Slc9a1 (solute carrier family 9 member A1) - Rat Genome Database

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Gene: Slc9a1 (solute carrier family 9 member A1) Rattus norvegicus
Analyze
Symbol: Slc9a1
Name: solute carrier family 9 member A1
RGD ID: 3718
Description: Enables sodium:proton antiporter activity. Involved in several processes, including cellular response to electrical stimulus; positive regulation of mitochondrial membrane permeability; and regulation of apoptotic process. Located in several cellular components, including T-tubule; basolateral plasma membrane; and intercalated disc. Used to study cataract; middle cerebral artery infarction; and proteinuria. Biomarker of hyperthyroidism; hypothyroidism; renovascular hypertension; and type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in autosomal recessive spinocerebellar ataxia 19 and congestive heart failure. Orthologous to human SLC9A1 (solute carrier family 9 member A1); PARTICIPATES IN endothelin signaling pathway; bile acid transport pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 3-iodobenzyl-5'-N-methylcarboxamidoadenosine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: na(+)/H(+) exchanger 1; NHE-1; Nhe1; sodium/hydrogen exchanger 1; Solute carrier family 9 (sodium/hydrogen exchanger 1) antiporter Na+/H+ (amiloride sensitive); Solute carrier family 9 (sodium/hydrogen exchanger 1), antiporter, Na+/H+, (amiloride sensitive); solute carrier family 9 (sodium/hydrogen exchanger), member 1; solute carrier family 9 member 1; solute carrier family 9, member 1; solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25145,576,341 - 145,629,630 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl5145,576,334 - 145,629,624 (+)Ensembl
Rnor_6.05151,573,122 - 151,626,360 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5151,573,092 - 151,627,316 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05155,237,482 - 155,290,410 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45151,680,696 - 151,748,460 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15151,690,734 - 151,758,499 (-)NCBI
Celera5143,998,303 - 144,051,177 (+)NCBICelera
RH 3.4 Map5977.9RGD
Cytogenetic Map5q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrobenzenesulfonic acid  (ISO)
2-methylcholine  (ISO)
3-iodobenzyl-5'-N-methylcarboxamidoadenosine  (EXP)
8-Br-cAMP  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
aldosterone  (EXP)
ammonium chloride  (EXP)
aristolochic acid  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (EXP)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bisphenol A  (EXP)
cadmium dichloride  (ISO)
calcium atom  (EXP)
calcium(0)  (EXP)
carbachol  (ISO)
carbon dioxide  (EXP)
CGS-21680  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
cyclosporin A  (ISO)
DDT  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dicrotophos  (ISO)
digoxin  (EXP)
disodium selenite  (ISO)
doxorubicin  (ISO)
endosulfan  (ISO)
eplerenone  (EXP)
ethanol  (ISO)
ethylisopropylamiloride  (EXP,ISO)
folic acid  (ISO)
formaldehyde  (ISO)
hydrogen peroxide  (EXP)
ketamine  (EXP)
Licochalcone B  (ISO)
lithium atom  (ISO)
lithium hydride  (ISO)
mercaptoethanol  (ISO)
methapyrilene  (ISO)
nickel atom  (ISO)
ouabain  (EXP)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
pentanal  (ISO)
perfluorooctanoic acid  (EXP)
phenanthrolines  (ISO)
phenylephrine  (EXP)
phloretin  (ISO)
pirinixic acid  (EXP,ISO)
progesterone  (EXP)
quercetin  (ISO)
reactive nitrogen species  (EXP)
reactive oxygen species  (EXP)
resveratrol  (EXP,ISO)
sodium arsenite  (ISO)
sodium atom  (ISO)
sodium chloride  (ISO)
tebuconazole  (ISO)
tetrachloromethane  (EXP)
tetrodotoxin  (ISO)
troglitazone  (ISO)
