Rgn (regucalcin) - Rat Genome Database

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Gene: Rgn (regucalcin) Rattus norvegicus
Analyze
Symbol: Rgn
Name: regucalcin
RGD ID: 3560
Description: Exhibits calcium ion binding activity and gluconolactonase activity. Involved in several processes, including negative regulation of hydrolase activity; negative regulation of nitrogen compound metabolic process; and positive regulation of hydrolase activity. Localizes to cytosol and nucleus. Used to study familial hyperlipidemia. Biomarker of hepatocellular carcinoma. Orthologous to human RGN (regucalcin); PARTICIPATES IN ascorbate and aldarate metabolic pathway; pentose phosphate pathway; INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: gluconolactonase; GNL; Rc; Reguc; regucalcin (senescence marker protein-30); senescence marker protein 30; SMP-30
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: Strains:   SD-Tg(CAG-Rgn)Slc  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X1,619,030 - 1,634,456 (-)NCBI
Rnor_6.0 EnsemblX1,833,492 - 1,848,904 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X1,833,484 - 1,848,904 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X2,626,525 - 2,641,949 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X13,037,171 - 13,052,846NCBIRGSC3.4rn4RGSC3.4
CeleraX2,182,952 - 2,198,371 (-)NCBICelera
Cytogenetic MapXq11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
1-naphthyl isothiocyanate  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-acetamidofluorene  (EXP)
3-chloropropane-1,2-diol  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-diaminodiphenylmethane  (EXP)
5-Hydroxythalidomide  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
amiodarone  (EXP)
ammonium chloride  (EXP)
antirheumatic drug  (ISO)
aristolochic acid  (EXP)
Aroclor 1254  (ISO)
bacitracin  (EXP)
benzo[a]pyrene  (ISO)
beta-naphthoflavone  (EXP)
bexarotene  (EXP)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP)
bromobenzene  (EXP)
buta-1,3-diene  (ISO)
carbon nanotube  (ISO)
cefaloridine  (EXP)
chromium trinitrate  (ISO)
cisplatin  (EXP)
clofibrate  (EXP,ISO)
clofibric acid  (EXP)
clotrimazole  (EXP)
cobalt dichloride  (EXP)
copper atom  (EXP)
copper(0)  (EXP)
copper(II) sulfate  (ISO)
coumarin  (EXP)
cycloheximide  (ISO)
cyclosporin A  (EXP,ISO)
cyproconazole  (ISO)
dexamethasone  (EXP)
Diallyl sulfide  (EXP)
diclofenac  (EXP)
dicrotophos  (ISO)
diisopropyl fluorophosphate  (ISO)
dioscin  (ISO)
dorsomorphin  (ISO)
entinostat  (ISO)
epoxiconazole  (ISO)
ethanol  (EXP)
flavonoids  (EXP)
fumonisin B1  (ISO)
furan  (EXP)
Hexachloro-1,3-butadiene  (EXP)
hydrazine  (EXP)
indoxyl sulfate  (ISO)
melatonin  (ISO)
methapyrilene  (EXP)
methylmercury chloride  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
N-nitrosomorpholine  (EXP)
nefazodone  (EXP)
nickel atom  (ISO)
nickel dichloride  (EXP)
nimesulide  (EXP)
O-methyleugenol  (ISO)
ochratoxin A  (EXP)
paracetamol  (EXP,ISO)
pent-4-enoic acid  (EXP)
perfluorododecanoic acid  (EXP)
perfluorooctanoic acid  (EXP)
phenobarbital  (EXP)
phenylmercury acetate  (ISO)
pioglitazone  (ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (EXP,ISO)
polaprezinc  (ISO)
potassium chromate  (ISO)
potassium dichromate  (EXP,ISO)
pregnenolone 16alpha-carbonitrile  (EXP)
propiconazole  (ISO)
Propiverine  (EXP)
quercetin  (ISO)
rac-1,2-dichloropropane  (ISO)
resveratrol  (EXP)
rotenone  (EXP)
sarin  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (EXP,ISO)
sodium dichromate  (EXP,ISO)
Soman  (ISO)
tacrolimus hydrate  (EXP)
tert-butyl hydroperoxide  (EXP)
testosterone  (EXP)
testosterone enanthate  (ISO)
tetrachloromethane  (EXP,ISO)
tetracycline  (EXP)
titanium dioxide  (ISO)
tremolite asbestos  (ISO)
triclosan  (ISO)
triptonide  (ISO)
urethane  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
zinc sulfate  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
aging  (IEP)
cellular calcium ion homeostasis  (IDA)
kidney development  (IEP)
L-ascorbic acid biosynthetic process  (IBA,ISO,ISS)
liver development  (IEP)
liver regeneration  (IEP)
negative regulation of apoptotic process  (IDA)
negative regulation of bone development  (IDA,IMP)
negative regulation of calcium-dependent ATPase activity  (IMP)
negative regulation of cyclic-nucleotide phosphodiesterase activity  (IDA)
negative regulation of DNA biosynthetic process  (IMP)
negative regulation of DNA catabolic process  (IDA)
negative regulation of epithelial cell proliferation  (IDA)
negative regulation of flagellated sperm motility  (IDA)
negative regulation of GTPase activity  (IMP)
negative regulation of leucine-tRNA ligase activity  (IDA)
negative regulation of nitric oxide biosynthetic process  (IMP)
negative regulation of phosphoprotein phosphatase activity  (IMP)
negative regulation of protein kinase activity  (IMP)
negative regulation of protein phosphorylation  (IMP)
negative regulation of RNA biosynthetic process  (IMP)
positive regulation of ATPase activity  (IDA)
positive regulation of ATPase-coupled calcium transmembrane transporter activity  (IDA)
positive regulation of dUTP diphosphatase activity  (IDA)
positive regulation of fatty acid biosynthetic process  (IDA)
positive regulation of glucose metabolic process  (IDA)
positive regulation of GTPase activity  (IDA)
positive regulation of phosphatase activity  (IMP)
positive regulation of proteolysis involved in cellular protein catabolic process  (IDA)
positive regulation of superoxide dismutase activity  (IDA)
positive regulation of triglyceride biosynthetic process  (IDA)
regulation of calcium-mediated signaling  (IDA)
spermatogenesis  (IDA)

