Slc30a9 (solute carrier family 30 member 9) - Rat Genome Database

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Gene: Slc30a9 (solute carrier family 30 member 9) Rattus norvegicus
Analyze
Symbol: Slc30a9
Name: solute carrier family 30 member 9
RGD ID: 1593180
Description: Predicted to enable several functions, including nuclear receptor binding activity; nuclear receptor coactivator activity; and zinc ion transmembrane transporter activity. Predicted to be involved in intracellular zinc ion homeostasis; regulation of mitochondrion organization; and zinc ion transport. Predicted to act upstream of or within positive regulation of transcription by RNA polymerase II. Predicted to be located in several cellular components, including cytoplasmic vesicle; cytoskeleton; and mitochondrial membrane. Predicted to be active in endoplasmic reticulum. Orthologous to human SLC30A9 (solute carrier family 30 member 9); INTERACTS WITH bisphenol A; fenvalerate; flutamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC498358; proton-coupled zinc antiporter SLC30A9, mitochondrial; similar to solute carrier family 30 (zinc transporter), member 9; solute carrier family 30 (zinc transporter), member 9; zinc transporter 9
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81441,170,164 - 41,224,861 (-)NCBIGRCr8
mRatBN7.21440,816,284 - 40,870,992 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1440,816,290 - 40,870,929 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1441,163,614 - 41,217,044 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01442,463,696 - 42,517,124 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01440,944,484 - 40,997,919 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01442,464,814 - 42,519,760 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1442,465,807 - 42,520,020 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01442,260,670 - 42,315,608 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41443,423,677 - 43,477,106 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1439,971,799 - 40,024,874 (-)NCBICelera
Cytogenetic Map14p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10409434   PMID:15988012   PMID:28334855   PMID:36889209  


Genomics

Comparative Map Data
Slc30a9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81441,170,164 - 41,224,861 (-)NCBIGRCr8
mRatBN7.21440,816,284 - 40,870,992 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1440,816,290 - 40,870,929 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1441,163,614 - 41,217,044 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01442,463,696 - 42,517,124 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01440,944,484 - 40,997,919 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01442,464,814 - 42,519,760 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1442,465,807 - 42,520,020 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01442,260,670 - 42,315,608 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41443,423,677 - 43,477,106 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1439,971,799 - 40,024,874 (-)NCBICelera
Cytogenetic Map14p11NCBI
SLC30A9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38441,990,530 - 42,090,461 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl441,990,502 - 42,090,461 (+)EnsemblGRCh38hg38GRCh38
GRCh37441,992,547 - 42,092,478 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36441,687,280 - 41,784,308 (+)NCBINCBI36Build 36hg18NCBI36
Build 34441,833,450 - 41,930,478NCBI
Celera442,436,367 - 42,535,251 (+)NCBICelera
Cytogenetic Map4p13NCBI
HuRef441,314,384 - 41,411,336 (+)NCBIHuRef
CHM1_1441,992,998 - 42,089,827 (+)NCBICHM1_1
T2T-CHM13v2.0441,964,357 - 42,064,385 (+)NCBIT2T-CHM13v2.0
Slc30a9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39567,464,298 - 67,513,485 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl567,464,298 - 67,515,786 (+)EnsemblGRCm39 Ensembl
GRCm38567,306,955 - 67,356,142 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl567,306,955 - 67,358,443 (+)EnsemblGRCm38mm10GRCm38
MGSCv37567,698,196 - 67,747,384 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36567,586,092 - 67,635,277 (+)NCBIMGSCv36mm8
Celera564,609,485 - 64,658,412 (+)NCBICelera
Cytogenetic Map5C3.1NCBI
cM Map536.02NCBI
Slc30a9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554435,642,828 - 5,716,071 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554435,641,372 - 5,716,188 (-)NCBIChiLan1.0ChiLan1.0
SLC30A9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2342,172,118 - 42,271,944 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1442,365,508 - 42,465,365 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0436,315,959 - 36,412,653 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1442,163,547 - 42,260,175 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl442,163,724 - 42,255,318 (+)Ensemblpanpan1.1panPan2
SLC30A9
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11339,053,613 - 39,138,117 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1339,055,252 - 39,134,956 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1339,034,325 - 39,113,858 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01339,548,803 - 39,628,746 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1339,545,614 - 39,617,572 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11339,238,687 - 39,317,575 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01339,349,922 - 39,429,370 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01339,815,084 - 39,894,643 (+)NCBIUU_Cfam_GSD_1.0
Slc30a9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528537,015,591 - 37,112,184 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364829,186,198 - 9,281,242 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364829,186,044 - 9,282,646 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC30A9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl833,058,618 - 33,113,283 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1833,058,666 - 33,111,775 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2834,713,130 - 34,766,670 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLC30A9
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1278,263,287 - 8,367,549 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl278,260,355 - 8,367,395 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604754,568,926 - 54,678,061 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc30a9
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476124,869,491 - 24,944,258 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476124,869,370 - 24,944,410 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slc30a9
193 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:712
Count of miRNA genes:301
Interacting mature miRNAs:399
Transcripts:ENSRNOT00000065550
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)143999825175582726Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat

