Mt3 (metallothionein 3) - Rat Genome Database

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Gene: Mt3 (metallothionein 3) Rattus norvegicus
Analyze
Symbol: Mt3
Name: metallothionein 3
RGD ID: 621252
Description: Enables copper ion binding activity and zinc ion binding activity. Involved in brain development; negative regulation of hydrogen peroxide catabolic process; and negative regulation of neuron death. Located in several cellular components, including astrocyte end-foot; mitochondrial outer membrane; and synaptic vesicle. Used to study motor neuron disease. Biomarker of borna disease; cerebrovascular disease (multiple); hypothyroidism; median neuropathy; and visual epilepsy. Human ortholog(s) of this gene implicated in Alzheimer's disease. Orthologous to human MT3 (metallothionein 3); INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: GIF; growth inhibitory factor; metallothionein III; metallothionein-3; metallothionein-III; Mt-3; MT-III
RGD Orthologs
Human
Mouse
Bonobo
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21910,848,754 - 10,850,158 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1910,848,755 - 10,850,158 (-)Ensembl
Rnor_6.01911,324,708 - 11,326,112 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1911,324,698 - 11,326,139 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01911,300,014 - 11,301,422 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41911,284,554 - 11,286,402 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11911,289,380 - 11,291,228 (-)NCBI
Celera1910,734,686 - 10,736,090 (-)NCBICelera
Cytogenetic Map19p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-catechin  (ISO)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-estradiol  (EXP)
17beta-estradiol 3-benzoate  (EXP)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,7-dihydropurine-6-thione  (EXP)
4-hydroxyphenyl retinamide  (ISO)
4-tert-Octylphenol  (EXP)
5-aza-2'-deoxycytidine  (ISO)
6-aminonicotinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
7,8-dihydro-8-oxoguanine  (ISO)
alachlor  (EXP)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bifenthrin  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
cadmium atom  (EXP,ISO)
cadmium dichloride  (EXP,ISO)
cadmium sulfate  (ISO)
carbon nanotube  (EXP,ISO)
chlordecone  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
cobalt atom  (ISO)
cobalt dichloride  (EXP)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
D-glucose  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
dichromium trioxide  (ISO)
diethylstilbestrol  (EXP)
dioxygen  (EXP,ISO)
disulfiram  (ISO)
dithionitrobenzoic acid  (ISO)
doxorubicin  (ISO)
elemental selenium  (EXP)
entinostat  (ISO)
ethanol  (ISO)
ethylenediaminetetraacetic acid  (ISO)
eugenol  (ISO)
fipronil  (ISO)
folic acid  (ISO)
fonofos  (ISO)
glucose  (ISO)
hydrogen peroxide  (ISO)
hydroxyl  (ISO)
iron(III) nitrilotriacetate  (ISO)
L-ascorbic acid  (EXP,ISO)
lead diacetate  (EXP,ISO)
LY294002  (ISO)
manganese(II) chloride  (EXP)
mercaptopurine  (EXP)
mercury atom  (EXP,ISO)
mercury dichloride  (ISO)
mercury(0)  (EXP,ISO)
methamphetamine  (EXP)
methapyrilene  (ISO)
methylmercury chloride  (ISO)
N,N-diethyl-m-toluamide  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-ethylmaleimide  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
naringin  (ISO)
nicotine  (ISO)
nitric oxide  (EXP)
nitrogen dioxide  (ISO)
