Calca (calcitonin-related polypeptide alpha) - Rat Genome Database

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Gene: Calca (calcitonin-related polypeptide alpha) Rattus norvegicus
Analyze
Symbol: Calca
Name: calcitonin-related polypeptide alpha
RGD ID: 2254
Description: Predicted to have calcitonin receptor binding activity and identical protein binding activity. Involved in several processes, including cellular response to nerve growth factor stimulus; cellular response to tumor necrosis factor; and vasodilation. Localizes to several cellular components, including axon; extracellular space; and neuronal cell body. Used to study brain disease; ischemia; and stomach disease. Biomarker of prediabetes syndrome and type 2 diabetes mellitus. Human ortholog(s) of this gene implicated in migraine and osteoporosis. Orthologous to human CALCA (calcitonin related polypeptide alpha); INTERACTS WITH (6aR,9R)-N-[(2S)-1-hydroxybutan-2-yl]-4,7-dimethyl-6,6a,8,9-tetrahydroindolo[4,3-fg]quinoline-9-carboxamide; (D-Ala(2)-mephe(4)-gly-ol(5))enkephalin; (R)-adrenaline.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: alpha-type CGRP; Cal1; CAL6; Calc; calcitonin; calcitonin gene-related peptide 1; calcitonin gene-related peptide I; calcitonin/calcitonin-related polypeptide, alpha; CGRP; CGRP-I; RATCAL6
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Is Marker For: Strains:   SHRSP.WKY-(Calca-D1Arb21)/IzmTkyo  
QTLs:   Bp138  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21168,878,212 - 168,883,176 (-)NCBI
Rnor_6.0 Ensembl1184,184,020 - 184,188,911 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01184,184,018 - 184,188,922 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01191,158,061 - 191,162,954 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41172,686,168 - 172,691,061 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11172,824,299 - 172,827,127 (-)NCBI
Celera1166,711,610 - 166,716,491 (-)NCBICelera
RH 3.4 Map11317.6RGD
RH 2.0 Map1757.3RGD
Cytogenetic Map1q35NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(6aR,9R)-N-[(2S)-1-hydroxybutan-2-yl]-4,7-dimethyl-6,6a,8,9-tetrahydroindolo[4,3-fg]quinoline-9-carboxamide  (EXP)
(D-Ala(2)-mephe(4)-gly-ol(5))enkephalin  (EXP)
(R)-adrenaline  (EXP)
(R)-noradrenaline  (EXP)
(S)-amphetamine  (EXP)
1,2-dichloroethane  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-(3,4-dimethoxyphenyl)-5-\{[2-(3,4-dimethoxyphenyl)ethyl](methyl)amino\}-2-(propan-2-yl)pentanenitrile  (ISO)
3',5'-cyclic AMP  (EXP,ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
3,5-dichloro-N-[[(2S)-1-ethyl-2-pyrrolidinyl]methyl]-2-hydroxy-6-methoxybenzamide  (EXP)
4-(4-methylpiperazin-1-yl)-7-(trifluoromethyl)pyrrolo[1,2-a]quinoxaline dimaleate  (EXP)
4-hydroxynon-2-enal  (EXP)
4-methyl-3-[[1-oxo-2-(propylamino)propyl]amino]-2-thiophenecarboxylic acid methyl ester  (ISO)
4-methylcatechol  (ISO)
5-azacytidine  (ISO)
6-oxoprostaglandin F1alpha  (EXP,ISO)
6-propyl-2-thiouracil  (EXP)
acetylcholine  (EXP)
acetylsalicylic acid  (EXP)
acrolein  (EXP)
aflatoxin B1  (ISO)
alachlor  (EXP)
aldehydo-D-glucose  (ISO)
all-trans-retinoic acid  (ISO)
allyl isothiocyanate  (EXP)
amiloride  (ISO)
aminoguanidine  (EXP)
ammonium chloride  (EXP)
Anetholtrithion  (ISO)