Markers in Region
BF386044  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21440,870,537 - 40,870,690 (+)MAPPERmRatBN7.2
Rnor_6.01442,519,304 - 42,519,456NCBIRnor6.0
Rnor_5.01442,315,160 - 42,315,312UniSTSRnor5.0
RGSC_v3.41443,476,731 - 43,476,883UniSTSRGSC3.4
Celera1440,024,499 - 40,024,651UniSTS
Cytogenetic Map14p11UniSTS


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 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000065550   ⟹   ENSRNOP00000059961
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1440,819,524 - 40,870,929 (-)Ensembl
Rnor_6.0 Ensembl1442,465,807 - 42,520,020 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000097270   ⟹   ENSRNOP00000093811
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1440,816,290 - 40,870,929 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100697   ⟹   ENSRNOP00000082378
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1440,816,290 - 40,870,929 (-)Ensembl
RefSeq Acc Id: NM_001109088   ⟹   NP_001102558
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81441,171,356 - 41,224,788 (-)NCBI
mRatBN7.21440,817,476 - 40,870,913 (-)NCBI
Rnor_6.01442,466,006 - 42,519,679 (-)NCBI
Rnor_5.01442,260,670 - 42,315,608 (-)NCBI
RGSC_v3.41443,423,677 - 43,477,106 (-)RGD
Celera1439,971,799 - 40,024,874 (-)RGD
Sequence:
RefSeq Acc Id: XM_006250963   ⟹   XP_006251025
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81441,170,164 - 41,224,861 (-)NCBI
mRatBN7.21440,816,284 - 40,870,992 (-)NCBI
Rnor_6.01442,464,814 - 42,519,760 (-)NCBI
Rnor_5.01442,260,670 - 42,315,608 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001102558 (Get FASTA)   NCBI Sequence Viewer  
  XP_006251025 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL90027 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000059961.2
  ENSRNOP00000082378
  ENSRNOP00000082378.1
  ENSRNOP00000093811.1
Reference Protein Sequences
RefSeq Acc Id: NP_001102558   ⟸   NM_001109088
- UniProtKB: D3ZWW5 (UniProtKB/TrEMBL),   A0A8I5ZUD8 (UniProtKB/TrEMBL),   A6JDA5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006251025   ⟸   XM_006250963
- Peptide Label: isoform X1
- UniProtKB: D3ZWW5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000059961   ⟸   ENSRNOT00000065550
RefSeq Acc Id: ENSRNOP00000093811   ⟸   ENSRNOT00000097270
RefSeq Acc Id: ENSRNOP00000082378   ⟸   ENSRNOT00000100697

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZWW5-F1-model_v2 AlphaFold D3ZWW5 1-567 view protein structure

Transcriptome

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

Promoters
RGD ID:13699304
Promoter ID:EPDNEW_R9829
Type:initiation region
Name:Slc30a9_1
Description:solute carrier family 30 member 9
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_6.01442,519,715 - 42,519,775EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1593180 AgrOrtholog
BioCyc Gene G2FUF-15775 BioCyc
Ensembl Genes ENSRNOG00000002246 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000065550.4 UniProtKB/TrEMBL
  ENSRNOT00000097270.1 UniProtKB/TrEMBL
  ENSRNOT00000100697 ENTREZGENE
  ENSRNOT00000100697.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1510.10 UniProtKB/TrEMBL
  3.90.530.10 UniProtKB/TrEMBL
InterPro Cation_efflux UniProtKB/TrEMBL
  Cation_efflux_TMD UniProtKB/TrEMBL
  DNA-bd_dom_put UniProtKB/TrEMBL
  SLC30A9 UniProtKB/TrEMBL
  XPA_C_sf UniProtKB/TrEMBL
KEGG Report rno:498358 UniProtKB/TrEMBL
NCBI Gene 498358 ENTREZGENE
PANTHER PTHR13414 UniProtKB/TrEMBL
  ZINC TRANSPORTER 9 UniProtKB/TrEMBL
Pfam Cation_efflux UniProtKB/TrEMBL
PhenoGen Slc30a9 PhenoGen
RatGTEx ENSRNOG00000002246 RatGTEx
Superfamily-SCOP Putativ_DNA_bind UniProtKB/TrEMBL
  SSF161111 UniProtKB/TrEMBL
UniProt A0A8I5ZUD8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AXK2_RAT UniProtKB/TrEMBL
  A6JDA5 ENTREZGENE, UniProtKB/TrEMBL
  D3ZWW5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-24 Slc30a9  solute carrier family 30 member 9  Slc30a9  solute carrier family 30 (zinc transporter), member 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Slc30a9  solute carrier family 30 (zinc transporter), member 9  LOC498358  similar to solute carrier family 30 (zinc transporter), member 9  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC498358  similar to solute carrier family 30 (zinc transporter), member 9      Symbol and Name status set to provisional 70820 PROVISIONAL