Slc31a1 (solute carrier family 31 member 1) - Rat Genome Database

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Gene: Slc31a1 (solute carrier family 31 member 1) Rattus norvegicus
Analyze
Symbol: Slc31a1
Name: solute carrier family 31 member 1
RGD ID: 620059
Description: Enables copper ion transmembrane transporter activity. Involved in cellular response to cisplatin; copper ion import; and copper ion import across plasma membrane. Located in cytoplasm; neuronal cell body; and plasma membrane. Orthologous to human SLC31A1 (solute carrier family 31 member 1); PARTICIPATES IN cisplatin drug pathway; cisplatin response pathway; INTERACTS WITH 17alpha-ethynylestradiol; 17beta-estradiol; 17beta-estradiol 3-benzoate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: copper transporter 1; Copper uptake transporter 1; Ctr1; high affinity copper uptake protein 1; liver regeneration-related protein LRRGT00200; LRRGT00200; rCTR1; solute carrier family 31 (copper transporter), member 1; solute carrier family 31 (copper transporters), member 1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2575,814,744 - 75,844,241 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl575,814,743 - 75,844,228 (+)Ensembl
Rnor_6.0578,222,504 - 78,249,358 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl578,222,504 - 78,249,358 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0582,341,969 - 82,371,285 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4579,359,420 - 79,385,988 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1579,364,532 - 79,391,101 (+)NCBI
Celera574,756,941 - 74,783,647 (+)NCBICelera
Cytogenetic Map5q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-epigallocatechin 3-gallate  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
17beta-estradiol 3-benzoate  (EXP)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
2,2,2-tetramine  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-hydroxypropanoic acid  (ISO)
3,3',4,4'-tetrachlorobiphenyl  (ISO)
3-Iodothyronamine  (ISO)
4,4'-diaminodiphenylmethane  (EXP)
4,4'-sulfonyldiphenol  (ISO)
5-aza-2'-deoxycytidine  (ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
amiloride  (ISO)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
Aroclor 1254  (ISO)
bathocuproine disulfonic acid  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
C60 fullerene  (EXP)
cadmium dichloride  (ISO)
carboplatin  (EXP,ISO)
casticin  (ISO)
celecoxib  (ISO)
chlorpromazine  (ISO)
chromium(6+)  (ISO)
cisplatin  (EXP,ISO)
clofibric acid  (EXP)
cobalt dichloride  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
copper(II) chloride  (EXP,ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
CU-O LINKAGE  (ISO)
Cuprizon  (EXP)
cytochalasin D  (ISO)
D-penicillamine  (ISO)
diazinon  (ISO)
diethylstilbestrol  (EXP)
dioxygen  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
ethyl methanesulfonate  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
fructose  (EXP)
fumonisin B1  (ISO)
genistein  (ISO)
gentamycin  (EXP)
glutathione  (ISO)
graphite  (EXP)
hydrogen peroxide  (ISO)
irinotecan  (EXP)
isotretinoin  (ISO)
ivermectin  (ISO)