Cellular Component
cytoplasm  (ISO,ISS)
cytosol  (IDA)
nucleus  (IDA,ISO,ISS)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Akhter T, etal., Int J Mol Med. 2006 Jul;18(1):171-6.
2. Albrethsen J, etal., Biochim Biophys Acta. 2011 Oct;1814(10):1367-76. Epub 2011 Jun 6.
3. Correia S, etal., Mol Hum Reprod. 2013 Sep;19(9):581-9. doi: 10.1093/molehr/gat030. Epub 2013 Apr 23.
4. Fujita T, etal., Biochim Biophys Acta 1992 Oct 20;1132(3):297-305.
5. Fujita T, etal., Mech Ageing Dev. 1996 Jun 25;87(3):219-29.
6. Fukaya Y and Yamaguchi M, Int J Mol Med. 2005 May;15(5):853-7.
7. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
8. Hanahisa Y and Yamaguchi M, Brain Res Bull. 1998 Jul 1;46(4):347-51.
9. Ichikawa E and Yamaguchi M, Int J Mol Med. 2004 Oct;14(4):691-5.
10. Inagaki S and Yamaguchi M, J Cell Biochem Suppl. 2001;Suppl 36:12-8.
11. Inagaki S and Yamaguchi M, J Cell Biochem. 2001;82(4):704-11.
12. Inagaki S, etal., Mol Cell Biochem. 2000 Oct;213(1-2):43-50.
13. Isogai M, etal., Mol Cell Biochem. 1997 Mar;168(1-2):67-72.
14. Katsumata T and Yamaguchi M, J Cell Biochem. 1998 Dec 15;71(4):569-76.
15. Kondo Y, etal., Proc Natl Acad Sci U S A. 2006 Apr 11;103(15):5723-8. Epub 2006 Apr 3.
16. MGD data from the GO Consortium
17. Nakagawa T and Yamaguchi M, Int J Mol Med. 2008 May;21(5):605-10.
18. Nakagawa T and Yamaguchi M, J Cell Biochem. 2005 Dec 15;96(6):1274-85.
19. Nakagawa T, etal., Int J Mol Med. 2005 Oct;16(4):637-43.
20. Nakashima C and Yamaguchi M, J Cell Biochem. 2006 Dec 15;99(6):1582-92.
21. NCBI rat LocusLink and RefSeq merged data July 26, 2002
22. Omura M and Yamaguchi M, J Cell Biochem. 1999 Dec 1;75(3):437-45.
23. Pipeline to import KEGG annotations from KEGG into RGD
24. RGD automated data pipeline
25. RGD automated import pipeline for gene-chemical interactions
26. Shimokawa N and Yamaguchi M, FEBS Lett 1993 Aug 2;327(3):251-5.
27. Son TG, etal., J Neurosci Res. 2009 Oct;87(13):2890-7. doi: 10.1002/jnr.22122.
28. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
29. Takahashi H and Yamaguchi M, J Cell Biochem. 2000 Apr;78(1):121-30.
30. Takahashi H and Yamaguchi M, Mol Cell Biochem. 2001 Aug;224(1-2):117-22.
31. Tobisawa M and Yamaguchi M, J Neurol Sci. 2003 May 15;209(1-2):47-54.
32. Tsurusaki Y and Yamaguchi M, Biol Pharm Bull. 2001 Aug;24(8):958-61.
33. Tsurusaki Y and Yamaguchi M, J Cell Biochem. 2000 Jun 12;78(4):541-9.
34. Tsurusaki Y and Yamaguchi M, J Cell Biochem. 2002;87(4):450-7.
35. Yamaguchi M and Kanayama Y, J Cell Biochem. 1995 Feb;57(2):185-90.
36. Yamaguchi M and Mori S, Mol Cell Biochem. 1990 Dec 3;99(1):25-32.
37. Yamaguchi M and Nakajima R, J Cell Biochem 2002;86(1):184-93.
38. Yamaguchi M and Sakurai T, FEBS Lett. 1991 Feb 25;279(2):281-4.
39. Yamaguchi M and Sakurai T, Mol Cell Biochem. 1992 Mar 4;110(1):25-9.
40. Yamaguchi M and Tai H, Mol Cell Biochem. 1991 Jul 24;106(1):25-30.
41. Yamaguchi M and Tai H, Mol Cell Biochem. 1992 May 13;112(1):89-95.
42. Yamaguchi M and Ueoka S, Mol Cell Biochem. 1998 Jan;178(1-2):283-7.
43. Yamaguchi M and Yamamoto T, Chem Pharm Bull (Tokyo). 1978 Jun;26(6):1915-8.
44. Yamaguchi M, etal., Brain Res Bull. 2000 Jul 15;52(5):343-8.
45. Yamaguchi M, etal., Int J Mol Med. 2002 Oct;10(4):377-83.
46. Yamaguchi M, etal., Int J Mol Med. 2004 Oct;14(4):647-51.
47. Yamaguchi M, etal., J Cell Biochem 2002;86(3):520-9.
48. Yamaguchi M, etal., J Cell Biochem 2003 Apr 15;88(6):1092-100.
Additional References at PubMed
PMID:8569761   PMID:8979263   PMID:11936841   PMID:11967991   PMID:12368201   PMID:12647304   PMID:12851718   PMID:12851719   PMID:12964038   PMID:14767576   PMID:15108356   PMID:15251439  
PMID:15254778   PMID:15289895   PMID:15289899   PMID:15340235   PMID:15489334   PMID:15578574   PMID:16052480   PMID:16273285   PMID:16676356   PMID:16677110   PMID:16767692   PMID:17334641  
PMID:17671736   PMID:17912465   PMID:18157649   PMID:18181158   PMID:18442420   PMID:20329768   PMID:21347421   PMID:21431902   PMID:21680783   PMID:22652898   PMID:23349732   PMID:24519986  
PMID:26171977   PMID:26553531   PMID:27553527   PMID:29602294  


