Slc9a6 (solute carrier family 9 member A6) - Rat Genome Database

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Gene: Slc9a6 (solute carrier family 9 member A6) Rattus norvegicus
Analyze
Symbol: Slc9a6
Name: solute carrier family 9 member A6
RGD ID: 1563582
Description: Predicted to enable identical protein binding activity; potassium:proton antiporter activity; and sodium:proton antiporter activity. Involved in glial cell activation and regulation of synaptic vesicle lumen acidification. Is active in presynapse. Human ortholog(s) of this gene implicated in Christianson syndrome. Orthologous to human SLC9A6 (solute carrier family 9 member A6); PARTICIPATES IN angiotensin II signaling pathway via AT2 receptor; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,6-dinitrotoluene; 2-methoxyethanol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC302863; Na(+)/H(+) exchanger 6; NHE-6; RGD1563582; similar to mKIAA0267 protein; sodium/hydrogen exchanger 6; solute carrier family 9 (sodium/hydrogen exchanger), isoform 6; solute carrier family 9 (sodium/hydrogen exchanger), member 6; solute carrier family 9 member 6; solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: Slc9a6 em1Moro  
Genetic Models: SD-Slc9a6 em1Moro SD-Slc9a6 em1Moro/Rrrc
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X139,468,045 - 139,524,111 (+)NCBIGRCr8
mRatBN7.2X134,430,677 - 134,486,747 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX134,420,756 - 134,485,375 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X158,979,081 - 159,045,019 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX158,978,755 - 159,045,044 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X153,620,082 - 153,675,717 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X141,146,237 - 141,201,234 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX142,471,399 - 142,536,119 (+)NCBICelera
Cytogenetic MapXq36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. SCAMP5 plays a critical role in axonal trafficking and synaptic localization of NHE6 to adjust quantal size at glutamatergic synapses. Lee U, etal., Proc Natl Acad Sci U S A. 2021 Jan 12;118(2):e2011371118. doi: 10.1073/pnas.2011371118.
3. Early lysosome defects precede neurodegeneration with amyloid-β and tau aggregation in NHE6-null rat brain. Lee Y, etal., Brain. 2021 Dec 20. pii: 6470622. doi: 10.1093/brain/awab467.
4. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Comprehensive gene review and curation RGD comprehensive gene curation
8. An ATIPical family of angiotensin II AT2 receptor-interacting proteins. Rodrigues-Ferreira S and Nahmias C, Trends Endocrinol Metab. 2010 Nov;21(11):684-90.
Additional References at PubMed
PMID:11641397   PMID:11940519   PMID:14651853   PMID:23303939   PMID:24035762   PMID:33663553   PMID:36621975  


Genomics

Comparative Map Data
Slc9a6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X139,468,045 - 139,524,111 (+)NCBIGRCr8
mRatBN7.2X134,430,677 - 134,486,747 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX134,420,756 - 134,485,375 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.0X158,979,081 - 159,045,019 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX158,978,755 - 159,045,044 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X153,620,082 - 153,675,717 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X141,146,237 - 141,201,234 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX142,471,399 - 142,536,119 (+)NCBICelera
Cytogenetic MapXq36NCBI
SLC9A6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X135,973,837 - 136,047,269 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX135,973,841 - 136,047,269 (+)EnsemblGRCh38hg38GRCh38
GRCh37X135,055,996 - 135,129,428 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X134,895,252 - 134,957,094 (+)NCBINCBI36Build 36hg18NCBI36
Build 34X134,793,146 - 134,854,812NCBI
CeleraX135,428,360 - 135,490,286 (+)NCBICelera
Cytogenetic MapXq26.3NCBI
HuRefX124,341,164 - 124,403,216 (+)NCBIHuRef
CHM1_1X134,978,471 - 135,040,349 (+)NCBICHM1_1
T2T-CHM13v2.0X134,282,570 - 134,355,980 (+)NCBIT2T-CHM13v2.0
Slc9a6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X55,654,921 - 55,709,590 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX55,655,117 - 55,709,590 (+)EnsemblGRCm39 Ensembl
GRCm38X56,609,556 - 56,664,230 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX56,609,757 - 56,664,230 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X53,863,012 - 53,917,407 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X52,956,638 - 53,008,677 (+)NCBIMGSCv36mm8
CeleraX43,091,843 - 43,146,238 (+)NCBICelera
Cytogenetic MapXA5- A6NCBI
cM MapX30.06NCBI
Slc9a6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554899,019,425 - 9,078,705 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554899,020,719 - 9,078,375 (-)NCBIChiLan1.0ChiLan1.0
SLC9A6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X135,398,673 - 135,460,202 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X135,402,314 - 135,463,798 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X125,099,378 - 125,171,161 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X135,378,091 - 135,439,781 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX135,378,094 - 135,439,781 (+)Ensemblpanpan1.1panPan2
SLC9A6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X106,408,789 - 106,465,504 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX106,398,850 - 106,463,252 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX92,228,868 - 92,285,695 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X108,385,561 - 108,442,397 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX108,375,657 - 108,440,140 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X105,522,975 - 105,586,115 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X107,706,620 - 107,763,439 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X107,355,362 - 107,412,198 (+)NCBIUU_Cfam_GSD_1.0
Slc9a6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X104,399,038 - 104,455,882 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493651311,158,730 - 11,215,568 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493651311,158,609 - 11,215,477 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC9A6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX111,176,495 - 111,233,099 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X111,176,461 - 111,233,108 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X127,098,575 - 127,154,902 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLC9A6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X110,997,985 - 111,060,164 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX110,998,281 - 111,060,252 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606548,664,039 - 48,725,734 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc9a6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462480811,107,125 - 11,157,913 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slc9a6
133 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:45
Count of miRNA genes:35
Interacting mature miRNAs:45
Transcripts:ENSRNOT00000066809
Prediction methods:Miranda, Pita, 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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598872Memor14Memory QTL 144.5exploratory 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)X93956491138956491Rat
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat
1598809Memor15Memory QTL 154.4exploratory 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)X103312877148312877Rat
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX112934952138400867Rat
10059603Bw174Body weight QTL 1743.40.025body mass (VT:0001259)body weight (CMO:0000012)X113937816152453651Rat
1598837Memor13Memory QTL 133.2exploratory 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)X41052407146860749Rat