lactacystin  (ISO)
lamivudine  (ISO)
lead diacetate  (EXP,ISO)
lead(0)  (EXP)
lead(2+)  (EXP)
lipopolysaccharide  (ISO)
lovastatin  (EXP)
manganese(II) chloride  (EXP)
methapyrilene  (EXP)
methyl beta-cyclodextrin  (ISO)
methyl methanesulfonate  (ISO)
Methylazoxymethanol acetate  (EXP)
methylmercury chloride  (ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
N-nitrosodiethylamine  (EXP)
nitrofen  (EXP)
oxaliplatin  (EXP,ISO)
paclitaxel  (ISO)
paracetamol  (EXP,ISO)
paraquat  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
platinum  (ISO)
platinum(0)  (ISO)
rac-lactic acid  (ISO)
resveratrol  (ISO)
S-butyl-DL-homocysteine (S,R)-sulfoximine  (ISO)
SB 431542  (ISO)
silver atom  (EXP)
silver(0)  (EXP)
silver(1+) nitrate  (ISO)
sodium dichromate  (EXP)
streptozocin  (EXP)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP,ISO)
tetrathiomolybdate(2-)  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
trichostatin A  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vanadium atom  (ISO)
vanadium(0)  (ISO)
Y-27632  (ISO)
zearalenone  (ISO)
zidovudine  (ISO)
zinc acetate  (ISO)
zinc atom  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Membrane transporters as mediators of Cisplatin effects and side effects. Ciarimboli G Scientifica (Cairo). 2012;2012:473829. doi: 10.6064/2012/473829. Epub 2012 Nov 25.
2. Iron deficiency in the pregnant rat has differential effects on maternal and fetal copper levels. Gambling L, etal., J Nutr Biochem 2004 Jun;15(6):366-72.
3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. The N-terminus of the human copper transporter 1 (hCTR1) is localized extracellularly, and interacts with itself. Klomp AE, etal., Biochem J 2003 Mar 15;370(Pt 3):881-9.
6. Contributions of rat Ctr1 to the uptake and toxicity of copper and platinum anticancer drugs in dorsal root ganglion neurons. Liu JJ, etal., Biochem Pharmacol. 2013 Jan 15;85(2):207-15. doi: 10.1016/j.bcp.2012.10.023. Epub 2012 Nov 1.
7. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
8. Mechanism of copper transport at the blood-cerebrospinal fluid barrier: influence of iron deficiency in an in vitro model. Monnot AD, etal., Exp Biol Med (Maywood). 2012 Mar;237(3):327-33. doi: 10.1258/ebm.2011.011170.
9. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
10. GOA pipeline RGD automated data pipeline
11. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
12. Subcellular targets of cisplatin cytotoxicity: an integrated view. Sancho-Martinez SM, etal., Pharmacol Ther. 2012 Oct;136(1):35-55. doi: 10.1016/j.pharmthera.2012.07.003. Epub 2012 Jul 14.
13. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
14. Dysregulation of intracellular copper trafficking pathway in a mouse model of mutant copper/zinc superoxide dismutase-linked familial amyotrophic lateral sclerosis. Tokuda E, etal., J Neurochem. 2009 Oct;111(1):181-91. doi: 10.1111/j.1471-4159.2009.06310.x. Epub 2009 Jul 27.
Additional References at PubMed
PMID:12177073   PMID:15489334   PMID:16501047   PMID:16637264   PMID:16741141   PMID:19240214   PMID:20004225   PMID:20699218   PMID:20836889   PMID:22465424   PMID:24167251   PMID:24316150  


