Slc8a3 (solute carrier family 8 member A3) - Rat Genome Database

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Gene: Slc8a3 (solute carrier family 8 member A3) Rattus norvegicus
Analyze
Symbol: Slc8a3
Name: solute carrier family 8 member A3
RGD ID: 620197
Description: Enables calcium:cation antiporter activity involved in regulation of postsynaptic cytosolic calcium ion concentration and calcium:sodium antiporter activity. Involved in cellular response to cAMP; metal ion transport; and telencephalon development. Acts upstream of or within cellular calcium ion homeostasis. Located in several cellular components, including dendritic spine; neuronal cell body; and sarcolemma. Is integral component of postsynaptic membrane. Biomarker of brain ischemia and status epilepticus. Orthologous to human SLC8A3 (solute carrier family 8 member A3); PARTICIPATES IN calcium transport pathway; calcium/calcium-mediated signaling pathway; INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; acrylamide; amiodarone.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: na(+)/Ca(2+)-exchange protein 3; Ncx3; sodium/calcium exchanger 3; solute carrier family 8 (sodium/calcium exchanger), member 3; solute carrier family 8 member 3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26100,874,359 - 101,007,989 (-)NCBI
Rnor_6.0 Ensembl6104,891,376 - 105,097,054 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06104,889,500 - 105,099,408 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06113,212,215 - 113,244,454 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.06113,051,977 - 113,067,568 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46105,012,888 - 105,159,942 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16105,016,343 - 105,163,398 (-)NCBI
Celera698,727,252 - 98,860,656 (-)NCBICelera
Cytogenetic Map6q24NCBI
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
Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Bojarski C, etal., Brain Res. 2008 Jan 16;1189:198-202. Epub 2007 Nov 1.
2. Boscia F, etal., J Cereb Blood Flow Metab. 2006 Apr;26(4):502-17.
3. Cross JL, etal., Neurosci Res. 2012 Jul;73(3):191-8. doi: 10.1016/j.neures.2012.04.007. Epub 2012 Apr 27.
4. Fraysse B, etal., Am J Physiol Cell Physiol. 2001 Jan;280(1):C146-54.
5. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6. Ketelaars SO, etal., Epilepsia. 2004 Oct;45(10):1189-201.