Aroclor 1254  (EXP)
arsenite(3-)  (ISO)
ATP  (EXP)
atropine  (EXP)
Bay-K-8644  (EXP)
benzo[a]pyrene  (ISO)
bethanechol  (EXP)
bis(2-ethylhexyl) phthalate  (EXP)
bisphenol A  (EXP,ISO)
Botulinum toxin type A  (EXP)
buta-1,3-diene  (ISO)
butanal  (ISO)
cadmium atom  (ISO)
calcium atom  (EXP,ISO)
calcium(0)  (EXP,ISO)
capsaicin  (EXP,ISO)
capsazepine  (EXP,ISO)
carbon dioxide  (EXP)
carbon nanotube  (ISO)
carvedilol  (EXP)
chelerythrine  (EXP)
chloroprene  (ISO)
cobalt atom  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
corticosterone  (EXP)
corticotropin  (EXP)
crocidolite asbestos  (EXP)
D-glucose  (ISO)
decabromodiphenyl ether  (EXP)
dexamethasone  (EXP,ISO)
dextran sulfate  (ISO)
dibutyl phthalate  (EXP)
diclofenac  (EXP)
diethylstilbestrol  (EXP)
disodium cromoglycate  (EXP)
disodium selenite  (ISO)
dorsomorphin  (ISO)
eletriptan  (EXP)
entinostat  (ISO)
epothilone B  (EXP)
ergotamine  (EXP)
ethanol  (EXP,ISO)
etoposide  (ISO)
fentanyl  (EXP)
fenvalerate  (EXP)
flavonoids  (EXP)
flurbiprofen  (EXP)
folic acid  (ISO)
fructose  (ISO)
Gallopamil  (EXP)
genistein  (ISO)
gentamycin  (EXP)
Ginkgolide A  (ISO)
glucose  (ISO)
glycidol  (EXP)
glyphosate  (EXP)
GR 127935  (EXP)
haloperidol  (EXP)
histamine  (EXP)
hydrogen chloride  (EXP)
ibuprofen  (EXP)
ICI 118551  (EXP)
indometacin  (EXP)
ionomycin  (EXP,ISO)
isoflurane  (ISO)
isoprenaline  (EXP)
KT 5720  (EXP)
Lafutidine  (EXP,ISO)
lead diacetate  (EXP)
lidocaine  (EXP,ISO)
linsidomine  (EXP)
lipopolysaccharide  (EXP,ISO)
LY294002  (ISO)
lycopene  (EXP)
magnesium atom  (ISO)
methylene blue  (EXP)
methylmercury chloride  (ISO)
methysergide  (EXP)
Mibefradil  (EXP)
morphine  (EXP,ISO)
N1'-[2-[[5-[(dimethylamino)methyl]-2-furanyl]methylthio]ethyl]-N1-methyl-2-nitroethene-1,1-diamine  (ISO)
naloxone  (EXP)
nefopam  (EXP)
nimodipine  (EXP)
nitrendipine  (EXP)
nitrofen  (EXP)
nitroglycerin  (EXP,ISO)
nitroprusside  (EXP)
nizatidine  (ISO)
NONOate(1-)  (ISO)
ozone  (ISO)
paclitaxel  (EXP)
panobinostat  (ISO)
paracetamol  (ISO)
pemirolast  (EXP)
phenol  (EXP)
Phenoxybenzamine  (EXP)
phenylephrine  (EXP,ISO)
phenytoin  (EXP)
pirinixic acid  (EXP)
potassium atom  (EXP,ISO)
potassium chloride  (EXP)
potassium dichromate  (ISO)
procaine  (ISO)
progesterone  (EXP,ISO)
propanal  (ISO)
propranolol  (EXP)
prostaglandin E2  (EXP)
ranitidine  (ISO)
rebaudioside A  (ISO)
resiniferatoxin  (ISO)
resveratrol  (EXP)
Rizatriptan benzoate  (EXP)
rofecoxib  (EXP)
ruthenium red  (EXP)
S-nitroso-N-acetyl-D-penicillamine  (EXP)
safranal  (EXP,ISO)
SB 431542  (ISO)
SCH 23390  (EXP)
serotonin  (EXP)
sevoflurane  (ISO)
silicon carbide  (EXP)
silicon dioxide  (EXP,ISO)
sodium chloride  (EXP,ISO)
Soman  (EXP)
steviol  (ISO)
stevioside  (ISO)
streptozocin  (EXP)
sulprostone  (EXP)
sumatriptan  (EXP,ISO)
suramin  (EXP)
tetrachloromethane  (ISO)
thapsigargin  (ISO)
titanium dioxide  (ISO)
topiramate  (EXP)
trichostatin A  (ISO)
tropan-3alpha-yl 3-hydroxy-2-phenylpropanoate  (EXP)
Tryptanthrine  (ISO)
Tungsten carbide  (ISO)
UTP  (EXP)
valproic acid  (ISO)
verapamil  (ISO)
veratridine  (EXP)
vorinostat  (ISO)
zinc atom  (EXP)
zinc protoporphyrin  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
activation of adenylate cyclase activity  (ISO)
