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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in TCGA

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Exon skipping events with PSIs in GTEx

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Open reading frame (ORF) annotation in the exon skipping event

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Exon skipping events in the canonical protein sequence

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SNVs in the skipped exons with depth of coverage

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

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Related drugs with this gene

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Related diseases with this gene

Gene summary for SLC6A4

check button Gene summary
Gene informationGene symbol

SLC6A4

Gene ID

6532

Gene namesolute carrier family 6 member 4
Synonyms5-HTT|5-HTTLPR|5HTT|HTT|OCD1|SERT|SERT1|hSERT
Cytomap

17q11.2

Type of geneprotein-coding
Descriptionsodium-dependent serotonin transporter5-hydroxytryptamine (serotonin) transporter5HT transporterNa+/Cl- dependent serotonin transporterserotonin transporter 1solute carrier family 6 (neurotransmitter transporter), member 4solute carrier family 6 (ne
Modification date20180527
UniProtAcc

P31645

ContextPubMed: SLC6A4 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract]
- Title (PMID)

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
SLC6A4

GO:0006837

serotonin transport

19270731

SLC6A4

GO:0009636

response to toxic substance

17575980

SLC6A4

GO:0015844

monoamine transport

16024787

SLC6A4

GO:0051610

serotonin uptake

8987735|16870614|17506858|18227069|19270731


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Exon skipping events across known transcript of Ensembl for SLC6A4 from UCSC genome browser

check buttonSkipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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Gene isoform structures and expression levels for SLC6A4

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


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Exon skipping events with PSIs in TCGA for SLC6A4

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_2880451728530189:28530357:28534749:28534850:28536160:2853626028534749:28534850ENSG00000108576.5ENST00000401766.2,ENST00000394821.2,ENST00000261707.3
exon_skip_2880461728530189:28530357:28534749:28534850:28537532:2853766428534749:28534850ENSG00000108576.5ENST00000579221.1
exon_skip_2880481728534749:28534850:28536160:28536260:28537532:2853766428536160:28536260ENSG00000108576.5ENST00000401766.2,ENST00000394821.2,ENST00000261707.3
exon_skip_2880491728545135:28545355:28545814:28545949:28548633:2854909928545814:28545949ENSG00000108576.5ENST00000401766.2,ENST00000394821.2,ENST00000261707.3
exon_skip_2880511728548889:28549099:28549836:28549933:28562630:2856271628549836:28549933ENSG00000108576.5ENST00000394821.2,ENST00000261707.3

check button PSI values of skipped exons in TCGA.
psi tcga

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Exon skipping events with PSIs in GTEx for SLC6A4

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_2880451728530189:28530357:28534749:28534850:28536160:2853626028534749:28534850ENSG00000108576.5ENST00000401766.2,ENST00000261707.3,ENST00000394821.2
exon_skip_2880461728530189:28530357:28534749:28534850:28537532:2853766428534749:28534850ENSG00000108576.5ENST00000579221.1
exon_skip_2880481728534749:28534850:28536160:28536260:28537532:2853766428536160:28536260ENSG00000108576.5ENST00000401766.2,ENST00000261707.3,ENST00000394821.2
exon_skip_2880491728545135:28545355:28545814:28545949:28548633:2854909928545814:28545949ENSG00000108576.5ENST00000401766.2,ENST00000261707.3,ENST00000394821.2
exon_skip_2880511728548889:28549099:28549836:28549933:28562630:2856271628549836:28549933ENSG00000108576.5ENST00000261707.3,ENST00000394821.2

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for SLC6A4

check button Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST0000026170728549836285499333UTR-3UTR
ENST000002617072853474928534850Frame-shift
ENST000004017662853474928534850Frame-shift
ENST000002617072853616028536260Frame-shift
ENST000004017662853616028536260Frame-shift
ENST000002617072854581428545949In-frame
ENST000004017662854581428545949In-frame

check button Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST0000026170728549836285499333UTR-3UTR
ENST000002617072853474928534850Frame-shift
ENST000004017662853474928534850Frame-shift
ENST000002617072853616028536260Frame-shift
ENST000004017662853616028536260Frame-shift
ENST000002617072854581428545949In-frame
ENST000004017662854581428545949In-frame