Genomics

Comparative Map Data
Slc31a1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2575,814,744 - 75,844,241 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl575,814,743 - 75,844,228 (+)Ensembl
Rnor_6.0578,222,504 - 78,249,358 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl578,222,504 - 78,249,358 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0582,341,969 - 82,371,285 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4579,359,420 - 79,385,988 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1579,364,532 - 79,391,101 (+)NCBI
Celera574,756,941 - 74,783,647 (+)NCBICelera
Cytogenetic Map5q24NCBI
SLC31A1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389113,221,544 - 113,264,492 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl9113,221,544 - 113,264,492 (+)EnsemblGRCh38hg38GRCh38
GRCh379115,983,824 - 116,026,772 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369115,023,689 - 115,066,593 (+)NCBINCBI36hg18NCBI36
Build 349113,063,421 - 113,106,325NCBI
Celera986,631,426 - 86,674,386 (+)NCBI
Cytogenetic Map9q32ENTREZGENE
HuRef985,591,243 - 85,634,236 (+)NCBIHuRef
CHM1_19116,130,594 - 116,173,508 (+)NCBICHM1_1
T2T-CHM13v2.09125,420,370 - 125,463,332 (+)NCBI
Slc31a1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39462,278,821 - 62,310,006 (+)NCBIGRCm39mm39
GRCm39 Ensembl462,278,964 - 62,310,006 (+)Ensembl
GRCm38462,360,583 - 62,391,769 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl462,360,727 - 62,391,769 (+)EnsemblGRCm38mm10GRCm38
MGSCv37462,021,735 - 62,052,803 (+)NCBIGRCm37mm9NCBIm37
MGSCv36461,847,110 - 61,878,123 (+)NCBImm8
Celera461,032,896 - 61,063,964 (+)NCBICelera
Cytogenetic Map4B3NCBI
Slc31a1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541914,220,495 - 14,264,699 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541914,221,258 - 14,264,288 (-)NCBIChiLan1.0ChiLan1.0
SLC31A1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19112,691,503 - 112,734,352 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9112,691,503 - 112,734,352 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0984,319,304 - 84,362,288 (+)NCBIMhudiblu_PPA_v0panPan3
SLC31A1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11167,590,087 - 67,628,947 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1167,591,080 - 67,625,798 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1165,994,878 - 66,033,741 (+)NCBI
ROS_Cfam_1.01168,714,951 - 68,753,806 (+)NCBI
ROS_Cfam_1.0 Ensembl1168,715,210 - 68,812,959 (+)Ensembl
UMICH_Zoey_3.11167,232,618 - 67,271,432 (+)NCBI
UNSW_CanFamBas_1.01167,254,684 - 67,293,582 (+)NCBI
UU_Cfam_GSD_1.01168,000,439 - 68,039,329 (+)NCBI
Slc31a1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947182,901,798 - 182,934,079 (+)NCBI
SpeTri2.0NW_004936559333,461 - 364,737 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SLC31A1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1253,868,332 - 253,894,449 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11253,868,389 - 253,893,135 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21284,727,786 - 284,753,055 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Pig Cytomap1q28-q2.13NCBI
SLC31A1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11226,307,308 - 26,348,701 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1226,311,334 - 26,348,694 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603516,453,718 - 16,495,422 (+)NCBIVero_WHO_p1.0
Slc31a1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476021,832,908 - 21,849,576 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462476021,832,924 - 21,879,089 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH129201  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2575,841,763 - 75,841,976 (+)MAPPERmRatBN7.2
Rnor_6.0578,249,080 - 78,249,292NCBIRnor6.0
Rnor_5.0582,368,812 - 82,369,024UniSTSRnor5.0
RGSC_v3.4579,385,710 - 79,385,922UniSTSRGSC3.4
Celera574,783,369 - 74,783,581UniSTS
RH 3.4 Map5559.0UniSTS
Cytogenetic Map5q24UniSTS
RH133724  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2575,822,418 - 75,823,125 (+)MAPPERmRatBN7.2
Rnor_6.0578,229,663 - 78,230,369NCBIRnor6.0
Rnor_5.0582,349,514 - 82,350,220UniSTSRnor5.0
RGSC_v3.4579,366,579 - 79,367,285UniSTSRGSC3.4
Celera574,764,120 - 74,764,826UniSTS
RH 3.4 Map5558.4UniSTS
Cytogenetic Map5q24UniSTS
RH128029  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2575,841,747 - 75,841,937 (+)MAPPERmRatBN7.2
Rnor_6.0578,249,064 - 78,249,253NCBIRnor6.0
Rnor_5.0582,368,796 - 82,368,985UniSTSRnor5.0
RGSC_v3.4579,385,694 - 79,385,883UniSTSRGSC3.4
Celera574,783,353 - 74,783,542UniSTS
RH 3.4 Map5559.9UniSTS
Cytogenetic Map5q24UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5190450412Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51131345958Rat
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)572947086724018Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)52138965166875058Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)5982326699753708Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512789751113558310Rat
2290448Scl54Serum cholesterol level QTL 542.93blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)531663789131345958Rat
1598807Glom12Glomerulus QTL 122.7kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)53321566578215665Rat
1298067Scl15Serum cholesterol level QTL 154.80.001blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)53321566578215665Rat