activation of protein kinase activity  (ISO)
adenylate cyclase-activating G protein-coupled receptor signaling pathway  (IBA,ISO)
aging  (IEP)
amylin receptor signaling pathway  (ISO)
artery vasodilation involved in baroreceptor response to increased systemic arterial blood pressure  (ISO)
calcitonin gene-related peptide receptor signaling pathway  (ISO)
cellular calcium ion homeostasis  (ISO)
cellular response to nerve growth factor stimulus  (IEP,ISO)
cellular response to tumor necrosis factor  (IEP)
detection of temperature stimulus involved in sensory perception of pain  (ISO)
embryo implantation  (ISO)
endothelial cell migration  (ISO)
endothelial cell proliferation  (ISO)
feeding behavior  (ISO)
G protein-coupled receptor internalization  (ISO)
inflammatory response  (IEP,ISO)
leukocyte cell-cell adhesion  (ISO)
monocyte chemotaxis  (ISO)
negative regulation of blood pressure  (IMP,ISO)
negative regulation of bone resorption  (IEA,ISO)
negative regulation of calcium ion transport into cytosol  (ISO)
negative regulation of nervous system process  (ISO)
negative regulation of ossification  (ISO)
negative regulation of osteoclast differentiation  (ISO)
negative regulation of smooth muscle contraction  (IMP,ISO)
negative regulation of transcription, DNA-templated  (ISO)
nervous system process involved in regulation of systemic arterial blood pressure  (ISO)
neuromuscular junction development  (ISO)
neuropeptide signaling pathway  (ISO)
positive regulation of cell adhesion  (ISO)
positive regulation of cytosolic calcium ion concentration  (ISO)
positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G protein-coupled signaling pathway  (IEA,ISO)
positive regulation of interleukin-1 alpha production  (ISO)
positive regulation of interleukin-8 production  (ISO)
positive regulation of macrophage differentiation  (ISO)
positive regulation of ossification  (ISO)
protein phosphorylation  (ISO)
receptor internalization  (ISO)
regulation of blood pressure  (ISO)
regulation of cytosolic calcium ion concentration  (IBA,ISO)
regulation of heart contraction  (IDA)
regulation of heart rate  (ISO)
response to heat  (ISO)
response to pain  (ISO)
signal transduction  (IEA)
vasculature development  (ISO)
vasodilation  (IDA,ISO)

Cellular Component

Molecular Function

References

References - curated
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2. Adeghate E, etal., Ann N Y Acad Sci. 2006 Nov;1084:296-303.
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4. Amara SG, etal., J Biol Chem 1982 Mar 10;257(5):2129-32.
5. Amara SG, etal., Mol Cell Biol 1984 Oct;4(10):2151-60.
6. Amara SG, etal., Nature 1982 Jul 15;298(5871):240-4.
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16. GOA data from the GO Consortium
17. Hang CH, etal., World J Gastroenterol. 2004 Mar 15;10(6):875-80.
18. Hartmann P, etal., Naunyn Schmiedebergs Arch Pharmacol. 2011 Feb;383(2):179-89. Epub 2010 Dec 23.
19. Husum H, etal., Neuropharmacology 2002 May;42(6):798-806.
20. Jacobs JW, etal., Science 1981 Jul 24;213(4506):457-9.
21. Kaygisiz Z, etal., Acta Physiol Hung. 2003;90(2):133-46.
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24. Larson SD, etal., Am J Physiol Lung Cell Mol Physiol. 2004 Aug;287(2):L286-95. Epub 2004 Apr 2.
