Slc24a3 (solute carrier family 24 member 3) - Rat Genome Database

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Gene: Slc24a3 (solute carrier family 24 member 3) Rattus norvegicus
Analyze
Symbol: Slc24a3
Name: solute carrier family 24 member 3
RGD ID: 69256
Description: Enables calcium, potassium:sodium antiporter activity. Involved in cation transport. Located in plasma membrane. Orthologous to human SLC24A3 (solute carrier family 24 member 3); PARTICIPATES IN calcium transport pathway; calcium/calcium-mediated signaling pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: na(+)/K(+)/Ca(2+)-exchange protein 3; Nckx3; potassium-dependent sodium-calcium exchanger NCKX3 (SLC24A3); sodium/potassium/calcium exchanger 3; solute carrier family 24 (sodium/potassium/calcium exchanger) member 3; solute carrier family 24 (sodium/potassium/calcium exchanger), member 3; solute carrier family 24, member 3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Slc24a3Tn(sb-T2/Bart3)2.188Mcwi   Slc24a3Tn(sb-T2/Bart3)2.178Mcwi  
Genetic Models: F344-Slc24a3Tn(sb-T2/Bart3)2.178Mcwi F344-Slc24a3Tn(sb-T2/Bart3)2.188Mcwi
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23132,552,119 - 133,051,192 (+)NCBI
Rnor_6.0 Ensembl3139,695,028 - 139,833,967 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03139,333,942 - 139,835,728 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03145,760,074 - 146,259,491 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43133,734,890 - 134,249,326 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13133,640,575 - 134,153,200 (+)NCBI
Celera3131,419,773 - 131,916,131 (+)NCBICelera
Cytogenetic Map3q41NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:19464262   PMID:19474185   PMID:21321244   PMID:26631410   PMID:28602864  


Genomics

Comparative Map Data
Slc24a3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23132,552,119 - 133,051,192 (+)NCBI
Rnor_6.0 Ensembl3139,695,028 - 139,833,967 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.03139,333,942 - 139,835,728 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.03145,760,074 - 146,259,491 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43133,734,890 - 134,249,326 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.13133,640,575 - 134,153,200 (+)NCBI
Celera3131,419,773 - 131,916,131 (+)NCBICelera
Cytogenetic Map3q41NCBI
SLC24A3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2019,212,642 - 19,722,926 (+)EnsemblGRCh38hg38GRCh38
GRCh382019,212,642 - 19,722,926 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372019,193,286 - 19,703,570 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362019,141,290 - 19,651,541 (+)NCBINCBI36hg18NCBI36
Build 342019,141,289 - 19,651,540NCBI
Celera2019,267,475 - 19,777,636 (+)NCBI
Cytogenetic Map20p11.23NCBI
HuRef2019,155,790 - 19,666,236 (+)NCBIHuRef
CHM1_12019,262,244 - 19,704,077 (+)NCBICHM1_1
Slc24a3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392145,009,695 - 145,484,086 (+)NCBIGRCm39mm39
GRCm39 Ensembl2145,009,674 - 145,484,086 (+)Ensembl
GRCm382145,167,775 - 145,642,166 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2145,167,754 - 145,642,166 (+)EnsemblGRCm38mm10GRCm38
MGSCv372145,068,347 - 145,467,689 (+)NCBIGRCm37mm9NCBIm37
MGSCv362144,934,052 - 145,333,394 (+)NCBImm8
Celera2146,442,567 - 146,852,275 (+)NCBICelera
Cytogenetic Map2G1NCBI
Slc24a3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541527,477,819 - 27,928,383 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495541527,477,801 - 27,930,108 (+)NCBIChiLan1.0ChiLan1.0
SLC24A3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12019,137,943 - 19,648,235 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2019,137,938 - 19,646,475 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02019,168,820 - 19,680,706 (+)NCBIMhudiblu_PPA_v0panPan3
SLC24A3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1243,593,562 - 4,014,366 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl243,593,513 - 3,784,467 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha243,620,103 - 3,818,880 (-)NCBI
ROS_Cfam_1.0244,000,491 - 4,482,100 (-)NCBI
UMICH_Zoey_3.1243,595,752 - 4,077,406 (-)NCBI
UNSW_CanFamBas_1.0243,699,250 - 4,181,348 (-)NCBI
UU_Cfam_GSD_1.0243,977,410 - 4,458,938 (-)NCBI
Slc24a3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640152,206,337 - 152,654,468 (-)NCBI
SpeTri2.0NW_004936485637,715 - 1,085,860 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC24A3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1727,270,214 - 27,780,529 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11727,270,232 - 27,780,535 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21731,405,580 - 31,468,072 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC24A3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1248,238,872 - 48,736,517 (+)NCBI
Vero_WHO_p1.0NW_0236660783,017,793 - 3,516,931 (+)NCBI
Slc24a3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474119,808,186 - 20,298,772 (+)NCBI

Position Markers
D3Rat85  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23133,042,352 - 133,042,572 (+)MAPPER
Rnor_6.03139,826,887 - 139,827,106NCBIRnor6.0
Rnor_5.03146,250,650 - 146,250,869UniSTSRnor5.0
RGSC_v3.43134,240,485 - 134,240,704UniSTSRGSC3.4
RGSC_v3.13134,146,057 - 134,146,277RGD
Celera3131,907,298 - 131,907,517UniSTS
FHH x ACI Map381.3799UniSTS
FHH x ACI Map381.3799RGD
Cytogenetic Map3q41UniSTS
D3Got97  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23133,006,585 - 133,006,885 (+)MAPPER
Rnor_6.03139,791,762 - 139,792,061NCBIRnor6.0
Rnor_5.03146,215,525 - 146,215,824UniSTSRnor5.0
RGSC_v3.43134,203,881 - 134,204,181RGDRGSC3.4
RGSC_v3.43134,203,882 - 134,204,181UniSTSRGSC3.4
RGSC_v3.13134,109,454 - 134,109,754RGD
Celera3131,871,677 - 131,871,976UniSTS
Cytogenetic Map3q41UniSTS
D3Got240  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23132,954,388 - 132,954,605 (+)MAPPER
Rnor_6.03139,741,825 - 139,742,041NCBIRnor6.0
Rnor_5.03146,164,940 - 146,165,156UniSTSRnor5.0
RGSC_v3.43134,151,226 - 134,151,442UniSTSRGSC3.4
Celera3131,819,702 - 131,819,918UniSTS
Cytogenetic Map3q41UniSTS
BE115278  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23132,683,693 - 132,683,843 (+)MAPPER
Rnor_6.03139,470,660 - 139,470,809NCBIRnor6.0
Rnor_5.03145,896,571 - 145,896,720UniSTSRnor5.0
RGSC_v3.43133,867,704 - 133,867,853UniSTSRGSC3.4
Celera3131,551,007 - 131,551,156UniSTS
RH 3.4 Map31178.6UniSTS
Cytogenetic Map3q41UniSTS
UniSTS:225330  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23132,583,428 - 132,583,591 (+)MAPPER
Rnor_6.03139,365,125 - 139,365,287NCBIRnor6.0
Rnor_5.03145,791,227 - 145,791,389UniSTSRnor5.0
RGSC_v3.43133,766,199 - 133,766,361UniSTSRGSC3.4
Celera3131,451,011 - 131,451,173UniSTS
Cytogenetic Map3q41UniSTS
Slc24a3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23133,049,999 - 133,050,949 (+)MAPPER
Rnor_6.03139,834,536 - 139,835,485NCBIRnor6.0
Rnor_5.03146,258,299 - 146,259,248UniSTSRnor5.0
Celera3131,914,939 - 131,915,888UniSTS
Cytogenetic Map3q41UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)330846101172879276Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3114376250159376250Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3138374177177699992Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)345406058177699992Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3103141944170934860Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)3101058963146058963Rat
1331758Bp207Blood pressure QTL 2072.848arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3117303473141971336Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)394788365139788365Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3136876155170935007Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)3103141814176418101Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)3103141814176418101Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3103141814176418101Rat
1581546Pur13Proteinuria QTL 132.930.0335total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)381136227154416635Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3138374177177699992Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3129787213177699992Rat
1581568Rf53Renal function QTL 53total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)358204463170534769Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128986468173986468Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)399465522168732722Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3125848628170848628Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3119471263164471263Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3126575595165355668Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3126575595153412619Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)339248391140271184Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)3102466149147466149Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)343295930163640485Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)343295930163640485Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)3120917788141971336Rat
1358204Insglur1Insulin/glucose ratio QTL 13.8blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)3120917788141971336Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)348561928155263151Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3132875075176418101Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)3102152812155263151Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3139578365177699992Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)397009185142009185Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)361241033165369047Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3130006659175006659Rat


