Slc6a4 (solute carrier family 6 member 4) - Rat Genome Database

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Gene: Slc6a4 (solute carrier family 6 member 4) Rattus norvegicus
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Symbol: Slc6a4
Name: solute carrier family 6 member 4
RGD ID: 3714
Description: Enables several functions, including cocaine binding activity; monoatomic cation transmembrane transporter activity; and syntaxin-1 binding activity. Involved in several processes, including cellular response to cGMP; negative regulation of dopaminergic synaptic transmission; and positive regulation of serotonin secretion. 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 and borna disease. Human ortholog(s) of this gene implicated in several diseases, including alcohol use disorder; alexithymia; anxiety disorder (multiple); depressive disorder (multiple); and heart disease (multiple). Orthologous to human SLC6A4 (solute carrier family 6 member 4); PARTICIPATES IN alfentanil pharmacodynamics pathway; bupivacaine pharmacodynamics pathway; buprenorphine pharmacodynamics pathway; INTERACTS WITH (S)-amphetamine; 1,2-dimethylhydrazine; 1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 5HT transporter; 5HTT; serotonin transporter; SERT; sodium-dependent serotonin transporter; solute carrier family 6 (neurotransmitter transporter serotonin) member 4; solute carrier family 6 (neurotransmitter transporter serotonin) member 4 (5-hydroxytryptamine (serotonin) transporter); solute carrier family 6 (neurotransmitter transporter serotonin) member 4 (5-hydroxytryptamine (serotonin) transporter); solute carrier family 6 (neurotransmitter transporter), member 4; solute carrier family 6 (neurotransmitter transporter, serotonin), member 4; solute carrier family 6, member 4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Slc6a4m1Hubr  
Genetic Models: WI-Slc6a4m1Hubr+/- WI-Slc6a4m1Hubr-/-
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21061,824,208 - 61,858,924 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1061,826,123 - 61,858,384 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1066,483,857 - 66,505,046 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01065,989,335 - 66,010,524 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01061,459,175 - 61,480,332 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01063,153,656 - 63,188,377 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1063,153,651 - 63,176,463 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01062,851,326 - 62,872,481 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41067,134,790 - 67,155,891 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11067,148,412 - 67,197,988 (-)NCBI
Celera1060,845,942 - 60,866,725 (+)NCBICelera
Cytogenetic Map10q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(R)-noradrenaline  (ISO)
(R)-octopamine  (ISO)
(S)-amphetamine  (EXP,ISO)
(S)-colchicine  (ISO)
(S)-fenfluramine  (ISO)
1,2-dimethylhydrazine  (EXP,ISO)
1-(3-chlorophenyl)piperazine  (ISO)
1-[(4-chlorophenyl)-phenylmethyl]-4-methylpiperazine  (EXP)
1-[3-(dimethylamino)propyl]-1-(4-fluorophenyl)-1,3-dihydro-2-benzofuran-5-carbonitrile  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP)
2,3,7,8-Tetrachlorodibenzofuran  (EXP)
2,5-dimethoxy-4-bromophenethylamine  (ISO)
2-phenylethylamine  (ISO)
3,4-methylenedioxymethamphetamine  (EXP,ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (EXP,ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
8-OH-DPAT  (EXP)
aflatoxin B1  (ISO)
alendronic acid  (EXP)
aminorex  (EXP)
ammonium chloride  (EXP)
amphetamine  (ISO)
antirheumatic drug  (ISO)
aripiprazole  (ISO)
aristolochic acid A  (ISO)
Aroclor 1254  (EXP)
arsane  (EXP)
arsenic atom  (EXP)
atorvastatin calcium  (EXP)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP,ISO)
bupropion  (ISO)
cadmium atom  (ISO)
cannabidiol  (ISO)
cantharidin  (ISO)
carbon nanotube  (ISO)
carbonyl sulfide  (EXP)
CGP 52608  (ISO)
chlorpyrifos  (EXP)
citalopram  (ISO)
clomipramine  (ISO)
clozapine  (EXP,ISO)
cocaine  (EXP,ISO)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
cyhalothrin  (EXP)
dexamethasone  (EXP)
dextromethorphan  (EXP)
diazinon  (EXP)
dieldrin  (EXP)
diquat  (ISO)
dopamine  (ISO)
ethanol  (ISO)
excitatory amino acid agonist  (EXP)
fluoxetine  (EXP,ISO)
fluoxetine hydrochloride  (EXP)
folic acid  (ISO)
formaldehyde  (ISO)
forskolin  (ISO)
fulvestrant  (ISO)
fumonisin B1  (ISO)
gabapentin  (ISO)
genistein  (EXP,ISO)
glyphosate  (ISO)
haloperidol  (EXP)
hydrogen peroxide  (ISO)
hydroxyurea  (ISO)
imipramine  (EXP)
ketanserin  (ISO)
lamivudine  (ISO)
lithium chloride  (ISO)
Mazindol  (ISO)
mephedrone  (EXP,ISO)
mepyramine  (ISO)
mercury atom  (ISO)
mercury dichloride  (EXP)
mercury(0)  (ISO)
methamidophos  (ISO)
methamphetamine  (EXP,ISO)
monensin A  (ISO)
monocrotaline  (EXP,ISO)
N-ethyl-N-nitrosourea  (EXP)
N-Nitrosopyrrolidine  (ISO)
nickel atom  (EXP)
nisoxetine  (ISO)
nitrofen  (EXP)
nomifensine  (ISO)
nortriptyline  (ISO)
O-methyleugenol  (ISO)
ochratoxin A  (ISO)
octopamine  (ISO)
oxaliplatin  (EXP)
oxidopamine  (EXP)
paracetamol  (EXP)
parathion  (EXP)
paroxetine  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
phorbol 13-acetate 12-myristate  (EXP)
piperazines  (ISO)
pirinixic acid  (EXP,ISO)
quercetin  (ISO)
raloxifene  (EXP)
reserpine  (EXP)
ribavirin  (ISO)
serotonin  (EXP,ISO)
sertraline  (EXP,ISO)
