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    Snx27 sorting nexin 27 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 260323, updated on 9-Dec-2024

    Summary

    Official Symbol
    Snx27provided by RGD
    Official Full Name
    sorting nexin 27provided by RGD
    Primary source
    RGD:628705
    See related
    EnsemblRapid:ENSRNOG00000020893 AllianceGenome:RGD:628705
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Mrt1
    Summary
    Enables calcium-dependent protein binding activity; ionotropic glutamate receptor binding activity; and phosphatidylinositol-3-phosphate binding activity. Involved in several processes, including negative regulation of inward rectifier potassium channel activity; positive regulation of AMPA glutamate receptor clustering; and vesicle-mediated transport to the plasma membrane. Located in early endosome. Orthologous to human SNX27 (sorting nexin 27). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 145.2), Adrenal (RPKM 131.9) and 9 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See Snx27 in Genome Data Viewer
    Location:
    2q34
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 2 NC_086020.1 (184824930..184907931, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 2 NC_051337.1 (182135904..182218906, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 2 NC_005101.4 (195738613..195821608, complement)

    Chromosome 2 - NC_086020.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102556390 Neighboring gene regulatory subunit of type II PKA R-subunit domain containing 1 Neighboring gene CUGBP, Elav-like family member 3 Neighboring gene uncharacterized LOC134485647 Neighboring gene nuclear receptor binding factor 2 like 1 Neighboring gene tuftelin 1 Neighboring gene uncharacterized LOC120100872

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables calcium-dependent protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables ionotropic glutamate receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables phosphatidylinositol binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables phosphatidylinositol-3-phosphate binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables phosphatidylinositol-3-phosphate binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables phosphatidylinositol-3-phosphate binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in cellular response to nerve growth factor stimulus IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in endocytic recycling IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in endocytic recycling IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in endocytic recycling ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in endocytic recycling ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in endosomal transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    acts_upstream_of_or_within endosomal transport ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in endosomal transport ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in endosome to lysosome transport IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within endosome to lysosome transport ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in endosome to plasma membrane protein transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in establishment of protein localization to plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in intracellular protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in intracellular protein transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in intracellular protein transport ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of inward rectifier potassium channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in nervous system development NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in neurotransmitter receptor transport to plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of AMPA glutamate receptor clustering IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of postsynaptic membrane neurotransmitter receptor levels IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of postsynaptic membrane neurotransmitter receptor levels ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of synapse maturation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of synapse maturation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in response to methamphetamine hydrochloride IEP
    Inferred from Expression Pattern
    more info
    PubMed 
    involved_in signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in Schaffer collateral - CA1 synapse IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in Schaffer collateral - CA1 synapse ISO
    Inferred from Sequence Orthology
    more info
     
    part_of WASH complex IEA
    Inferred from Electronic Annotation
    more info
     
    part_of WASH complex ISO
    Inferred from Sequence Orthology
    more info
     
    part_of WASH complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in early endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in early endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in early endosome ISO
    Inferred from Sequence Orthology
    more info
     
    located_in early endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in endosome ISO
    Inferred from Sequence Orthology
    more info
     
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in glutamatergic synapse ISO
    Inferred from Sequence Orthology
    more info
     
    located_in immunological synapse IEA
    Inferred from Electronic Annotation
    more info
     
    located_in immunological synapse ISO
    Inferred from Sequence Orthology
    more info
     
    located_in immunological synapse ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in intracellular membrane-bounded organelle ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in postsynapse ISO
    Inferred from Sequence Orthology
    more info
     
    located_in postsynaptic early endosome IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in postsynaptic early endosome ISO
    Inferred from Sequence Orthology
    more info
     
    located_in postsynaptic recycling endosome IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in postsynaptic recycling endosome ISO
    Inferred from Sequence Orthology
    more info
     
    part_of retromer complex IEA
    Inferred from Electronic Annotation
    more info
     
    part_of retromer complex ISO
    Inferred from Sequence Orthology
    more info
     
    part_of retromer complex ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    sorting nexin-27
    Names
    MAP-responsive gene protein
    PDZ-protein Mrt1
    methamphetamine (MAP) responsive transcript 1
    methamphetamine-responsive transcript 1 protein
    sorting nexin family member 27

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001110151.1NP_001103621.1  sorting nexin-27 isoform a

      See identical proteins and their annotated locations for NP_001103621.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (a).
      Source sequence(s)
      AB051816, AC133978, BF524912
      UniProtKB/Swiss-Prot
      Q8K4T6, Q8K4V4
      UniProtKB/TrEMBL
      A6K2S0
      Related
      ENSRNOP00000107295.1, ENSRNOT00000126858.1
      Conserved Domains (4) summary
      cd06886
      Location:158263
      PX_SNX27; The phosphoinositide binding Phox Homology domain of Sorting Nexin 27
      cd00992
      Location:39131
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cd13338
      Location:423524
      FERM-like_C_SNX27; Atypical FERM-like domain C-lobe of Sorting nexin 27
      cd01777
      Location:271363
      FERM_F1_SNX27; FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in sorting nexin protein 27 (SNX27)
    2. NM_152847.2NP_690060.2  sorting nexin-27 isoform b

      See identical proteins and their annotated locations for NP_690060.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice junction at the 5' end of a coding exon compared to variant 1. The resulting isoform (b) is shorter and has a distinct C-terminus compared to isoform a.
      Source sequence(s)
      AB051816, AC133978, BF524912
      UniProtKB/TrEMBL
      A6K2S3, G3V8U4
      Related
      ENSRNOP00000028389.8, ENSRNOT00000028389.8
      Conserved Domains (4) summary
      cd06886
      Location:158263
      PX_SNX27; The phosphoinositide binding Phox Homology domain of Sorting Nexin 27
      cd00992
      Location:39131
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      cd13338
      Location:423524
      FERM-like_C_SNX27; Atypical FERM-like domain C-lobe of Sorting nexin 27
      cd01777
      Location:271363
      FERM_F1_SNX27; FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in sorting nexin protein 27 (SNX27)

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086020.1 Reference GRCr8

      Range
      184824930..184907931 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)