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Aliases for SLC6A4 Gene

Aliases for SLC6A4 Gene

  • Solute Carrier Family 6 Member 4 2 3 4
  • Solute Carrier Family 6 (Neurotransmitter Transporter), Member 4 2 3 5
  • Solute Carrier Family 6 (Neurotransmitter Transporter, Serotonin), Member 4 2 3
  • 5-Hydroxytryptamine (Serotonin) Transporter 2 3
  • Serotonin Transporter 1 2 3
  • 5HT Transporter 3 4
  • 5HTT 3 4
  • SERT 3 4
  • HTT 3 4
  • Na+/Cl- Dependent Serotonin Transporter 3
  • Obsessive-Compulsive Disorder 1 2
  • 5-HTTLPR 3
  • 5-HTT 3
  • SERT1 3
  • HSERT 3
  • OCD1 3

External Ids for SLC6A4 Gene

Previous HGNC Symbols for SLC6A4 Gene

  • HTT
  • OCD1

Previous GeneCards Identifiers for SLC6A4 Gene

  • GC17M028278
  • GC17M030431
  • GC17M028670
  • GC17M025549
  • GC17M028521
  • GC17M024733

Summaries for SLC6A4 Gene

Entrez Gene Summary for SLC6A4 Gene

  • This gene encodes an integral membrane protein that transports the neurotransmitter serotonin from synaptic spaces into presynaptic neurons. The encoded protein terminates the action of serotonin and recycles it in a sodium-dependent manner. This protein is a target of psychomotor stimulants, such as amphetamines and cocaine, and is a member of the sodium:neurotransmitter symporter family. A repeat length polymorphism in the promoter of this gene has been shown to affect the rate of serotonin uptake and may play a role in sudden infant death syndrome, aggressive behavior in Alzheimer disease patients, and depression-susceptibility in people experiencing emotional trauma. [provided by RefSeq, Jul 2008]

GeneCards Summary for SLC6A4 Gene

SLC6A4 (Solute Carrier Family 6 Member 4) is a Protein Coding gene. Diseases associated with SLC6A4 include obsessive-compulsive disorder and slc6a4-related altered drug metabolism. Among its related pathways are EGFR1 Signaling Pathway and SIDS Susceptibility Pathways. GO annotations related to this gene include protein homodimerization activity and Rab GTPase binding. An important paralog of this gene is SLC6A6.

UniProtKB/Swiss-Prot for SLC6A4 Gene

  • Serotonin transporter whose primary function in the central nervous system involves the regulation of serotonergic signaling via transport of serotonin molecules from the synaptic cleft back into the pre-synaptic terminal for re-utilization. Plays a key role in mediating regulation of the availability of serotonin to other receptors of serotonergic systems. Terminates the action of serotonin and recycles it in a sodium-dependent manner.

Tocris Summary for SLC6A4 Gene

  • 5-HT transporters (serotonin transporters, SERT) are sodium- and chloride-dependent members of the solute carrier family 6 (SLC6) found widely distributed throughout the brain. They are responsible for re-uptake of 5-HT and undergo a conformational change to move molecules.

Gene Wiki entry for SLC6A4 Gene

No data available for PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SLC6A4 Gene

Genomics for SLC6A4 Gene

Regulatory Elements for SLC6A4 Gene

Genomic Location for SLC6A4 Gene

Chromosome:
17
Start:
30,194,319 bp from pter
End:
30,236,002 bp from pter
Size:
41,684 bases
Orientation:
Minus strand

Genomic View for SLC6A4 Gene

Genes around SLC6A4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SLC6A4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SLC6A4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SLC6A4 Gene

Proteins for SLC6A4 Gene

  • Protein details for SLC6A4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    P31645-SC6A4_HUMAN
    Recommended name:
    Sodium-dependent serotonin transporter
    Protein Accession:
    P31645
    Secondary Accessions:
    • Q5EE02

    Protein attributes for SLC6A4 Gene

    Size:
    630 amino acids
    Molecular mass:
    70325 Da
    Quaternary structure:
    • Monomer or homooligomer (By similarity). Interacts with TGFB1I1. Interacts (via sialylated form) with MYH9. Interacts with SEC23A, SEC24C and INADL. Interacts with NOS1; the interaction may diminish the cell surface localization of SERT in the brain and, correspondingly, reduce serotonin reuptake. Interacts with filamentous actin and STX1A (By similarity). Interacts (via C-terminus) with VIM. Interacts (via C-terminus) with SCAMP2; the interaction is direct and retains transporter molecules intracellularly. Interacts with RAB4 (GTP-bound form); the interaction retains transporter molecules intracellularly.
    Miscellaneous:
    • This protein is the target of psychomotor stimulants such as amphetamines or cocaine.

