Slc9a4 (solute carrier family 9 member A4) - Rat Genome Database
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Gene: Slc9a4 (solute carrier family 9 member A4) Rattus norvegicus
Analyze
Symbol: Slc9a4
Name: solute carrier family 9 member A4
RGD ID: 3721
Description: Predicted to have sodium:proton antiporter activity. Predicted to be involved in epithelial cell development and gastric acid secretion. Predicted to localize to several cellular components, including apical plasma membrane; basolateral plasma membrane; and vacuolar membrane. Orthologous to human SLC9A4 (solute carrier family 9 member A4); INTERACTS WITH 17beta-estradiol; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: na(+)/H(+) exchanger 4; NHE-4; Nhe4; sodium/hydrogen exchanger 4; solute carrier family 9 (sodium/hydrogen exchanger) isoform 4; Solute carrier family 9 (sodium/hydrogen exchanger), isoform 4; solute carrier family 9 (sodium/hydrogen exchanger), member 4; solute carrier family 9 member 4; solute carrier family 9, member 4; solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4
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
mRatBN7.2942,824,468 - 42,879,767 (+)NCBI
Rnor_6.0 Ensembl947,281,961 - 47,328,839 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0947,281,821 - 47,334,755 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0946,965,557 - 47,018,293 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4939,725,135 - 39,773,368 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1939,726,548 - 39,774,782 (+)NCBI
Celera940,568,530 - 40,616,779 (+)NCBICelera
Cytogenetic Map9q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Acidoses  (ISO)

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:15684419   PMID:22049213   PMID:23509787   PMID:26078707  


Genomics

Comparative Map Data
Slc9a4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2942,824,468 - 42,879,767 (+)NCBI
Rnor_6.0 Ensembl947,281,961 - 47,328,839 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0947,281,821 - 47,334,755 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0946,965,557 - 47,018,293 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4939,725,135 - 39,773,368 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1939,726,548 - 39,774,782 (+)NCBI
Celera940,568,530 - 40,616,779 (+)NCBICelera
Cytogenetic Map9q22NCBI
SLC9A4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2102,473,226 - 102,533,972 (+)EnsemblGRCh38hg38GRCh38
GRCh382102,473,226 - 102,533,974 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372103,089,685 - 103,150,431 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362102,456,194 - 102,516,863 (+)NCBINCBI36hg18NCBI36
Celera297,290,912 - 97,351,604 (+)NCBI
Cytogenetic Map2q12.1NCBI
HuRef296,854,147 - 96,914,821 (+)NCBIHuRef
CHM1_12103,094,074 - 103,154,769 (+)NCBICHM1_1
Slc9a4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39140,619,146 - 40,669,891 (+)NCBIGRCm39mm39
GRCm39 Ensembl140,619,241 - 40,669,885 (+)Ensembl
GRCm38140,579,986 - 40,630,731 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl140,580,081 - 40,630,725 (+)EnsemblGRCm38mm10GRCm38
MGSCv37140,637,072 - 40,687,576 (+)NCBIGRCm37mm9NCBIm37
MGSCv36140,524,747 - 40,574,199 (+)NCBImm8
Celera140,395,812 - 40,446,178 (+)NCBICelera
Cytogenetic Map1BNCBI
cM Map119.51NCBI
Slc9a4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554707,936,532 - 7,984,777 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554707,936,677 - 7,989,946 (+)NCBIChiLan1.0ChiLan1.0
SLC9A4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A103,566,298 - 103,626,975 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A103,566,128 - 103,626,975 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A99,280,738 - 99,341,618 (-)NCBIMhudiblu_PPA_v0panPan3
SLC9A4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1040,492,613 - 40,560,472 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11040,492,031 - 40,560,423 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Slc9a4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049367131,134,059 - 1,186,145 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC9A4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl351,686,672 - 51,750,073 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1351,686,001 - 51,749,996 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2354,166,243 - 54,230,077 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC9A4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1146,136,179 - 6,197,632 (+)NCBI
ChlSab1.1 Ensembl146,137,368 - 6,195,786 (+)Ensembl
Slc9a4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247496,972,364 - 7,025,929 (+)NCBI