simvastatin  (ISO)
staurosporine  (ISO)
streptozocin  (ISO)
sulfadiazine  (ISO)
Sunset Yellow FCF  (ISO)
tetrachloroethene  (ISO)
tianeptine  (ISO)
titanium dioxide  (ISO)
topotecan  (EXP)
triclosan  (ISO)
triphenyl phosphate  (EXP)
triptonide  (ISO)
trisodium vanadate  (EXP)
trovafloxacin  (ISO)
tryptamine  (ISO)
tyramine  (ISO)
urethane  (ISO)
valproic acid  (EXP,ISO)
vancomycin  (ISO)
venlafaxine hydrochloride  (ISO)
vortioxetine  (EXP,ISO)
zinc atom  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
alfentanil pharmacodynamics pathway  (ISO)
bupivacaine pharmacodynamics pathway  (ISO)
buprenorphine pharmacodynamics pathway  (ISO)
chloroprocaine pharmacodynamics pathway  (ISO)
citalopram pharmacodynamics pathway  (ISO)
citalopram pharmacokinetics pathway  (ISO)
cocaine pharmacodynamics pathway  (ISO)
codeine and morphine pharmacodynamics pathway  (ISO)
desipramine pharmacodynamics pathway  (ISO)
desipramine pharmacokinetics pathway  (ISO)
diphenoxylate pharmacodynamics pathway  (ISO)
escitalopram pharmacodynamics pathway  (ISO)
ethylmorphine pharmacodynamics pathway  (ISO)
fentanyl pharmacodynamics pathway  (ISO)
fluoxetine pharmacodynamics pathway  (ISO)
fluoxetine pharmacokinetics pathway  (ISO)
heroin pharmacodynamics pathway  (ISO)
hydrocodone pharmacodynamics pathway  (ISO)
hydromorphone pharmacodynamics pathway  (ISO)
imipramine pharmacodynamics pathway  (ISO)
imipramine pharmacokinetics pathway  (ISO)
levacetylmethadol pharmacodynamics pathway  (ISO)
levobupivacaine phgarmacodynamics pathway  (ISO)
levorphanol pharmacodynamics pathway  (ISO)
lidocaine pharmacodynamics pathway  (ISO)
mepivacaine pharmacodynamics pathway  (ISO)
methadone pharmacodynamics pathway  (ISO)
nalbuphine pharmacodynamics pathway  (ISO)
naloxone pharmacodynamics pathway  (ISO)
naltrexone pharmacodynamics pathway  (ISO)
nicotine pharmacodynamics pathway  (ISO)
oxybuprocaine pharmacodynamics pathway  (ISO)
oxycodone pharmacodynamics pathway  (ISO)
oxymorphone pharmacodynamics pathway  (ISO)
pathogenic Escherichia coli infection pathway  (ISO)
pentazocine pharmacodynamics pathway  (ISO)
prilocaine pharmacodynamics pathway  (ISO)
procaine pharmacodynamics pathway  (ISO)
remifentanil pharmacodynamics pathway  (ISO)
ropivacaine pharmacodynamics pathway  (ISO)
tramadol pharmacodynamics pathway  (ISO)
venlafaxine pharmacokinetics pathway  (ISO)

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. No Influence of a functional polymorphism within the serotonin transporter gene on partial sleep deprivation in major depression. Baghai TC, etal., World J Biol Psychiatry. 2003 Jul;4(3):111-4. doi: 10.1080/15622970310029903.
2. Serotonin transporter polymorphism moderates the effects of caregiver intrusiveness on ADHD symptoms among institutionalized preschoolers. Baptista J, etal., Eur Child Adolesc Psychiatry. 2017 Mar;26(3):303-313. doi: 10.1007/s00787-016-0890-x. Epub 2016 Jul 18.
3. Three autism candidate genes: a synthesis of human genetic analysis with other disciplines. Bartlett CW, etal., Int J Dev Neurosci 2005 Apr-May;23(2-3):221-34.
4. Influence of a functional polymorphism within the promoter of the serotonin transporter gene on the effects of total sleep deprivation in bipolar depression. Benedetti F, etal., Am J Psychiatry. 1999 Sep;156(9):1450-2. doi: 10.1176/ajp.156.9.1450.
5. A Western Diet Increases Serotonin Availability in Rat Small Intestine. Bertrand RL, etal., Endocrinology. 2010 Nov 10.
6. Effects of 3,4-methylenedioxymethamphetamine (MDMA) on serotonin transporter and vesicular monoamine transporter 2 protein and gene expression in rats: implications for MDMA neurotoxicity. Biezonski DK and Meyer JS, J Neurochem. 2010 Feb;112(4):951-62. Epub 2009 Nov 30.
7. Cloning and expression of a functional serotonin transporter from rat brain. Blakely RD, etal., Nature. 1991 Nov 7;354(6348):66-70. doi: 10.1038/354066a0.
8. Association study of serotonin transporter gene polymorphisms and ventricular septal defects related possible pulmonary arterial hypertension in Chinese population. Cao H, etal., Clin Exp Hypertens. 2009 Oct;31(7):605-14.
9. The Serotonin Transporter Plays an Important Role in Male Sexual Behavior: A Study in Serotonin Transporter Knockout Rats. Chan JS, etal., J Sex Med. 2010 Aug 5.
10. Association of the serotonin transporter gene with serum cholesterol levels and heart disease. Comings DE, etal., Mol Genet Metab. 1999 Jul;67(3):248-53.
11. Serotonin signaling in diverticular disease. Costedio MM, etal., J Gastrointest Surg. 2008 Aug;12(8):1439-45. doi: 10.1007/s11605-008-0536-5. Epub 2008 May 20.
12. The serotonin transporter and 5HT2A receptor in rat brain after localized lesions. Dam H, etal., Neurol Res. 2007 Oct;29(7):717-22.
13. Prenatal exposure to maternal depressed mood and the MTHFR C677T variant affect SLC6A4 methylation in infants at birth. Devlin AM, etal., PLoS One. 2010 Aug 16;5(8):e12201. doi: 10.1371/journal.pone.0012201.
14. Serotonin transporter gene hypomethylation predicts impaired antidepressant treatment response. Domschke K, etal., Int J Neuropsychopharmacol. 2014 Aug;17(8):1167-76. doi: 10.1017/S146114571400039X. Epub 2014 Mar 28.
15. Sequence variations of ABCB1, SLC6A2, SLC6A3, SLC6A4, CREB1, CRHR1 and NTRK2: association with major depression and antidepressant response in Mexican-Americans. Dong C, etal., Mol Psychiatry. 2009 Dec;14(12):1105-18. Epub 2009 Oct 20.