    Alternative splice isoforms for SLC6A4 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SLC6A4 Gene

Proteomics data for SLC6A4 Gene at MOPED

Post-translational modifications for SLC6A4 Gene

  • Glycosylated; modification with sialylated N-glycans is a requirement for transporters to associate with each other and to function as homooligomeric forms.
  • Phosphorylation at Thr-276 increases 5-HT uptake and is required for cGMP-mediated SERT regulation. Phosphorylation upon PKC stimulation modifies the SERT distribution and density in the membrane, and diminishes the uptake capacity.
  • Glycosylation at Asn 208 and Asn 217
  • Modification sites at PhosphoSitePlus

Other Protein References for SLC6A4 Gene

Antibody Products

No data available for DME Specific Peptides for SLC6A4 Gene

Domains & Families for SLC6A4 Gene

Gene Families for SLC6A4 Gene

HGNC:
IUPHAR :

Graphical View of Domain Structure for InterPro Entry

P31645

UniProtKB/Swiss-Prot:

SC6A4_HUMAN :
  • Belongs to the sodium:neurotransmitter symporter (SNF) (TC 2.A.22) family. SLC6A4 subfamily.
Family:
  • Belongs to the sodium:neurotransmitter symporter (SNF) (TC 2.A.22) family. SLC6A4 subfamily.
genes like me logo Genes that share domains with SLC6A4: view

Function for SLC6A4 Gene

Molecular function for SLC6A4 Gene

GENATLAS Biochemistry:
solute carrier family 6,member A4,neurotransmitter transporter,serotonin
UniProtKB/Swiss-Prot Function:
Serotonin transporter whose primary function in the central nervous system involves the regulation of serotonergic signaling via transport of serotonin molecules from the synaptic cleft back into the pre-synaptic terminal for re-utilization. Plays a key role in mediating regulation of the availability of serotonin to other receptors of serotonergic systems. Terminates the action of serotonin and recycles it in a sodium-dependent manner.
UniProtKB/Swiss-Prot Induction:
Down-regulated when plasma serotonin is elevated.

Gene Ontology (GO) - Molecular Function for SLC6A4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA,IPI 11343649
GO:0019811 cocaine binding IEA --
GO:0051015 actin filament binding IEA,ISS --
genes like me logo Genes that share ontologies with SLC6A4: view
genes like me logo Genes that share phenotypes with SLC6A4: view

Animal Models for SLC6A4 Gene

MGI Knock Outs for SLC6A4:

Animal Model Products

  • Taconic Biosciences Mouse Models for SLC6A4

CRISPR Products

miRNA for SLC6A4 Gene

miRTarBase miRNAs that target SLC6A4

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for SLC6A4 Gene

Localization for SLC6A4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SLC6A4 Gene

Cell membrane; Multi-pass membrane protein. Endomembrane system; Multi-pass membrane protein. Endosome membrane; Multi-pass membrane protein. Note=Could be part of recycling endosomes (PubMed:18227069) (PubMed:16870614). Density of transporter molecules on the plasma membrane is itself regulated by STX1A (By similarity). Density of transporter molecules on the plasma membrane is also regulated by serotonin (PubMed:17506858) (PubMed:18227069). {ECO:0000250 UniProtKB:P31652, ECO:0000269 PubMed:16870614, ECO:0000269 PubMed:17506858, ECO:0000269 PubMed:18227069}.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for SLC6A4 Gene COMPARTMENTS Subcellular localization image for SLC6A4 gene
Compartment Confidence
cytosol 5
plasma membrane 5
endosome 3
extracellular 3
nucleus 2
cytoskeleton 1
endoplasmic reticulum 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for SLC6A4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005829 cytosol IDA 19270731
GO:0043005 neuron projection IEA,IBA --
genes like me logo Genes that share ontologies with SLC6A4: view

Pathways & Interactions for SLC6A4 Gene

genes like me logo Genes that share pathways with SLC6A4: view

SIGNOR curated interactions for SLC6A4 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for SLC6A4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006837 serotonin transport IEA,IDA 19270731
GO:0007584 response to nutrient IEA --
GO:0007613 memory IEA --
GO:0007623 circadian rhythm IEA --
GO:0009636 response to toxic substance IDA 17575980
genes like me logo Genes that share ontologies with SLC6A4: view