Position Markers
D9Rat124  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0947,319,756 - 47,319,888NCBIRnor6.0
Rnor_5.0947,004,007 - 47,004,139UniSTSRnor5.0
RGSC_v3.4939,764,582 - 39,764,715RGDRGSC3.4
RGSC_v3.4939,764,583 - 39,764,715UniSTSRGSC3.4
RGSC_v3.1939,765,996 - 39,766,129RGD
Celera940,608,076 - 40,608,208UniSTS
SHRSP x BN Map937.7198UniSTS
SHRSP x BN Map937.7198RGD
Cytogenetic Map9q21UniSTS
D9Mco26  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0947,287,912 - 47,288,120NCBIRnor6.0
Rnor_5.0946,972,136 - 46,972,344UniSTSRnor5.0
RGSC_v3.4939,731,087 - 39,731,295UniSTSRGSC3.4
Celera940,574,481 - 40,574,689UniSTS
Cytogenetic Map9q21UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9235572247355722Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9235572247355722Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9288097747375681Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9288097747880977Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9498609549986095Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9498609549986095Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)91221677157216771Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)91242546357425463Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)91242546357425463Rat
631680Cm11Cardiac mass QTL 113.10.00089heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)92488509969885099Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92569234292741406Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)92569237370692373Rat
1598823Memor16Memory QTL 161.9exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)92575432054885226Rat
7207805Bmd88Bone mineral density QTL 884femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)92748603663264281Rat
1300180Bw14Body weight QTL 143.776body mass (VT:0001259)body weight (CMO:0000012)92748603666757620Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92748615588333183Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92907507983686404Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)929466970107878528Rat
1641894Alcrsp12Alcohol response QTL 12response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)93238513377385133Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93764235182642351Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93764235182642351Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)94126103490024806Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94126103498606834Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)941261034102531865Rat
6903941Pur31Proteinuria QTL 310.036total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94657976991579769Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94657976991579769Rat
61352Bp34Blood pressure QTL 345arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94695242783686153Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94724896594124663Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:54
Count of miRNA genes:43
Interacting mature miRNAs:50
Transcripts:ENSRNOT00000065234
Prediction methods: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

endocrine system hemolymphoid system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 1 9
Low 1 1 34 24 8
Below cutoff 1 1 8 9 13 2 14 6 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000065234   ⟹   ENSRNOP00000059258
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl947,281,961 - 47,328,839 (+)Ensembl
RefSeq Acc Id: NM_173098   ⟹   NP_775121
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2942,825,064 - 42,873,819 (+)NCBI
Rnor_6.0947,281,961 - 47,328,845 (+)NCBI
Rnor_5.0946,965,557 - 47,018,293 (+)NCBI
RGSC_v3.4939,725,135 - 39,773,368 (+)RGD
Celera940,568,530 - 40,616,779 (+)RGD
Sequence:
RefSeq Acc Id: XM_006244738   ⟹   XP_006244800
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2942,824,468 - 42,879,767 (+)NCBI
Rnor_6.0947,281,821 - 47,334,755 (+)NCBI
Rnor_5.0946,965,557 - 47,018,293 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008766991   ⟹   XP_008765213
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0947,282,644 - 47,334,755 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_775121 (Get FASTA)   NCBI Sequence Viewer  
  XP_006244800 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA41703 (Get FASTA)   NCBI Sequence Viewer  
  EDL99168 (Get FASTA)   NCBI Sequence Viewer  
  EDL99169 (Get FASTA)   NCBI Sequence Viewer  
  P26434 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_775121   ⟸   NM_173098
- Peptide Label: precursor
- Sequence:
RefSeq Acc Id: XP_006244800   ⟸   XM_006244738
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008765213   ⟸   XM_008766991
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000059258   ⟸   ENSRNOT00000065234
Protein Domains
Na_H_Exchanger   NEXCaM_BD

Transcriptome

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

Promoters
RGD ID:13696633
Promoter ID:EPDNEW_R7158
Type:single initiation site
Name:Slc9a4_1
Description:solute carrier family 9 member A4
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_6.0947,281,938 - 47,281,998EPDNEW

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)
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
MNS/Gib (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
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:3721 AgrOrtholog
Ensembl Genes ENSRNOG00000015306 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000059258 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000065234 ENTREZGENE, UniProtKB/TrEMBL
InterPro Cation/H_exchanger UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cation/H_exchanger_CPA1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na/H_exchanger_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NaH_exchanger UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NHE_CaM-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NHX4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24785 UniProtKB/Swiss-Prot
NCBI Gene 24785 ENTREZGENE
PANTHER PTHR10110 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10110:SF103 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Na_H_Exchanger UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NEXCaM_BD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc9a4 PhenoGen
PRINTS NAHEXCHNGR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NAHEXCHNGR2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs b_cpa1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G3V9T3_RAT UniProtKB/TrEMBL
  P26434 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-01 Slc9a4  solute carrier family 9 member A4  Slc9a4  solute carrier family 9 member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-02-24 Slc9a4  solute carrier family 9 member 4  Slc9a4  solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-16 Slc9a4  solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4  Slc9a4  solute carrier family 9 (sodium/hydrogen exchanger), member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-15 Slc9a4  solute carrier family 9 (sodium/hydrogen exchanger), member 4  Slc9a4  solute carrier family 9, member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Slc9a4  solute carrier family 9, member 4    Solute carrier family 9 (sodium/hydrogen exchanger), isoform 4  Name updated 629478 APPROVED
2002-06-10 Slc9a4  Solute carrier family 9 (sodium/hydrogen exchanger), isoform 4      Symbol and Name status set to approved 70586 APPROVED