1302786Kidm8Kidney mass QTL 828.15kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)53321566578215665Rat
1576317Eutr2Estrogen induced uterine response QTL 20.01uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)534730116104251008Rat
2316959Gluco59Glucose level QTL 594.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)534944474113558310Rat
1641912Alcrsp18Alcohol response QTL 18response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)535189153141643988Rat
1549845Scl44Serum cholesterol level QTL 446blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)540128307148607290Rat
1331773Scl26Serum cholesterol level QTL 263.065blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)54372665686724018Rat
1331801Rf33Renal function QTL 334.149kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)543726656129132602Rat
1578766Tcas11Tongue tumor susceptibility QTL 114.12tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)546711509161317411Rat
1300115Hrtrt7Heart rate QTL 72.76heart pumping trait (VT:2000009)heart rate (CMO:0000002)54786906290099692Rat
9589025Epfw7Epididymal fat weight QTL 720.660.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)54946360094463600Rat
7411561Bw134Body weight QTL 134240.001body mass (VT:0001259)body weight gain (CMO:0000420)54946360094463600Rat
1576312Emca8Estrogen-induced mammary cancer QTL 84.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)550328551141643988Rat
2303615Vencon7Ventilatory control QTL 70.001respiration trait (VT:0001943)respiration rate (CMO:0000289)55098389595983895Rat
2303574Gluco42Glucose level QTL 422blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)55349671998496719Rat
61359EaexExperimental allergic encephalomyelitis QTL x3nervous system integrity trait (VT:0010566)post-insult time to onset of experimental autoimmune encephalomyelitis (CMO:0001422)555715622100715622Rat
70189Mcs5Mammary carcinoma susceptibility QTL 510.51mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)555805606132207589Rat
1358895Bp254Blood pressure QTL 2543.60.0003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)558829236128034027Rat
61426Scl2Serum cholesterol level QTL 27.30.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)559793399143070159Rat
2316954Rf57Renal function QTL 570kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)55979352890450144Rat
2316957Pur21Proteinuria QTL 216.2urine protein amount (VT:0005160)urine protein level (CMO:0000591)559793528113558156Rat
61386Bp49Blood pressure QTL 4916.6cerebrum integrity trait (VT:0010549)brain infarction volume (CMO:0001013)56029343498603051Rat
61393Bp7Blood pressure QTL 74.50.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)560293434161481680Rat
2290005Mcs24Mammary carcinoma susceptibility QTL 24mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)564719390109719390Rat
2306971Anxrr21Anxiety related response QTL 219.47fear/anxiety-related behavior trait (VT:1000241)number of entries into a discrete space in an experimental apparatus (CMO:0000960)566174080124160948Rat
2312671Scl64Serum cholesterol level QTL 640.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)568984307104251008Rat
61380Edpm5Estrogen-dependent pituitary mass QTL 54.50.92pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)568984307104251008Rat
1357396Bw44Body weight QTL 444.19body mass (VT:0001259)body weight (CMO:0000012)568984307104251008Rat
1357402Bw46Body weight QTL 464.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)568984307104251008Rat
2302381Bw84Body weight QTL 844.47body mass (VT:0001259)body mass index (BMI) (CMO:0000105)568984307104251008Rat
1354598Srn6Serum renin concentration QTL 63.8blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)569540295151018848Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:67
Count of miRNA genes:63
Interacting mature miRNAs:64
Transcripts:ENSRNOT00000019544
Prediction methods:Miranda, Rnahybrid
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 31 57 41 19 41 2 2 74 35 41 11 2
Low 12 6 9 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000019544   ⟹   ENSRNOP00000019544
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl575,814,743 - 75,840,470 (+)Ensembl
Rnor_6.0 Ensembl578,222,504 - 78,249,358 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000114775   ⟹   ENSRNOP00000096861
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl575,815,254 - 75,844,228 (+)Ensembl
RefSeq Acc Id: NM_133600   ⟹   NP_598284
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2575,815,258 - 75,842,042 (+)NCBI
Rnor_6.0578,222,504 - 78,249,358 (+)NCBI
Rnor_5.0582,341,969 - 82,371,285 (+)NCBI
RGSC_v3.4579,359,420 - 79,385,988 (+)RGD
Celera574,756,941 - 74,783,647 (+)RGD
Sequence:
RefSeq Acc Id: XM_039109221   ⟹   XP_038965149
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2575,815,236 - 75,844,241 (+)NCBI
RefSeq Acc Id: XM_039109222   ⟹   XP_038965150
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2575,814,744 - 75,844,241 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_598284   ⟸   NM_133600
- UniProtKB: Q9JK41 (UniProtKB/Swiss-Prot),   Q53YN6 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000019544   ⟸   ENSRNOT00000019544
RefSeq Acc Id: XP_038965150   ⟸   XM_039109222
- Peptide Label: isoform X1
- UniProtKB: Q53YN6 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_038965149   ⟸   XM_039109221
- Peptide Label: isoform X1
- UniProtKB: Q53YN6 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: ENSRNOP00000096861   ⟸   ENSRNOT00000114775