tungsten  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zidovudine  (ISO)
zinc dichloride  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
anion transmembrane transport  (IEA)
cardiac muscle cell contraction  (IEP)
cardiac muscle cell differentiation  (ISO)
cell differentiation  (IEP)
cellular response to acidic pH  (ISO,ISS)
cellular response to antibiotic  (IEP)
cellular response to cold  (IEP)
cellular response to electrical stimulus  (IEP)
cellular response to epinephrine stimulus  (ISO)
cellular response to hypoxia  (IDA)
cellular response to insulin stimulus  (IDA)
cellular response to organic cyclic compound  (IEP)
cellular sodium ion homeostasis  (ISO)
negative regulation of apoptotic process  (IMP)
neuron death  (IMP)
positive regulation of action potential  (IMP)
positive regulation of apoptotic process  (IMP)
positive regulation of calcineurin-NFAT signaling cascade  (ISO)
positive regulation of calcium:sodium antiporter activity  (ISO)
positive regulation of cardiac muscle hypertrophy  (ISO)
positive regulation of cell growth  (IMP)
positive regulation of intracellular signal transduction  (IMP)
positive regulation of mitochondrial membrane permeability  (IMP)
positive regulation of the force of heart contraction  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
potassium ion transmembrane transport  (IBA)
proton transmembrane transport  (ISO)
regulation of cardiac muscle contraction by calcium ion signaling  (ISO)
regulation of intracellular pH  (IBA,IMP,ISO,ISS)
regulation of pH  (ISO,ISS)
regulation of sensory perception of pain  (IMP)
regulation of the force of heart contraction  (IMP)
regulation of the force of heart contraction by cardiac conduction  (ISO)
response to acidic pH  (IDA,ISO,ISS)
response to muscle stretch  (ISO)
response to organic cyclic compound  (IDA)
sodium ion export across plasma membrane  (ISS)
sodium ion import across plasma membrane  (IBA,ISO)
sodium ion transport  (ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Carraro-Lacroix LR, etal., Am J Physiol Renal Physiol. 2006 Jul;291(1):F129-39. Epub 2006 Feb 21.
2. Castaneda-Corral G, etal., Neurosci Lett. 2011 Aug 21;501(1):4-9. Epub 2011 Jul 6.
3. Gan XT, etal., Cardiovasc Res. 2010 Jan 1;85(1):79-89. Epub .
4. Gan XT, etal., J Pharmacol Exp Ther. 2005 Jan;312(1):27-34. Epub 2004 Sep 27.
5. Garciarena CD, etal., J Appl Physiol. 2009 Apr;106(4):1325-31. Epub 2009 Jan 29.
6. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
7. GOA data from the GO Consortium
8. Hileeto D, etal., Diabetes Metab Res Rev 2002 Sep-Oct;18(5):386-94.
9. Howarth FC, etal., Mol Cell Biochem. 2012 Feb;361(1-2):267-80. Epub 2011 Oct 19.
10. Huber JD, etal., J Med Chem. 2012 Jul 17.
11. Huc L, etal., Cancer Res. 2007 Feb 15;67(4):1696-705.
12. Inoue H, etal., Biol Pharm Bull 2003 Feb;26(2):148-55.
13. Khan I, etal., Nephron 2002 Oct;92(2):346-55.
14. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
15. Lawrence SP, etal., Biochem J. 2010 Dec 15;432(3):515-23. doi: 10.1042/BJ20100717.
16. Li W, etal., Physiol Rep. 2019 Aug;7(13):e14142. doi: 10.14814/phy2.14142.
17. Li X, etal., J Biol Chem 2002 Aug 9;277(32):28656-62.
18. Lin CY, etal., J Biol Chem 2003 Apr 25;278(17):15128-35. Epub 2003 Feb 3.
19. Lin M, etal., Nan Fang Yi Ke Da Xue Xue Bao. 2012 May;32(5):734-7.
20. Lin X, etal., Sheng Wu Yi Xue Gong Cheng Xue Za Zhi. 2010 Feb;27(1):132-7.
21. Liu CN and Somps CJ, Toxicol Sci. 2008 Jun;103(2):346-53. Epub 2008 Mar 3.
22. Lupachyk S, etal., Int J Mol Med. 2012 Jun;29(6):989-98. doi: 10.3892/ijmm.2012.933. Epub 2012 Mar 7.
23. Manucha W, etal., BJU Int. 2007 Jul;100(1):191-8.
24. Matsushita M, etal., Am J Physiol Cell Physiol. 2011 Aug;301(2):C280-8. doi: 10.1152/ajpcell.00404.2010. Epub 2011 May 4.