25. Lemos C, etal., Cephalalgia. 2010 Nov;30(11):1375-82. Epub 2010 May 10.
26. Li XQ, etal., J Neuropathol Exp Neurol. 2004 Oct;63(10):1092-103.
27. Lin YT, etal., J Neuroinflammation. 2011 Sep 30;8:126. doi: 10.1186/1742-2094-8-126.
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29. Menon S, etal., Brain Res. 2011 Mar 10;1378:119-24. Epub 2010 Dec 31.
30. MGD data from the GO Consortium
31. Mizutani A, etal., Anesthesiology. 2009 Feb;110(2):361-9. doi: 10.1097/ALN.0b013e3181942f3c.
32. Morrison JF, etal., Auton Neurosci. 2009 Mar 12;146(1-2):76-80. Epub 2009 Jan 17.
33. NCBI rat LocusLink and RefSeq merged data July 26, 2002
34. Pecile P, etal., Pediatrics. 2004 Aug;114(2):e249-54.
35. Pokabla MJ, etal., Peptides. 2002 Mar;23(3):507-14.
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37. Qiu H, etal., Lancet Infect Dis. 2020 Jun;20(6):689-696. doi: 10.1016/S1473-3099(20)30198-5. Epub 2020 Mar 25.
38. RGD automated data pipeline
39. RGD automated import pipeline for gene-chemical interactions
40. Ringer C, etal., Neurobiol Dis. 2012 Jan;45(1):547-54. Epub 2011 Sep 21.
41. Schneider L, etal., Pancreatology. 2009;9(5):662-9. Epub 2009 Aug 14.
42. Sun YP, etal., Endocrinology 2002 Oct;143(10):4056-64.
43. Supowit SC, etal., Hypertension 2001 Feb;37(2 Part 2):728-32.
44. Supowit SC, etal., Hypertension. 2005 Jan;45(1):109-14. Epub 2004 Dec 6.
45. Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
46. Wan S, etal., J Med Virol. 2020 Jul;92(7):797-806. doi: 10.1002/jmv.25783. Epub 2020 Apr 1.
47. Yan Y, etal., BMJ Open Diabetes Res Care. 2020 Apr;8(1). pii: 8/1/e001343. doi: 10.1136/bmjdrc-2020-001343.
Additional References at PubMed
PMID:1278175   PMID:1317267   PMID:1326102   PMID:2408883   PMID:3266556   PMID:6400492   PMID:6933496   PMID:7521790   PMID:7698182   PMID:7955356   PMID:8078488   PMID:8261138  
PMID:8278635   PMID:8453761   PMID:8582325   PMID:8735980   PMID:8889548   PMID:8940110   PMID:9271704   PMID:9322931   PMID:9685362   PMID:9838101   PMID:9853118   PMID:10208559  
PMID:10532808   PMID:10642343   PMID:10715114   PMID:10822112   PMID:10882736   PMID:11014233   PMID:11166483   PMID:11276224   PMID:11466438   PMID:11551509   PMID:11717154   PMID:12030813  
PMID:12060780   PMID:12488435   PMID:12507435   PMID:12531473   PMID:12531474   PMID:12697724   PMID:12832107   PMID:12888222   PMID:14567394   PMID:14624932   PMID:14722252   PMID:14736738  
PMID:14765981   PMID:15193773   PMID:15205172   PMID:15248232   PMID:15277470   PMID:15385550   PMID:15512786   PMID:15537449   PMID:15582720   PMID:15629546   PMID:15643132   PMID:15879482  
PMID:15882801   PMID:16014619   PMID:16039054   PMID:16118273   PMID:16238469   PMID:16284585   PMID:16337713   PMID:16399878   PMID:16541240   PMID:16847357   PMID:16875511   PMID:16904178  
PMID:16935424   PMID:16973914   PMID:16997465   PMID:17033093   PMID:17184994   PMID:17194737   PMID:17241109   PMID:17267696   PMID:17455082   PMID:17457027   PMID:17640046   PMID:17660394  
PMID:17666428   PMID:17932220   PMID:17950540   PMID:17964731   PMID:17983652   PMID:18035338   PMID:18057382   PMID:18167349   PMID:18186028   PMID:18328477   PMID:18521856   PMID:18539096  
PMID:18650319   PMID:18662828   PMID:18806620   PMID:18809208   PMID:19018584   PMID:19076981   PMID:19095023   PMID:19130224   PMID:19141408   PMID:19225405   PMID:19247856   PMID:19387418  
PMID:19422825   PMID:19429062   PMID:19457095   PMID:19691152   PMID:19735698   PMID:19864020   PMID:20138125   PMID:20139325   PMID:20354476   PMID:20375903   PMID:20385119   PMID:20519072  
PMID:20534813   PMID:20559810   PMID:20596610   PMID:20851839   PMID:20936354   PMID:20955764   PMID:21040789   PMID:21057386   PMID:21171370   PMID:21216873   PMID:21289190   PMID:21289592  
PMID:21394197   PMID:21514666   PMID:21561603   PMID:21606356   PMID:21671799   PMID:21694766   PMID:21763400   PMID:21809559   PMID:22038198   PMID:22038237   PMID:22074408   PMID:22145886  
PMID:22208649   PMID:22233274   PMID:22472888   PMID:22500019   PMID:22688302   PMID:22706400   PMID:22742729   PMID:22763971   PMID:22881710   PMID:22935198   PMID:23056625   PMID:23112192  
