Slc39a2 (solute carrier family 39 member 2) - Rat Genome Database

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Gene: Slc39a2 (solute carrier family 39 member 2) Rattus norvegicus
Analyze
Symbol: Slc39a2
Name: solute carrier family 39 member 2
RGD ID: 1306291
Description: Predicted to enable zinc ion transmembrane transporter activity. Predicted to be involved in zinc ion transmembrane transport. Predicted to act upstream of or within zinc ion transport. Predicted to be located in cytoplasmic ribonucleoprotein granule and cytoplasmic vesicle. Predicted to be active in plasma membrane. Orthologous to human SLC39A2 (solute carrier family 39 member 2); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC305846; solute carrier family 39 (zinc transporter), member 2; zinc transporter ZIP2
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
mRatBN7.21524,590,738 - 24,592,850 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1524,590,738 - 24,592,850 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1527,361,775 - 27,363,891 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01528,317,522 - 28,319,634 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01526,570,466 - 26,572,578 (+)NCBIRnor_WKY
Rnor_6.01528,295,044 - 28,297,688 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1528,295,368 - 28,297,684 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01532,108,556 - 32,110,668 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41527,328,308 - 27,330,420 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11527,344,131 - 27,345,845 (+)NCBI
Celera1524,896,195 - 24,898,307 (+)NCBICelera
Cytogenetic Map15p14NCBI
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

Biological Process

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14525987   PMID:14612438   PMID:18346199   PMID:20148757  


Genomics

Comparative Map Data
Slc39a2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21524,590,738 - 24,592,850 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1524,590,738 - 24,592,850 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1527,361,775 - 27,363,891 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01528,317,522 - 28,319,634 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01526,570,466 - 26,572,578 (+)NCBIRnor_WKY
Rnor_6.01528,295,044 - 28,297,688 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1528,295,368 - 28,297,684 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01532,108,556 - 32,110,668 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41527,328,308 - 27,330,420 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11527,344,131 - 27,345,845 (+)NCBI
Celera1524,896,195 - 24,898,307 (+)NCBICelera
Cytogenetic Map15p14NCBI
SLC39A2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381420,999,293 - 21,001,871 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1420,999,255 - 21,001,871 (+)EnsemblGRCh38hg38GRCh38
GRCh371421,467,452 - 21,470,030 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361420,537,259 - 20,539,870 (+)NCBINCBI36Build 36hg18NCBI36
Build 341420,537,309 - 20,539,870NCBI
Celera141,328,279 - 1,330,899 (+)NCBICelera
Cytogenetic Map14q11.2NCBI
HuRef141,588,520 - 1,591,140 (+)NCBIHuRef
CHM1_11421,469,515 - 21,472,135 (+)NCBICHM1_1
T2T-CHM13v2.01415,196,693 - 15,199,271 (+)NCBIT2T-CHM13v2.0
Slc39a2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391452,130,539 - 52,134,202 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1452,130,346 - 52,134,202 (+)EnsemblGRCm39 Ensembl
GRCm381451,893,082 - 51,896,745 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1451,892,889 - 51,896,745 (+)EnsemblGRCm38mm10GRCm38
MGSCv371452,513,285 - 52,516,420 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361450,815,559 - 50,818,696 (+)NCBIMGSCv36mm8
Celera1448,878,496 - 48,881,630 (+)NCBICelera
Cytogenetic Map14C2NCBI
Slc39a2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555501,762,907 - 1,765,254 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555501,762,905 - 1,765,254 (+)NCBIChiLan1.0ChiLan1.0
SLC39A2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11419,896,112 - 19,898,728 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1419,896,112 - 19,898,728 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0141,813,992 - 1,818,226 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SLC39A2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11518,099,310 - 18,102,884 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1518,100,785 - 18,102,896 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1518,584,806 - 18,588,423 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01518,360,111 - 18,363,728 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1518,361,630 - 18,363,726 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11518,041,468 - 18,045,085 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01518,097,460 - 18,101,077 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01518,225,334 - 18,228,951 (+)NCBIUU_Cfam_GSD_1.0
Slc39a2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440864032,298,786 - 32,302,504 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936880209,738 - 211,531 (+)EnsemblSpeTri2.0
SpeTri2.0NW_004936880207,810 - 211,876 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC39A2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl778,129,237 - 78,131,819 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1778,127,628 - 78,132,900 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SLC39A2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12921,472,627 - 21,475,549 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2921,473,123 - 21,475,252 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605924,960,605 - 24,963,604 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc39a2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248256,999,039 - 7,002,141 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248256,996,864 - 7,011,917 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slc39a2
3 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:226
Count of miRNA genes:157
Interacting mature miRNAs:176
Transcripts:ENSRNOT00000013786
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
1354657Despr13Despair related QTL 130.0022locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)15129912054Rat
8552920Pigfal8Plasma insulin-like growth factor 1 level QTL 83blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)15134723002Rat
8694361Abfw6Abdominal fat weight QTL 610.20.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)15134723002Rat
9589149Insul29Insulin level QTL 299.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)15134723002Rat
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
5685002Bss103Bone structure and strength QTL 1032.8tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)151448116528469888Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
631550Bw7Body weight QTL 73.6body mass (VT:0001259)body weight (CMO:0000012)151985656634924750Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat

Markers in Region
RH138780  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21524,592,156 - 24,592,631 (+)MAPPERmRatBN7.2
Rnor_6.01528,296,995 - 28,297,469NCBIRnor6.0
Rnor_5.01532,109,975 - 32,110,449UniSTSRnor5.0
RGSC_v3.41527,329,727 - 27,330,201UniSTSRGSC3.4
Celera1524,897,614 - 24,898,088UniSTS
Cytogenetic Map15p14UniSTS
UniSTS:547105  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21524,592,388 - 24,593,318 (+)MAPPERmRatBN7.2
Rnor_6.01528,297,227 - 28,298,156NCBIRnor6.0
Rnor_5.01532,110,207 - 32,111,136UniSTSRnor5.0
Celera1524,897,846 - 24,898,775UniSTS
Cytogenetic Map15p14UniSTS


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

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 8
Low 41 2 7 7 3
Below cutoff 10 4 8 4 6 7 61 22 17 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000013786   ⟹   ENSRNOP00000013786
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1524,590,738 - 24,592,850 (+)Ensembl
Rnor_6.0 Ensembl1528,295,368 - 28,297,684 (+)Ensembl
RefSeq Acc Id: NM_001107260   ⟹   NP_001100730
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21524,590,738 - 24,592,850 (+)NCBI
Rnor_6.01528,295,576 - 28,297,688 (+)NCBI
Rnor_5.01532,108,556 - 32,110,668 (+)NCBI
RGSC_v3.41527,328,308 - 27,330,420 (+)RGD
Celera1524,896,195 - 24,898,307 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001100730 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL88446 (Get FASTA)   NCBI Sequence Viewer  
  EDL88447 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100730   ⟸   NM_001107260
- UniProtKB: D3ZIN1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000013786   ⟸   ENSRNOT00000013786

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZIN1-F1-model_v2 AlphaFold D3ZIN1 1-309 view protein structure

Transcriptome

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

Promoters
RGD ID:13699631
Promoter ID:EPDNEW_R10155
Type:single initiation site
Name:Slc39a2_1
Description:solute carrier family 39 member 2
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_6.01528,295,426 - 28,295,486EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306291 AgrOrtholog
BioCyc Gene G2FUF-14003 BioCyc
Ensembl Genes ENSRNOG00000010375 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000013786 ENTREZGENE
  ENSRNOP00000013786.5 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000013786 ENTREZGENE
  ENSRNOT00000013786.7 UniProtKB/TrEMBL
InterPro ZIP UniProtKB/TrEMBL
KEGG Report rno:305846 UniProtKB/TrEMBL
NCBI Gene 305846 ENTREZGENE
Pfam Zip UniProtKB/TrEMBL
PhenoGen Slc39a2 PhenoGen
UniProt D3ZIN1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-24 Slc39a2  solute carrier family 39 member 2  Slc39a2  solute carrier family 39 (zinc transporter), member 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Slc39a2  solute carrier family 39 (zinc transporter), member 2   Slc39a2_predicted  solute carrier family 39 (zinc transporter), member 2 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Slc39a2_predicted  solute carrier family 39 (zinc transporter), member 2 (predicted)      Symbol and Name status set to approved 70820 APPROVED