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

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, Nov 2024]
Expression: Biased expression in Brain (RPKM 145.2), Adrenal (RPKM 131.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

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_086020.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Sorting Nexin 27 Regulates the Lysosomal Degradation of Aquaporin-2 Protein in the Kidney Collecting Duct.
Title: Sorting Nexin 27 Regulates the Lysosomal Degradation of Aquaporin-2 Protein in the Kidney Collecting Duct.
SNX27-Mediated Recycling of Neuroligin-2 Regulates Inhibitory Signaling.
Title: SNX27-Mediated Recycling of Neuroligin-2 Regulates Inhibitory Signaling.
these data indicate that NLGs are SNX27-retromer cargoes and suggest that SNX27-retromer controls inhibitory synapse number, at least in part through trafficking of NLG2.
Title: Sorting nexin 27 rescues neuroligin 2 from lysosomal degradation to control inhibitory synapse number.
SNX27 is required for the exocytosis of NHE3 from early endosome to plasma membrane and the regulation of the retention of NHE3 on the plasma membrane.
Title: Sorting nexin 27 regulates basal and stimulated brush border trafficking of NHE3.
The regulation of the VPS26A-SNX27 interaction modifies mGluR5 trafficking which mediates neuropathic pain.
Title: VPS26A-SNX27 Interaction-Dependent mGluR5 Recycling in Dorsal Horn Neurons Mediates Neuropathic Pain in Rats.
SNX27 is synaptically enriched and its level of expression regulates targeting of AMPARs to the neuronal surface. Loss of SNX27 abolishes recruitment of surface AMPARs during chemical LTP.
Title: Sorting Nexin 27 regulates basal and activity-dependent trafficking of AMPARs.
The surface expression of neuronal GIRK channels is regulated by the psychostimulant-sensitive sorting nexin 27 (SNX27) protein through a class I PDZ-binding interaction.
Title: Mechanism underlying selective regulation of G protein-gated inwardly rectifying potassium channels by the psychostimulant-sensitive sorting nexin 27.
SNX27 promotes the endosomal movement of Kir3 (GIRK) channels, leading to reduced surface expression, increased degradation and smaller Kir3 potassium currents.
Title: A unique sorting nexin regulates trafficking of potassium channels via a PDZ domain interaction.
Gene is developmentally regulated and stimulated by methamphetamine in the neocortex.
Title: A developmentally regulated and psychostimulant-inducible novel rat gene mrt1 encoding PDZ-PX proteins isolated in the neocortex.
These findings suggest the differential regulation by stimulant of neocortical mrt1 expression and supports the view that stimulant induction of mrt1 may be involved in the early molecular signalings for stimulant sensitization.
Title: Differential regulation by stimulants of neocortical expression of mrt1, arc, and homer1a mRNA in the rats treated with repeated methamphetamine.

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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

RH125229 (e-PCR)
- UniSTS:162051

REN34946 (e-PCR)
- UniSTS:359746

R75405 (e-PCR), detects polymorphism
- UniSTS:143031

C79375 (e-PCR), detects polymorphism
- UniSTS:143033

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

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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)

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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)

NM_001110151.1 → NP_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:158 → 263

PX_SNX27; The phosphoinositide binding Phox Homology domain of Sorting Nexin 27

cd00992
Location:39 → 131

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:423 → 524

FERM-like_C_SNX27; Atypical FERM-like domain C-lobe of Sorting nexin 27

cd01777
Location:271 → 363

FERM_F1_SNX27; FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in sorting nexin protein 27 (SNX27)
NM_152847.2 → NP_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:158 → 263

PX_SNX27; The phosphoinositide binding Phox Homology domain of Sorting Nexin 27

cd00992
Location:39 → 131

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:423 → 524

FERM-like_C_SNX27; Atypical FERM-like domain C-lobe of Sorting nexin 27

cd01777
Location:271 → 363

FERM_F1_SNX27; FERM (Four.1 protein, Ezrin, Radixin, Moesin) domain, F1 sub-domain, found in sorting nexin protein 27 (SNX27)