25. MGD data from the GO Consortium
26. Mukhin YV, etal., J Biol Chem. 2004 Jan 16;279(3):1845-52. Epub 2003 Nov 4.
27. Nakamura TY, etal., Circ Res. 2008 Oct 10;103(8):891-9. Epub 2008 Sep 5.
28. NCBI rat LocusLink and RefSeq merged data July 26, 2002
29. Orlowski J, etal., J Biol Chem 1992 May 5;267(13):9331-9.
30. Park SL, etal., Brain Res. 2010 Dec 17;1366:189-96. Epub 2010 Sep 29.
31. Perez NG, etal., J Appl Physiol. 2011 Sep;111(3):874-80. Epub 2011 Jun 9.
32. Pipeline to import KEGG annotations from KEGG into RGD
33. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
34. RGD automated data pipeline
35. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
36. RGD automated import pipeline for gene-chemical interactions
37. Rutherford PA, etal., Exp Nephrol. 1997 Nov-Dec;5(6):490-7.
38. Sangan P, etal., J Biol Chem 2002 Mar 22;277(12):9668-75.
39. Serafino A, etal., Biochim Biophys Acta. 2012 Jun;1822(6):1004-18. Epub 2012 Feb 25.
40. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
41. Vial G, etal., Mol Cell Biochem. 2008 Mar;310(1-2):93-102. Epub 2007 Dec 5.
42. Villa-Abrille MC, etal., Am J Physiol Heart Circ Physiol. 2011 Apr;300(4):H1237-51. Epub 2011 Feb 4.
43. Wang Y, etal., Toxicon. 2009 Aug;54(2):95-102. Epub 2009 Mar 26.
44. Westhoff TH, etal., Physiol Genomics. 2005 Sep 21;23(1):46-53. Epub 2005 Jun 7.
45. Williams IA, etal., Pflugers Arch. 2007 Mar 14;.
46. Willoughby D, etal., J Biol Chem. 2005 Sep 2;280(35):30864-72. Epub 2005 Jul 7.
47. Wu D, etal., Crit Care Med. 2009 Jun;37(6):1994-9.
48. Young M and Funder J, Endocrinology 2003 Sep;144(9):3848-51.
49. Zaun HC, etal., J Biol Chem. 2008 May 2;283(18):12456-67. doi: 10.1074/jbc.M800267200. Epub 2008 Mar 5.
Additional References at PubMed
PMID:8901634   PMID:9688597   PMID:10666043   PMID:10673550   PMID:11350981   PMID:11369779   PMID:12619893   PMID:12791686   PMID:14610099   PMID:14724181   PMID:14737747   PMID:14753440  
PMID:15009712   PMID:15035633   PMID:15105296   PMID:15523538   PMID:15644322   PMID:16306134   PMID:16396499   PMID:16575514   PMID:16707501   PMID:16859700   PMID:17429605   PMID:18095144  
PMID:18448627   PMID:18650245   PMID:18660503   PMID:18703017   PMID:18715944   PMID:19011045   PMID:19028724   PMID:19199708   PMID:19248819   PMID:19419999   PMID:19458287   PMID:19542484  
PMID:19710385   PMID:19949839   PMID:20427472   PMID:20712402   PMID:20886221   PMID:21207853   PMID:21325644   PMID:21359875   PMID:21423176   PMID:21553168   PMID:21613418   PMID:21705333  
PMID:21856903   PMID:22154810   PMID:22688515   PMID:22731252   PMID:22898152   PMID:23055051   PMID:23059814   PMID:23509787   PMID:23545808   PMID:23677982   PMID:23709596   PMID:23837875  
PMID:24049114   PMID:24126173   PMID:24566932   PMID:24840010   PMID:25216745   PMID:25240639   PMID:25749446   PMID:25830299   PMID:26063808   PMID:26078707   PMID:26459736   PMID:26521941  
PMID:26724742   PMID:27009277   PMID:27633736   PMID:28019659   PMID:28719339   PMID:30627552   PMID:30838887   PMID:31622577   PMID:31694264   PMID:31742355   PMID:31811544   PMID:32469979  
PMID:32496418   PMID:33957206   PMID:34063987  


Genomics

Comparative Map Data
Slc9a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.25145,576,341 - 145,629,630 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl5145,576,334 - 145,629,624 (+)Ensembl
Rnor_6.05151,573,122 - 151,626,360 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5151,573,092 - 151,627,316 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05155,237,482 - 155,290,410 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45151,680,696 - 151,748,460 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.15151,690,734 - 151,758,499 (-)NCBI
Celera5143,998,303 - 144,051,177 (+)NCBICelera
RH 3.4 Map5977.9RGD
Cytogenetic Map5q36NCBI
SLC9A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl127,098,809 - 27,166,981 (-)EnsemblGRCh38hg38GRCh38
GRCh38127,098,809 - 27,155,125 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37127,425,300 - 27,481,616 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36127,297,894 - 27,353,990 (-)NCBINCBI36hg18NCBI36