16. Association of polymorphisms in serotonin and nitric oxide genes with clinical outcome of dengue in Brazilian northeast population. Dos Santos ACM, etal., Acta Trop. 2019 Feb;190:144-148. doi: 10.1016/j.actatropica.2018.11.015. Epub 2018 Nov 16.
17. The serotonin transporter polymorphism, 5HTTLPR, is associated with a faster response time to sertraline in an elderly population with major depressive disorder. Durham LK, etal., Psychopharmacology (Berl). 2004 Aug;174(4):525-9. doi: 10.1007/s00213-003-1562-3. Epub 2003 Sep 4.
18. Dexfenfluramine-associated changes in 5-hydroxytryptamine transporter expression and development of hypoxic pulmonary hypertension in rats. Eddahibi S, etal., J Pharmacol Exp Ther. 2001 Apr;297(1):148-54.
19. Functional genetic variants that increase synaptic serotonin and 5-HT3 receptor sensitivity predict alcohol and drug dependence. Enoch MA, etal., Mol Psychiatry. 2011 Nov;16(11):1139-46. doi: 10.1038/mp.2010.94. Epub 2010 Sep 14.
20. Enteropathogenic Escherichia coli infection inhibits intestinal serotonin transporter function and expression. Esmaili A, etal., Gastroenterology. 2009 Dec;137(6):2074-83. doi: 10.1053/j.gastro.2009.09.002. Epub 2009 Sep 10.
21. Association between the Stin2 VNTR polymorphism of the serotonin transporter gene and treatment outcome in alcohol-dependent patients. Florez G, etal., Alcohol Alcohol. 2008 Sep-Oct;43(5):516-22. doi: 10.1093/alcalc/agn048. Epub 2008 Jun 14.
22. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
23. Serotonin transport is modulated differently by tetanus toxin and growth factors. Gil C, etal., Neurochem Int. 2003 Jun;42(7):535-42. doi: 10.1016/s0197-0186(02)00187-0.
24. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
25. [The role of the 5-HTTLPR polymorphism of the serotonin transporter gene in the development of depression in patients with coronary heart disease]. Golimbet VE, etal., Zh Nevrol Psikhiatr Im S S Korsakova. 2012;112(8):63-9.
26. The pulmonary hypertensive fawn-hooded rat has a normal serotonin transporter coding sequence. Gonzalez AM, etal., Am J Respir Cell Mol Biol 1998 Aug;19(2):245-9.
27. Regulation of the serotonin transporter by interacting proteins. Haase J, etal., Biochem Soc Trans. 2001 Nov;29(Pt 6):722-8.
28. Cerebral glucose utilisation in hepatitis C virus infection-associated encephalopathy. Heeren M, etal., J Cereb Blood Flow Metab. 2011 Nov;31(11):2199-208. doi: 10.1038/jcbfm.2011.82. Epub 2011 Jun 1.
29. Cloning of a serotonin transporter affected by antidepressants. Hoffman BJ, etal., Science 1991 Oct 25;254(5031):579-80.
30. Upregulation of serotonin-receptor-2a and serotonin transporter expression in the pulmonary vasculature of nitrofen-induced congenital diaphragmatic hernia. Hofmann AD, etal., J Pediatr Surg. 2014 Jun;49(6):871-4; discussion 874-5. doi: 10.1016/j.jpedsurg.2014.01.015. Epub 2014 Jan 31.
31. Adaptations in pre- and postsynaptic 5-HT1A receptor function and cocaine supersensitivity in serotonin transporter knockout rats. Homberg JR, etal., Psychopharmacology (Berl). 2008 Oct;200(3):367-80. Epub 2008 Jun 27.
32. Association of SLC6A4 5-HTTLPR and TRPV1 945G>C with functional dyspepsia in Korea. Hwang SW, etal., J Gastroenterol Hepatol. 2014 Oct;29(10):1770-7. doi: 10.1111/jgh.12596.
33. Association of serotonin transporter gene variation with smoking, chronic obstructive pulmonary disease, and its depressive symptoms. Ishii T, etal., J Hum Genet. 2010 Oct 28.
34. The CC genotype in HTR2A T102C polymorphism is associated with behavioral impulsivity in alcohol-dependent patients. Jakubczyk A, etal., J Psychiatr Res. 2012 Jan;46(1):44-9. doi: 10.1016/j.jpsychires.2011.09.001. Epub 2011 Sep 17.
35. Controlled clinical comparison of paroxetine and fluvoxamine considering the serotonin transporter promoter polymorphism. Kato M, etal., Int Clin Psychopharmacol. 2005 May;20(3):151-6. doi: 10.1097/00004850-200505000-00005.
36. Oligomerization of serotonin transporter and its functional consequences. Kilic F and Rudnick G, Proc Natl Acad Sci U S A. 2000 Mar 28;97(7):3106-11.
37. Body image, sexual function and depression in Korean patients with breast cancer: modification by 5-HTT polymorphism. Kim KR, etal., Support Care Cancer. 2012 Sep;20(9):2177-82. doi: 10.1007/s00520-011-1329-z. Epub 2011 Dec 2.
38. Transmission disequilibrium mapping at the serotonin transporter gene (SLC6A4) region in autistic disorder. Kim SJ, etal., Mol Psychiatry. 2002;7(3):278-88.
39. [Chronic administration of serotonin transporter inhibitor (fluoxetine) decreases monocrotaline-induced pulmonary hypertension in rats] Kozhevnikova VV and Medvedeva NA, Eksp Klin Farmakol. 2007 Sep-Oct;70(5):15-8.
40. Serotonin transporter gene polymorphism associated with short-term treatment response to venlafaxine. Lee SH, etal., Neuropsychobiology. 2010 Aug;62(3):198-206. doi: 10.1159/000319362. Epub 2010 Jul 22.
41. Single-channel currents produced by the serotonin transporter and analysis of a mutation affecting ion permeation. Lin F, etal., Biophys J. 1996 Dec;71(6):3126-35. doi: 10.1016/S0006-3495(96)79506-1.
42. Vascular reactivity, 5-HT uptake, and blood pressure in the serotonin transporter knockout rat. Linder AE, etal., Am J Physiol Heart Circ Physiol. 2008 Apr;294(4):H1745-52. Epub 2008 Feb 8.
43. Postnatal changes in tryptophan hydroxylase and serotonin transporter immunoreactivity in multiple brainstem nuclei of the rat: implications for a sensitive period. Liu Q and Wong-Riley MT, J Comp Neurol. 2010 Apr 1;518(7):1082-97.