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9JK41-F1-model_v2 AlphaFold Q9JK41 1-187 view protein structure

Transcriptome

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

Promoters
RGD ID:13693787
Promoter ID:EPDNEW_R4311
Type:initiation region
Name:Slc31a1_1
Description:solute carrier family 31 member 1
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_6.0578,222,526 - 78,222,586EPDNEW

Strain Variation

Strain Sequence Variants (mRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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-Lx/CubMcwi (2019)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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
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)
Visual CSV TAB Printer
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
BUF/N (2020)
Visual CSV TAB Printer
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
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
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
DA/OlaHsd (2019)
Visual CSV TAB Printer
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
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
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
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/Stm (2019)
Visual CSV TAB Printer
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
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
FXLE16/Stm (2020)
Visual CSV TAB Printer
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
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
GK/FarMcwi (2019)
Visual CSV TAB Printer
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
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
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
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
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
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
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
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
LEW/Crl (2019)
Visual CSV TAB Printer
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
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
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
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
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
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
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
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
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/MavRrrcAek (2020)
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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/MavRrrcAek (2020)
Visual CSV TAB Printer
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/MavRrrcAek (2020)
Visual CSV TAB Printer
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
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/NRrrcMcwi (2019)
Visual CSV TAB Printer
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
MR/N (2020)
Visual CSV TAB Printer
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
MWF/Hsd (2019)
Visual CSV TAB Printer
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
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
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
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
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
SR/JrHsd (2020)
Visual CSV TAB Printer
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
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
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
WAG/RijCrl (2020)
Visual CSV TAB Printer
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/N (2020)
Visual CSV TAB Printer
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/NCrl (2019)
Visual CSV TAB Printer
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
WN/N (2020)
Visual CSV TAB Printer
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620059 AgrOrtholog
BioCyc Gene G2FUF-41100 BioCyc
Ensembl Genes ENSRNOG00000014475 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000019544.3 UniProtKB/TrEMBL
  ENSRNOP00000096861 ENTREZGENE
  ENSRNOP00000096861.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000019544.5 UniProtKB/TrEMBL
  ENSRNOT00000114775 ENTREZGENE
  ENSRNOT00000114775.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7126088 IMAGE-MGC_LOAD
InterPro Cop_transporter UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:171135 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93210 IMAGE-MGC_LOAD
NCBI Gene 171135 ENTREZGENE
PANTHER PTHR12483 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Ctr UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Slc31a1 PhenoGen
UniProt A0A8I6AQ78_RAT UniProtKB/TrEMBL
  A0A8L2QA41_RAT UniProtKB/TrEMBL
  COPT1_RAT UniProtKB/Swiss-Prot
  Q53YN6 ENTREZGENE
  Q9JK41 ENTREZGENE
UniProt Secondary Q53YN6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-24 Slc31a1  solute carrier family 31 member 1  Slc31a1  solute carrier family 31 (copper transporter), member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-02 Slc31a1  solute carrier family 31 (copper transporter), member 1  Slc31a1  solute carrier family 31 (copper transporters), member 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Slc31a1  solute carrier family 31 (copper transporters), member 1      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Slc31a1  solute carrier family 31 (copper transporters), member 1      Symbol and Name status set to provisional 70820 PROVISIONAL