Genomics

Comparative Map Data
Rgn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X1,619,030 - 1,634,456 (-)NCBI
Rnor_6.0 EnsemblX1,833,492 - 1,848,904 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X1,833,484 - 1,848,904 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X2,626,525 - 2,641,949 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X13,037,171 - 13,052,846NCBIRGSC3.4rn4RGSC3.4
CeleraX2,182,952 - 2,198,371 (-)NCBICelera
Cytogenetic MapXq11NCBI
RGN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX47,078,355 - 47,093,314 (+)EnsemblGRCh38hg38GRCh38
GRCh38X47,078,414 - 47,093,313 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X46,937,842 - 46,952,712 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X46,822,719 - 46,837,656 (+)NCBINCBI36hg18NCBI36
Build 34X46,696,510 - 46,708,966NCBI
CeleraX51,129,720 - 51,148,035 (+)NCBI
Cytogenetic MapXp11.3NCBI
HuRefX44,651,176 - 44,667,384 (+)NCBIHuRef
CHM1_1X46,969,543 - 46,984,508 (+)NCBICHM1_1
Rgn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X20,416,005 - 20,428,328 (+)NCBIGRCm39mm39
GRCm39 EnsemblX20,416,026 - 20,428,328 (+)Ensembl
GRCm38X20,549,766 - 20,562,089 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX20,549,787 - 20,562,089 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X20,126,944 - 20,139,213 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X19,706,777 - 19,719,046 (+)NCBImm8
CeleraX18,681,357 - 18,693,626 (+)NCBICelera
Cytogenetic MapXA1.3NCBI
Rgn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955516955,680 - 978,910 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955516958,416 - 978,829 (-)NCBIChiLan1.0ChiLan1.0
RGN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X47,371,225 - 47,388,881 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX47,371,226 - 47,388,881 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X39,513,135 - 39,530,188 (+)NCBIMhudiblu_PPA_v0panPan3
RGN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X40,697,292 - 40,715,491 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX40,698,768 - 40,715,490 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX15,074,578 - 15,090,960 (+)NCBI
ROS_Cfam_1.0X40,818,343 - 40,849,916 (+)NCBI
UMICH_Zoey_3.1X40,806,174 - 40,837,694 (+)NCBI
UNSW_CanFamBas_1.0X40,793,810 - 40,825,378 (+)NCBI
UU_Cfam_GSD_1.0X40,886,864 - 40,918,439 (+)NCBI
Rgn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X33,032,122 - 33,050,817 (+)NCBI
SpeTri2.0NW_00493650212,872,938 - 12,891,270 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RGN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX41,726,526 - 41,749,726 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X41,725,660 - 41,749,736 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X46,902,494 - 46,926,414 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RGN
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X44,282,825 - 44,299,027 (+)NCBI
ChlSab1.1 EnsemblX44,285,601 - 44,299,258 (+)Ensembl
Rgn
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248873,881,624 - 3,900,144 (+)NCBI