Build 34127,109,448 - 27,165,543NCBI
Celera125,822,106 - 25,878,256 (-)NCBI
Cytogenetic Map1p36.11NCBI
HuRef125,679,019 - 25,736,027 (-)NCBIHuRef
CHM1_1127,539,712 - 27,596,211 (-)NCBICHM1_1
Slc9a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm394133,097,022 - 133,151,013 (+)NCBIGRCm39mm39
GRCm39 Ensembl4133,097,017 - 133,151,013 (+)Ensembl
GRCm384133,369,711 - 133,423,702 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl4133,369,706 - 133,423,702 (+)EnsemblGRCm38mm10GRCm38
MGSCv374132,925,687 - 132,979,613 (+)NCBIGRCm37mm9NCBIm37
MGSCv364132,642,305 - 132,695,773 (+)NCBImm8
Celera4131,535,491 - 131,589,316 (+)NCBICelera
Cytogenetic Map4D2.3NCBI
cM Map466.25NCBI
Slc9a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554526,409,833 - 6,467,841 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554526,409,833 - 6,467,841 (-)NCBIChiLan1.0ChiLan1.0
SLC9A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1127,414,937 - 27,475,089 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl127,414,937 - 27,475,089 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0126,359,818 - 26,418,910 (-)NCBIMhudiblu_PPA_v0panPan3
SLC9A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1273,054,742 - 73,103,364 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl273,054,742 - 73,103,364 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha269,631,268 - 69,679,864 (+)NCBI
ROS_Cfam_1.0273,616,211 - 73,664,827 (+)NCBI
UMICH_Zoey_3.1270,441,943 - 70,490,513 (+)NCBI
UNSW_CanFamBas_1.0271,447,299 - 71,495,908 (+)NCBI
UU_Cfam_GSD_1.0272,450,107 - 72,498,704 (+)NCBI
Slc9a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505845,635,479 - 45,692,666 (-)NCBI
SpeTri2.0NW_00493647411,460,266 - 11,517,420 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC9A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl684,372,649 - 84,426,997 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1684,373,921 - 84,426,447 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2677,944,221 - 77,996,927 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC9A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.120105,613,289 - 105,670,868 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl20105,613,338 - 105,674,208 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603310,772,194 - 10,834,851 (-)NCBIVero_WHO_p1.0
Slc9a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476411,041,118 - 11,095,892 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH94564  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25145,628,911 - 145,629,016 (+)MAPPERmRatBN7.2
Rnor_6.05151,625,642 - 151,625,746NCBIRnor6.0
Rnor_5.05155,289,692 - 155,289,796UniSTSRnor5.0
RGSC_v3.45151,681,310 - 151,681,414UniSTSRGSC3.4
Celera5144,050,459 - 144,050,563UniSTS
RH 3.4 Map5977.9UniSTS
Cytogenetic Map5q36UniSTS
Slc9a1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.25145,626,755 - 145,628,174 (+)MAPPERmRatBN7.2
Rnor_6.05151,623,486 - 151,624,904NCBIRnor6.0
Rnor_5.05155,287,536 - 155,288,954UniSTSRnor5.0
RGSC_v3.45151,682,152 - 151,683,570UniSTSRGSC3.4
Celera5144,048,303 - 144,049,721UniSTS
Cytogenetic Map5q36UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat
1302790Scl20Serum cholesterol level QTL 206.40.0001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)582394392166664054Rat
1331796Thshl2Thyroid stimulating hormone level QTL 22.3blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)597059760147465714Rat
1358187Emca1Estrogen-induced mammary cancer QTL 14.4mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)599216724148607142Rat
1578673Bmd13Bone mineral density QTL 134.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)5103689353148689353Rat
2317056Wbc3White blood cell count QTL 32.510.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)5105999803150999803Rat
7207488Bss110Bone structure and strength QTL 18.4femur strength trait (VT:0010010)femur stiffness (CMO:0001674)5106906205151906205Rat
