Slc39a12 (solute carrier family 39 member 12) - Rat Genome Database

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Gene: Slc39a12 (solute carrier family 39 member 12) Rattus norvegicus
Analyze
Symbol: Slc39a12
Name: solute carrier family 39 member 12
RGD ID: 1309305
Description: Predicted to enable monoatomic cation:bicarbonate symporter activity and zinc ion transmembrane transporter activity. Involved in positive regulation of sprouting angiogenesis and response to decreased oxygen levels. Predicted to be located in perinuclear region of cytoplasm and plasma membrane. Orthologous to human SLC39A12 (solute carrier family 39 member 12); INTERACTS WITH 3-chloropropane-1,2-diol; bisphenol A; copper atom.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC291328; solute carrier family 39 (zinc transporter), member 12; zinc transporter ZIP12
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Slc39a12em77Tja  
Genetic Models: WKY-Slc39a12em77Tja-/- WKY-Slc39a12em77Tja+/- WKY-Slc39a12em77Tja
Candidate Gene For: Cm15
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81782,262,303 - 82,348,974 (+)NCBIGRCr8
mRatBN7.21777,353,761 - 77,440,384 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1777,353,805 - 77,440,353 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1780,811,544 - 80,890,227 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01784,646,963 - 84,725,647 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01778,694,864 - 78,773,553 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01781,455,731 - 81,541,742 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1781,455,955 - 81,541,759 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01783,202,775 - 83,288,616 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41788,525,527 - 88,605,947 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11788,513,119 - 88,616,376 (+)NCBI
Celera1776,696,501 - 76,773,017 (+)NCBICelera
Cytogenetic Map17q12.3NCBI
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

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
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
4. The zinc transporter ZIP12 regulates the pulmonary vascular response to chronic hypoxia. Zhao L, etal., Nature. 2015 Aug 20;524(7565):356-60. doi: 10.1038/nature14620. Epub 2015 Aug 10.
Additional References at PubMed
PMID:23716681   PMID:24769233   PMID:34347342   PMID:34635097   PMID:35346134  