Drugs & Compounds for SLC6A4 Gene

(133) Drugs for SLC6A4 Gene - From: Novoseek, DrugBank, HMDB, DGIdb, IUPHAR, PharmGKB, Tocris, and ApexBio

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Paroxetine Approved, Investigational Pharma Inhibition, Inhibitor, inhibitor, Target 221
Sertraline Approved Pharma Inhibition, Inhibitor, inhibitor, Target 282
Citalopram Approved Pharma inhibitor, Target, Transporter, substrate 494
Clomipramine Approved Pharma inhibitor, Target 24
Escitalopram Approved, Investigational Pharma inhibitor, Target 0

(52) Additional Compounds for SLC6A4 Gene - From: Novoseek, Tocris, and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
N-Desmethylcitalopram
O-Desmethylverapamil (D-702)
sodium
  • Sodium
  • Sodium ion
7440-23-5
Citalopram hydrobromide
59729-32-7
Clomipramine hydrochloride
17321-77-6
genes like me logo Genes that share compounds with SLC6A4: view

Drug Products

Transcripts for SLC6A4 Gene

mRNA/cDNA for SLC6A4 Gene

(1) REFSEQ mRNAs :
(7) Additional mRNA sequences :
(15) Selected AceView cDNA sequences:
(5) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for SLC6A4 Gene

Solute carrier family 6 (neurotransmitter transporter, serotonin), member 4:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for SLC6A4 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15a · 15b
SP1: -
SP2: - -
SP3:
SP4: -
SP5:

Relevant External Links for SLC6A4 Gene

GeneLoc Exon Structure for
SLC6A4
ECgene alternative splicing isoforms for
SLC6A4

Expression for SLC6A4 Gene

mRNA expression in normal human tissues for SLC6A4 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SLC6A4 Gene

This gene is overexpressed in Lung (x32.4) and Small Intestine - Terminal Ileum (x5.7).

Protein differential expression in normal tissues from HIPED for SLC6A4 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (22.0), Lung (15.0), Placenta (11.4), Platelet (9.7), and Pancreatic juice (9.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for SLC6A4 Gene



SOURCE GeneReport for Unigene cluster for SLC6A4 Gene Hs.29792

mRNA Expression by UniProt/SwissProt for SLC6A4 Gene

P31645-SC6A4_HUMAN
Tissue specificity: Expressed in platelets (at protein level).
genes like me logo Genes that share expression patterns with SLC6A4: view

Protein tissue co-expression partners for SLC6A4 Gene

Primer Products

In Situ Assay Products

Orthologs for SLC6A4 Gene

This gene was present in the common ancestor of animals.

Orthologs for SLC6A4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SLC6A4 35
  • 99.26 (n)
  • 99.37 (a)
SLC6A4 36
  • 93 (a)
OneToOne
cow
(Bos Taurus)
Mammalia SLC6A4 36
  • 92 (a)
OneToOne
SLC6A4 35
  • 89.74 (n)
  • 93.02 (a)
dog
(Canis familiaris)
Mammalia SLC6A4 35
  • 90.32 (n)
  • 93.49 (a)
SLC6A4 36
  • 94 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Slc6a4 16
Slc6a4 36
  • 93 (a)
OneToOne
Slc6a4 35
  • 87.83 (n)
  • 92.54 (a)
oppossum
(Monodelphis domestica)
Mammalia SLC6A4 36
  • 87 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia SLC6A4 36
  • 76 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Slc6a4 35
  • 88.15 (n)
  • 91.75 (a)
chicken
(Gallus gallus)
Aves SLC6A4 36
  • 76 (a)
OneToOne
SLC6A4 35
  • 76.89 (n)
  • 81.88 (a)
lizard
(Anolis carolinensis)
Reptilia SLC6A4 36
  • 74 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100493853 35
  • 71.08 (n)
  • 76.81 (a)
zebrafish
(Danio rerio)
Actinopterygii slc6a4a 36
  • 67 (a)
OneToOne
slc6a4a 35
  • 68.29 (n)
  • 70.83 (a)
fruit fly
(Drosophila melanogaster)
Insecta SerT 36
  • 52 (a)
OneToOne
SerT 37
  • 56 (a)
DAT 37
  • 50 (a)
CG8850 37
  • 37 (a)
CG7075 37
  • 35 (a)
CG4476 37
  • 34 (a)
CG1698 37
  • 35 (a)
CG10804 37
  • 36 (a)
worm
(Caenorhabditis elegans)
Secernentea mod-5 36
  • 42 (a)
OneToOne
snf-9 37
  • 30 (a)
snf-8 37
  • 25 (a)
snf-6 37
  • 31 (a)
snf-3 37
  • 36 (a)
snf-12 37
  • 32 (a)
mod-5 37
  • 49 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 55 (a)
OneToOne
Species with no ortholog for SLC6A4:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for SLC6A4 Gene