ozone  (ISO)
p-tert-Amylphenol  (EXP)
paraquat  (ISO)
parathion  (ISO)
perfluorooctanoic acid  (ISO)
platinum  (ISO)
platinum(0)  (ISO)
potassium dichromate  (EXP)
purine-6-thiol  (EXP)
quercetin  (ISO)
rotenone  (ISO)
SB 203580  (ISO)
selenium atom  (EXP)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
silver(1+) nitrate  (ISO)
sodium arsenite  (ISO)
streptozocin  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
superoxide  (ISO)
tamibarotene  (ISO)
terbufos  (ISO)
testosterone  (EXP)
thimerosal  (ISO)
triclosan  (ISO)
Tungsten carbide  (ISO)
valproic acid  (ISO)
vitamin E  (EXP)
wortmannin  (ISO)
zinc atom  (EXP,ISO)
zinc dichloride  (ISO)
zinc(0)  (EXP,ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of protein kinase B activity  (ISO,ISS)
apoptotic process  (IEA)
astrocyte development  (ISO,ISS)
brain development  (IEP)
cadmium ion homeostasis  (ISO,ISS)
cellular lipid catabolic process  (ISO,ISS)
cellular metal ion homeostasis  (ISO)
cellular response to cadmium ion  (IBA,ISO,ISS)
cellular response to copper ion  (IBA)
cellular response to hypoxia  (ISO)
cellular response to nitric oxide  (ISO,ISS)
cellular response to oxidative stress  (ISO,ISS)
cellular response to zinc ion  (IBA)
cellular zinc ion homeostasis  (IBA,ISO,ISS)
cholesterol catabolic process  (ISO,ISS)
detoxification of copper ion  (IBA)
energy reserve metabolic process  (ISO,ISS)
ERK1 and ERK2 cascade  (ISO,ISS)
histone modification  (ISO,ISS)
leptin-mediated signaling pathway  (ISO,ISS)
negative regulation of apoptotic process  (ISO,ISS)
negative regulation of autophagy  (ISO,ISS)
negative regulation of axon extension  (ISO,ISS)
negative regulation of cell growth  (ISO,ISS,NAS)
negative regulation of cysteine-type endopeptidase activity  (ISO,ISS)
negative regulation of cysteine-type endopeptidase activity involved in apoptotic process  (ISO,ISS)
negative regulation of dendrite morphogenesis  (NAS)
negative regulation of hydrogen peroxide catabolic process  (IDA)
negative regulation of necrotic cell death  (ISO,ISS)
negative regulation of neurogenesis  (ISO,NAS)
negative regulation of neuron apoptotic process  (ISO,ISS)
negative regulation of neuron death  (IDA)
negative regulation of oxidoreductase activity  (ISO,ISS)
negative regulation of reactive oxygen species metabolic process  (ISO,ISS)
negative regulation of transcription, DNA-templated  (ISO,ISS)
positive regulation of catalytic activity  (ISO,ISS)
positive regulation of cell death  (ISO,ISS)
positive regulation of ERK1 and ERK2 cascade  (IBA,ISO,ISS)
positive regulation of gene expression  (ISO,ISS)
positive regulation of lysosomal membrane permeability  (ISO,ISS)
positive regulation of necrotic cell death  (ISO,ISS)
positive regulation of oxygen metabolic process  (ISO,ISS)
positive regulation of protein phosphorylation  (ISO,ISS)
positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress  (ISO,ISS)
positive regulation of transcription, DNA-templated  (ISO,ISS)
positive regulation of vascular endothelial growth factor receptor signaling pathway  (ISO,ISS)
protein kinase B signaling  (ISO,ISS)
protein stabilization  (ISO,ISS)
regulation of protein glycosylation  (ISO,ISS)
regulation of response to food  (ISO,ISS)
removal of superoxide radicals  (ISO,ISS)
response to hypoxia  (ISO,ISS)
response to oxidative stress  (ISO)
zinc ion homeostasis  (ISO,ISS)
zinc ion transport  (ISO,ISS)