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Infer the effects of exon skipping event on protein functional features for SLC6A4

check button Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.
prot feature distribution

check button Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000261707453363028545814285459498881022114159
ENST0000040176665606302854581428545949857991114159

check button Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000261707453363028545814285459498881022114159
ENST0000040176665606302854581428545949857991114159

check button Lost protein functional features of individual exon skipping events in TCGA.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
P316451141591630ChainID=PRO_0000214757;Note=Sodium-dependent serotonin transporter
P316451141591630ChainID=PRO_0000214757;Note=Sodium-dependent serotonin transporter
P31645114159114117HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I6X
P31645114159114117HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I6X
P31645114159118127HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I6X
P31645114159118127HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I6X
P31645114159129143HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I6X
P31645114159129143HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I6X
P31645114159149152HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I6X
P31645114159149152HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I6X
P31645114159156159HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I6X
P31645114159156159HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I6X
P31645114159142142Modified residueNote=Phosphotyrosine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21992875;Dbxref=PMID:21992875
P31645114159142142Modified residueNote=Phosphotyrosine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21992875;Dbxref=PMID:21992875
P31645114159113115Topological domainNote=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305
P31645114159113115Topological domainNote=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305
P31645114159136160Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
P31645114159136160Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
P31645114159116135TransmembraneNote=Helical%3B Name%3D2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:27049939;Dbxref=PMID:27049939
P31645114159116135TransmembraneNote=Helical%3B Name%3D2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:27049939;Dbxref=PMID:27049939


check button Lost protein functional features of individual exon skipping events in GTEx.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
P316451141591630ChainID=PRO_0000214757;Note=Sodium-dependent serotonin transporter
P316451141591630ChainID=PRO_0000214757;Note=Sodium-dependent serotonin transporter
P31645114159114117HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I6X
P31645114159114117HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I6X
P31645114159118127HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I6X
P31645114159118127HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I6X
P31645114159129143HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I6X
P31645114159129143HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I6X
P31645114159149152HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I6X
P31645114159149152HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I6X
P31645114159156159HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I6X
P31645114159156159HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:5I6X
P31645114159142142Modified residueNote=Phosphotyrosine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21992875;Dbxref=PMID:21992875
P31645114159142142Modified residueNote=Phosphotyrosine;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21992875;Dbxref=PMID:21992875
P31645114159113115Topological domainNote=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305
P31645114159113115Topological domainNote=Extracellular;Ontology_term=ECO:0000305;evidence=ECO:0000305
P31645114159136160Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
P31645114159136160Topological domainNote=Cytoplasmic;Ontology_term=ECO:0000305;evidence=ECO:0000305
P31645114159116135TransmembraneNote=Helical%3B Name%3D2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:27049939;Dbxref=PMID:27049939
P31645114159116135TransmembraneNote=Helical%3B Name%3D2;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:27049939;Dbxref=PMID:27049939


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SNVs in the skipped exons for SLC6A4

check button - Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.
lollipop

check button - Differential PSIs between mutated versus non-mutated samples.

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
ESCATCGA-IG-A7DP-01exon_skip_288049
28545815285459492854583328545833Frame_Shift_DelT-p.I154fs
LUSCTCGA-22-5480-01exon_skip_288049
28545815285459492854594728545947Frame_Shift_DelC-p.A116fs
SKCMTCGA-FW-A3R5-06exon_skip_288046
exon_skip_288045
28534750285348502853479628534796Nonsense_MutationCTp.W535*
UCECTCGA-AX-A05Z-01exon_skip_288049
28545815285459492854585728545857Nonsense_MutationCAp.G146*

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
MERO14_LUNG28534750285348502853476428534765Frame_Shift_Ins-GCp.P546fs
KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE28534750285348502853480428534804Missense_MutationGTp.S532R
SNU1040_LARGE_INTESTINE28536161285362602853617928536179Missense_MutationCTp.A511T
YD8_UPPER_AERODIGESTIVE_TRACT28536161285362602853619728536197Missense_MutationCTp.A505T
HEC59_ENDOMETRIUM28545815285459492854588128545881Missense_MutationCTp.A138T
NCIH661_LUNG28534750285348502853485028534850Splice_SiteCAp.G517V

