Slc40a1 (solute carrier family 40 member 1) - Rat Genome Database
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Gene: Slc40a1 (solute carrier family 40 member 1) Rattus norvegicus
Analyze
Symbol: Slc40a1
Name: solute carrier family 40 member 1
RGD ID: 620180
Description: Predicted to have ferrous iron transmembrane transporter activity; identical protein binding activity; and peptide hormone binding activity. Predicted to be involved in several processes, including iron ion export across plasma membrane; iron ion homeostasis; and regulation of transcription by RNA polymerase II. Predicted to localize to several cellular components, including basolateral plasma membrane; nucleoplasm; and synaptic vesicle. Human ortholog(s) of this gene implicated in hemochromatosis type 4. Orthologous to human SLC40A1 (solute carrier family 40 member 1); PARTICIPATES IN iron efflux pathway; INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: CAR1; cell adhesion regulator; ferroportin 1; ferroportin-1; Fpn1; Slc11a3; Slc39a1; solute carrier family 39 (iron-regulated transporter), member 1; solute carrier family 40 (iron-regulated transporter), member 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
NCBI Annotation Information: Annotation category: partial on reference assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0952,819,451 - 52,830,461 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl952,894,365 - 52,912,293 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0952,560,116 - 52,579,079 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4944,977,430 - 44,995,358 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1944,979,984 - 44,996,778 (-)NCBI
Celera945,700,875 - 45,718,803 (-)NCBICelera
Cytogenetic Map9q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
1,2-dimethylhydrazine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-acetamidofluorene  (EXP)
2-tert-butylhydroquinone  (ISO)
3,3',4,4',5-pentachlorobiphenyl  (EXP,ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,4-dihydroxybenzoate  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-tert-Octylphenol  (EXP)
5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole  (ISO)
acetamide  (EXP)
acrylamide  (EXP)
actinomycin D  (ISO)
aflatoxin B1  (ISO)
alcohol  (ISO)
all-trans-retinoic acid  (EXP,ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
apocynin  (ISO)
Aroclor 1254  (EXP)
arsenous acid  (ISO)
azathioprine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
busulfan  (ISO)
buta-1,3-diene  (ISO)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
chloroprene  (ISO)
chlorpyrifos  (ISO)
chromium(6+)  (EXP,ISO)
ciguatoxin CTX1B  (ISO)
cisplatin  (ISO)
cobalt atom  (ISO)
cobalt dichloride  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) sulfate  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
cytarabine  (ISO)
desferrioxamine B  (ISO)
dexamethasone  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
diazinon  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
diethyl maleate  (ISO)
diethylstilbestrol  (EXP)
diquat  (EXP)
dorsomorphin  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
ethanol  (ISO)
ferric ammonium citrate  (EXP,ISO)
flutamide  (EXP)
folic acid  (ISO)
gadolinium trichloride  (EXP)
Gastrodin  (ISO)
glycidol  (EXP)
hexane  (ISO)
hypochlorous acid  (ISO)
indometacin  (ISO)
iron atom  (EXP,ISO)
iron(0)  (EXP,ISO)
iron(2+) sulfate (anhydrous)  (ISO)
iron(III) nitrilotriacetate  (ISO)
isoprenaline  (ISO)
L-glutamic acid  (ISO)
lamivudine  (ISO)
lead diacetate  (EXP,ISO)
lipopolysaccharide  (ISO)
maneb  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (EXP)
mercury dibromide  (ISO)
mercury dichloride  (EXP)
methamphetamine  (EXP)
methapyrilene  (ISO)
methimazole  (EXP)
methylmercury chloride  (ISO)
mithramycin  (EXP)
N-acetyl-L-cysteine  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
naphthalene  (EXP)
nefazodone  (EXP)
nickel atom  (ISO)
nickel dichloride  (EXP)
nickel sulfate  (ISO)
nitric oxide  (EXP)
omeprazole  (ISO)
oxidopamine  (EXP,ISO)
p-chloromercuribenzoic acid  (ISO)
p-tert-Amylphenol  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
paraquat  (ISO)
pentachlorophenol  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctanoic acid  (EXP)
permethrin  (EXP)
phenacetin  (EXP)
phenobarbital  (ISO)
phenylhydrazine  (EXP)
phenylmercury acetate  (ISO)
phorone  (EXP)
pirinixic acid  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
quercetin  (EXP,ISO)
reactive oxygen species  (ISO)
rotenone  (EXP)
SB 431542  (ISO)
SCH 23390  (EXP)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
succimer  (ISO)
sulforaphane  (ISO)
tamoxifen  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
titanium dioxide  (ISO)
toluene  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
tunicamycin  (ISO)
valproic acid  (ISO)
zidovudine  (ISO)
zinc atom  (EXP,ISO)
zinc(0)  (EXP,ISO)
zoledronic acid  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:8889548   PMID:10477520   PMID:10828623   PMID:12091367   PMID:12431995   PMID:14972659   PMID:15084469   PMID:15114483   PMID:15342464   PMID:15514116   PMID:15888661   PMID:15944915  
PMID:16081696   PMID:17383861   PMID:17561842   PMID:18189270   PMID:18839536   PMID:18974313   PMID:19234114   PMID:19252488   PMID:19596281   PMID:19766498   PMID:19913091   PMID:20007457  
PMID:20019163   PMID:20530874   PMID:20564203   PMID:21473866   PMID:21570398   PMID:21700773   PMID:21785164   PMID:22469696   PMID:22659129   PMID:22682227   PMID:23395172   PMID:23506423  
PMID:24174620   PMID:25115800   PMID:25318588   PMID:25745840   PMID:26617777   PMID:26788496   PMID:28273797   PMID:29757912   PMID:30027341  