PMID:23123284   PMID:23155193   PMID:23218524   PMID:23324931   PMID:23392237   PMID:23395606   PMID:23468996   PMID:23570731   PMID:23571710   PMID:23649215   PMID:23821557   PMID:23958278  
PMID:24004534   PMID:24051030   PMID:24076003   PMID:24140435   PMID:24269509   PMID:24321404   PMID:24328744   PMID:24384662   PMID:24508136   PMID:24701588   PMID:24760869   PMID:24877063  
PMID:24887115   PMID:24998872   PMID:25219961   PMID:25489075   PMID:25563479   PMID:26164378   PMID:26713069   PMID:26930007   PMID:27082317   PMID:27306412   PMID:27345362   PMID:27470397  
PMID:27579553   PMID:27737007   PMID:27919019   PMID:27939448   PMID:27990431   PMID:28393079   PMID:28560441   PMID:28599085   PMID:29730242   PMID:29846865   PMID:31035923   PMID:31298358  
PMID:31386894   PMID:32212492   PMID:32853530  


Genomics

Candidate Gene Status
Calca is a candidate Gene for QTL Bp138
Comparative Map Data
Calca
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21168,878,212 - 168,883,176 (-)NCBI
Rnor_6.0 Ensembl1184,184,020 - 184,188,911 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01184,184,018 - 184,188,922 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01191,158,061 - 191,162,954 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41172,686,168 - 172,691,061 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11172,824,299 - 172,827,127 (-)NCBI
Celera1166,711,610 - 166,716,491 (-)NCBICelera
RH 3.4 Map11317.6RGD
RH 2.0 Map1757.3RGD
Cytogenetic Map1q35NCBI
CALCA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1114,966,668 - 14,972,351 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p13 Ensembl1114,966,668 - 14,972,354 (-)EnsemblGRCh38hg38GRCh38
GRCh381114,966,668 - 14,972,361 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371114,988,214 - 14,993,897 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361114,944,792 - 14,950,408 (-)NCBINCBI36hg18NCBI36
Build 341114,946,625 - 14,950,427NCBI
Celera1115,115,335 - 15,120,952 (-)NCBI
Cytogenetic Map11p15.2NCBI
HuRef1114,671,857 - 14,677,473 (-)NCBIHuRef
CHM1_11114,987,226 - 14,992,843 (-)NCBICHM1_1
Calca
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm397114,225,223 - 114,236,145 (-)NCBIGRCm39mm39
GRCm39 Ensembl7114,230,713 - 114,235,592 (-)Ensembl
GRCm387114,625,981 - 114,636,910 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl7114,631,478 - 114,636,357 (-)EnsemblGRCm38mm10GRCm38
MGSCv377121,774,992 - 121,779,871 (-)NCBIGRCm37mm9NCBIm37
MGSCv367114,422,640 - 114,427,439 (-)NCBImm8
Celera7114,584,937 - 114,589,792 (-)NCBICelera
Cytogenetic Map7F1NCBI
cM Map759.99NCBI
CALCA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11114,745,588 - 14,751,267 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1114,745,588 - 14,751,267 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01115,055,897 - 15,061,539 (-)NCBIMhudiblu_PPA_v0panPan3
CRSP-3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12137,676,841 - 37,680,643 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2137,676,841 - 37,680,645 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2137,176,307 - 37,180,108 (+)NCBI
ROS_Cfam_1.02138,770,713 - 38,774,520 (+)NCBI
UNSW_CanFamBas_1.02137,993,320 - 37,997,114 (+)NCBI
UU_Cfam_GSD_1.02138,281,026 - 38,284,825 (+)NCBI
Calca
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494747,766,690 - 47,772,207 (+)NCBI
SpeTri2.0NW_0049365283,800,801 - 3,806,000 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CALCB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1244,043,135 - 44,048,651 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2247,248,414 - 47,253,904 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LOC103239768
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1149,946,574 - 49,956,010 (+)NCBI
ChlSab1.1 Ensembl149,951,694 - 49,954,092 (+)Ensembl
Calca
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247666,764,388 - 6,771,396 (-)NCBI

Position Markers
D1Smu11  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21168,879,333 - 168,879,526 (+)MAPPER
Rnor_6.01184,185,140 - 184,185,332NCBIRnor6.0
Rnor_5.01191,159,183 - 191,159,375UniSTSRnor5.0
RGSC_v3.41172,687,290 - 172,687,482UniSTSRGSC3.4
Celera1166,712,732 - 166,712,912UniSTS
Cytogenetic Map1q34UniSTS