Position Markers
DXWox11  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X1,623,715 - 1,623,851 (+)MAPPER
Rnor_6.0X1,838,166 - 1,838,301NCBIRnor6.0
Rnor_5.0X2,631,211 - 2,631,346UniSTSRnor5.0
RGSC_v3.4X13,041,853 - 13,041,988UniSTSRGSC3.4
CeleraX2,187,634 - 2,187,769UniSTS
Cytogenetic MapXq11-q12UniSTS
RH142290  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X1,620,629 - 1,621,248 (+)MAPPER
Rnor_6.0X1,835,084 - 1,835,702NCBIRnor6.0
Rnor_5.0X2,628,129 - 2,628,747UniSTSRnor5.0
RGSC_v3.4X13,038,771 - 13,039,389UniSTSRGSC3.4
CeleraX2,184,552 - 2,185,170UniSTS
Cytogenetic MapXq11-q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X144092703Rat
70166Bp65Blood pressure QTL 655.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X166245312370298Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X166245321592783Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X166260933443848Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X183816624331837Rat


Related Rat Strains
The following Strains have been annotated to Rgn

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:588
Count of miRNA genes:268
Interacting mature miRNAs:337
Transcripts:ENSRNOT00000010984
Prediction methods:Microtar, Miranda, Pita
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 3 3 3
Medium 44 36 36 25 3 1
Low 3 43 10 2 13 2 8 11 70 10 36 10 8
Below cutoff 6 4 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000010984   ⟹   ENSRNOP00000010984
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX1,833,492 - 1,848,904 (-)Ensembl
RefSeq Acc Id: NM_031546   ⟹   NP_113734
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X1,619,030 - 1,634,456 (-)NCBI
Rnor_6.0X1,833,484 - 1,848,904 (-)NCBI
Rnor_5.0X2,626,525 - 2,641,949 (-)NCBI
RGSC_v3.4X13,037,171 - 13,052,846 (-)RGD
CeleraX2,182,952 - 2,198,371 (-)RGD
Sequence:
Reference Sequences
RefSeq Acc Id: NP_113734   ⟸   NM_031546
- UniProtKB: Q03336 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000010984   ⟸   ENSRNOT00000010984

Transcriptome

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

Promoters
RGD ID:13701698
Promoter ID:EPDNEW_R12222
Type:multiple initiation site
Name:Rgn_1
Description:regucalcin
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_6.0X1,848,910 - 1,848,970EPDNEW

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)
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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
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)
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)
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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:3560 AgrOrtholog
Ensembl Genes ENSRNOG00000007949 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000010984 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000010984 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.120.10.30 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7126233 IMAGE-MGC_LOAD
InterPro 6-blade_b-propeller_TolB-like UniProtKB/Swiss-Prot
  Regucalcin UniProtKB/Swiss-Prot
  SGL UniProtKB/Swiss-Prot
  SMP-30 UniProtKB/Swiss-Prot
KEGG Report rno:25106 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93360 IMAGE-MGC_LOAD
NCBI Gene 25106 ENTREZGENE
Pfam SGL UniProtKB/Swiss-Prot
PhenoGen Rgn PhenoGen
PRINTS REGUCALCIN UniProtKB/Swiss-Prot
  SMP30FAMILY UniProtKB/Swiss-Prot
UniProt Q03336 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q63496 UniProtKB/Swiss-Prot
  Q925W3 UniProtKB/Swiss-Prot
  Q9QWP2 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-08-07 Rgn  regucalcin  Rgn  regucalcin (senescence marker protein-30)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-09 Rgn  regucalcin (senescence marker protein-30)  Rgn  regucalcin  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Rgn  Regucalcin      Symbol and Name status set to approved 70586 APPROVED