Slc6a4 solute carrier family 6 member 4 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Slc6a4provided by RGD
Official Full Name: solute carrier family 6 member 4provided by RGD
Primary source: RGD:3714
See related: EnsemblRapid:ENSRNOG00000003476 AllianceGenome:RGD:3714
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: SERT
Summary: Enables several functions, including cocaine binding activity; monoatomic cation transmembrane transporter activity; and syntaxin-1 binding activity. Involved in several processes, including behavioral response to cocaine; cellular response to cGMP; and learning or memory. Located in endomembrane system and plasma membrane. Is active in postsynaptic membrane; presynaptic membrane; and serotonergic synapse. Used to study anxiety disorder; depressive disorder; and pulmonary hypertension. Biomarker of Parkinsonism; borna disease; congenital diaphragmatic hernia; and fetal alcohol spectrum disorder. Human ortholog(s) of this gene implicated in several diseases, including alcohol dependence; anxiety disorder (multiple); depressive disorder (multiple); heart disease (multiple); and substance abuse (multiple). Orthologous to human SLC6A4 (solute carrier family 6 member 4). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Lung (RPKM 107.1), Adrenal (RPKM 71.6) and 4 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 10q24

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	10	NC_086028.1 (62322688..62357060)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	10	NC_051345.1 (61824208..61858924)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	10	NC_005109.4 (63153656..63188377, complement)

Chromosome 10 - NC_086028.1 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?

Serotonin transporter knockout in rats reduces beta- and gamma-band functional connectivity between the orbitofrontal cortex and amygdala during auditory discrimination.
Title: Serotonin transporter knockout in rats reduces beta- and gamma-band functional connectivity between the orbitofrontal cortex and amygdala during auditory discrimination.
Offspring's own serotonin transporter genotype, independently from the maternal one, increases anxiety- and depression-like behavior and alters neuroplasticity markers in rats.
Title: Offspring's own serotonin transporter genotype, independently from the maternal one, increases anxiety- and depression-like behavior and alters neuroplasticity markers in rats.
Regional expression differences of SERT and TSPAN8 in hippocampus, cerebellum and cortex of wild-type young, adult and middle-aged rats.
Title: Regional expression differences of SERT and TSPAN8 in hippocampus, cerebellum and cortex of wild-type young, adult and middle-aged rats.
Alteration of the alpha5 GABA receptor and 5HTT lead to cognitive deficits associated with major depressive-like behaviors in a 14-day combined stress rat model.
Title: Alteration of the α5 GABA receptor and 5HTT lead to cognitive deficits associated with major depressive-like behaviors in a 14-day combined stress rat model.
The serotonin reuptake transporter modulates mitochondrial copy number and mitochondrial respiratory complex gene expression in the frontal cortex and cerebellum in a sexually dimorphic manner.
Title: The serotonin reuptake transporter modulates mitochondrial copy number and mitochondrial respiratory complex gene expression in the frontal cortex and cerebellum in a sexually dimorphic manner.
Genetic Knockout of the Serotonin Reuptake Transporter Results in the Reduction of Dendritic Spines in In vitro Rat Cortical Neuronal Culture.
Title: Genetic Knockout of the Serotonin Reuptake Transporter Results in the Reduction of Dendritic Spines in In vitro Rat Cortical Neuronal Culture.
Reduced emission of alarm 22-kHz ultrasonic vocalizations during fear conditioning in rats lacking the serotonin transporter.
Title: Reduced emission of alarm 22-kHz ultrasonic vocalizations during fear conditioning in rats lacking the serotonin transporter.
Knockout of the Serotonin Transporter in the Rat Mildly Modulates Decisional Anhedonia.
Title: Knockout of the Serotonin Transporter in the Rat Mildly Modulates Decisional Anhedonia.
Fear Extinction and Predictive Trait-Like Inter-Individual Differences in Rats Lacking the Serotonin Transporter.
Title: Fear Extinction and Predictive Trait-Like Inter-Individual Differences in Rats Lacking the Serotonin Transporter.
BDNF Overexpression in the Ventral Hippocampus Promotes Antidepressant- and Anxiolytic-Like Activity in Serotonin Transporter Knockout Rats.
Title: BDNF Overexpression in the Ventral Hippocampus Promotes Antidepressant- and Anxiolytic-Like Activity in Serotonin Transporter Knockout Rats.