Genomics

Comparative Map Data
Slc40a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0952,819,451 - 52,830,461 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl952,894,365 - 52,912,293 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0952,560,116 - 52,579,079 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4944,977,430 - 44,995,358 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1944,979,984 - 44,996,778 (-)NCBI
Celera945,700,875 - 45,718,803 (-)NCBICelera
Cytogenetic Map9q22NCBI
SLC40A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2189,560,579 - 189,583,758 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl2189,560,590 - 189,583,758 (-)EnsemblGRCh38hg38GRCh38
GRCh382189,560,590 - 189,580,811 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372190,425,316 - 190,448,478 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362190,133,561 - 190,153,858 (-)NCBINCBI36hg18NCBI36
Build 342190,250,823 - 190,271,119NCBI
Celera2184,020,234 - 184,040,455 (-)NCBI
Cytogenetic Map2q32.2NCBI
HuRef2182,284,805 - 182,305,032 (-)NCBIHuRef
CHM1_12190,431,102 - 190,451,326 (-)NCBICHM1_1
Slc40a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39145,947,230 - 45,965,690 (-)NCBIGRCm39mm39
GRCm38145,908,070 - 45,926,532 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl145,908,068 - 45,926,523 (-)EnsemblGRCm38mm10GRCm38
MGSCv37145,964,915 - 45,982,439 (-)NCBIGRCm37mm9NCBIm37
MGSCv36145,852,630 - 45,870,079 (-)NCBImm8
Celera146,240,344 - 46,257,933 (-)NCBICelera
Cytogenetic Map1C1.1NCBI
Slc40a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554039,253,734 - 9,271,916 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554039,253,734 - 9,271,732 (+)NCBIChiLan1.0ChiLan1.0
SLC40A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B194,787,575 - 194,808,129 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B194,787,575 - 194,810,993 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B76,867,908 - 76,888,403 (-)NCBIMhudiblu_PPA_v0panPan3
SLC40A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl37303,104 - 368,865 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.137308,054 - 329,037 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Slc40a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365068,396,593 - 8,415,069 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC40A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1594,140,725 - 94,168,210 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11594,140,635 - 94,161,793 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215105,177,377 - 105,198,528 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SLC40A1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11075,076,286 - 75,097,742 (-)NCBI
ChlSab1.1 Ensembl1075,075,971 - 75,096,271 (-)Ensembl
Slc40a1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_004624899685,166 - 701,725 (+)NCBI