44. NEUROPSYCHOBIOLOGICAL MECHANISMS OF AFFECTIVE AND COGNITIVE DISORDERS IN THE CHORNOBYL CLEAN-UP WORKERS TAKING INTO ACCOUNT THE SPECIFIC GENE POLYMORPHISMS. Loganovsky KN, etal., Probl Radiac Med Radiobiol. 2018 Dec;23:373-409. doi: 10.33145/2304-8336-2018-23-373-409.
45. Interaction between polymorphisms in serotonin transporter (SLC6A4) and serotonin receptor 2A (HTR2A) genes predict treatment response to venlafaxine XR in generalized anxiety disorder. Lohoff FW, etal., Pharmacogenomics J. 2013 Oct;13(5):464-9. doi: 10.1038/tpj.2012.33. Epub 2012 Aug 21.
46. Genetic association of the serotonin transporter in pulmonary arterial hypertension. Machado RD, etal., Am J Respir Crit Care Med. 2006 Apr 1;173(7):793-7. Epub 2006 Jan 6.
47. Partitioning of the serotonin transporter into lipid microdomains modulates transport of serotonin. Magnani F, etal., J Biol Chem. 2004 Sep 10;279(37):38770-8. Epub 2004 Jun 29.
48. Serotonin transporter gene (SLC6A4) polymorphisms are associated with response to fluoxetine in south Indian major depressive disorder patients. Manoharan A, etal., Eur J Clin Pharmacol. 2016 Oct;72(10):1215-1220. doi: 10.1007/s00228-016-2099-9. Epub 2016 Jul 20.
49. Serotonin transporter protein overexpression and association to Th17 and T regulatory cells in lupoid leishmaniasis. Mashayekhi Goyonlo V, etal., Arch Dermatol Res. 2014 Mar;306(2):181-8. doi: 10.1007/s00403-013-1395-9. Epub 2013 Aug 29.
50. Deletion of the serotonin transporter in rats disturbs serotonin homeostasis without impairing liver regeneration. Matondo RB, etal., Am J Physiol Gastrointest Liver Physiol. 2009 Apr;296(4):G963-8. Epub 2009 Feb 26.
51. Isolation of cDNAs encoding a novel member of the neurotransmitter transporter gene family. Mayser W, etal., FEBS Lett 1991 Dec 16;295(1-3):203-6.
52. Deficiency of the 5-hydroxytryptamine transporter gene leads to cardiac fibrosis and valvulopathy in mice. Mekontso-Dessap A, etal., Circulation. 2006 Jan 3;113(1):81-9. Epub 2005 Dec 27.
53. Maintenance of Chronic Fatigue Syndrome (CFS) in Young CFS Patients Is Associated with the 5-HTTLPR and SNP rs25531 A > G Genotype. Meyer B, etal., PLoS One. 2015 Oct 16;10(10):e0140883. doi: 10.1371/journal.pone.0140883. eCollection 2015.
54. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
55. Role of C-terminal region in the functional regulation of rat serotonin transporter (SERT). Mochizuki H, etal., Neurochem Int. 2005 Jan;46(2):93-105. Epub 2004 Nov 26.
56. In vivo effects of a combined 5-HT1B receptor/SERT antagonist in experimental pulmonary hypertension. Morecroft I, etal., Cardiovasc Res. 2010 Feb 1;85(3):593-603. Epub 2009 Sep 7.
57. Molecular cloning, expression and characterization of a bovine serotonin transporter. Mortensen OV, etal., Brain Res Mol Brain Res. 1999 Jul 23;71(1):120-6. doi: 10.1016/s0169-328x(99)00178-3.
58. Serotonin receptor 3A polymorphism c.-42C > T is associated with severe dyspepsia. Mujakovic S, etal., BMC Med Genet. 2011 Oct 20;12:140. doi: 10.1186/1471-2350-12-140.
59. Subcellular redistribution of the serotonin transporter by secretory carrier membrane protein 2. Muller HK, etal., J Biol Chem. 2006 Sep 29;281(39):28901-9. Epub 2006 Jul 26.
60. Unaltered susceptibility to scrapie in serotonin transporter deficient mice. Mössner R, etal., Neurochem Int. 2006 Oct;49(5):454-8. doi: 10.1016/j.neuint.2006.03.008. Epub 2006 May 30.
61. Serotonin transporter phosphorylation modulated by tetanus toxin. Najib A, etal., FEBS Lett. 2000 Dec 8;486(2):136-42. doi: 10.1016/s0014-5793(00)02294-8.
62. Association between serotonin transporter gene polymorphism and chronic fatigue syndrome. Narita M, etal., Biochem Biophys Res Commun. 2003 Nov 14;311(2):264-6. doi: 10.1016/j.bbrc.2003.09.207.
63. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
64. Selective serotonin reuptake inhibitors and raft inhibitors shorten the period of Period1-driven circadian bioluminescence rhythms in rat-1 fibroblasts. Nomura K, etal., Life Sci. 2008 Jun 6;82(23-24):1169-74. Epub 2008 Apr 16.
65. Consequences of Citrobacter rodentium infection on enteroendocrine cells and the enteric nervous system in the mouse colon. O'Hara JR, etal., Cell Microbiol. 2006 Apr;8(4):646-60. doi: 10.1111/j.1462-5822.2005.00657.x.
66. 13-cis-Retinoic acid alters intracellular serotonin, increases 5-HT1A receptor, and serotonin reuptake transporter levels in vitro. O'Reilly KC, etal., Exp Biol Med (Maywood). 2007 Oct;232(9):1195-203.
67. Time course of opioid and cannabinoid gene transcription alterations induced by repeated administration with fluoxetine in the rat brain. Oliva JM, etal., Neuropharmacology. 2005 Oct;49(5):618-26. doi: 10.1016/j.neuropharm.2005.04.014.
68. A study in male and female 5-HT transporter knockout rats: an animal model for anxiety and depression disorders. Olivier JD, etal., Neuroscience. 2008 Mar 27;152(3):573-84. Epub 2008 Jan 1.
69. Repeat length polymorphism of the serotonin transporter gene influences pulmonary artery pressure in heart failure. Olson TP, etal., Am Heart J. 2007 Mar;153(3):426-32.
70. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
71. Serotonin transporter missense mutation associated with a complex neuropsychiatric phenotype. Ozaki N, etal., Mol Psychiatry. 2003 Nov;8(11):933-6.