PMC109322P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21168,880,516 - 168,881,338 (+)MAPPER
Rnor_6.01184,186,323 - 184,187,144NCBIRnor6.0
Rnor_5.01191,160,366 - 191,161,187UniSTSRnor5.0
RGSC_v3.41172,688,473 - 172,689,294UniSTSRGSC3.4
Celera1166,713,903 - 166,714,724UniSTS
Cytogenetic Map1q34UniSTS
RH94470  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21168,878,272 - 168,878,451 (+)MAPPER
Rnor_6.01184,184,079 - 184,184,257NCBIRnor6.0
Rnor_5.01191,158,122 - 191,158,300UniSTSRnor5.0
RGSC_v3.41172,686,229 - 172,686,407UniSTSRGSC3.4
Celera1166,711,671 - 166,711,849UniSTS
RH 3.4 Map11317.6UniSTS
Cytogenetic Map1q34UniSTS
RH131181  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21168,880,115 - 168,880,318 (+)MAPPER
Rnor_6.01184,185,922 - 184,186,124NCBIRnor6.0
Rnor_5.01191,159,965 - 191,160,167UniSTSRnor5.0
RGSC_v3.41172,688,072 - 172,688,274UniSTSRGSC3.4
Celera1166,713,502 - 166,713,704UniSTS
RH 3.4 Map11317.59UniSTS
Cytogenetic Map1q34UniSTS
RH137698  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21168,878,416 - 168,878,596 (+)MAPPER
Rnor_6.01184,184,223 - 184,184,402NCBIRnor6.0
Rnor_5.01191,158,266 - 191,158,445UniSTSRnor5.0
RGSC_v3.41172,686,373 - 172,686,552UniSTSRGSC3.4
Celera1166,711,815 - 166,711,994UniSTS
RH 3.4 Map11317.29UniSTS
Cytogenetic Map1q34UniSTS
Calca  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21168,880,512 - 168,881,370 (+)MAPPER
Rnor_6.01184,186,319 - 184,187,176NCBIRnor6.0
Rnor_5.01191,160,362 - 191,161,219UniSTSRnor5.0
RGSC_v3.41172,688,469 - 172,689,326UniSTSRGSC3.4
Celera1166,713,899 - 166,714,756UniSTS
Cytogenetic Map1q34UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149578693217054291Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)182788437239853971Rat
724521Uae1Urinary albumin excretion QTL 13.80.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)194201400184846632Rat
1358902Bw47Body weight QTL 471.67body mass (VT:0001259)body weight (CMO:0000012)194201400197187904Rat
1331793Bp200Blood pressure QTL 2003.71601arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)199983293188289386Rat
1331751Bp199Blood pressure QTL 1993.60022arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)199983293198656062Rat
1331749Hrtrt11Heart rate QTL 112.973heart pumping trait (VT:2000009)heart rate (CMO:0000002)199983293216213510Rat
70209Niddm23Non-insulin dependent diabetes mellitus QTL 232.82blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)199983293216325819Rat
731168Bp154Blood pressure QTL 1543.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1100131562236763528Rat
8655649Arrd1Age-related retinal degeneration QTL 14.89retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1106002252202571904Rat
1354591Cm36Cardiac mass QTL 364.1heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1108986301219232156Rat
1354615Cm32Cardiac mass QTL 325.2heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1108986301219232156Rat
1354606Bp246Blood pressure QTL 2463.6arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)1108986301238830534Rat
1300158Bp173Blood pressure QTL 1733.48arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1122614824201146953Rat
7794788Mcs32Mammary carcinoma susceptibility QTL 322.61mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)1122614824262664716Rat
631199Cm23Cardiac mass QTL 234.60.0004heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)1124603592188289386Rat
7421630Bp362Blood pressure QTL 3620.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1125875758262433692Rat
631205Bp196Blood pressure QTL 19640.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1126240667217054291Rat
631544Bp84Blood pressure QTL 845.6arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1130779148198585664Rat
1358189Cstrr1Cold stress response QTL 10.0001catecholamine amount (VT:0010543)urine norepinephrine level (CMO:0001629)1130779148199254774Rat
1578770Stresp23Stress response QTL 23kidney sympathetic nerve activity (VT:0004050)stimulated renal sympathetic nerve activity to basal renal sympathetic nerve activity ratio (CMO:0001786)1130779148199254774Rat
1641895Bp298Blood pressure QTL 298arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1130779148199254774Rat
