Slc39a4 (solute carrier family 39 member 4) - Rat Genome Database
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Gene: Slc39a4 (solute carrier family 39 member 4) Rattus norvegicus
Analyze
Symbol: Slc39a4
Name: solute carrier family 39 member 4
RGD ID: 1306701
Description: Predicted to have zinc ion transmembrane transporter activity. Predicted to be involved in cellular response to zinc ion starvation; cellular zinc ion homeostasis; and zinc ion import across plasma membrane. Predicted to localize to apical plasma membrane; endosome; and integral component of plasma membrane. Human ortholog(s) of this gene implicated in acrodermatitis enteropathica. Orthologous to human SLC39A4 (solute carrier family 39 member 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC300051; MGC156705; solute carrier family 39 (zinc transporter), member 4; zinc transporter ZIP4; ZIP-4; zrt- and Irt-like protein 4
Orthologs:
Homo sapiens (human) : SLC39A4 (solute carrier family 39 member 4)  HGNC  Alliance
Mus musculus (house mouse) : Slc39a4 (solute carrier family 39 (zinc transporter), member 4)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Slc39a4 (solute carrier family 39 member 4)
Pan paniscus (bonobo/pygmy chimpanzee) : SLC39A4 (solute carrier family 39 member 4)
Canis lupus familiaris (dog) : SLC39A4 (solute carrier family 39 member 4)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Slc39a4 (solute carrier family 39 member 4)
Sus scrofa (pig) : SLC39A4 (solute carrier family 39 member 4)
Chlorocebus sabaeus (African green monkey) : SLC39A4 (solute carrier family 39 member 4)
Heterocephalus glaber (naked mole-rat) : Slc39a4 (solute carrier family 39 member 4)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.07117,675,718 - 117,682,586 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7117,675,720 - 117,680,004 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07117,663,813 - 117,667,986 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47114,661,925 - 114,666,098 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17114,696,147 - 114,700,327 (-)NCBI
Celera7104,683,583 - 104,687,756 (-)NCBICelera
Cytogenetic Map7q34NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
actinomycin D  (ISO)
ammonium chloride  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
cadmium dichloride  (EXP)
calcitriol  (ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
cefaloridine  (EXP)
cisplatin  (ISO)
cobalt dichloride  (ISO)
coumestrol  (ISO)
cycloheximide  (ISO)
cyclosporin A  (ISO)
dextran sulfate  (ISO)
dibutyl phthalate  (EXP)
diethylstilbestrol  (ISO)
dioxygen  (ISO)
ethyl methanesulfonate  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
furan  (EXP)
genistein  (ISO)
hydrogen peroxide  (ISO)
indole-3-methanol  (EXP)
irinotecan  (EXP)
lead diacetate  (EXP)
leflunomide  (EXP)
methimazole  (EXP)
methyl beta-cyclodextrin  (ISO)
methyl methanesulfonate  (ISO)
N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-nitrosodiethylamine  (ISO)
nickel dichloride  (EXP)
nimesulide  (EXP)
oxycodone  (EXP)
phenobarbital  (EXP,ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
propiconazole  (ISO)
quercetin  (ISO)
rotenone  (EXP,ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sucrose  (ISO)
tetrachloromethane  (ISO)
titanium dioxide  (ISO)
triphenyl phosphate  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)
zinc atom  (ISO)
zinc dichloride  (EXP,ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:12801924   PMID:14612438   PMID:15358787   PMID:15489334   PMID:19530166   PMID:22242765   PMID:23013362   PMID:23376485   PMID:26702153  


Genomics

Comparative Map Data
Slc39a4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.07117,675,718 - 117,682,586 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7117,675,720 - 117,680,004 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07117,663,813 - 117,667,986 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47114,661,925 - 114,666,098 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.17114,696,147 - 114,700,327 (-)NCBI
Celera7104,683,583 - 104,687,756 (-)NCBICelera
Cytogenetic Map7q34NCBI
SLC39A4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl8144,409,742 - 144,416,895 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl8144,409,742 - 144,416,844 (-)EnsemblGRCh38hg38GRCh38
GRCh388144,412,414 - 144,417,146 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh378145,637,798 - 145,642,279 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 368145,608,606 - 145,613,081 (-)NCBINCBI36hg18NCBI36
Build 348145,608,606 - 145,613,081NCBI
Celera8141,812,232 - 141,816,707 (-)NCBI
Cytogenetic Map8q24.3NCBI
HuRef8140,751,031 - 140,755,512 (-)NCBIHuRef
CHM1_18145,676,089 - 145,680,570 (-)NCBICHM1_1
Slc39a4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391576,496,583 - 76,501,579 (-)NCBI
GRCm381576,612,383 - 76,618,506 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1576,612,383 - 76,617,384 (-)EnsemblGRCm38mm10GRCm38
MGSCv371576,442,813 - 76,447,282 (-)NCBIGRCm37mm9NCBIm37
MGSCv361576,439,638 - 76,444,107 (-)NCBImm8
Celera1578,105,998 - 78,110,467 (-)NCBICelera
Cytogenetic Map15D3NCBI
Slc39a4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554543,040,877 - 3,046,250 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554543,041,316 - 3,047,419 (-)NCBIChiLan1.0ChiLan1.0
SLC39A4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.18144,169,089 - 144,173,517 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl8144,169,089 - 144,173,517 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v08141,178,792 - 141,183,565 (-)NCBIMhudiblu_PPA_v0panPan3
SLC39A4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1337,833,156 - 37,838,522 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11337,833,073 - 37,838,304 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Slc39a4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364707,836,612 - 7,842,262 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC39A4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4372,660 - 378,516 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14372,681 - 378,519 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24464,005 - 469,123 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SLC39A4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl8138,622,224 - 138,626,376 (-)Ensembl
ChlSab1.18138,622,100 - 138,626,749 (-)NCBI
Slc39a4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473512,433,024 - 12,438,406 (+)NCBI