Genetic Models
This gene Slc24a3 is modified in the following models/strains
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:191
Count of miRNA genes:147
Interacting mature miRNAs:165
Transcripts:ENSRNOT00000012683
Prediction methods:Miranda, Rnahybrid
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 1 18 4 2 60 29 11
Low 2 25 35 23 17 23 8 10 14 35 12 8
Below cutoff 18 18 18 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000089098   ⟹   ENSRNOP00000071351
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl3139,695,028 - 139,833,967 (+)Ensembl
RefSeq Acc Id: NM_053505   ⟹   NP_445957
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23132,552,119 - 133,051,192 (+)NCBI
Rnor_6.03139,333,942 - 139,835,728 (+)NCBI
Rnor_5.03145,760,074 - 146,259,491 (+)NCBI
RGSC_v3.43133,734,890 - 134,249,326 (+)RGD
Celera3131,419,773 - 131,916,131 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039106001   ⟹   XP_038961929
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23132,593,668 - 133,049,651 (+)NCBI
Protein Sequences
Protein RefSeqs NP_445957 (Get FASTA)   NCBI Sequence Viewer  
  XP_038961929 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAG32680 (Get FASTA)   NCBI Sequence Viewer  
  EDL95148 (Get FASTA)   NCBI Sequence Viewer  
  EDL95149 (Get FASTA)   NCBI Sequence Viewer  
  Q9EPQ0 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_445957   ⟸   NM_053505
- UniProtKB: Q9EPQ0 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000071351   ⟸   ENSRNOT00000089098
RefSeq Acc Id: XP_038961929   ⟸   XM_039106001
- Peptide Label: isoform X1
Protein Domains
Na_Ca_ex

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
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 (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/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 (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)
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
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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
LL/MavRrrc (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
LN/MavRrrc (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
M520/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
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 (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
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)
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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/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
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 (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 (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)
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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/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
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 (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 (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 (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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:69256 AgrOrtholog
Ensembl Genes ENSRNOG00000060687 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000071351 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000089098 ENTREZGENE, UniProtKB/TrEMBL
InterPro K/Na/Ca-exchanger UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NaCa_Exmemb UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SLC24A3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:85267 UniProtKB/Swiss-Prot
NCBI Gene 85267 ENTREZGENE
PANTHER PTHR10846 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10846:SF22 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Na_Ca_ex UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc24a3 PhenoGen
TIGRFAMs TIGR00367 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K092_RAT UniProtKB/TrEMBL
  NCKX3_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Slc24a3  solute carrier family 24 (sodium/potassium/calcium exchanger), member 3    solute carrier family 24, member 3  Name updated 1299863 APPROVED
2002-06-10 Slc24a3  solute carrier family 24, member 3      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression mRNA highly expressed in brain, especially in thalamic nuclei, hippocampal CA1 neurons, and in layer IV of the cerebral cortex 68852
gene_process transports one calcium and one potassium in exchange for four sodium ions 68852
gene_protein predicted protein contains 644 aa residues 68852