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SLC6A4

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SLC6A4


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SLC6A4


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RelatedDrugs for SLC6A4

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
P31645DB00215CitalopramSodium-dependent serotonin transportersmall moleculeapproved
P31645DB00245BenzatropineSodium-dependent serotonin transportersmall moleculeapproved
P31645DB00285VenlafaxineSodium-dependent serotonin transportersmall moleculeapproved
P31645DB00289AtomoxetineSodium-dependent serotonin transportersmall moleculeapproved
P31645DB00321AmitriptylineSodium-dependent serotonin transportersmall moleculeapproved
P31645DB00344ProtriptylineSodium-dependent serotonin transportersmall moleculeapproved
P31645DB00370MirtazapineSodium-dependent serotonin transportersmall moleculeapproved
P31645DB00408LoxapineSodium-dependent serotonin transportersmall moleculeapproved
P31645DB00454MeperidineSodium-dependent serotonin transportersmall moleculeapproved
P31645DB00458ImipramineSodium-dependent serotonin transportersmall moleculeapproved
P31645DB00476DuloxetineSodium-dependent serotonin transportersmall moleculeapproved
P31645DB00514DextromethorphanSodium-dependent serotonin transportersmall moleculeapproved
P31645DB00540NortriptylineSodium-dependent serotonin transportersmall moleculeapproved
P31645DB00543AmoxapineSodium-dependent serotonin transportersmall moleculeapproved
P31645DB00661VerapamilSodium-dependent serotonin transportersmall moleculeapproved
P31645DB00726TrimipramineSodium-dependent serotonin transportersmall moleculeapproved
P31645DB00805MinaprineSodium-dependent serotonin transportersmall moleculeapproved
P31645DB00852PseudoephedrineSodium-dependent serotonin transportersmall moleculeapproved
P31645DB00988DopamineSodium-dependent serotonin transportersmall moleculeapproved
P31645DB01104SertralineSodium-dependent serotonin transportersmall moleculeapproved
P31645DB01114ChlorphenamineSodium-dependent serotonin transportersmall moleculeapproved
P31645DB06204TapentadolSodium-dependent serotonin transportersmall moleculeapproved
P31645DB09016ButriptylineSodium-dependent serotonin transportersmall moleculeapproved
P31645DB09167DosulepinSodium-dependent serotonin transportersmall moleculeapproved
P31645DB00191PhentermineSodium-dependent serotonin transportersmall moleculeapproved|illicit
P31645DB00907CocaineSodium-dependent serotonin transportersmall moleculeapproved|illicit
P31645DB01577MetamfetamineSodium-dependent serotonin transportersmall moleculeapproved|illicit
P31645DB00182AmphetamineSodium-dependent serotonin transportersmall moleculeapproved|illicit|investigational
P31645DB00574FenfluramineSodium-dependent serotonin transportersmall moleculeapproved|illicit|investigational|withdrawn
P31645DB01105SibutramineSodium-dependent serotonin transportersmall moleculeapproved|illicit|investigational|withdrawn
P31645DB01191DexfenfluramineSodium-dependent serotonin transportersmall moleculeapproved|illicit|investigational|withdrawn
P31645DB00176FluvoxamineSodium-dependent serotonin transportersmall moleculeapproved|investigational
P31645DB00193TramadolSodium-dependent serotonin transportersmall moleculeapproved|investigational
P31645DB00422MethylphenidateSodium-dependent serotonin transportersmall moleculeapproved|investigational
P31645DB00579MazindolSodium-dependent serotonin transportersmall moleculeapproved|investigational
P31645DB00656TrazodoneSodium-dependent serotonin transportersmall moleculeapproved|investigational
P31645DB00715ParoxetineSodium-dependent serotonin transportersmall moleculeapproved|investigational
P31645DB01142DoxepinSodium-dependent serotonin transportersmall moleculeapproved|investigational
P31645DB01151DesipramineSodium-dependent serotonin transportersmall moleculeapproved|investigational
P31645DB01175EscitalopramSodium-dependent serotonin transportersmall moleculeapproved|investigational
P31645DB04896MilnacipranSodium-dependent serotonin transportersmall moleculeapproved|investigational
P31645DB06148MianserinSodium-dependent serotonin transportersmall moleculeapproved|investigational
P31645DB06700DesvenlafaxineSodium-dependent serotonin transportersmall moleculeapproved|investigational
P31645DB06701DexmethylphenidateSodium-dependent serotonin transportersmall moleculeapproved|investigational
P31645DB09068VortioxetineSodium-dependent serotonin transportersmall moleculeapproved|investigational
P31645DB01242ClomipramineSodium-dependent serotonin transportersmall moleculeapproved|investigational|vet_approved
P31645DB09225ZotepineSodium-dependent serotonin transportersmall moleculeapproved|investigational|withdrawn
P31645DB00472FluoxetineSodium-dependent serotonin transportersmall moleculeapproved|vet_approved
P31645DB01149NefazodoneSodium-dependent serotonin transportersmall moleculeapproved|withdrawn
P31645DB04821NomifensineSodium-dependent serotonin transportersmall moleculeapproved|withdrawn
P31645DB04832ZimelidineSodium-dependent serotonin transportersmall moleculeapproved|withdrawn