72. Glycosyl modification facilitates homo- and hetero-oligomerization of the serotonin transporter. A specific role for sialic acid residues. Ozaslan D, etal., J Biol Chem. 2003 Nov 7;278(45):43991-4000. Epub 2003 Aug 27.
73. Genetic determinants of alcohol addiction and metabolism: a survey in Italy. Pastorelli R, etal., Alcohol Clin Exp Res. 2001 Feb;25(2):221-7.
74. Tetanus toxin modulates serotonin transport in rat-brain neuronal cultures. Pelliccioni P, etal., J Mol Neurosci. 2001 Dec;17(3):303-10. doi: 10.1385/JMN:17:3:303.
75. Ultrastructural localization of the serotonin transporter in limbic and motor compartments of the nucleus accumbens. Pickel VM and Chan J, J Neurosci. 1999 Sep 1;19(17):7356-66.
76. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
77. Effects of genetic background on neonatal Borna disease virus infection-induced neurodevelopmental damage. II. Neurochemical alterations and responses to pharmacological treatments. Pletnikov MV, etal., Brain Res. 2002 Jul 19;944(1-2):108-23. doi: 10.1016/s0006-8993(02)02724-5.
78. Genetic Associations of Alexithymia in Predicting Interferon-Induced Depression in Chronic Hepatitis C. Porcelli P, etal., Psychopathology. 2015;48(6):417-20. doi: 10.1159/000441682. Epub 2015 Nov 27.
79. Regulating the conducting states of a mammalian serotonin transporter. Quick MW Neuron. 2003 Oct 30;40(3):537-49.
80. Cyclic AMP-independent up-regulation of the human serotonin transporter by staurosporine in choriocarcinoma cells. Ramamoorthy JD, etal., J Biol Chem. 1995 Jul 21;270(29):17189-95. doi: 10.1074/jbc.270.29.17189.
81. Regulation of the human serotonin transporter. Cholera toxin-induced stimulation of serotonin uptake in human placental choriocarcinoma cells is accompanied by increased serotonin transporter mRNA levels and serotonin transporter-specific ligand binding. Ramamoorthy S, etal., J Biol Chem. 1993 Oct 15;268(29):21626-31.
82. Phosphorylation of threonine residue 276 is required for acute regulation of serotonin transporter by cyclic GMP. Ramamoorthy S, etal., J Biol Chem. 2007 Apr 20;282(16):11639-47. Epub 2007 Feb 19.
83. GOA pipeline RGD automated data pipeline
84. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
85. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
86. Estradiol increases Pet-1 and serotonin transporter mRNA in the midbrain raphe nuclei of ovariectomized rats. Rivera HM, etal., Brain Res. 2009 Mar 9;1259:51-8. Epub 2009 Jan 10.
87. Chronic buspirone treatment decreases 5-HT1B receptor densities and the serotonin transporter but increases the density of 5-HT2A receptors in the bulbectomized rat model of depression: an autoradiographic study. Sato H, etal., Brain Res. 2010 Jul 23;1345:28-44. Epub 2010 May 23.
88. Effects of S-citalopram, citalopram, and R-citalopram on the firing patterns of dopamine neurons in the ventral tegmental area, N-methyl-D-aspartate receptor-mediated transmission in the medial prefrontal cortex and cognitive function in the rat. Schilstrom B, etal., Synapse. 2010 Aug 20.
89. Interaction of paroxetine with mitochondrial proteins mediates neuroprotection. Steiner JP, etal., Neurotherapeutics. 2015 Jan;12(1):200-16. doi: 10.1007/s13311-014-0315-9.
90. Pentylenetetrazol-kindling of seizures selectively decreases -citalopram binding in the CA-3 area of rat hippocampus. Szyndler J, etal., Neurosci Lett 2002 Dec 19;335(1):49-53.
91. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
92. Serotonin and interleukin-6: the role of genetic polymorphisms in IFN-induced neuropsychiatric symptoms. Udina M, etal., Psychoneuroendocrinology. 2013 Sep;38(9):1803-13. doi: 10.1016/j.psyneuen.2013.03.007. Epub 2013 Apr 6.
93. Genetic polymorphisms of the serotonin transporter, but not the 2a receptor or nitric oxide synthetase, are associated with pulmonary hypertension in chronic obstructive pulmonary disease. Ulrich S, etal., Respiration. 2010;79(4):288-95. Epub 2009 Jun 24.
94. Reduced cocaine-induced serotonin, but not dopamine and noradrenaline, release in rats with a genetic deletion of serotonin transporters. Verheij MM, etal., Eur Neuropsychopharmacol. 2014 Nov;24(11):1850-4. doi: 10.1016/j.euroneuro.2014.09.004. Epub 2014 Sep 16.
95. Localization and function of a 5-HT transporter in crypt epithelia of the gastrointestinal tract. Wade PR, etal., J Neurosci. 1996 Apr 1;16(7):2352-64. doi: 10.1523/JNEUROSCI.16-07-02352.1996.
96. In vivo studies of the SERT-selective FPBM and VMAT2-selective [18F]AV-133 radiotracers in a rat model of Parkinson's disease. Wang JL, etal., Nucl Med Biol. 2010 May;37(4):479-86.
97. [Association of 5-hydroxytryptamine transporter gene polymorphism with asthma and comorbid depression] Wang L, etal., Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2009 Oct;26(5):575-9.
98. Potentiation of 5-hydroxytryptamine (5-HT) responses by a 5-HT uptake inhibitor in pulmonary and systemic vessels: effects of exposing rats to hypoxia. Wanstall JC, etal., Naunyn Schmiedebergs Arch Pharmacol. 2003 Dec;368(6):520-7. Epub 2003 Nov 6.
99. Enterochromaffin cell hyperplasia and decreased serotonin transporter in a mouse model of postinfectious bowel dysfunction. Wheatcroft J, etal., Neurogastroenterol Motil. 2005 Dec;17(6):863-70. doi: 10.1111/j.1365-2982.2005.00719.x.
100. Serotonin transporter polymorphisms in familial and idiopathic pulmonary arterial hypertension. Willers ED, etal., Am J Respir Crit Care Med. 2006 Apr 1;173(7):798-802. Epub 2005 Dec 9.