7. Kuroda H, etal., Mol Pain. 2013 Apr 29;9:22. doi: 10.1186/1744-8069-9-22.
8. Linck B, etal., Am J Physiol. 1998 Feb;274(2 Pt 1):C415-23.
9. Lu J, etal., Neurosci Lett 2002 Oct 25;332(1):21-4.
10. Lytton J Biochem J. 2007 Sep 15;406(3):365-82.
11. MGD data from the GO Consortium
12. Minelli A, etal., Cell Calcium. 2007 Mar;41(3):221-34. Epub 2006 Aug 17.
13. NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. Nicoll DA, etal., J Biol Chem 1996 Oct 4;271(40):24914-21.
15. Pipeline to import KEGG annotations from KEGG into RGD
16. RGD automated data pipeline
17. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
18. RGD automated import pipeline for gene-chemical interactions
19. Sakaue M, etal., Brain Res. 2000 Oct 27;881(2):212-6.
20. Scorziello A, etal., J Cell Sci. 2013 Dec 15;126(Pt 24):5566-77. doi: 10.1242/jcs.129668. Epub 2013 Oct 7.
21. Secondo A, etal., Cell Calcium. 2007 Dec;42(6):521-35. Epub 2007 Mar 6.
22. Sokolow S, etal., Cell Calcium. 2011 Apr;49(4):208-16. doi: 10.1016/j.ceca.2010.12.008. Epub 2011 Mar 5.
23. Thurneysen T, etal., Ann N Y Acad Sci 2002 Nov;976:367-75.
Additional References at PubMed
PMID:12502534   PMID:12722103   PMID:14722618   PMID:15472108   PMID:15680332   PMID:15681692   PMID:16679322   PMID:18079274   PMID:18234895   PMID:20628398   PMID:20928830   PMID:21593315  
PMID:21959935   PMID:23403180   PMID:23688374   PMID:23919677   PMID:24029230   PMID:24632945   PMID:26041911   PMID:26608990   PMID:26924806   PMID:28428550   PMID:29274751   PMID:29763795  


Genomics

Comparative Map Data
Slc8a3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.26100,874,359 - 101,007,989 (-)NCBI
Rnor_6.0 Ensembl6104,891,376 - 105,097,054 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.06104,889,500 - 105,099,408 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06113,212,215 - 113,244,454 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.06113,051,977 - 113,067,568 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46105,012,888 - 105,159,942 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.16105,016,343 - 105,163,398 (-)NCBI
Celera698,727,252 - 98,860,656 (-)NCBICelera
Cytogenetic Map6q24NCBI
SLC8A3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1470,044,215 - 70,189,070 (-)EnsemblGRCh38hg38GRCh38
GRCh381470,044,215 - 70,189,626 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371470,510,932 - 70,655,668 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361469,580,687 - 69,725,540 (-)NCBINCBI36hg18NCBI36
Build 341469,580,686 - 69,725,540NCBI
Celera1450,575,050 - 50,719,920 (-)NCBI
Cytogenetic Map14q24.2NCBI
HuRef1450,679,036 - 50,824,067 (-)NCBIHuRef
CHM1_11470,448,984 - 70,593,925 (-)NCBICHM1_1
Slc8a3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391281,244,689 - 81,380,506 (-)NCBIGRCm39mm39
GRCm39 Ensembl1281,244,689 - 81,379,954 (-)Ensembl
GRCm381281,197,915 - 81,333,732 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1281,197,915 - 81,333,180 (-)EnsemblGRCm38mm10GRCm38
MGSCv371282,298,902 - 82,434,167 (-)NCBIGRCm37mm9NCBIm37
MGSCv361282,118,294 - 82,252,028 (-)NCBImm8
Celera1282,663,653 - 82,799,351 (-)NCBICelera
Cytogenetic Map12D1NCBI
cM Map1237.44NCBI
Slc8a3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955466220,099 - 360,851 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955466220,346 - 359,627 (+)NCBIChiLan1.0ChiLan1.0
SLC8A3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11469,505,703 - 69,650,382 (-)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v01450,634,091 - 50,779,712 (-)NCBIMhudiblu_PPA_v0panPan3
SLC8A3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1843,780,363 - 43,926,142 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl843,781,120 - 43,926,343 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha843,468,296 - 43,609,170 (-)NCBI
ROS_Cfam_1.0844,007,522 - 44,148,880 (-)NCBI
UMICH_Zoey_3.1843,621,943 - 43,763,260 (-)NCBI
UNSW_CanFamBas_1.0843,695,111 - 43,836,566 (-)NCBI
UU_Cfam_GSD_1.0844,055,432 - 44,196,751 (-)NCBI
Slc8a3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864060,820,218 - 60,955,215 (+)NCBI
SpeTri2.0NW_00493649513,236,480 - 13,370,973 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC8A3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl793,643,613 - 93,797,254 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1793,643,609 - 93,797,483 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2799,955,640 - 100,109,379 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC8A3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12447,287,487 - 47,428,608 (-)NCBI
ChlSab1.1 Ensembl2447,288,256 - 47,427,776 (-)Ensembl
Vero_WHO_p1.0NW_02366605335,512,872 - 35,653,693 (-)NCBI
Slc8a3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473430,889,302 - 31,033,098 (+)NCBI

Position Markers
AU046738  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26100,874,568 - 100,874,723 (+)MAPPER
Rnor_6.06104,891,225 - 104,891,379NCBIRnor6.0
Rnor_5.06113,051,824 - 113,051,978UniSTSRnor5.0
RGSC_v3.46105,012,735 - 105,012,889UniSTSRGSC3.4
Celera698,727,452 - 98,727,606UniSTS
Cytogenetic Map6q24UniSTS
AW742262  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26100,875,098 - 100,875,342 (+)MAPPER
