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

Gene ID: 55988, updated on 5-Mar-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 act upstream of or within protein 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, Apr 2022]
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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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. BioID screening of biotinylation sites using the avidin-like protein Tamavidin 2-REV identifies global interactors of stimulator of interferon genes (STING). Motani K, et al. J Biol Chem, 2020 Aug 7. PMID 32554809, Free PMC Article
  5. The central role of EED in the orchestration of polycomb group complexes. Cao Q, et al. Nat Commun, 2014. PMID 24457600, Free PMC Article

See all (21) 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)
  • Gene trapped (1) 
  • 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 enzyme binding ISO
Inferred from Sequence Orthology
more info
  
enables lipid 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
  
acts_upstream_of_or_within 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

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