101. Reduction of serotonin transporters of patients with chronic fatigue syndrome. Yamamoto S, etal., Neuroreport. 2004 Dec 3;15(17):2571-4. doi: 10.1097/00001756-200412030-00002.
102. Association of serotonin transporter gene polymorphism with obstructive sleep apnea syndrome. Ylmaz M, etal., Laryngoscope. 2005 May;115(5):832-6.
103. Association study of serotonin transporter gene polymorphisms with obstructive sleep apnea syndrome in Chinese Han population. Yue W, etal., Sleep. 2008 Nov 1;31(11):1535-41.
104. Zhonghua yi xue yi chuan xue za zhi = Zhonghua yixue yichuanxue zazhi = Chinese journal of medical genetics Yue WH, etal., Zhonghua Yi Xue Yi Chuan Xue Za Zhi. 2005 Oct;22(5):533-6.
105. Serotonin transporter binding increases in caudate-putamen and nucleus accumbens after neonatal 6-hydroxydopamine lesions in rats: implications for motor hyperactivity. Zhang K, etal., Brain Res Dev Brain Res 2002 Aug 30;137(2):135-8.
106. Cysteine-scanning mutagenesis of serotonin transporter intracellular loop 2 suggests an alpha-helical conformation. Zhang YW and Rudnick G, J Biol Chem. 2005 Sep 2;280(35):30807-13. Epub 2005 Jul 1.
107. Continuous fluoxetine administration prevents recurrence of pulmonary arterial hypertension and prolongs survival in rats. Zhu SP, etal., Clin Exp Pharmacol Physiol. 2009 Aug;36(8):e1-5. Epub 2009 Mar 26.
108. Fluoxetine-induced proliferation and differentiation of neural progenitor cells isolated from rat postnatal cerebellum. Zusso M, etal., Biochem Pharmacol. 2008 Aug 1;76(3):391-403. Epub 2008 May 23.
Additional References at PubMed
PMID:7681602   PMID:8889548   PMID:8987735   PMID:9037532   PMID:9547354   PMID:12124434   PMID:14515341   PMID:14622117   PMID:15126130   PMID:15222762   PMID:15634764   PMID:15997417  
PMID:16024787   PMID:16341932   PMID:16452989   PMID:16677634   PMID:17008313   PMID:17110048   PMID:17298851   PMID:17398000   PMID:17452640   PMID:17467186   PMID:17506858   PMID:17575980  
PMID:17897403   PMID:17949903   PMID:18207350   PMID:18307099   PMID:18378990   PMID:18414394   PMID:18534635   PMID:18573249   PMID:18581270   PMID:18778441   PMID:18794345   PMID:19207716  
PMID:19208814   PMID:19308295   PMID:19444235   PMID:19656393   PMID:19698744   PMID:19740092   PMID:19781533   PMID:19968967   PMID:20034565   PMID:20170186   PMID:20345836   PMID:20388545  
PMID:21186266   PMID:21371073   PMID:21463019   PMID:21549766   PMID:21683764   PMID:21719351   PMID:21730057   PMID:22505721   PMID:22511363   PMID:22525280   PMID:23164505   PMID:23274951  
PMID:23321813   PMID:23564488   PMID:23594365   PMID:23711978   PMID:24269496   PMID:24878716   PMID:25087780   PMID:25309082   PMID:25640835   PMID:26132384   PMID:26180184   PMID:26223876  
PMID:26302762   PMID:26386116   PMID:26612383   PMID:26707058   PMID:26723990   PMID:26924154   PMID:26987216   PMID:27082144   PMID:27208789   PMID:27789384   PMID:27826101   PMID:28158484  
PMID:29038237   PMID:29233642   PMID:29427306   PMID:29560525   PMID:30101500   PMID:30144237   PMID:30176268   PMID:30614673   PMID:30670681   PMID:30915622   PMID:31037750   PMID:32800867  
PMID:33403594   PMID:34068707   PMID:34182055   PMID:34209318   PMID:34937496   PMID:35043462   PMID:37572802  


Genomics

Comparative Map Data
Slc6a4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21061,824,208 - 61,858,924 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1061,826,123 - 61,858,384 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1066,483,857 - 66,505,046 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01065,989,335 - 66,010,524 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01061,459,175 - 61,480,332 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01063,153,656 - 63,188,377 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1063,153,651 - 63,176,463 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01062,851,326 - 62,872,481 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41067,134,790 - 67,155,891 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11067,148,412 - 67,197,988 (-)NCBI
Celera1060,845,942 - 60,866,725 (+)NCBICelera
Cytogenetic Map10q24NCBI
SLC6A4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381730,194,319 - 30,235,697 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1730,194,319 - 30,236,002 (-)EnsemblGRCh38hg38GRCh38
GRCh371728,521,337 - 28,562,715 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361725,549,032 - 25,586,841 (-)NCBINCBI36Build 36hg18NCBI36
Build 341725,549,031 - 25,586,831NCBI
Celera1725,385,103 - 25,424,627 (-)NCBICelera
Cytogenetic Map17q11.2NCBI
HuRef1724,731,684 - 24,773,327 (-)NCBIHuRef
CHM1_11728,583,810 - 28,625,471 (-)NCBICHM1_1
T2T-CHM13v2.01731,138,872 - 31,180,231 (-)NCBIT2T-CHM13v2.0
Slc6a4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391176,889,423 - 76,923,169 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1176,889,429 - 76,923,166 (+)EnsemblGRCm39 Ensembl
GRCm381176,998,597 - 77,032,343 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1176,998,603 - 77,032,340 (+)EnsemblGRCm38mm10GRCm38
MGSCv371176,812,099 - 76,845,845 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361176,814,792 - 76,848,536 (+)NCBIMGSCv36mm8
Celera1184,497,023 - 84,530,633 (+)NCBICelera
Cytogenetic Map11B5NCBI
cM Map1146.18NCBI
Slc6a4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554813,088,416 - 3,125,711 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554813,088,440 - 3,122,421 (+)NCBIChiLan1.0ChiLan1.0
SLC6A4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan11736,108,094 - 36,136,018 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01726,546,177 - 26,572,301 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11727,050,900 - 27,089,444 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1727,050,900 - 27,092,882 (+)Ensemblpanpan1.1panPan2
SLC6A4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1944,224,026 - 44,259,655 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl944,224,229 - 44,259,736 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha943,375,681 - 43,398,433 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0945,040,878 - 45,077,650 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl945,042,211 - 45,077,764 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1943,823,112 - 43,845,857 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0944,109,908 - 44,132,663 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0944,194,421 - 44,217,174 (-)NCBIUU_Cfam_GSD_1.0
Slc6a4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560243,327,307 - 43,361,581 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365386,205,251 - 6,239,083 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365386,205,268 - 6,239,062 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC6A4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1246,285,997 - 46,314,378 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11246,285,995 - 46,328,377 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21248,106,444 - 48,135,338 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC6A4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11623,929,196 - 23,969,665 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1623,927,311 - 23,955,616 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660756,110,560 - 6,136,546 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc6a4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247862,672,552 - 2,710,914 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247862,673,285 - 2,711,432 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slc6a4