Rnor_6.06104,891,755 - 104,891,998NCBIRnor6.0
Rnor_5.06113,052,354 - 113,052,597UniSTSRnor5.0
RGSC_v3.46105,013,265 - 105,013,508UniSTSRGSC3.4
Celera698,727,982 - 98,728,225UniSTS
Cytogenetic Map6q24UniSTS
BE110255  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26100,949,606 - 100,949,807 (+)MAPPER
Rnor_6.06104,966,732 - 104,966,932NCBIRnor6.0
Rnor_5.06113,127,651 - 113,127,851UniSTSRnor5.0
RGSC_v3.46105,090,055 - 105,090,255UniSTSRGSC3.4
Celera698,802,336 - 98,802,536UniSTS
RH 3.4 Map6704.6UniSTS
Cytogenetic Map6q24UniSTS
BF413600  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26100,882,609 - 100,882,742 (+)MAPPER
Rnor_6.06104,899,265 - 104,899,397NCBIRnor6.0
Rnor_5.06113,059,865 - 113,059,997UniSTSRnor5.0
RGSC_v3.46105,020,776 - 105,020,908UniSTSRGSC3.4
Celera698,735,493 - 98,735,625UniSTS
RH 3.4 Map6716.4UniSTS
Cytogenetic Map6q24UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)648432758108268790Rat
1558641Cm47Cardiac mass QTL 472.90.001heart mass (VT:0007028)heart wet weight (CMO:0000069)660606431108154445Rat
6893332Cm74Cardiac mass QTL 740.40.64heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)660606431108154445Rat
70176Mcsm1Mammary carcinoma susceptibility modifier QTL 1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)662263348107263348Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)666129520111129520Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)671206251116206251Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)675449871120449871Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)675623277120276465Rat
70196BpQTLcluster7Blood pressure QTL cluster 76.82arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)675623277120623277Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)675623277136143011Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)675623277136426962Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)675623393136142742Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)675623393136142742Rat
724524Uae2Urinary albumin excretion QTL 22.70.0005urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)676902247114203334Rat
2293837Kiddil1Kidney dilation QTL 13.7kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)684763275108464097Rat
2293842Kiddil3Kidney dilation QTL 34.3kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)684763275108464097Rat
737827Hcar11Hepatocarcinoma resistance QTL 114.4liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)686422697115379601Rat
1576302Schws4Schwannoma susceptibility QTL 40.0078nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)687418448111129520Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)688507712133507712Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)688996335139410483Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)689631358134631358Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)689631358134631358Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)691703409136703409Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (CMO:0000132)692879510137879510Rat
1331722Thshl1Thyroid stimulating hormone level QTL 111.70.0001blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)693706176111134673Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)697949772133849286Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)699273921144273921Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)699273921144792678Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)6101207574147991367Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6104363890147991367Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6104381930138066274Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:582
Count of miRNA genes:251
Interacting mature miRNAs:303
Transcripts:ENSRNOT00000048606
Prediction methods:Microtar, Miranda, 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 5 52 3
Low 2 2 10 2 2 5 6 22 22 33 11 5
Below cutoff 1 40 42 34 16 34 13 8

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_078620 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593987 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593988 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593989 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593990 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593991 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593992 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593993 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017593995 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111700 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111701 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111702 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039111703 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC122625 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473982 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000166 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000048606   ⟹   ENSRNOP00000041987
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6104,891,376 - 105,097,054 (-)Ensembl
RefSeq Acc Id: NM_078620   ⟹   NP_511175
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26100,874,369 - 101,007,272 (-)NCBI