Cellular Component

Molecular Function

References

References - curated
1. Acarin L, etal., J Neuropathol Exp Neurol. 1999 Apr;58(4):389-97.
2. Amoureux MC, etal., Biochem Biophys Res Commun 1995 Sep 14;214(2):639-45.
3. Byun HR, etal., Neurobiol Dis. 2011 Oct;44(1):125-32. Epub 2011 Jun 25.
4. Carrasco J, etal., J Neurotrauma. 1999 Nov;16(11):1115-29.
5. Choi KH, etal., BMC Psychiatry. 2008 Nov 7;8:87.
6. Chung RS, etal., Exp Neurol 2002 Nov;178(1):1-12.
7. Erickson JC, etal., Brain Res. 1994 Jun 27;649(1-2):297-304.
8. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
9. GOA data from the GO Consortium
10. Gomi F, etal., Brain Res. 2005 Feb 1;1033(1):113-6.
11. Honda A, etal., J Toxicol Sci. 2010 Apr;35(2):209-15.
12. Hozumi I, etal., Brain Res. 1996 Nov 25;741(1-2):197-204.
13. Hozumi I, etal., Neurosci Lett. 2006 Mar 13;395(3):220-3. Epub 2005 Nov 28.
14. Inuzuka T, etal., Brain Res. 1996 Feb 12;709(1):151-31.
15. Ishigaki S, etal., FEBS Lett. 2002 Nov 6;531(2):354-8.
16. Koumura A, etal., Brain Res. 2009 Oct 6;1292:148-54. Epub 2009 Jul 25.
17. Koumura A, etal., Neurosci Lett. 2009 Dec 18;467(1):11-4. Epub 2009 Sep 30.
18. Lanza C, etal., J Neurochem. 2009 Sep;110(5):1674-84. Epub 2009 Jul 8.
19. Lanza C, etal., J Neurosci Res. 2012 Apr;90(4):842-8. doi: 10.1002/jnr.22778. Epub 2012 Jan 18.
20. Martin BL, etal., Mol Cell Biochem. 2006 Feb;283(1-2):129-37.
21. MGD data from the GO Consortium
22. Miyazaki I, etal., Neurosci Res. 2002 Aug;43(4):323-33.
23. Mocchegiani E, etal., Brain Res Bull 2004 Mar 15;63(2):133-42.
24. NCBI rat LocusLink and RefSeq merged data July 26, 2002
25. Ni H, etal., Toxicol Lett. 2013 Feb 27;217(2):162-9. doi: 10.1016/j.toxlet.2012.12.010. Epub 2012 Dec 21.
26. Pountney DL, etal., Neurotox Res. 2011 Jan;19(1):115-22. Epub 2009 Dec 29.
27. Puttaparthi K, etal., J Neurosci. 2002 Oct 15;22(20):8790-6.
28. RGD automated data pipeline
29. RGD automated import pipeline for gene-chemical interactions
30. Sakamoto T, etal., Neuroreport. 2003 Dec 2;14(17):2147-51.
31. Somji S, etal., Toxicol Sci. 2006 Apr;90(2):369-76. Epub 2005 Dec 30.
32. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
33. Tokuda E, etal., Toxicology. 2007 Jan 5;229(1-2):33-41. Epub 2006 Sep 29.
34. Tougu V, etal., J Neurochem. 2009 Sep;110(6):1784-95. Epub 2009 Jul 8.
35. Tsuji S, etal., EMBO J. 1992 Dec;11(13):4843-50.
36. Tsuruma K, etal., Invest Ophthalmol Vis Sci. 2012 Nov 29;53(12):7896-903. doi: 10.1167/iovs.12-10165.
37. Uchida Y, etal., J Biol Chem 2002 Aug 30;277(35):32353-9.
38. Watabe K, etal., Neuropathology. 2005 Dec;25(4):371-80.
39. Williams BL, etal., Brain Pathol. 2006 Jan;16(1):1-14.
40. Yamada M, etal., Brain Res. 1996 Oct 7;735(2):257-64.
41. Yamashita M, etal., Endocrinology 2002 Nov;143(11):4464-76.
42. Yanagitani S, etal., Life Sci. 1999;64(8):707-15.
43. Yeiser EC, etal., Brain Res Dev Brain Res. 1999 Jun 2;115(2):195-200.
Additional References at PubMed
PMID:7931547   PMID:8412560   PMID:10355541   PMID:10366715   PMID:12130647   PMID:12383939   PMID:12692462   PMID:12763630   PMID:14998173   PMID:15129022   PMID:15489334   PMID:16336778  
PMID:16601975   PMID:16945328   PMID:17712581   PMID:18157556   PMID:18206644   PMID:18295594   PMID:18479819   PMID:18554677   PMID:19536566   PMID:20544854   PMID:21320589   PMID:21359432  
PMID:21818286   PMID:22367221   PMID:25778834   PMID:27939232  


