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 (Ensembl:solute carrier family 9 (sodium/hydrogen exchanger), member 6)
RGD ID: 1563582
Description: Predicted to enable identical protein binding activity; potassium:proton antiporter activity; and sodium:proton antiporter activity. Predicted to be involved in several processes, including monoatomic cation transmembrane transport; regulation of intracellular pH; and regulation of postsynaptic membrane neurotransmitter receptor levels. Predicted to act upstream of or within several processes, including brain-derived neurotrophic factor receptor signaling pathway; neuron projection development; and regulation of neurotrophin TRK receptor signaling pathway. Predicted to be located in several cellular components, including axon; endoplasmic reticulum membrane; and endosome. Predicted to be active in several cellular components, including Schaffer collateral - CA1 synapse; glutamatergic synapse; and recycling endosome. 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: MODEL
Previously known as: LOC302863; 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, subfamily A (NHE6, cation proton antiporter 6), member 6
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Slc9a6 em1Moro  
Genetic Models: SD-Slc9a6 em1Moro
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X134,430,588 - 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 MapXq37NCBI
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
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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Comprehensive gene review and curation RGD comprehensive gene curation
6. 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  


Genomics

Comparative Map Data
Slc9a6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X134,430,588 - 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 MapXq37NCBI
SLC9A6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X135,973,837 - 136,047,269 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 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
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
PanPan1.1X135,378,091 - 135,439,781 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX135,378,094 - 135,439,781 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X125,099,378 - 125,171,161 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
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 (-)EnsemblSpeTri2.0
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
122 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
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
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
738025Stresp3Stress response QTL 34.610.0066stress-related behavior trait (VT:0010451)defensive burying - approachX100567703150256146Rat
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
1598856Memor1Memory QTL 11.9exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)X103312877148312877Rat
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
634346Insul4Insulin level QTL 40blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)X126975089152453651Rat

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 MapX39.09UniSTS
FHH x ACI MapX39.09RGD
Cytogenetic MapXq36UniSTS


Genetic Models
This gene Slc9a6 is modified in the following models/strains

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 2 12 11 4 4 74 32 33 11
Low 1 31 46 37 19 37 8 11 3 8 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000066809   ⟹   ENSRNOP00000060014
RefSeq Status:
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: XM_039100496   ⟹   XP_038956424
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X134,430,728 - 134,486,747 (+)NCBI
RefSeq Acc Id: XM_039100497   ⟹   XP_038956425
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X134,430,588 - 134,486,747 (+)NCBI
RefSeq Acc Id: XM_217630   ⟹   XP_217630
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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:
Protein Sequences
Protein RefSeqs XP_038956424 (Get FASTA)   NCBI Sequence Viewer  
  XP_038956425 (Get FASTA)   NCBI Sequence Viewer  
  XP_217630 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL75145 (Get FASTA)   NCBI Sequence Viewer  
  EDL75146 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_217630   ⟸   XM_217630
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000060014   ⟸   ENSRNOT00000066809
RefSeq Acc Id: XP_038956425   ⟸   XM_039100497
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038956424   ⟸   XM_039100496
- Peptide Label: isoform X1
Protein Domains
Na_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, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000060014 ENTREZGENE
  ENSRNOP00000060014.3 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000066809 ENTREZGENE
  ENSRNOT00000066809.4 UniProtKB/TrEMBL
InterPro Cation/H_exchanger UniProtKB/TrEMBL
  Cation/H_exchanger_cons-reg UniProtKB/TrEMBL
  Na/H_exchanger_6 UniProtKB/TrEMBL
  NaH_exchanger_subfam UniProtKB/TrEMBL
NCBI Gene 302863 ENTREZGENE
PANTHER Cation/H_exchanger_cons-reg UniProtKB/TrEMBL
Pfam Na_H_Exchanger UniProtKB/TrEMBL
PhenoGen Slc9a6 PhenoGen
PRINTS NAHEXCHNGR UniProtKB/TrEMBL
  NAHEXCHNGR6 UniProtKB/TrEMBL
TIGRFAMs b_cpa1 UniProtKB/TrEMBL
UniProt D3ZJ86_RAT UniProtKB/TrEMBL


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