189 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:99
Count of miRNA genes:76
Interacting mature miRNAs:90
Transcripts:ENSRNOT00000004717
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
2303118Mamtr7Mammary tumor resistance QTL 70.003mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)109658275104670812Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101448701189062041Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014487011104060283Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1598852Anxrr19Anxiety related response QTL 195.07body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)101816784163167841Rat
2313055Bw96Body weight QTL 963.60.0001body mass (VT:0001259)body weight (CMO:0000012)101960648364606483Rat
2313087Bmd80Bone mineral density QTL 803.20.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)101960648364606483Rat
1554317Bmd4Bone mineral density QTL 49.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)101981604299406971Rat
724556Pur2Proteinuria QTL 25.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)102242750090627625Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023444813104060283Rat
1298069Bp168Blood pressure QTL 1685.5blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)102652195798003205Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102652195798952741Rat
2300171Bmd58Bone mineral density QTL 584.90.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)102694462871944628Rat
10402859Bp381Blood pressure QTL 3810.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
2292441Bp308Blood pressure QTL 308arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102760646872606468Rat
724527Bp148Blood pressure QTL 1480.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)102845313673453136Rat
1331762Rf40Renal function QTL 403.873kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)102929950464155584Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
631557Bp136Blood pressure QTL 1360.003arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)103063205375632053Rat
1576311Pia26Pristane induced arthritis QTL 26joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103122402675632053Rat
1578779Tcas10Tongue tumor susceptibility QTL 103.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)103129743976297439Rat
1576319Cia29Collagen induced arthritis QTL 29joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)103397392178973921Rat
1358897Stresp6Stress response QTL 64.170.022blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)103539226764155584Rat
61441Btemp1Thermal response to stress QTL 14body temperature trait (VT:0005535)core body temperature (CMO:0001036)103539245763642539Rat
2317042Aia20Adjuvant induced arthritis QTL 203.38joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)103756507982565079Rat
2317043Aia7Adjuvant induced arthritis QTL 73.82joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)103756507982565079Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040035094102359817Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040035094104060283Rat
631552Vetf2Vascular elastic tissue fragility QTL 24.50.0002aorta elastic tissue integrity trait (VT:0010556)artery internal elastic lamina non-tumorous lesion count (CMO:0001913)104114263386142633Rat
61463Bp12Blood pressure QTL 126.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104133325886333258Rat
8552805Bw145Body weight QTL 1452.2body mass (VT:0001259)change in body weight to body weight ratio (CMO:0002216)104194452678307017Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042045676104670812Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)14232313287323132Rat
70188BpQTLcluster1Blood pressure QTL cluster 14.864arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)14232313287323132Rat
70198BpQTLcluster9Blood pressure QTL cluster 92.94arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)104232313287323132Rat
6893342Cm78Cardiac mass QTL 780.10.88heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)104287676679813922Rat
9589030Epfw9Epididymal fat weight QTL 919.240.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)104444169989441699Rat
7411614Foco18Food consumption QTL 180.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)104444169989441699Rat
8694173Bw149Body weight QTL 1494.380.001body mass (VT:0001259)body weight gain (CMO:0000420)104444169989441699Rat
2300218Hpcl2Hepatic cholesterol level QTL 2liver cholesterol amount (VT:0010498)liver cholesterol level (CMO:0001597)104502965095600334Rat
631547Bp87Blood pressure QTL 874.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)104736947092369470Rat
2293705Bmd25Bone mineral density QTL 257.10.0001femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)104944455181709989Rat
7207811Bmd90Bone mineral density QTL 905.2femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)104944455181709989Rat
2293652Bmd22Bone mineral density QTL 224.90.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
2293669Bmd33Bone mineral density QTL 334.50.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)104944455181709989Rat
2293679Bmd30Bone mineral density QTL 303.50.0001femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)104944455181709989Rat
1549846Scl47Serum cholesterol level QTL 473.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)105057470795574707Rat
70364Bp72Blood pressure QTL 72arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)105112110096121100Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
1359017Hrtrt21Heart rate QTL 212.4heart pumping trait (VT:2000009)heart rate (CMO:0000002)105177294096772940Rat
631530Tls3T-lymphoma susceptibility QTL 300.0001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)105177461295600334Rat
631535Cm51Cardiac mass QTL 513heart mass (VT:0007028)calculated heart weight (CMO:0000073)105178628291669536Rat
2306787Ean3Experimental allergic neuritis QTL 33.1nervous system integrity trait (VT:0010566)body weight loss (CMO:0001399)105379738566979128Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105379749498952626Rat
1354608Cm33Cardiac mass QTL 332.8heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)105480929299809292Rat
2312662Slep8Serum leptin concentration QTL 80.05blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1057134272102134272Rat
2312668Scl65Serum cholesterol level QTL 650.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1057134272102134272Rat
2312672Insul15Insulin level QTL 150.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1057134272102134272Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1057576521102576521Rat