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RelatedDiseases for SLC6A4

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
SLC6A4C0011581Depressive disorder9CTD_human;PSYGENET
SLC6A4C0001973Alcoholic Intoxication, Chronic7CTD_human;PSYGENET
SLC6A4C0005586Bipolar Disorder7CTD_human;PSYGENET
SLC6A4C0525045Mood Disorders6CTD_human;PSYGENET
SLC6A4C1269683Major Depressive Disorder6CTD_human;PSYGENET
SLC6A4C0004352Autistic Disorder5CTD_human
SLC6A4C0011570Mental Depression5PSYGENET
SLC6A4C0025193Melancholia5PSYGENET
SLC6A4C0041696Unipolar Depression5PSYGENET
SLC6A4C0085159Seasonal Affective Disorder5PSYGENET
SLC6A4C0221074Depression, Postpartum5PSYGENET
SLC6A4C0344315Depressed mood5PSYGENET
SLC6A4C0581391Chronic depression4PSYGENET
SLC6A4C0600427Cocaine Dependence4PSYGENET
SLC6A4C0221480Recurrent depression3PSYGENET
SLC6A4C0233477Dysphoric mood3PSYGENET
SLC6A4C2063866Depressive Disorder, Treatment-Resistant3PSYGENET
SLC6A4C0001723Affective Disorders, Psychotic2PSYGENET
SLC6A4C0005587Depression, Bipolar2PSYGENET
SLC6A4C0025261Memory Disorders2CTD_human
SLC6A4C0085762Alcohol abuse2PSYGENET
SLC6A4C0178417Anhedonia2PSYGENET
SLC6A4C0338715Drug-induced depressive state2PSYGENET
SLC6A4C0001969Alcoholic Intoxication1PSYGENET
SLC6A4C0003469Anxiety Disorders1CTD_human
SLC6A4C0009241Cognition Disorders1CTD_human
SLC6A4C0013415Dysthymic Disorder1PSYGENET
SLC6A4C0020542Pulmonary Hypertension1CTD_human
SLC6A4C0024809Marijuana Abuse1PSYGENET
SLC6A4C0028768Obsessive-Compulsive Disorder1CTD_human
SLC6A4C0031212Personality Disorders1CTD_human
SLC6A4C0036341Schizophrenia1CTD_human
SLC6A4C0038587Substance Withdrawal Syndrome1CTD_human
SLC6A4C0038644Sudden infant death syndrome1CTD_human
SLC6A4C0236733Amphetamine-Related Disorders1CTD_human
SLC6A4C0236736Cocaine-Related Disorders1CTD_human
SLC6A4C0236792Asperger Syndrome1CTD_human
SLC6A4C0236969Substance-Related Disorders1CTD_human
SLC6A4C0588008Severe depression1PSYGENET
SLC6A4C3160814Cannabis use1PSYGENET