Markers in Region
DXRat55  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X134,429,057 - 134,429,259 (+)MAPPERmRatBN7.2
Rnor_6.0X158,987,252 - 158,987,453NCBIRnor6.0
Rnor_5.0X153,618,494 - 153,618,695UniSTSRnor5.0
RGSC_v3.4X141,144,544 - 141,144,746RGDRGSC3.4
RGSC_v3.4X141,144,545 - 141,144,746UniSTSRGSC3.4
RGSC_v3.1X141,217,811 - 141,218,264RGD
CeleraX142,479,570 - 142,479,771UniSTS
FHH x ACI MapX39.09RGD
FHH x ACI MapX39.09UniSTS
Cytogenetic MapXq36UniSTS


Genetic Models
This gene Slc9a6 is modified in the following models/strains:
SD-Slc9a6 em1Moro     SD-Slc9a6 em1Moro/Rrrc    


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000066809   ⟹   ENSRNOP00000060014
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX134,420,756 - 134,485,375 (+)Ensembl
Rnor_6.0 EnsemblX158,978,755 - 159,045,044 (+)Ensembl
RefSeq Acc Id: NM_001419592   ⟹   NP_001406521
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X139,468,045 - 139,524,111 (+)NCBI
mRatBN7.2X134,430,677 - 134,486,747 (+)NCBI
RefSeq Acc Id: XM_039100496   ⟹   XP_038956424
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X139,468,097 - 139,524,109 (+)NCBI
mRatBN7.2X134,430,728 - 134,486,747 (+)NCBI
RefSeq Acc Id: XM_217630   ⟹   XP_217630
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X139,468,097 - 139,524,109 (+)NCBI
mRatBN7.2X134,430,728 - 134,486,747 (+)NCBI
Rnor_6.0X158,988,928 - 159,045,019 (+)NCBI
Rnor_5.0X153,620,082 - 153,675,717 (+)NCBI
RGSC_v3.4X141,146,237 - 141,201,234 (+)RGD
Sequence:
RefSeq Acc Id: XP_217630   ⟸   XM_217630
- Peptide Label: isoform X1
- UniProtKB: A6KSN8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000060014   ⟸   ENSRNOT00000066809
RefSeq Acc Id: XP_038956424   ⟸   XM_039100496
- Peptide Label: isoform X2
- UniProtKB: A6KSN8 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001406521   ⟸   NM_001419592
Protein Domains
Cation/H+ exchanger

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZJ86-F1-model_v2 AlphaFold D3ZJ86 1-721 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563582 AgrOrtholog
BioCyc Gene G2FUF-919 BioCyc
Ensembl Genes ENSRNOG00000000879 Ensembl, UniProtKB/Swiss-Prot
  ENSRNOG00055027658 UniProtKB/Swiss-Prot
  ENSRNOG00060022838 UniProtKB/Swiss-Prot
  ENSRNOG00065028401 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000066809.4 UniProtKB/Swiss-Prot
  ENSRNOT00055048079 UniProtKB/Swiss-Prot
  ENSRNOT00060040117 UniProtKB/Swiss-Prot
  ENSRNOT00065048991 UniProtKB/Swiss-Prot
Gene3D-CATH 6.10.140.1330 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Cation/H_exchanger UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cation/H_exchanger_CPA1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NaH_exchanger UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NHE-6/7/9 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 302863 ENTREZGENE
PANTHER SODIUM/HYDROGEN EXCHANGER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SODIUM/HYDROGEN EXCHANGER 6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Na_H_Exchanger UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc9a6 PhenoGen
PRINTS NAHEXCHNGR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NAHEXCHNGR6 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000879 RatGTEx
  ENSRNOG00055027658 RatGTEx
  ENSRNOG00060022838 RatGTEx
  ENSRNOG00065028401 RatGTEx
UniProt A6KSN8 ENTREZGENE, UniProtKB/TrEMBL
  D3ZJ86 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-01 Slc9a6  solute carrier family 9 member A6  Slc9a6  solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-16 Slc9a6  solute carrier family 9, subfamily A (NHE6, cation proton antiporter 6), member 6  Slc9a6  solute carrier family 9 (sodium/hydrogen exchanger), member 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-05-02 Slc9a6  solute carrier family 9 (sodium/hydrogen exchanger), member 6  Slc9a6  solute carrier family 9 (sodium/hydrogen exchanger), isoform 6  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-07 Slc9a6  solute carrier family 9 (sodium/hydrogen exchanger), isoform 6  Slc9a6_predicted  solute carrier family 9 (sodium/hydrogen exchanger), member 6 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Slc9a6_predicted  solute carrier family 9 (sodium/hydrogen exchanger), member 6 (predicted)  RGD1563582_predicted  similar to mKIAA0267 protein (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1563582_predicted  similar to mKIAA0267 protein (predicted)  LOC302863  similar to mKIAA0267 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC302863  similar to mKIAA0267 protein      Symbol and Name status set to provisional 70820 PROVISIONAL