631549Bp89Blood pressure QTL 895.7arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1130779320219238476Rat
634348Bp138Blood pressure QTL 138arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1133076978184188922Rat
724562Rends1Renal damage susceptibility QTL 10.05kidney glomerulus integrity trait (VT:0010546)index of glomerular damage (CMO:0001135)1137787261236763528Rat
61341Bp26Blood pressure QTL 26arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1137787261236763528Rat
738006Anxrr14Anxiety related response QTL 1440.00035locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1141296374186296374Rat
738028Anxrr12Anxiety related response QTL 124.90.00001locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)1141296374186296374Rat
1558645Bw55Body weight QTL 553.20.004body mass (VT:0001259)body weight (CMO:0000012)1144395993189395993Rat
6893347Bw98Body weight QTL 980.20.53body mass (VT:0001259)body weight (CMO:0000012)1144395993189395993Rat
6893361Bw104Body weight QTL 1040.590.27body mass (VT:0001259)body weight (CMO:0000012)1144395993189395993Rat
7771612Cm80Cardiac mass QTL 808.4heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)1144634295241482368Rat
71118Thym1Thymus enlargement QTL 110.170.001thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1153655976198655976Rat
724550Thym3Thymus enlargement QTL 37.820.001thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1153655976198655976Rat
631519Pia11Pristane induced arthritis QTL 115.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1153656062198656062Rat
1598853Memor3Memory QTL 34.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)1153834077232297227Rat
61348Bp30Blood pressure QTL 302.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1154337847215828102Rat
70160Bw18Body weight QTL 185.7body mass (VT:0001259)body weight (CMO:0000012)1156446196214277437Rat
737828Hcas3Hepatocarcinoma susceptibility QTL 34.9liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)1156446196243311614Rat
2302378Insul11Insulin level QTL 113.25blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1156446196274977688Rat
634315Niddm45Non-insulin dependent diabetes mellitus QTL 457.16blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1156446783188289244Rat
61379Bp44Blood pressure QTL 4419.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1156446783189514504Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1161321152273792054Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1161321256273791893Rat
1578778Pur4Proteinuria QTL 43.30.003total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1161321256273791893Rat
1354634Kidm12Kidney mass QTL 123.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)1161784169219232156Rat
1354636Lmblg1Limb length QTL 16.4tibia length (VT:0004357)tibia length (CMO:0000450)1161784169219232156Rat
1354602Bw35Body weight QTL 3512.2body mass (VT:0001259)body weight (CMO:0000012)1161784169219232156Rat
1354620Kidm19Kidney mass QTL 194kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1161784169219232156Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1161784169278228889Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1161784169278228889Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1161784169278228889Rat
1358886Bp260Blood pressure QTL 2603.67arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1161784422246226103Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1163796316282763074Rat
1582204Livw1Liver weight QTL 13.60.0003liver mass (VT:0003402)liver weight as percentage of body weight (CMO:0000141)1166100317188289386Rat
4889428Stresp24Stress response QTL 240.05heart pumping trait (VT:2000009)absolute change in electrocardiographic low frequency R-R spectral component to high frequency R-R spectral component ratio (CMO:0002162)1166577232211577232Rat
61343Bp28Blood pressure QTL 28arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1167027868212027868Rat
631548Bp88Blood pressure QTL 8850.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1167394665191883991Rat
1354618Kidm15Kidney mass QTL 155kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)1167394665219232156Rat
