Slc6a9 solute carrier family 6 member 9 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Slc6a9provided by RGD
Official Full Name: solute carrier family 6 member 9provided by RGD
Primary source: RGD:621243
See related: EnsemblRapid:ENSRNOG00000019484 AllianceGenome:RGD:621243
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: Glyt1; GLYT-1; GLYT-1b
Summary: Enables glycine:sodium symporter activity. Involved in glycine import across plasma membrane. Located in dense core granule; endosome; and plasma membrane. Is active in several cellular components, including hippocampal mossy fiber to CA3 synapse; parallel fiber to Purkinje cell synapse; and synaptic membrane. Orthologous to human SLC6A9 (solute carrier family 6 member 9). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Brain (RPKM 173.1), Liver (RPKM 105.1) and 8 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q36

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (136660022..136694173)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (131374562..131408733)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (136669674..136703702)

Chromosome 5 - NC_086023.1 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?

Regulation of the Glycine Transporter GLYT1 by microRNAs.
Title: Regulation of the Glycine Transporter GLYT1 by microRNAs.
Study demonstrated a biphasic response of GlyT1 expression during epileptogenesis with initial downregulation of GlyT1 after epileptogenesis-precipitating seizures followed by sustained pathological overexpression of GlyT1 in chronic epilepsy
Title: Glycine transporter 1 is a target for the treatment of epilepsy.
Study showed that glycine uptake mediated by GlyT1 and GlyT2 in astrocytes is modulated by BDNF
Title: BDNF, via truncated TrkB receptor, modulates GlyT1 and GlyT2 in astrocytes.
astrocytes express functional GlyT2, which challenge previous findings that those cells would express only GlyT1
Title: GlyT1 and GlyT2 in brain astrocytes: expression, distribution and function.
Double labeling for GLYT1 and synaptophysin of this vesicular fraction revealed that more of ninety percent of them were synaptic vesicles
Title: Localization of the glycine transporter GLYT1 in glutamatergic synaptic vesicles.
Inhibition of GlyT1 reduces the frequency of spontaneous network events in the hippocampus.
Title: Glycine transporter-1 controls nonsynaptic inhibitory actions of glycine receptors in the neonatal rat hippocampus.
Glycine transport by GLYT1 is inhibited by lithium whereas GLYT2 transport is stimulated, and this effect is more evident at increased glycine concentrations.
Title: Molecular basis of the differential interaction with lithium of glycine transporters GLYT1 and GLYT2.
study analyzed transient currents of recombinant GlyT1b variant protein and related their properties to characteristics of steady transport currents; numerical simulations show a simplified, 3-state model explains main features of GlyT1b operation
Title: Transient currents in the glycine cotransporter GlyT1 reveal different steps in transport mechanism.
In conclusion, GlyT1 most likely mediates glycine transport at the inner BRB and is expected to play an important role in regulating the glycine concentration in the neural retina.
Title: Characteristics of glycine transport across the inner blood-retinal barrier.
Results show that endocytosis is impaired in an ubiquitination-deficient cell line.
Title: Constitutive and regulated endocytosis of the glycine transporter GLYT1b is controlled by ubiquitination.

Submit: New GeneRIF Correction See all GeneRIFs (18)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH143473 (e-PCR)
- UniSTS:232720

D5Wox28 (e-PCR)
- UniSTS:239931

Glyt1 (e-PCR), detects polymorphism
- UniSTS:143225

RH141917 (e-PCR)
- UniSTS:223908

D5MIT14 (e-PCR)
- UniSTS:122067

AA943440 (e-PCR)
- UniSTS:250110

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables amino acid:sodium symporter activity	IEA Inferred from Electronic Annotation more info
enables glycine transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
enables glycine transmembrane transporter activity	ISO Inferred from Sequence Orthology more info
enables glycine transmembrane transporter activity	TAS Traceable Author Statement more info	PubMed
enables glycine:sodium symporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables glycine:sodium symporter activity	IDA Inferred from Direct Assay more info	PubMed
enables glycine:sodium symporter activity	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in amino acid transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in glycine import across plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
involved_in glycine import across plasma membrane	IDA Inferred from Direct Assay more info	PubMed
involved_in glycine import across plasma membrane	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within glycine secretion, neurotransmission	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within glycine transport	ISO Inferred from Sequence Orthology more info
involved_in glycine transport	ISO Inferred from Sequence Orthology more info
acts_upstream_of negative regulation of NMDA glutamate receptor activity	ISO Inferred from Sequence Orthology more info
involved_in neurotransmitter transport	IEA Inferred from Electronic Annotation more info
involved_in neurotransmitter uptake	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of heme biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of hemoglobin biosynthetic process	ISO Inferred from Sequence Orthology more info
involved_in regulation of synaptic transmission, glycinergic	ISO Inferred from Sequence Orthology more info
involved_in regulation of synaptic transmission, glycinergic	ISS Inferred from Sequence or Structural Similarity more info
involved_in sodium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in sodium ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in synaptic transmission, glycinergic	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in apical plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in asymmetric synapse	IDA Inferred from Direct Assay more info	PubMed
located_in basal plasma membrane	ISO Inferred from Sequence Orthology more info
located_in basolateral plasma membrane	ISO Inferred from Sequence Orthology more info
located_in dense core granule	IDA Inferred from Direct Assay more info	PubMed
located_in endosome	IDA Inferred from Direct Assay more info	PubMed
is_active_in hippocampal mossy fiber to CA3 synapse	IDA Inferred from Direct Assay more info	PubMed
located_in lateral plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in parallel fiber to Purkinje cell synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in postsynaptic density	IDA Inferred from Direct Assay more info	PubMed
is_active_in postsynaptic membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in presynaptic membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in synaptic vesicle membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: sodium- and chloride-dependent glycine transporter 1

Names: glycine transporter 1; solute carrier family 6 (neurotransmitter transporter, glycine), member 9

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_053818.3 → NP_446270.1 sodium- and chloride-dependent glycine transporter 1

See identical proteins and their annotated locations for NP_446270.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

A6JZE5

Related

ENSRNOP00000040252.4, ENSRNOT00000048770.5

Conserved Domains (1) summary

cd11498
Location:11 → 594

SLC6sbd_GlyT1; Na(+)- and Cl(-)-dependent glycine transporter GlyT1; solute-binding domain

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

NC_086023.1 Reference GRCr8

Range

136660022..136694173

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039109142.2 → XP_038965070.1 sodium- and chloride-dependent glycine transporter 1 isoform X2

UniProtKB/TrEMBL

A0A8L2ULJ7

Conserved Domains (1) summary

cl00456
Location:26 → 556

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain
XM_006238625.5 → XP_006238687.1 sodium- and chloride-dependent glycine transporter 1 isoform X1

See identical proteins and their annotated locations for XP_006238687.1

UniProtKB/Swiss-Prot

A1A5N0, P28572, Q63322, Q63323

Related

ENSRNOP00000070161.1, ENSRNOT00000085527.3

Conserved Domains (1) summary

cd11498
Location:16 → 599

SLC6sbd_GlyT1; Na(+)- and Cl(-)-dependent glycine transporter GlyT1; solute-binding domain
XM_039109143.2 → XP_038965071.1 sodium- and chloride-dependent glycine transporter 1 isoform X2

UniProtKB/TrEMBL

A0A8L2ULJ7

Conserved Domains (1) summary

cl00456
Location:26 → 556

SLC5-6-like_sbd; Solute carrier families 5 and 6-like; solute binding domain