ENSEMBL:
Gene Tree for SLC6A4 (if available)
TreeFam:
Gene Tree for SLC6A4 (if available)

Paralogs for SLC6A4 Gene

genes like me logo Genes that share paralogs with SLC6A4: view

Variants for SLC6A4 Gene

Polymorphic Variants from UniProtKB/Swiss-Prot for SLC6A4 Gene

P31645-SC6A4_HUMAN
A polymorphism in the promoter region (5-HTT gene-linked polymorphic region, 5-HTTLPR) is located approximately 1 kb upstream of the transcription initiation site and is composed of 16 repeat elements. The polymorphism consists of a 44-bp insertion or deletion involving repeat elements 6 to 8. The short allele is associated with lower transcriptional efficiency of the promoter compared with the long allele. Over half of the Caucasian population has a short allele. Individuals with one or two copies of the short allele exhibit more depressive symptoms, diagnosable depression and suicidality in relation to stressful life events than individuals homozygous for the long allele.

Sequence variations from dbSNP and Humsavar for SLC6A4 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
rs6353 -- 30,211,312(-) AGCAC(A/C/G)GTGAG reference, synonymous-codon
rs6354 -- 30,222,880(-) CCTCT(A/C)TTGCA utr-variant-5-prime
rs140699 -- 30,218,107(-) TGCAC(A/G/T)TAAGT intron-variant
rs745706 -- 30,198,997(-) TACAG(G/T)GGCTG intron-variant
rs1972305 -- 30,206,862(-) tgggc(A/G)tggta intron-variant

Structural Variations from Database of Genomic Variants (DGV) for SLC6A4 Gene

Variant ID Type Subtype PubMed ID
esv2715808 CNV Deletion 23290073

Variation tolerance for SLC6A4 Gene

Residual Variation Intolerance Score: 12.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.34; 41.64% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for SLC6A4 Gene

HapMap Linkage Disequilibrium report
SLC6A4
Human Gene Mutation Database (HGMD)
SLC6A4

Disorders for SLC6A4 Gene

MalaCards: The human disease database

(88) MalaCards diseases for SLC6A4 Gene - From: OMIM, GeneTests, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
obsessive-compulsive disorder
  • obsessive-compulsive disorder, protection against
slc6a4-related altered drug metabolism
  • serotonin transporter
slc6a4-related behavior disorders
personality disorder
  • character disorder
postpartum depression
  • maternity blues
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for SLC6A4

Genetic Association Database (GAD)
SLC6A4
Human Genome Epidemiology (HuGE) Navigator
SLC6A4
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
SLC6A4
genes like me logo Genes that share disorders with SLC6A4: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SLC6A4 Gene

Publications for SLC6A4 Gene

  1. Antidepressant- and cocaine-sensitive human serotonin transporter: molecular cloning, expression, and chromosomal localization. (PMID: 7681602) Ramamoorthy S. … Blakely R.D. (Proc. Natl. Acad. Sci. U.S.A. 1993) 2 3 4 23 67
  2. Alteration of gastric functions and candidate genes associated with weight reduction in response to sibutramine. (PMID: 17544870) Vazquez Roque M.I. … Zinsmeister A.R. (Clin. Gastroenterol. Hepatol. 2007) 3 23 25 26
  3. Age-dependent antidepressant pharmacogenomics: polymorphisms of the serotonin transporter and G protein beta3 subunit as predictors of response to fluoxetine and nortriptyline. (PMID: 14604448) Joyce P.R. … Kennedy M.A. (Int. J. Neuropsychopharmacol. 2003) 3 23 25 26
  4. Influence of the serotonin transporter gene-linked polymorphic region on the antidepressant response to fluvoxamine in Japanese depressed patients. (PMID: 11817517) Yoshida K. … Otani K. (Prog. Neuropsychopharmacol. Biol. Psychiatry 2002) 3 23 25 26
  5. Allelic variation in the serotonin transporter promoter affects onset of paroxetine treatment response in late-life depression. (PMID: 11027924) Pollock B.G. … Kupfer D.J. (Neuropsychopharmacology 2000) 3 23 25 26

Products for SLC6A4 Gene

Sources for SLC6A4 Gene

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