2293698Bss43Bone structure and strength QTL 435.330.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)1059209888104209888Rat
1331839Eae18bExperimental allergic encephalomyelitis QTL 18b5.80.03nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)106124830367785171Rat
70363Bp71Blood pressure QTL 710.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)106134527681714865Rat
2306970Anxrr22Anxiety related response QTL 225.95fear/anxiety-related behavior trait (VT:1000241)number of periods of voluntary immobility (CMO:0001045)106134527698211570Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)106134527699703528Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)106134527699703528Rat
631526Bp76Blood pressure QTL 760.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)106134541366743655Rat
61402Niddm3Non-insulin dependent diabetes mellitus QTL 34.58blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)106134541382564856Rat

Markers in Region
D10Rat242  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21061,852,309 - 61,852,455 (-)MAPPERmRatBN7.2
Rnor_6.01063,160,125 - 63,160,270NCBIRnor6.0
Rnor_5.01062,857,786 - 62,857,931UniSTSRnor5.0
RGSC_v3.41067,141,195 - 67,141,341RGDRGSC3.4
RGSC_v3.41067,141,196 - 67,141,341UniSTSRGSC3.4
RGSC_v3.11067,154,818 - 67,154,964RGD
Celera1060,860,505 - 60,860,642UniSTS
SHRSP x BN Map1046.5699RGD
SHRSP x BN Map1046.5699UniSTS
Cytogenetic Map10q26UniSTS
RH142224  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21061,858,283 - 61,858,390 (-)MAPPERmRatBN7.2
Rnor_6.01063,154,190 - 63,154,296NCBIRnor6.0
Rnor_5.01062,851,851 - 62,851,957UniSTSRnor5.0
RGSC_v3.41067,135,261 - 67,135,367UniSTSRGSC3.4
Celera1060,866,471 - 60,866,577UniSTS
Cytogenetic Map10q26UniSTS
BE097677  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21061,839,006 - 61,839,145 (-)MAPPERmRatBN7.2
Rnor_6.01063,173,435 - 63,173,573NCBIRnor6.0
Rnor_5.01062,871,096 - 62,871,234UniSTSRnor5.0
RGSC_v3.41067,154,506 - 67,154,644UniSTSRGSC3.4
Celera1060,847,189 - 60,847,327UniSTS
Cytogenetic Map10q26UniSTS


Genetic Models
This gene Slc6a4 is modified in the following models/strains:
WI-Slc6a4m1Hubr+/-     WI-Slc6a4m1Hubr-/-    


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 2 14 11
Low 2 35 34 20 19 20 4 4 40 33 36 4
Below cutoff 8 18 18 18 4 7 20 2 5 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000004717   ⟹   ENSRNOP00000004717
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1061,826,123 - 61,858,384 (+)Ensembl
Rnor_6.0 Ensembl1063,153,651 - 63,176,463 (-)Ensembl
RefSeq Acc Id: NM_013034   ⟹   NP_037166
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21061,837,760 - 61,858,924 (+)NCBI
Rnor_6.01063,153,656 - 63,174,820 (-)NCBI
Rnor_5.01062,851,326 - 62,872,481 (-)NCBI
RGSC_v3.41067,134,790 - 67,155,891 (-)RGD
Celera1060,845,942 - 60,866,725 (+)RGD
Sequence:
RefSeq Acc Id: XM_008767950   ⟹   XP_008766172
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21061,826,048 - 61,858,924 (+)NCBI
Rnor_6.01063,153,656 - 63,186,502 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597041   ⟹   XP_017452530
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21061,826,097 - 61,858,924 (+)NCBI
Rnor_6.01063,153,656 - 63,186,502 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597042   ⟹   XP_017452531
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21061,824,208 - 61,858,924 (+)NCBI
Rnor_6.01063,153,656 - 63,188,377 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039085288   ⟹   XP_038941216
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21061,826,146 - 61,858,924 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_037166   ⟸   NM_013034
- UniProtKB: P23976 (UniProtKB/Swiss-Prot),   P31652 (UniProtKB/Swiss-Prot),   A6HGX0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008766172   ⟸   XM_008767950
- Peptide Label: isoform X1
- UniProtKB: P23976 (UniProtKB/Swiss-Prot),   P31652 (UniProtKB/Swiss-Prot),   A6HGX0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017452531   ⟸   XM_017597042
- Peptide Label: isoform X1
- UniProtKB: P23976 (UniProtKB/Swiss-Prot),   P31652 (UniProtKB/Swiss-Prot),   A6HGX0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017452530   ⟸   XM_017597041
- Peptide Label: isoform X1
- UniProtKB: P23976 (UniProtKB/Swiss-Prot),   P31652 (UniProtKB/Swiss-Prot),   A6HGX0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000004717   ⟸   ENSRNOT00000004717
RefSeq Acc Id: XP_038941216   ⟸   XM_039085288
- Peptide Label: isoform X1
- UniProtKB: P31652 (UniProtKB/Swiss-Prot),   P23976 (UniProtKB/Swiss-Prot),   A6HGX0 (UniProtKB/TrEMBL)
Protein Domains
Sodium:neurotransmitter symporter serotonin N-

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P31652-F1-model_v2 AlphaFold P31652 1-630 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13697431
Promoter ID:EPDNEW_R7956
Type:multiple initiation site
Name:Slc6a4_1
Description:solute carrier family 6 member 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01063,175,883 - 63,175,943EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3714 AgrOrtholog
BioCyc Gene G2FUF-24137 BioCyc
Ensembl Genes ENSRNOG00000003476 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000004717 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro Na/ntran_symport UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na/ntran_symport_serotonin_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNS_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25553 UniProtKB/Swiss-Prot
NCBI Gene 25553 ENTREZGENE
PANTHER PTHR11616 UniProtKB/Swiss-Prot
  SODIUM-DEPENDENT SEROTONIN TRANSPORTER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SODIUM/CHLORIDE DEPENDENT TRANSPORTER UniProtKB/TrEMBL
Pfam 5HT_transport_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SNF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB SLC6A4 RGD
PhenoGen Slc6a4 PhenoGen
PRINTS 5HTTRANSPORT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NANEUSMPORT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE NA_NEUROTRAN_SYMP_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NA_NEUROTRAN_SYMP_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NA_NEUROTRAN_SYMP_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000003476 RatGTEx
Superfamily-SCOP SNF-like UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
TIGR TC208340
UniProt A6HGX0 ENTREZGENE, UniProtKB/TrEMBL
  P23976 ENTREZGENE
  P31652 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary P23976 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-09 Slc6a4  solute carrier family 6 member 4  Slc6a4  solute carrier family 6 (neurotransmitter transporter), member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Slc6a4  solute carrier family 6 (neurotransmitter transporter, serotonin), member 4    solute carrier family 6, member 4  Name updated 1299863 APPROVED
2003-04-09 Slc6a4  solute carrier family 6, member 4    Solute carrier family 6 (neurotransmitter transporter, serotonin), member 4  Name updated 629478 APPROVED
2001-11-02 Slc6a4  Solute carrier family 6 (neurotransmitter transporter, serotonin), member 4      Symbol and Name updated 68913 APPROVED