21. PMID 38187761, Free PMC Article
    5. USP7 represses lineage differentiation genes in mouse embryonic stem cells by both catalytic and noncatalytic activities. Liu C, et al. Sci Adv, 2023 May 19. PMID 37196079, Free PMC Article

    See all (24) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. These results suggest that SNX12 regulates neurite formation during cerebral cortical development.
      Title: Expression of sorting nexin 12 is regulated in developing cerebral cortical neurons.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Gene trapped (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 enzyme binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables phosphatidylinositol binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatidylinositol binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables phosphatidylinositol-3-phosphate binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in endocytic recycling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in late endosome to Golgi transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of early endosome to late endosome transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of protein catabolic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of protein processing ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in negative regulation of protein transport ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in regulation of endocytosis ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    located_in early endosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in early endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of retromer complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    sorting nexin-12

    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_001110310.2 → NP_001103780.1  sorting nexin-12 isoform 1

      See identical proteins and their annotated locations for NP_001103780.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the shortest isoform (1). An in-frame AUG is located 45 codons upstream of the annotated translation start site but is not being annotated as a start site since it is not conserved and is in a weak Kozak sequence context.
      Source sequence(s)
      AL671926
      Consensus CDS
      CCDS53151.1
      UniProtKB/TrEMBL
      Q6ZWQ5, Q99M52
      Related
      ENSMUSP00000113117.2, ENSMUST00000120389.8
      Conserved Domains (1) summary
      cd07294
      Location:27 → 158
      PX_SNX12; The phosphoinositide binding Phox Homology domain of Sorting Nexin 12

    2. NM_001110311.2 → NP_001103781.1  sorting nexin-12 isoform 2

      See identical proteins and their annotated locations for NP_001103781.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region, compared to variant 1. It encodes isoform 2 which has a longer, distinct C-terminus, compared to isoform 1. An in-frame AUG is located 45 codons upstream of the annotated translation start site but is not being annotated as a start site since it is not conserved and is in a weak Kozak sequence context.
      Source sequence(s)
      AL671926, AL672308
      Consensus CDS
      CCDS53152.1
      UniProtKB/TrEMBL
      Q3V2H3, Q99M52
      Related
      ENSMUSP00000119102.2, ENSMUST00000156473.8
      Conserved Domains (1) summary
      cd07294
      Location:27 → 158
      PX_SNX12; The phosphoinositide binding Phox Homology domain of Sorting Nexin 12

    3. NM_018875.3 → NP_061363.2  sorting nexin-12 isoform 3

      See identical proteins and their annotated locations for NP_061363.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 3' coding region and UTR, compared to variant 1. It encodes isoform 3 which has a longer, distinct C-terminus, compared to isoform 1. An in-frame AUG is located 45 codons upstream of the annotated translation start site but is not being annotated as a start site since it is not conserved and is in a weak Kozak sequence context.
      Source sequence(s)
      AL671926
      Consensus CDS
      CCDS41076.1
      UniProtKB/TrEMBL
      Q3TGS7, Q99M52
      Related
      ENSMUSP00000077038.4, ENSMUST00000077876.4
      Conserved Domains (1) summary
      cd07294
      Location:27 → 158
      PX_SNX12; The phosphoinositide binding Phox Homology domain of Sorting Nexin 12

    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_000086.8 Reference GRCm39 C57BL/6J

      Range
      100132973..100266185 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036162035.1 → XP_036017928.1  sorting nexin-12 isoform X1

      Conserved Domains (1) summary
      cd07294
      Location:72 → 203
      PX_SNX12; The phosphoinositide binding Phox Homology domain of Sorting Nexin 12

    2. XM_011247645.3 → XP_011245947.2  sorting nexin-12 isoform X1

      Conserved Domains (1) summary
      cd07294
      Location:72 → 203
      PX_SNX12; The phosphoinositide binding Phox Homology domain of Sorting Nexin 12

    3. XM_011247646.3 → XP_011245948.2  sorting nexin-12 isoform X2

      Conserved Domains (1) summary
      cd07294
      Location:72 → 203
      PX_SNX12; The phosphoinositide binding Phox Homology domain of Sorting Nexin 12
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    O70493.1 GenPept UniProtKB/Swiss-Prot:O70493

    Gene LinkOut

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

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