Genomics

Comparative Map Data
Mt3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21910,848,754 - 10,850,158 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl1910,848,755 - 10,850,158 (-)Ensembl
Rnor_6.01911,324,708 - 11,326,112 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1911,324,698 - 11,326,139 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01911,300,014 - 11,301,422 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41911,284,554 - 11,286,402 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11911,289,380 - 11,291,228 (-)NCBI
Celera1910,734,686 - 10,736,090 (-)NCBICelera
Cytogenetic Map19p12NCBI
MT3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1656,589,074 - 56,591,088 (+)EnsemblGRCh38hg38GRCh38
GRCh381656,589,528 - 56,591,085 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371656,623,440 - 56,624,997 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361655,180,768 - 55,182,501 (+)NCBINCBI36hg18NCBI36
Build 341655,180,767 - 55,182,500NCBI
Celera1641,120,754 - 41,122,487 (+)NCBI
Cytogenetic Map16q13NCBI
HuRef1642,492,901 - 42,494,634 (+)NCBIHuRef
CHM1_11658,029,740 - 58,031,473 (+)NCBICHM1_1
Mt3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39894,879,235 - 94,880,776 (+)NCBIGRCm39mm39
GRCm39 Ensembl894,879,235 - 94,880,774 (+)Ensembl
GRCm38894,152,607 - 94,154,148 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl894,152,607 - 94,154,146 (+)EnsemblGRCm38mm10GRCm38
MGSCv37896,676,507 - 96,678,048 (+)NCBIGRCm37mm9NCBIm37
MGSCv36897,041,873 - 97,043,260 (+)NCBImm8
Celera898,484,267 - 98,485,940 (+)NCBICelera
Cytogenetic Map8C5NCBI
cM Map846.29NCBI
MT3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11656,007,922 - 56,009,828 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1656,007,922 - 56,028,093 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01636,875,919 - 36,877,558 (+)NCBIMhudiblu_PPA_v0panPan3
Mt3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934950,722,559 - 50,724,569 (-)NCBI
SpeTri2.0NW_0049364758,864,512 - 8,866,516 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MT3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl618,634,721 - 18,789,137 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1618,634,735 - 18,636,134 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2626,377,693 - 26,380,233 (+)NCBISscrofa10.2Sscrofa10.2susScr3
MT3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1542,502,306 - 42,504,467 (+)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604733,859,328 - 33,861,438 (-)NCBIVero_WHO_p1.0


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
7411590Foco7Food consumption QTL 76.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)19124688055Rat
10054132Srcrt9Stress Responsive Cort QTL 92.870.0017blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19127355345Rat
631678Cm9Cardiac mass QTL 94.270.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)19128982497Rat
631681Cm12Cardiac mass QTL 123.330.00053heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)19128982497Rat
1549847Bss8Bone structure and strength QTL 84lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)19131963836Rat
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19136824771Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19136824771Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19136824771Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19136824771Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19997775339654489Rat
631840Niddm38Non-insulin dependent diabetes mellitus QTL 383.86blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)191032318023069265Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:73
Count of miRNA genes:66
Interacting mature miRNAs:72
Transcripts:ENSRNOT00000025669
Prediction methods: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 1
Medium 1 6 2 2 69 32 2
Low 2 37 20 4 14 4 6 9 4 28 7 8 6
Below cutoff 17 17 3 17 7 2 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000025669   ⟹   ENSRNOP00000025669
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1910,848,755 - 10,850,158 (-)Ensembl
Rnor_6.0 Ensembl1911,324,698 - 11,326,139 (-)Ensembl
RefSeq Acc Id: NM_053968   ⟹   NP_446420
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21910,848,754 - 10,850,158 (-)NCBI
Rnor_6.01911,324,708 - 11,326,112 (-)NCBI
Rnor_5.01911,300,014 - 11,301,422 (-)NCBI
RGSC_v3.41911,284,554 - 11,286,402 (-)RGD
Celera1910,734,686 - 10,736,090 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_446420 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB28366 (Get FASTA)   NCBI Sequence Viewer  
  AAH58453 (Get FASTA)   NCBI Sequence Viewer  
  CAA61762 (Get FASTA)   NCBI Sequence Viewer  
  EDL87352 (Get FASTA)   NCBI Sequence Viewer  
  P37361 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_446420   ⟸   NM_053968
- UniProtKB: P37361 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000025669   ⟸   ENSRNOT00000025669