Genomics

Comparative Map Data
Slc39a12
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81782,262,303 - 82,348,974 (+)NCBIGRCr8
mRatBN7.21777,353,761 - 77,440,384 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1777,353,805 - 77,440,353 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1780,811,544 - 80,890,227 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01784,646,963 - 84,725,647 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01778,694,864 - 78,773,553 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01781,455,731 - 81,541,742 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1781,455,955 - 81,541,759 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01783,202,775 - 83,288,616 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41788,525,527 - 88,605,947 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11788,513,119 - 88,616,376 (+)NCBI
Celera1776,696,501 - 76,773,017 (+)NCBICelera
Cytogenetic Map17q12.3NCBI
SLC39A12
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381017,951,918 - 18,043,285 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1017,951,839 - 18,043,292 (+)EnsemblGRCh38hg38GRCh38
GRCh371018,240,847 - 18,332,214 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361018,280,827 - 18,372,218 (+)NCBINCBI36Build 36hg18NCBI36
Build 341018,280,826 - 18,372,218NCBI
Celera1017,927,289 - 18,018,644 (+)NCBICelera
Cytogenetic Map10p12.33NCBI
HuRef1017,906,828 - 17,997,600 (+)NCBIHuRef
CHM1_11018,240,775 - 18,332,234 (+)NCBICHM1_1
T2T-CHM13v2.01017,971,349 - 18,062,603 (+)NCBIT2T-CHM13v2.0
Slc39a12
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39214,345,476 - 14,499,787 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl214,393,127 - 14,499,788 (+)EnsemblGRCm39 Ensembl
GRCm38214,388,316 - 14,494,977 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl214,388,316 - 14,494,977 (+)EnsemblGRCm38mm10GRCm38
MGSCv37214,310,025 - 14,416,604 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36214,306,158 - 14,412,731 (+)NCBIMGSCv36mm8
Celera214,289,501 - 14,395,951 (+)NCBICelera
Cytogenetic Map2A2NCBI
cM Map210.56NCBI
Slc39a12
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542910,052,968 - 10,116,727 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542910,053,022 - 10,116,713 (-)NCBIChiLan1.0ChiLan1.0
SLC39A12
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2830,795,318 - 30,888,370 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11030,800,639 - 30,893,691 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01018,270,652 - 18,362,558 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11018,540,473 - 18,699,305 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1018,541,859 - 18,698,851 (+)Ensemblpanpan1.1panPan2
SLC39A12
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1218,991,734 - 19,064,899 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl218,992,031 - 19,063,647 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha216,093,351 - 16,166,440 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0219,282,840 - 19,356,413 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl219,282,864 - 19,356,389 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1216,483,812 - 16,557,251 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0217,319,092 - 17,392,530 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0217,939,269 - 18,012,769 (-)NCBIUU_Cfam_GSD_1.0
Slc39a12
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934418,515,301 - 18,580,210 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365209,380,650 - 9,444,152 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365209,380,723 - 9,444,146 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC39A12
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1044,239,274 - 44,320,971 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11044,239,279 - 44,320,974 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21048,973,496 - 49,055,241 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLC39A12
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1917,887,821 - 17,970,593 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl917,888,748 - 17,970,580 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605123,536,156 - 23,618,931 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc39a12
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247969,940,176 - 10,008,234 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247969,940,228 - 10,008,526 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slc39a12
841 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:48
Count of miRNA genes:41
Interacting mature miRNAs:48
Transcripts:ENSRNOT00000044313
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354663Bvd5Brain ventricular dilatation QTL 53.510.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)173199078481292925Rat
2301412Kidm40Kidney mass QTL 400.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)173747984782479847Rat
2317054Aia12Adjuvant induced arthritis QTL 124.24joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)173828150983281509Rat
2317060Aia26Adjuvant induced arthritis QTL 263.22joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)173828150983281509Rat
1598871Memor5Memory QTL 55.3exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)174054004180387013Rat
1358295Aocep1Aortic cell protein QTL 16.10.00000071thoracic aorta cellular protein amount (VT:0010598)aortic cell percentage174099000585990005Rat
7411575Bw140Body weight QTL 14030.20.001body mass (VT:0001259)body weight gain (CMO:0000420)174856093586533673Rat
8694181Bw151Body weight QTL 1514.360.001body mass (VT:0001259)body weight gain (CMO:0000420)174856093586533673Rat
2317038Ginf3Gastrointestinal inflammation QTL 32.890.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)174992015486533673Rat
2303580Gluco49Glucose level QTL 492blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)175004027186533673Rat
4889894Eae33Experimental allergic encephalomyelitis QTL 335.20.0001nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)175090909986022412Rat
1354588Bvd4Brain ventricular dilatation QTL 45.310.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)175349882882479847Rat
2302365Gluco40Glucose level QTL 404.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)175724684382046127Rat
7488963Bp369Blood pressure QTL 3690.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)175900564977910000Rat
2317045Aia11Adjuvant induced arthritis QTL 114.06joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)176078142686533673Rat
7411577Bw141Body weight QTL 1410.001body mass (VT:0001259)body weight gain (CMO:0000420)176261951686533673Rat
631502Cm26Cardiac mass QTL 263.71heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)176570358081153923Rat
1300129Rf25Renal function QTL 253.03blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)177100332581153923Rat
12904736Cm121Cardiac mass QTL 1210.043heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)177177462182479847Rat


Genetic Models
This gene Slc39a12 is modified in the following models/strains:
WKY-Slc39a12em77Tja-/-     WKY-Slc39a12em77Tja+/-     WKY-Slc39a12em77Tja    