Rnor_6.06104,891,025 - 105,097,054 (-)NCBI
Rnor_5.06113,051,977 - 113,067,568 (-)NCBI
Rnor_5.06113,212,215 - 113,244,454 (-)NCBI
RGSC_v3.46105,012,888 - 105,159,942 (-)RGD
Celera698,727,252 - 98,860,656 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593987   ⟹   XP_017449476
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26100,874,359 - 101,007,453 (-)NCBI
Rnor_6.06104,889,500 - 105,097,254 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593992   ⟹   XP_017449481
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26100,874,359 - 101,007,453 (-)NCBI
Rnor_6.06104,889,500 - 105,097,255 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593993   ⟹   XP_017449482
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26100,874,359 - 101,007,452 (-)NCBI
Rnor_6.06104,889,500 - 105,097,254 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017593995   ⟹   XP_017449484
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26100,874,359 - 101,007,453 (-)NCBI
Rnor_6.06104,889,500 - 104,912,806 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039111700   ⟹   XP_038967628
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26100,874,359 - 101,007,453 (-)NCBI
RefSeq Acc Id: XM_039111701   ⟹   XP_038967629
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26100,874,359 - 101,007,989 (-)NCBI
RefSeq Acc Id: XM_039111702   ⟹   XP_038967630
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26100,874,359 - 101,007,454 (-)NCBI
RefSeq Acc Id: XM_039111703   ⟹   XP_038967631
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26100,874,359 - 101,007,454 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_511175   ⟸   NM_078620
- Peptide Label: precursor
- UniProtKB: P70549 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017449481   ⟸   XM_017593992
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017449482   ⟸   XM_017593993
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_017449476   ⟸   XM_017593987
- Peptide Label: isoform X2
- UniProtKB: P70549 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017449484   ⟸   XM_017593995
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000041987   ⟸   ENSRNOT00000048606
RefSeq Acc Id: XP_038967629   ⟸   XM_039111701
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038967631   ⟸   XM_039111703
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038967630   ⟸   XM_039111702
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038967628   ⟸   XM_039111700
- Peptide Label: isoform X1
Protein Domains
Calx-beta

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)
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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)
ACI/EurMcwi (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
ACI/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
BBDP/Wor (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
BN/SsN (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
Buf/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
COP/CrCrl (MCW & UW)
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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)
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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
F344/NRrrc (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
FHH/EurMcwi (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)
FHH/EurMcwi (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
FHL/EurMcwi (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)
FHL/EurMcwi (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
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:620197 AgrOrtholog
Ensembl Genes ENSRNOG00000029871 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000041987 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000048606 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.40.2030 UniProtKB/Swiss-Prot
InterPro CalX-like_sf UniProtKB/Swiss-Prot
  Calx_beta UniProtKB/Swiss-Prot
  Na_Ca_Ex UniProtKB/Swiss-Prot
  Na_Ca_Ex_C-exten UniProtKB/Swiss-Prot
  NaCa_Exmemb UniProtKB/Swiss-Prot
KEGG Report rno:140448 UniProtKB/Swiss-Prot
NCBI Gene 140448 ENTREZGENE
Pfam Calx-beta UniProtKB/Swiss-Prot
  Na_Ca_ex UniProtKB/Swiss-Prot
  Na_Ca_ex_C UniProtKB/Swiss-Prot
PhenoGen Slc8a3 PhenoGen
PRINTS NACAEXCHNGR UniProtKB/Swiss-Prot
SMART Calx_beta UniProtKB/Swiss-Prot
Superfamily-SCOP SSF141072 UniProtKB/Swiss-Prot
TIGRFAMs caca UniProtKB/Swiss-Prot
UniProt NAC3_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-01 Slc8a3  solute carrier family 8 member A3  Slc8a3  solute carrier family 8 member 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-24 Slc8a3  solute carrier family 8 member 3  Slc8a3  solute carrier family 8 (sodium/calcium exchanger), member 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-26 Slc8a3  solute carrier family 8 (sodium/calcium exchanger), member 3      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Slc8a3  solute carrier family 8 (sodium/calcium exchanger), member 3      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression mRNA expression restricted to brain and skeletal muscle 730187
gene_protein open reading frame of 2.8 kb encodes protein of 927 aa residues 730187