Slc39a5 (solute carrier family 39 member 5) - Rat Genome Database

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Gene: Slc39a5 (solute carrier family 39 member 5) Rattus norvegicus
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Symbol: Slc39a5
Name: solute carrier family 39 member 5
RGD ID: 1310322
Description: Predicted to enable zinc ion transmembrane transporter activity. Predicted to be involved in several processes, including BMP signaling pathway; intracellular zinc ion homeostasis; and zinc ion import across plasma membrane. Predicted to act upstream of or within cellular response to zinc ion starvation and positive regulation of mRNA splicing, via spliceosome. Predicted to be located in basolateral plasma membrane. Predicted to be active in plasma membrane. Human ortholog(s) of this gene implicated in myopia. Orthologous to human SLC39A5 (solute carrier family 39 member 5); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC362812; solute carrier family 39 (metal ion transporter), member 5; solute carrier family 39 (zinc transporter), member 5; zinc transporter ZIP5
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
mRatBN7.27822,873 - 830,865 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7824,818 - 830,242 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx73,586,578 - 3,591,992 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.075,462,559 - 5,467,973 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.075,760,340 - 5,765,764 (-)NCBIRnor_WKY
Rnor_6.072,813,875 - 2,819,917 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl72,813,875 - 2,819,299 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.072,792,038 - 2,798,370 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.471,686,969 - 1,692,393 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.171,687,705 - 1,692,002 (-)NCBI
Celera7698,310 - 703,734 (-)NCBICelera
Cytogenetic Map7q11NCBI
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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
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
Additional References at PubMed
PMID:15358787   PMID:19056867   PMID:23636947   PMID:24891338  


Genomics

Comparative Map Data
Slc39a5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27822,873 - 830,865 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7824,818 - 830,242 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx73,586,578 - 3,591,992 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.075,462,559 - 5,467,973 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.075,760,340 - 5,765,764 (-)NCBIRnor_WKY
Rnor_6.072,813,875 - 2,819,917 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl72,813,875 - 2,819,299 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.072,792,038 - 2,798,370 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.471,686,969 - 1,692,393 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.171,687,705 - 1,692,002 (-)NCBI
Celera7698,310 - 703,734 (-)NCBICelera
Cytogenetic Map7q11NCBI
SLC39A5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381256,230,051 - 56,237,846 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1256,230,049 - 56,237,846 (+)EnsemblGRCh38hg38GRCh38
GRCh371256,623,835 - 56,631,630 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361254,910,894 - 54,917,897 (+)NCBINCBI36Build 36hg18NCBI36
Build 341254,910,893 - 54,917,894NCBI
Celera1256,276,713 - 56,284,524 (+)NCBICelera
Cytogenetic Map12q13.3NCBI
HuRef1253,662,814 - 53,670,623 (+)NCBIHuRef
CHM1_11256,591,211 - 56,599,021 (+)NCBICHM1_1
T2T-CHM13v2.01256,197,676 - 56,205,471 (+)NCBIT2T-CHM13v2.0
Slc39a5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3910128,231,796 - 128,237,145 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl10128,231,800 - 128,237,098 (-)EnsemblGRCm39 Ensembl
GRCm3810128,395,927 - 128,401,276 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl10128,395,931 - 128,401,229 (-)EnsemblGRCm38mm10GRCm38
MGSCv3710127,832,987 - 127,838,280 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3610127,798,883 - 127,803,466 (-)NCBIMGSCv36mm8
Celera10130,784,187 - 130,789,483 (-)NCBICelera
Cytogenetic Map10D3NCBI
Slc39a5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554583,843,112 - 3,849,794 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554583,843,492 - 3,849,794 (+)NCBIChiLan1.0ChiLan1.0
SLC39A5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11232,929,033 - 32,936,826 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1232,929,033 - 32,936,158 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01232,677,330 - 32,685,316 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SLC39A5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.110552,755 - 557,319 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha10616,158 - 620,678 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.010561,381 - 565,902 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl10561,346 - 565,860 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.110538,832 - 543,351 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.010780,614 - 786,334 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.010905,885 - 910,417 (+)NCBIUU_Cfam_GSD_1.0
Slc39a5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494558,224,501 - 58,231,208 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936646640,253 - 645,617 (+)EnsemblSpeTri2.0
SpeTri2.0NW_004936646638,956 - 649,501 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC39A5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl521,631,924 - 21,637,646 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1521,631,874 - 21,640,476 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2523,030,339 - 23,036,253 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC39A5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11152,183,305 - 52,192,469 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1152,184,617 - 52,191,764 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037193,794,536 - 193,802,090 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Slc39a5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462480211,767,713 - 11,774,075 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462480211,767,713 - 11,774,074 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Slc39a5
17 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:224
Count of miRNA genes:146
Interacting mature miRNAs:167
Transcripts:ENSRNOT00000045547
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
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat

Markers in Region
RH139678  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map7q11UniSTS
RH140104  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27831,102 - 831,291 (+)MAPPERmRatBN7.2
Rnor_6.072,820,160 - 2,820,348NCBIRnor6.0
Rnor_5.072,798,624 - 2,798,812UniSTSRnor5.0
RGSC_v3.471,693,254 - 1,693,442UniSTSRGSC3.4
Celera7704,595 - 704,783UniSTS
Cytogenetic Map7q11UniSTS


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 29 29 2 29 2 29 1
Low 37 28 12 17 12 8 11 48 6 39 10 8
Below cutoff 6 24 2

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001108728 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006240760 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006240761 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006240762 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006240763 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006240764 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006240766 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006240767 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765027 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008765028 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079366 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079367 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079368 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079369 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039079370 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005486653 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005486654 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH474104 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ220010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000171 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000045547   ⟹   ENSRNOP00000042922
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7824,818 - 830,242 (-)Ensembl
Rnor_6.0 Ensembl72,813,875 - 2,819,299 (-)Ensembl
RefSeq Acc Id: NM_001108728   ⟹   NP_001102198
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27824,818 - 830,242 (-)NCBI
Rnor_6.072,813,875 - 2,819,299 (-)NCBI
Rnor_5.072,792,038 - 2,798,370 (-)NCBI
RGSC_v3.471,686,969 - 1,692,393 (-)RGD
Celera7698,310 - 703,734 (-)RGD
Sequence:
RefSeq Acc Id: XM_039079366   ⟹   XP_038935294
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27822,873 - 830,865 (-)NCBI
RefSeq Acc Id: XM_039079367   ⟹   XP_038935295
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27822,873 - 830,795 (-)NCBI
RefSeq Acc Id: XM_039079368   ⟹   XP_038935296
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27822,873 - 830,865 (-)NCBI
RefSeq Acc Id: XM_039079369   ⟹   XP_038935297
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27826,150 - 830,795 (-)NCBI
RefSeq Acc Id: XM_039079370   ⟹   XP_038935298
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27822,873 - 829,634 (-)NCBI
RefSeq Acc Id: XR_005486653
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27825,679 - 830,795 (-)NCBI
RefSeq Acc Id: XR_005486654
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27826,805 - 830,795 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001102198   ⟸   NM_001108728
- Peptide Label: precursor
- UniProtKB: D3ZSF7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000042922   ⟸   ENSRNOT00000045547
RefSeq Acc Id: XP_038935296   ⟸   XM_039079368
- Peptide Label: isoform X1
- UniProtKB: D3ZSF7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038935294   ⟸   XM_039079366
- Peptide Label: isoform X1
- UniProtKB: D3ZSF7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038935295   ⟸   XM_039079367
- Peptide Label: isoform X1
- UniProtKB: D3ZSF7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038935298   ⟸   XM_039079370
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038935297   ⟸   XM_039079369
- Peptide Label: isoform X2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZSF7-F1-model_v2 AlphaFold D3ZSF7 1-533 view protein structure

Transcriptome

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

Promoters
RGD ID:13694935
Promoter ID:EPDNEW_R5460
Type:single initiation site
Name:Slc39a5_1
Description:solute carrier family 39 member 5
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_6.072,819,327 - 2,819,387EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310322 AgrOrtholog
BioCyc Gene G2FUF-35373 BioCyc
Ensembl Genes ENSRNOG00000033361 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000042922 ENTREZGENE
  ENSRNOP00000042922.4 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000045547 ENTREZGENE
  ENSRNOT00000045547.5 UniProtKB/TrEMBL
InterPro ZIP UniProtKB/TrEMBL
KEGG Report rno:362812 UniProtKB/TrEMBL
NCBI Gene 362812 ENTREZGENE
Pfam Zip UniProtKB/TrEMBL
PhenoGen Slc39a5 PhenoGen
UniProt D3ZSF7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-24 Slc39a5  solute carrier family 39 member 5  Slc39a5  solute carrier family 39 (zinc transporter), member 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-02 Slc39a5  solute carrier family 39 (zinc transporter), member 5  Slc39a5  solute carrier family 39 (metal ion transporter), member 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Slc39a5  solute carrier family 39 (metal ion transporter), member 5   Slc39a5_predicted  solute carrier family 39 (metal ion transporter), member 5 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Slc39a5_predicted  solute carrier family 39 (metal ion transporter), member 5 (predicted)      Symbol and Name status set to approved 70820 APPROVED