Submit: New GeneRIF Correction See all GeneRIFs (102)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Slc6a4 (e-PCR), detects polymorphism
- UniSTS:547357

D10Rat242 (e-PCR), detects polymorphism
- UniSTS:226352

RH142224 (e-PCR)
- UniSTS:231474

Slc6a4 (e-PCR), detects polymorphism
- UniSTS:516847

BE097677 (e-PCR)
- UniSTS:244722

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables actin filament binding	IDA Inferred from Direct Assay more info	PubMed
enables antiporter activity	ISO Inferred from Sequence Orthology more info
enables cocaine binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables integrin binding	ISO Inferred from Sequence Orthology more info
enables integrin binding	ISS Inferred from Sequence or Structural Similarity more info
enables monoamine transmembrane transporter activity	ISO Inferred from Sequence Orthology more info
enables monoatomic cation channel activity	IDA Inferred from Direct Assay more info	PubMed
enables neurotransmitter transmembrane transporter activity	ISO Inferred from Sequence Orthology more info
enables nitric-oxide synthase binding	ISO Inferred from Sequence Orthology more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables serotonin binding	IBA Inferred from Biological aspect of Ancestor more info
enables serotonin binding	ISO Inferred from Sequence Orthology more info
enables serotonin binding	ISS Inferred from Sequence or Structural Similarity more info
enables serotonin:sodium:chloride symporter activity	IBA Inferred from Biological aspect of Ancestor more info
enables serotonin:sodium:chloride symporter activity	IDA Inferred from Direct Assay more info	PubMed
enables serotonin:sodium:chloride symporter activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables serotonin:sodium:chloride symporter activity	ISO Inferred from Sequence Orthology more info
enables serotonin:sodium:chloride symporter activity	TAS Traceable Author Statement more info	PubMed
enables sodium ion binding	ISO Inferred from Sequence Orthology more info
enables sodium ion binding	ISS Inferred from Sequence or Structural Similarity more info
enables syntaxin-1 binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in amino acid transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in behavioral response to cocaine	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in brain morphogenesis	ISO Inferred from Sequence Orthology more info
involved_in cellular response to cGMP	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to retinoic acid	IEP Inferred from Expression Pattern more info	PubMed
involved_in circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in conditioned place preference	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in enteric nervous system development	ISO Inferred from Sequence Orthology more info
involved_in locomotory behavior	NAS Non-traceable Author Statement more info	PubMed
involved_in male mating behavior	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in membrane depolarization	IDA Inferred from Direct Assay more info	PubMed
involved_in memory	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within monoamine transport	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cerebellar granule cell precursor proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of neuron differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of organ growth	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of synaptic transmission, dopaminergic	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neurotransmitter reuptake	ISO Inferred from Sequence Orthology more info
involved_in neurotransmitter transport	ISO Inferred from Sequence Orthology more info
involved_in platelet aggregation	ISO Inferred from Sequence Orthology more info
involved_in platelet aggregation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of cell cycle	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of serotonin secretion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of thalamus size	ISO Inferred from Sequence Orthology more info
involved_in regulation of thalamus size	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to estradiol	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to hypoxia	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to nutrient	IEP Inferred from Expression Pattern more info	PubMed
involved_in response to toxic substance	ISO Inferred from Sequence Orthology more info
involved_in response to xenobiotic stimulus	IEP Inferred from Expression Pattern more info	PubMed
involved_in serotonin transport	IDA Inferred from Direct Assay more info	PubMed
involved_in serotonin transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in serotonin transport	ISO Inferred from Sequence Orthology more info
involved_in serotonin transport	TAS Traceable Author Statement more info	PubMed
involved_in serotonin uptake	IBA Inferred from Biological aspect of Ancestor more info
involved_in serotonin uptake	IDA Inferred from Direct Assay more info	PubMed
involved_in serotonin uptake	ISO Inferred from Sequence Orthology more info
involved_in sodium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in vasoconstriction	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in endomembrane system	IDA Inferred from Direct Assay more info	PubMed
located_in endomembrane system	ISO Inferred from Sequence Orthology more info
located_in endomembrane system	NAS Non-traceable Author Statement more info	PubMed
located_in endosome membrane	IEA Inferred from Electronic Annotation more info
located_in focal adhesion	ISO Inferred from Sequence Orthology more info
located_in focal adhesion	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane raft	ISO Inferred from Sequence Orthology more info
is_active_in neuron projection	IBA Inferred from Biological aspect of Ancestor more info
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	ISO Inferred from Sequence Orthology more info
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 serotonergic synapse	IDA Inferred from Direct Assay more info	PubMed
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info
located_in synapse	ISO Inferred from Sequence Orthology more info
located_in synapse	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: sodium-dependent serotonin transporter