Position Markers
AU041686  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.07117,675,896 - 117,676,194NCBIRnor6.0
Rnor_5.07117,663,979 - 117,664,277UniSTSRnor5.0
RGSC_v3.47114,662,091 - 114,662,389UniSTSRGSC3.4
Celera7104,683,749 - 104,684,047UniSTS
Cytogenetic Map7q34UniSTS
RH131800  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.07117,675,727 - 117,675,906NCBIRnor6.0
Rnor_5.07117,663,810 - 117,663,989UniSTSRnor5.0
RGSC_v3.47114,661,922 - 114,662,101UniSTSRGSC3.4
Celera7104,683,580 - 104,683,759UniSTS
Cytogenetic Map7q34UniSTS
RH 3.4 Map7795.3UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)748118835128611831Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)750704769128085642Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)751251919118477612Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)751251919145729302Rat
2316947Rf58Renal function QTL 587.8kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)755072862123602998Rat
2316952Pur22Proteinuria QTL 225.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)755072862123602998Rat
2316955Stl24Serum triglyceride level QTL 247.1blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)755072862123602998Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)771448715145729302Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)777428105127748511Rat
1357338Stl17Serum triglyceride level QTL 173.23blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)777428234122421148Rat
634331Pia17Pristane induced arthritis QTL 174.7joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)781645773140745067Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)785595369130595369Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)785595369130595369Rat
631529Tls2T-lymphoma susceptibility QTL 200.001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)788365265119318087Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)788365265121986709Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)788365265133365265Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)788365265134673427Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)791018361136018361Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)791832949145158140Rat
71114Niddm14Non-insulin dependent diabetes mellitus QTL 144.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)793726906138726906Rat
2298475Eau6Experimental allergic uveoretinitis QTL 60.0029uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)793726906138726906Rat
1558655Swd4Spike wave discharge measurement QTL 43.680.0002brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge severity grade (CMO:0001988)796630946141630946Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)7100028953145729302Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)7100160423140335001Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)7100192194145192194Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)7103815550126525386Rat
1357336Gluco6Glucose level QTL 63.4blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)7103867802126080176Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)7106564316145729302Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7111519266143965591Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7112429186126525386Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7114825174145729302Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7115922628145729302Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:413
Count of miRNA genes:193
Interacting mature miRNAs:216
Transcripts:ENSRNOT00000040422, ENSRNOT00000071522
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.


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 15 15 15 9 11
Low 12 36 26 13 26 13 33 32
Below cutoff 26 6 6 8 10 61 2 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000040422   ⟹   ENSRNOP00000047376
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7117,675,720 - 117,680,004 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000071522   ⟹   ENSRNOP00000066561
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7117,676,948 - 117,679,219 (-)Ensembl
RefSeq Acc Id: NM_001077669   ⟹   NP_001071137
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07117,675,730 - 117,679,903 (-)NCBI
Rnor_5.07117,663,813 - 117,667,986 (-)NCBI
RGSC_v3.47114,661,925 - 114,666,098 (-)RGD
Celera7104,683,583 - 104,687,756 (-)RGD
Sequence:
RefSeq Acc Id: XM_008765563   ⟹   XP_008763785
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07117,675,718 - 117,682,586 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008765564   ⟹   XP_008763786
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.07117,675,718 - 117,682,048 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001071137   ⟸   NM_001077669
- Peptide Label: precursor
- UniProtKB: A0JPN2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008763785   ⟸   XM_008765563
- Peptide Label: isoform X1
- UniProtKB: A0A0H2UHY4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008763786   ⟸   XM_008765564
- Peptide Label: isoform X1
- UniProtKB: A0A0H2UHY4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000066561   ⟸   ENSRNOT00000071522
RefSeq Acc Id: ENSRNOP00000047376   ⟸   ENSRNOT00000040422
Protein Domains
ZIP4_domain

Transcriptome

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

Promoters
RGD ID:13695430
Promoter ID:EPDNEW_R5953
Type:multiple initiation site
Name:Slc39a4_1
Description:solute carrier family 39 member 4
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_6.07117,679,894 - 117,679,954EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306701 AgrOrtholog
Ensembl Genes ENSRNOG00000014314 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000047376 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000066561 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000040422 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000071522 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7100017 IMAGE-MGC_LOAD
InterPro ZIP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZIP4_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:300051 UniProtKB/Swiss-Prot
MGC_CLONE MGC:156705 IMAGE-MGC_LOAD
NCBI Gene 300051 ENTREZGENE
Pfam Zip UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZIP4_domain UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc39a4 PhenoGen
UniGene Rn.7960 ENTREZGENE
UniProt A0A0H2UHY4 ENTREZGENE, UniProtKB/TrEMBL
  A0JPN2 ENTREZGENE
  M0RAL0_RAT UniProtKB/TrEMBL
  S39A4_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-09 Slc39a4  solute carrier family 39 member 4  Slc39a4  solute carrier family 39 (zinc transporter), member 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Slc39a4  solute carrier family 39 (zinc transporter), member 4   Slc39a4_predicted  solute carrier family 39 (zinc transporter), member 4 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Slc39a4_predicted  solute carrier family 39 (zinc transporter), member 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED