Slc9c1 (solute carrier family 9 member C1) - Rat Genome Database

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Gene: Slc9c1 (solute carrier family 9 member C1) Rattus norvegicus
Analyze
Symbol: Slc9c1
Name: solute carrier family 9 member C1
RGD ID: 1309075
Description: Predicted to have solute:proton antiporter activity. Predicted to be involved in flagellated sperm motility. Predicted to localize to motile cilium. Orthologous to human SLC9C1 (solute carrier family 9 member C1); INTERACTS WITH 1,2-dichloroethane (ortholog); 2-hydroxypropanoic acid (ortholog); aflatoxin B1 (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: gene model 610, (NCBI); Gm610; LOC288117; Slc9a10; sodium/hydrogen exchanger 10; solute carrier family 9, member 10; solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1; sperm-specific sodium proton exchanger
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
mRatBN7.21155,211,774 - 55,278,285 (-)NCBI
Rnor_6.0 Ensembl1160,184,961 - 60,251,428 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01160,184,953 - 60,251,458 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01164,285,570 - 64,350,871 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41156,702,554 - 56,769,394 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11156,760,142 - 56,826,983 (-)NCBI
Celera1154,735,652 - 54,802,154 (-)NCBICelera
Cytogenetic Map11q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:12783626   PMID:14634667  


Genomics

Comparative Map Data
Slc9c1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21155,211,774 - 55,278,285 (-)NCBI
Rnor_6.0 Ensembl1160,184,961 - 60,251,428 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01160,184,953 - 60,251,458 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01164,285,570 - 64,350,871 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41156,702,554 - 56,769,394 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11156,760,142 - 56,826,983 (-)NCBI
Celera1154,735,652 - 54,802,154 (-)NCBICelera
Cytogenetic Map11q21NCBI
SLC9C1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl3112,140,898 - 112,294,227 (-)EnsemblGRCh38hg38GRCh38
GRCh383112,140,898 - 112,294,258 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh373111,859,745 - 112,013,063 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363113,342,442 - 113,495,764 (-)NCBINCBI36hg18NCBI36
Build 343113,342,442 - 113,495,764NCBI
Celera3110,258,818 - 110,421,777 (-)NCBI
Cytogenetic Map3q13.2NCBI
HuRef3109,234,451 - 109,397,162 (-)NCBIHuRef
CHM1_13111,823,766 - 111,977,173 (-)NCBICHM1_1
Slc9c1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391645,355,629 - 45,427,364 (+)NCBIGRCm39mm39
GRCm39 Ensembl1645,355,672 - 45,427,364 (+)Ensembl
GRCm381645,535,266 - 45,607,001 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1645,535,309 - 45,607,001 (+)EnsemblGRCm38mm10GRCm38
MGSCv371645,535,422 - 45,607,114 (+)NCBIGRCm37mm9NCBIm37
MGSCv361645,454,641 - 45,526,333 (+)NCBImm8
Celera1645,866,205 - 45,982,308 (+)NCBICelera
Cytogenetic Map16B5NCBI
Slc9c1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542712,541,286 - 12,644,604 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542712,541,396 - 12,644,543 (-)NCBIChiLan1.0ChiLan1.0
SLC9C1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.13116,219,881 - 116,358,397 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3116,219,887 - 116,358,397 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v03109,296,225 - 109,435,341 (-)NCBIMhudiblu_PPA_v0panPan3
SLC9C1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13316,762,824 - 16,844,780 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3316,762,837 - 16,845,003 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3316,866,751 - 16,948,860 (-)NCBI
ROS_Cfam_1.03317,009,322 - 17,091,214 (-)NCBI
UMICH_Zoey_3.13316,812,599 - 16,894,749 (-)NCBI
UNSW_CanFamBas_1.03316,858,459 - 16,941,889 (-)NCBI
UU_Cfam_GSD_1.03317,409,076 - 17,491,071 (-)NCBI
Slc9c1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602137,568,862 - 137,647,058 (+)NCBI
SpeTri2.0NW_004936834939,319 - 1,004,163 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC9C1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13147,517,663 - 147,603,247 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113147,517,985 - 147,612,667 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213157,110,613 - 157,154,008 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC9C1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12268,528,699 - 68,648,936 (+)NCBI
Slc9c1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473136,291,310 - 36,430,429 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11172720192Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)1132503169342559Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111901627290463843Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)111947517979734728Rat
1598811Bp291Blood pressure QTL 2911.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)112194422966944229Rat
1598841Memor7Memory QTL 7exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)112194422966944229Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112540112970401129Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112572003870720038Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112572003870720038Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112572003870720038Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112572003870720038Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112831466586994795Rat
1300130Rf20Renal function QTL 204.44kidney glomerulus integrity trait (VT:0010546)kidney glomerulus diameter (CMO:0001166)113043533963186373Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)113043533986714631Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)113215552082443118Rat
70180BpQTLcluster10Blood pressure QTL cluster 103.19arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)113590063480900634Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)114309033886714631Rat
634339Niddm50Non-insulin dependent diabetes mellitus QTL 503.32blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)114444434769649708Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)114658320986714631Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114726402386994547Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)114726402386994547Rat
4889859Pur28Proteinuria QTL 2819.50.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)114790104978471527Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)115785881090463843Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)115994302390463843Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)116010984287141948Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:123
Count of miRNA genes:97
Interacting mature miRNAs:105
Transcripts:ENSRNOT00000040908
Prediction methods:Microtar, 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 endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system reproductive system respiratory system appendage
High
Medium 7
Low 1 1 1 1 2 1
Below cutoff 2 9 2 10 2 1 1 1 9 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000040908   ⟹   ENSRNOP00000045235
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1160,190,782 - 60,249,165 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000080148   ⟹   ENSRNOP00000074847
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1160,184,964 - 60,251,415 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000086602   ⟹   ENSRNOP00000072593
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1160,184,961 - 60,251,428 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000093613
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1160,232,871 - 60,233,519 (-)Ensembl
RefSeq Acc Id: NM_001008762   ⟹   NP_001008762
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21155,211,792 - 55,278,285 (-)NCBI
Rnor_6.01160,184,973 - 60,251,458 (-)NCBI
Rnor_5.01164,285,570 - 64,350,871 (-)NCBI
Celera1154,735,652 - 54,802,154 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008768722   ⟹   XP_008766944
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21155,211,774 - 55,276,179 (-)NCBI
Rnor_6.01160,184,953 - 60,249,352 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597925   ⟹   XP_017453414
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21155,211,774 - 55,278,279 (-)NCBI
Rnor_6.01160,184,953 - 60,251,452 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597926   ⟹   XP_017453415
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21155,211,774 - 55,278,161 (-)NCBI
Rnor_6.01160,184,953 - 60,251,334 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017597927   ⟹   XP_017453416
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21155,211,774 - 55,278,002 (-)NCBI
Rnor_6.01160,184,953 - 60,251,184 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039088182   ⟹   XP_038944110
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21155,211,774 - 55,278,279 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001008762   ⟸   NM_001008762
- UniProtKB: A0A0G2K3D4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008766944   ⟸   XM_008768722
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K3D4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017453414   ⟸   XM_017597925
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K3D4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017453415   ⟸   XM_017597926
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K3D4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017453416   ⟸   XM_017597927
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K3D4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074847   ⟸   ENSRNOT00000080148
RefSeq Acc Id: ENSRNOP00000045235   ⟸   ENSRNOT00000040908
RefSeq Acc Id: ENSRNOP00000072593   ⟸   ENSRNOT00000086602
RefSeq Acc Id: XP_038944110   ⟸   XM_039088182
- Peptide Label: isoform X2
Transcriptome

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

Promoters
RGD ID:13698134
Promoter ID:EPDNEW_R8659
Type:initiation region
Name:Slc9c1_1
Description:solute carrier family 9 member C1
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_6.01160,251,379 - 60,251,439EPDNEW

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)
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/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
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 (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
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
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
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
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
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:1309075 AgrOrtholog
Ensembl Genes ENSRNOG00000022007 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000045235 UniProtKB/TrEMBL
  ENSRNOP00000072593 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074847 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000040908 UniProtKB/TrEMBL
  ENSRNOT00000080148 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000086602 UniProtKB/TrEMBL
Gene3D-CATH 1.20.120.350 UniProtKB/TrEMBL
  2.60.120.10 UniProtKB/TrEMBL
InterPro Cation/H_exchanger UniProtKB/TrEMBL
  Cation/H_exchanger_CPA1 UniProtKB/TrEMBL
  cNMP-bd-like UniProtKB/TrEMBL
  cNMP-bd_dom UniProtKB/TrEMBL
  N/H_exchanger_10 UniProtKB/TrEMBL
  RmlC-like_jellyroll UniProtKB/TrEMBL
  Volt_channel_dom_sf UniProtKB/TrEMBL
KEGG Report rno:288117 UniProtKB/TrEMBL
NCBI Gene 288117 ENTREZGENE
PANTHER Cation/H_exchanger_cons-reg UniProtKB/TrEMBL
  PTHR10110:SF87 UniProtKB/TrEMBL
Pfam cNMP_binding UniProtKB/TrEMBL
  Na_H_Exchanger UniProtKB/TrEMBL
PhenoGen Slc9c1 PhenoGen
PROSITE CNMP_BINDING_3 UniProtKB/TrEMBL
Superfamily-SCOP cNMP_binding UniProtKB/TrEMBL
UniProt A0A0G2K3D4 ENTREZGENE, UniProtKB/TrEMBL
  F1M7D9_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-24 Slc9c1  solute carrier family 9 member C1  Slc9c1  solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-16 Slc9c1  solute carrier family 9, subfamily C (Na+-transporting carboxylic acid decarboxylase), member 1  Slc9a10  solute carrier family 9, member 10  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Slc9a10  solute carrier family 9, member 10  Gm610  gene model 610, (NCBI)  Symbol and Name updated 1299863 APPROVED
2005-12-06 Gm610  gene model 610, (NCBI)  Gm610_predicted  gene model 610, (NCBI) (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Gm610_predicted  gene model 610, (NCBI) (predicted)      Symbol and Name status set to approved 70820 APPROVED