Names: 5HT transporter; 5HTT; Solute carrier family 6 (neurotransmitter transporter serotonin) member 4 (5-hydroxytryptamine (serotonin) transporter); serotonin transporter; solute carrier family 6 (neurotransmitter transporter), member 4; solute carrier family 6 (neurotransmitter transporter, serotonin), member 4

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_013034.4 → NP_037166.2 sodium-dependent serotonin transporter

See identical proteins and their annotated locations for NP_037166.2

Status: VALIDATED

Source sequence(s)

AI547408, BF548147, CB736426, JAXUCZ010000010, M79450

UniProtKB/Swiss-Prot

P23976, P31652

UniProtKB/TrEMBL

A6HGX0

Conserved Domains (2) summary

cd11513
Location:79 → 615

SLC6sbd_SERT; Na(+)- and Cl(-)-dependent serotonin transporter SERT; solute-binding domain

pfam03491
Location:24 → 64

5HT_transport_N; Serotonin (5-HT) neurotransmitter transporter, N-terminus

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_086028.1 Reference GRCr8

Range

62322688..62357060

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017597042.3 → XP_017452531.1 sodium-dependent serotonin transporter isoform X1

UniProtKB/Swiss-Prot

P23976, P31652

UniProtKB/TrEMBL

A6HGX0

Conserved Domains (2) summary

cd11513
Location:79 → 615

SLC6sbd_SERT; Na(+)- and Cl(-)-dependent serotonin transporter SERT; solute-binding domain

pfam03491
Location:24 → 64

5HT_transport_N; Serotonin (5-HT) neurotransmitter transporter, N-terminus
XM_008767950.4 → XP_008766172.1 sodium-dependent serotonin transporter isoform X1

See identical proteins and their annotated locations for XP_008766172.1

UniProtKB/Swiss-Prot

P23976, P31652

UniProtKB/TrEMBL

A6HGX0

Conserved Domains (2) summary

cd11513
Location:79 → 615

SLC6sbd_SERT; Na(+)- and Cl(-)-dependent serotonin transporter SERT; solute-binding domain

pfam03491
Location:24 → 64

5HT_transport_N; Serotonin (5-HT) neurotransmitter transporter, N-terminus
XM_017597041.3 → XP_017452530.1 sodium-dependent serotonin transporter isoform X1

UniProtKB/Swiss-Prot

P23976, P31652

UniProtKB/TrEMBL

A6HGX0

Related

ENSRNOP00000004717.4, ENSRNOT00000004717.8

Conserved Domains (2) summary

cd11513
Location:79 → 615

SLC6sbd_SERT; Na(+)- and Cl(-)-dependent serotonin transporter SERT; solute-binding domain

pfam03491
Location:24 → 64

5HT_transport_N; Serotonin (5-HT) neurotransmitter transporter, N-terminus
XM_039085288.2 → XP_038941216.1 sodium-dependent serotonin transporter isoform X1

UniProtKB/Swiss-Prot

P23976, P31652

UniProtKB/TrEMBL

A6HGX0

Conserved Domains (2) summary

cd11513
Location:79 → 615

SLC6sbd_SERT; Na(+)- and Cl(-)-dependent serotonin transporter SERT; solute-binding domain

pfam03491
Location:24 → 64

5HT_transport_N; Serotonin (5-HT) neurotransmitter transporter, N-terminus