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

integumental system musculoskeletal system nervous system renal system reproductive system appendage
High
Medium 11
Low 63 8 2
Below cutoff 5 5 10 19 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000044313   ⟹   ENSRNOP00000042204
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1777,353,805 - 77,440,353 (+)Ensembl
Rnor_6.0 Ensembl1781,455,955 - 81,541,759 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000111559   ⟹   ENSRNOP00000083440
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1777,353,805 - 77,440,353 (+)Ensembl
RefSeq Acc Id: NM_001106124   ⟹   NP_001099594
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81782,262,357 - 82,348,974 (+)NCBI
mRatBN7.21777,353,815 - 77,440,384 (+)NCBI
Rnor_6.01781,465,380 - 81,541,721 (+)NCBI
Rnor_5.01783,202,775 - 83,288,616 (+)NCBI
RGSC_v3.41788,525,527 - 88,605,947 (+)RGD
Celera1776,696,501 - 76,773,017 (+)RGD
Sequence:
RefSeq Acc Id: XM_017600498   ⟹   XP_017455987
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81782,262,303 - 82,348,971 (+)NCBI
mRatBN7.21777,353,761 - 77,440,381 (+)NCBI
Rnor_6.01781,455,731 - 81,541,742 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039095559   ⟹   XP_038951487
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81782,262,303 - 82,348,551 (+)NCBI
mRatBN7.21777,353,761 - 77,439,960 (+)NCBI
RefSeq Acc Id: XM_039095560   ⟹   XP_038951488
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81782,262,303 - 82,348,971 (+)NCBI
mRatBN7.21777,353,761 - 77,439,960 (+)NCBI
RefSeq Acc Id: XM_039095561   ⟹   XP_038951489
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81782,275,864 - 82,348,551 (+)NCBI
mRatBN7.21777,367,322 - 77,439,960 (+)NCBI
RefSeq Acc Id: XR_005495258
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81782,262,303 - 82,320,788 (+)NCBI
mRatBN7.21777,353,761 - 77,412,240 (+)NCBI
RefSeq Acc Id: XR_005495259
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81782,262,303 - 82,320,788 (+)NCBI
mRatBN7.21777,353,761 - 77,412,240 (+)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001099594   ⟸   NM_001106124
- Peptide Label: precursor
- UniProtKB: D4A8R5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455987   ⟸   XM_017600498
- Peptide Label: isoform X3
- UniProtKB: A0A8I6A003 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000042204   ⟸   ENSRNOT00000044313
RefSeq Acc Id: XP_038951487   ⟸   XM_039095559
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038951488   ⟸   XM_039095560
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038951489   ⟸   XM_039095561
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000083440   ⟸   ENSRNOT00000111559
Protein Domains
Zinc transporter ZIP4 N-terminal   Zinc transporter ZIP4/12 EF-hand

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A8R5-F1-model_v2 AlphaFold D4A8R5 1-688 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:1309305 AgrOrtholog
BioCyc Gene G2FUF-8598 BioCyc
Ensembl Genes ENSRNOG00000025639 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000044313 ENTREZGENE
  ENSRNOT00000044313.6 UniProtKB/TrEMBL
  ENSRNOT00000111559.1 UniProtKB/TrEMBL
InterPro ZIP UniProtKB/TrEMBL
  ZIP4_12_EF-hand UniProtKB/TrEMBL
  ZIP4_N UniProtKB/TrEMBL
KEGG Report rno:291328 UniProtKB/TrEMBL
NCBI Gene 291328 ENTREZGENE
PANTHER SOLUTE CARRIER FAMILY 39 UniProtKB/TrEMBL
  ZINC TRANSPORTER ZIP12 UniProtKB/TrEMBL
Pfam EF-hand_Zip UniProtKB/TrEMBL
  Zip UniProtKB/TrEMBL
  ZIP4_domain UniProtKB/TrEMBL
PhenoGen Slc39a12 PhenoGen
RatGTEx ENSRNOG00000025639 RatGTEx
UniProt A0A8I6A003 ENTREZGENE, UniProtKB/TrEMBL
  A6JM58_RAT UniProtKB/TrEMBL
  D4A8R5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Slc39a12  solute carrier family 39 (zinc transporter), member 12   Slc39a12_predicted  solute carrier family 39 (zinc transporter), member 12 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Slc39a12_predicted  solute carrier family 39 (zinc transporter), member 12 (predicted)      Symbol and Name status set to approved 70820 APPROVED