Position Markers
D9Rat60  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0952,896,774 - 52,896,896NCBIRnor6.0
Rnor_6.0952,821,860 - 52,821,982NCBIRnor6.0
Rnor_5.0952,487,676 - 52,487,798UniSTSRnor5.0
Rnor_5.0952,562,590 - 52,562,712UniSTSRnor5.0
RGSC_v3.4944,979,838 - 44,979,961RGDRGSC3.4
RGSC_v3.4944,979,839 - 44,979,961UniSTSRGSC3.4
RGSC_v3.1944,981,242 - 44,981,612RGD
Celera945,703,284 - 45,703,406UniSTS
Cytogenetic Map9q22UniSTS
SHRSP x BN Map941.0698UniSTS
SHRSP x BN Map941.0698RGD
FHH x ACI Map932.43RGD
RH129386  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0952,819,793 - 52,819,989NCBIRnor6.0
Rnor_6.0952,894,707 - 52,894,903NCBIRnor6.0
Rnor_5.0952,560,523 - 52,560,719UniSTSRnor5.0
Rnor_5.0952,485,609 - 52,485,805UniSTSRnor5.0
RGSC_v3.4944,977,772 - 44,977,968UniSTSRGSC3.4
Celera945,701,217 - 45,701,413UniSTS
Cytogenetic Map9q22UniSTS
RH136898  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0952,895,546 - 52,895,725NCBIRnor6.0
Rnor_6.0952,820,632 - 52,820,811NCBIRnor6.0
Rnor_5.0952,561,362 - 52,561,541UniSTSRnor5.0
Rnor_5.0952,486,448 - 52,486,627UniSTSRnor5.0
RGSC_v3.4944,978,611 - 44,978,790UniSTSRGSC3.4
Celera945,702,056 - 45,702,235UniSTS
Cytogenetic Map9q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)91221677157216771Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)91242546357425463Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)91242546357425463Rat
631680Cm11Cardiac mass QTL 113.10.00089heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)92488509969885099Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92569234292741406Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)92569237370692373Rat
1598823Memor16Memory QTL 161.9exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)92575432054885226Rat
7207805Bmd88Bone mineral density QTL 884femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)92748603663264281Rat
1300180Bw14Body weight QTL 143.776body mass (VT:0001259)body weight (CMO:0000012)92748603666757620Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92748615588333183Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92907507983686404Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)929466970107878528Rat
1641894Alcrsp12Alcohol response QTL 12response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)93238513377385133Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93764235182642351Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93764235182642351Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)94126103490024806Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94126103498606834Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)941261034102531865Rat
6903941Pur31Proteinuria QTL 310.036total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)94657976991579769Rat
11353949Bp393Blood pressure QTL 393arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94657976991579769Rat
61352Bp34Blood pressure QTL 345arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)94695242783686153Rat
10058949Gmadr5Adrenal mass QTL 520.014adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)94724896594124663Rat
6903937Bp356Blood pressure QTL 3560.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)95268687457216771Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:464
Count of miRNA genes:237
Interacting mature miRNAs:285
Transcripts:ENSRNOT00000005228, ENSRNOT00000073557
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 1 2 37 37 11 37 34 21 1
Low 2 41 20 4 8 4 8 11 74 1 20 10 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000005228   ⟹   ENSRNOP00000005228
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl952,894,365 - 52,912,293 (-)Ensembl
RefSeq Acc Id: NM_133315   ⟹   NP_579849
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0952,819,451 - 52,830,461 (-)NCBI
Rnor_5.0952,560,116 - 52,579,079 (-)NCBI
RGSC_v3.4944,977,430 - 44,995,358 (-)RGD
Celera945,700,875 - 45,718,803 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_579849 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAD00260 (Get FASTA)   NCBI Sequence Viewer  
  AAK77858 (Get FASTA)   NCBI Sequence Viewer  
  EDL99122 (Get FASTA)   NCBI Sequence Viewer  
  Q923U9 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_579849   ⟸   NM_133315
- UniProtKB: Q923U9 (UniProtKB/Swiss-Prot),   G3V6H7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000005228   ⟸   ENSRNOT00000005228

Transcriptome

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


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)
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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
COP/CrCrl (MCW & UW)
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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)
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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
F344/NRrrc (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
FHH/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)
FHH/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
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:620180 AgrOrtholog
Ensembl Genes ENSRNOG00000003872 Ensembl, UniProtKB/TrEMBL
  ENSRNOG00000049995 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000005228 UniProtKB/TrEMBL
  ENSRNOP00000064964 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000005228 UniProtKB/TrEMBL
  ENSRNOT00000073557 ENTREZGENE, UniProtKB/TrEMBL
InterPro Ferroportin-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  MFS_trans_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:108348131 UniProtKB/TrEMBL
  rno:170840 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 170840 ENTREZGENE
PANTHER PTHR11660 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam FPN1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc40a1 PhenoGen
Superfamily-SCOP SSF103473 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.15324 ENTREZGENE
UniProt G3V6H7 ENTREZGENE, UniProtKB/TrEMBL
  M0R6B7_RAT UniProtKB/TrEMBL
  Q923U9 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q9Z1C9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-03-09 Slc40a1  solute carrier family 40 member 1  Slc40a1  solute carrier family 40 (iron-regulated transporter), member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-16 Slc40a1  solute carrier family 40 (iron-regulated transporter), member 1  Slc40a1  solute carrier family 39 (iron-regulated transporter), member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Slc40a1  solute carrier family 39 (iron-regulated transporter), member 1  Slc39a1    Symbol and Name updated 1299863 APPROVED
2002-08-07 Slc39a1  solute carrier family 39 (iron-regulated transporter), member 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in many specific regions of the brain 634086
gene_regulation expression downregulated by hepcidin in an LPS-induced manner 1304454