7207491Bss112Bone structure and strength QTL 1127femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)5106906205151906205Rat
7207481Bss106Bone structure and strength QTL 1067.9femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5106906205151906205Rat
7207486Bss109Bone structure and strength QTL 109femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)5106906205151906205Rat
1549838Bss4Bone structure and strength QTL 49.2femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)5106906205151906205Rat
1298089Scl14Serum cholesterol level QTL 145.80.0004blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)5108845856153845856Rat
1598847Cm62Cardiac mass QTL 623.4heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5108845856153845856Rat
8657050Bw146Body weight QTL 14619.840.001body mass (VT:0001259)body weight gain (CMO:0000420)5108938288153938288Rat
8694441Bw169Body weight QTL 16917.610.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)5111416838156416838Rat
8694198Abfw3Abdominal fat weight QTL 316.130.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)5111416838156416838Rat
8694389Bw160Body weight QTL 1606.170.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)5111416838156416838Rat
8552960Pigfal15Plasma insulin-like growth factor 1 level QTL 15blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5111416838156416838Rat
2293642Bss37Bone structure and strength QTL 374.640.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)5120740824151018848Rat
1641920Colcs1Colorectal carcinoma susceptibility QTL 12.990.0055intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)5121846814166846814Rat
10053720Scort26Serum corticosterone level QTL 262.060.0147blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)5124965598166875058Rat
724525Bp147Blood pressure QTL 1474.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5126424772166875058Rat
1598819Bp292Blood pressure QTL 2924.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5127798274166875058Rat
1598861Cm64Cardiac mass QTL 642.9heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)5127798274166875058Rat
8552908Pigfal4Plasma insulin-like growth factor 1 level QTL 46.6blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)5128506074166875058Rat
8694169Bw148Body weight QTL 14850.001body mass (VT:0001259)body weight gain (CMO:0000420)5128506074166875058Rat
634349Bp139Blood pressure QTL 1390.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5128924607166875058Rat
70156Niddm30Non-insulin dependent diabetes mellitus QTL 303.98blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)5129132447151006154Rat
738018Anxrr4Anxiety related response QTL 45.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)5130130159166875058Rat
7794791Mcs33Mammary carcinoma susceptibility QTL 331.93mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)5131345754166875058Rat
631505Bp103Blood pressure QTL 1033.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)5132717196165560427Rat
631562Apr2Acute phase response QTL 23.7blood murinoglobulin 1 amount (VT:0010597)plasma murinoglobulin 1 level (CMO:0001931)5135927956166875058Rat
61444Strs2Sensitivity to stroke QTL 24.7cerebrum integrity trait (VT:0010549)post-insult time to onset of cerebrovascular lesion (CMO:0002343)5135929696166875058Rat
1331721Bp210Blood pressure QTL 2103.413arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5143069996166846814Rat
2302369Scl60Serum cholesterol level QTL 603.13blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)5143608201161165651Rat
631263Cm24Cardiac mass QTL 243.5heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)5143799107158428037Rat
1300119Bp180Blood pressure QTL 1803.82arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)5144358090157869054Rat
2313096Bmd78Bone mineral density QTL 783.10.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)5144377876161317411Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:200
Count of miRNA genes:126
Interacting mature miRNAs:157
Transcripts:ENSRNOT00000011049
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.


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 3 33 17 10 13 10 66 26 31 3
Low 10 40 31 6 31 8 11 8 9 10 8 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000011049   ⟹   ENSRNOP00000011049
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl5145,576,334 - 145,629,624 (+)Ensembl
Rnor_6.0 Ensembl5151,573,092 - 151,627,316 (+)Ensembl
RefSeq Acc Id: NM_012652   ⟹   NP_036784
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25145,576,390 - 145,629,630 (+)NCBI
Rnor_6.05151,573,122 - 151,626,360 (+)NCBI
Rnor_5.05155,237,482 - 155,290,410 (+)NCBI
RGSC_v3.45151,680,696 - 151,748,460 (-)RGD
Celera5143,998,303 - 144,051,177 (+)RGD
Sequence:
RefSeq Acc Id: XR_005504367
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25145,576,341 - 145,628,235 (+)NCBI
RefSeq Acc Id: XR_005504368
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.25145,576,341 - 145,627,457 (+)NCBI
Protein Sequences
Protein RefSeqs NP_036784 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA98479 (Get FASTA)   NCBI Sequence Viewer  
  EDL80666 (Get FASTA)   NCBI Sequence Viewer  
  P26431 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_036784   ⟸   NM_012652
- UniProtKB: P26431 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000011049   ⟸   ENSRNOT00000011049

Transcriptome

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

Promoters
RGD ID:13694114
Promoter ID:EPDNEW_R4637
Type:initiation region
Name:Slc9a1_1
Description:solute carrier family 9 member A1
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_6.05151,573,109 - 151,573,169EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BUF/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
DA/OlaHsd (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
F344/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FXLE16/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/OlalpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/RijCrl (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_6.0
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
5 151614248 151614249 A G snv WKY/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3718 AgrOrtholog
Ensembl Genes ENSRNOG00000007982 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000011049 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000011049 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro Cation/H_exchanger UniProtKB/Swiss-Prot
  Cation/H_exchanger_CPA1 UniProtKB/Swiss-Prot
  Na/H_exchanger_1 UniProtKB/Swiss-Prot
  NaH_exchanger UniProtKB/Swiss-Prot
  NHE_CaM-bd UniProtKB/Swiss-Prot
KEGG Report rno:24782 UniProtKB/Swiss-Prot
NCBI Gene 24782 ENTREZGENE
PANTHER PTHR10110 UniProtKB/Swiss-Prot
  PTHR10110:SF59 UniProtKB/Swiss-Prot
Pfam Na_H_Exchanger UniProtKB/Swiss-Prot
  NEXCaM_BD UniProtKB/Swiss-Prot
PhenoGen Slc9a1 PhenoGen
PRINTS NAHEXCHNGR UniProtKB/Swiss-Prot
  NAHEXCHNGR1 UniProtKB/Swiss-Prot
TIGR TC218885
TIGRFAMs b_cpa1 UniProtKB/Swiss-Prot
UniProt P26431 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-01 Slc9a1  solute carrier family 9 member A1  Slc9a1  solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-16 Slc9a1  solute carrier family 9, subfamily A (NHE1, cation proton antiporter 1), member 1  Slc9a1  solute carrier family 9 (sodium/hydrogen exchanger), member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-15 Slc9a1  solute carrier family 9 (sodium/hydrogen exchanger), member 1  Slc9a1  solute carrier family 9, member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Slc9a1  solute carrier family 9, member 1    Solute carrier family 9 (sodium/hydrogen exchanger 1), antiporter, Na+/H+, (amiloride sensitive)  Name updated 629478 APPROVED
2002-06-10 Slc9a1  Solute carrier family 9 (sodium/hydrogen exchanger 1), antiporter, Na+/H+, (amiloride sensitive)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease may participate in development of coronary vasculitis produced by excess mineralocorticoid and salt 1299036
gene_disease may mediate changes in diabetic cardiomyopathy associated with increased endothelin-1 expression 730152
gene_expression expressed in all tissues examined 1299035
gene_expression expressed in coronary vascular smooth muscle 1299036
gene_product member of the Na/H exchanger family 1299035
gene_regulation G-protein coupled somatostatin receptor subtypes SSTR1, -3, and -4 inhibit exchanger activity 1299037
gene_regulation transcription is regulated by the thyroid hormone receptor alpha (Thra) 625454