Transcriptome

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

Promoters
RGD ID:13700951
Promoter ID:EPDNEW_R11475
Type:single initiation site
Name:Mt3_1
Description:metallothionein 3
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_6.01911,326,112 - 11,326,172EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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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
BN-Lx/CubMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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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)
DA/OlaHsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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
F344/Stm (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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
FXLE16/Stm (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GH/OmrMcwi (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)
GK/FarMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/Ox (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
HXB10/IpcvMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (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
LEW/Crl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (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
LEW/NCrlBR (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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrc (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
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrc (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
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrc (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
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/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
M520/NRrrcMcwi (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MHS/Gib (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
MNS/Gib (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
MR/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/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
MWF/Hsd (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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)
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
SBN/Ygl (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: SBN/Ygl sequenced by MCW
SBN/Ygl (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
SHR/NHsd (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
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/Gcrc (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
SR/JrHsd (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (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: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (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
SS/Jr (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
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (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)
SS/JrHsdMcwi (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
WAG/Rij (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
WAG/RijCrl (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/Gcrc (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
WKY/N (2020)
Visual CSV TAB Printer
Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/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
WKY/NCrl (2019)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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 (2020)
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Sequenced By: MCW
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
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:621252 AgrOrtholog
Ensembl Genes ENSRNOG00000018958 Ensembl, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000025669 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000025669 UniProtKB/Swiss-Prot
Gene3D-CATH 4.10.10.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:6887014 IMAGE-MGC_LOAD
InterPro Metalthion UniProtKB/Swiss-Prot
  Metalthion_dom_sf UniProtKB/Swiss-Prot
  Metalthion_dom_sf_vert UniProtKB/Swiss-Prot
  Metalthion_vert UniProtKB/Swiss-Prot
  Metalthion_vert_metal_BS UniProtKB/Swiss-Prot
KEGG Report rno:117038 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72731 IMAGE-MGC_LOAD
NCBI Gene 117038 ENTREZGENE
PANTHER PTHR23299 UniProtKB/Swiss-Prot
Pfam Metallothio UniProtKB/Swiss-Prot
PhenoGen Mt3 PhenoGen
PRINTS MTVERTEBRATE UniProtKB/Swiss-Prot
PROSITE METALLOTHIONEIN_VRT UniProtKB/Swiss-Prot
Superfamily-SCOP SSF57868 UniProtKB/Swiss-Prot
UniProt MT3_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-01-20 Mt3  metallothionein 3      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Mt3  metallothionein 3      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_disease drastically reduced in Alzheimers disease brains 628363
gene_expression preferentially found in vasopressin (VP)-expressing magnocellular neurons (MCNs) 628363
gene_process inhibits the formation and growth of both axons and dendrites 727475
gene_process may inhibit growth of rat C6 glial cells 729282
gene_process may play a role in regulation of copper and zinc in the nervous system, in tissue repair after adult brain injury and in preventing neuronal sprouting 628363
gene_product brain-specific member of the metallothionein protein family 628363