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    snx12 sorting nexin 12 [ Danio rerio (zebrafish) ]

    Gene ID: 394098, updated on 9-Dec-2024

    Summary

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    Official Symbol
    snx12provided by ZNC
    Official Full Name
    sorting nexin 12provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-787
    See related
    Ensembl:ENSDARG00000019060 AllianceGenome:ZFIN:ZDB-GENE-040426-787
    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
    fc02c04; fc03c06; fj97e07; zgc:55728; zgc:77034; wu:fc02c04; wu:fc03c06; wu:fj97e07; zgc:158590
    Summary
    Predicted to enable phosphatidylinositol-3-phosphate binding activity. Predicted to be involved in endocytic recycling and late endosome to Golgi transport. Predicted to be located in membrane. Predicted to be part of retromer complex. Predicted to be active in early endosome membrane. Orthologous to human SNX12 (sorting nexin 12). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    human mouse all
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    Genomic context

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    See snx12 in Genome Data Viewer
    Location:
    chromosome: 21
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 21 NC_007132.7 (30470862..30487116)
    105 previous assembly GRCz10 (GCF_000002035.5) 21 NC_007132.6 (30434161..30450421)

    Chromosome 21 - NC_007132.7Genomic Context describing neighboring genes Neighboring gene GrpE-like 2, mitochondrial Neighboring gene actin filament associated protein 1-like 1b Neighboring gene uncharacterized LOC137488828 Neighboring gene solute carrier family 7 member 3a

    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. An antiapoptotic role of sorting nexin 7 is required for liver development in zebrafish. Xu L, et al. Hepatology, 2012 Jun. PMID 22213104
    2. Hematopoietic gene expression profile in zebrafish kidney marrow. Song HD, et al. Proc Natl Acad Sci U S A, 2004 Nov 16. PMID 15520368, Free PMC Article
    3. The zebrafish gene map defines ancestral vertebrate chromosomes. Woods IG, et al. Genome Res, 2005 Sep. PMID 16109975, Free PMC Article
    4. Evolution of complexity in the zebrafish synapse proteome. Bayés À, et al. Nat Commun, 2017 Mar 2. PMID 28252024, Free PMC Article
    5. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, Free PMC Article

    See all (8) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC55728, MGC77034

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables lipid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables phosphatidylinositol binding IEA
    Inferred from Electronic Annotation
    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
    		  
    Component Evidence Code Pubs
    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_001145892.1 → NP_001139364.1  sorting nexin-12 isoform 3

      See identical proteins and their annotated locations for NP_001139364.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the coding region compared to variant 1. The resulting protein (isoform 3) is shorter but has the same N- and C-termini compared to isoform 1.
      Source sequence(s)
      CR749164
      UniProtKB/TrEMBL
      A0A8N1TRW5, A2RV07
      Related
      ENSDARP00000106488.2, ENSDART00000126678.4
      Conserved Domains (1) summary
      cl02563
      Location:27 → 149
      PX_domain; The Phox Homology domain, a phosphoinositide binding module

    2. NM_001145893.1 → NP_001139365.1  sorting nexin-12 isoform 2

      See identical proteins and their annotated locations for NP_001139365.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      CR749164
      UniProtKB/TrEMBL
      Q6TNQ4, Q6TNQ5
      Related
      ENSDARP00000122910.1, ENSDART00000133478.3
      Conserved Domains (1) summary
      cd07294
      Location:27 → 158
      PX_SNX12; The phosphoinositide binding Phox Homology domain of Sorting Nexin 12

    3. NM_001145894.1 → NP_001139366.1  sorting nexin-12 isoform 4

      See identical proteins and their annotated locations for NP_001139366.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains multiple differences in the coding region and differs in the 3' UTR compared to variant 1. The resulting protein (isoform 4) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      CR749164
      UniProtKB/TrEMBL
      A0A8M1NQH6, Q6NYP1
      Related
      ENSDARP00000114138.1, ENSDART00000147375.2
      Conserved Domains (1) summary
      cl02563
      Location:27 → 149
      PX_domain; The Phox Homology domain, a phosphoinositide binding module

    4. NM_201123.2 → NP_957417.1  sorting nexin-12 isoform 1

      See identical proteins and their annotated locations for NP_957417.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      CR749164
      UniProtKB/TrEMBL
      B2GTL0, Q803J1
      Related
      ENSDARP00000008027.8, ENSDART00000003335.10
      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_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_007132.7 Reference GRCz11 Primary Assembly

      Range
      30470862..30487116
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068215813.1 → XP_068071914.1  sorting nexin-12 isoform X1

      Related
      ENSDARP00000134144.2, ENSDART00000171648.2
    Nucleotide Protein Strain
    Heading Accession and Version

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