2312420Pur17Proteinuria QTL 177.10.0001urine protein amount (VT:0005160)urine total protein excretion rate (CMO:0000756)1167394665238830534Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1167394665278228889Rat
2303622Vencon6Ventilatory control QTL 60.001respiration trait (VT:0001943)respiration rate (CMO:0000289)1169971964214971964Rat
2292222Bp307Blood pressure QTL 3073.060.0014arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1174905700233490237Rat
2292220Bp306Blood pressure QTL 3063.470.00087arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1174905700264802994Rat
619613Bp77Blood pressure QTL 770.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1175447029220447029Rat
619613Bp77Blood pressure QTL 770.01arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1175447029220447029Rat
737974Bp161Blood pressure QTL 1610.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1175447162197963658Rat
61347Bp197Blood pressure QTL 1974.2arterial blood pressure trait (VT:2000000)blood pressure measurement (CMO:0000003)1175462885220462885Rat
2312558Glom17Glomerulus QTL 173.90.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)1177235071208786962Rat


Related Rat Strains
The following Strains have been annotated to Calca

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:242
Count of miRNA genes:167
Interacting mature miRNAs:184
Transcripts:ENSRNOT00000014948, ENSRNOT00000055124
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium
Low 11 4 7 4 74 20 25 11
Below cutoff 2 14 4 1 5 1 1 1 13 10 1

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001033955 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001033956 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_017338 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008759676 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AH005313 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AW523601 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY702025 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BG663259 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB711853 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CB746609 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CF978038 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473956 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000043 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M11597 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M26137 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  V01228 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  V01229 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  V01230 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  V01231 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000014948   ⟹   ENSRNOP00000014948
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1184,186,041 - 184,188,911 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000055124   ⟹   ENSRNOP00000051997
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1184,184,020 - 184,188,911 (-)Ensembl
RefSeq Acc Id: NM_001033955   ⟹   NP_001029127
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21168,878,212 - 168,883,105 (-)NCBI
Rnor_6.01184,184,018 - 184,188,911 (-)NCBI
Rnor_5.01191,158,061 - 191,162,954 (-)NCBI
RGSC_v3.41172,686,168 - 172,691,061 (-)RGD
Celera1166,711,610 - 166,716,491 (-)RGD
Sequence:
RefSeq Acc Id: NM_001033956   ⟹   NP_001029128
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21168,878,212 - 168,883,105 (-)NCBI
Rnor_6.01184,184,018 - 184,188,911 (-)NCBI
Rnor_5.01191,158,061 - 191,162,954 (-)NCBI
RGSC_v3.41172,686,168 - 172,691,061 (-)RGD
Celera1166,711,610 - 166,716,491 (-)RGD
Sequence:
RefSeq Acc Id: NM_017338   ⟹   NP_059034
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21168,880,235 - 168,883,105 (-)NCBI
Rnor_6.01184,186,041 - 184,188,911 (-)NCBI
Rnor_5.01191,158,061 - 191,162,954 (-)NCBI
RGSC_v3.41172,686,168 - 172,691,061 (-)RGD
Celera1166,713,621 - 166,716,491 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008759676   ⟹   XP_008757898
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21168,880,094 - 168,883,176 (-)NCBI
Rnor_6.01184,185,900 - 184,188,922 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001029127   ⟸   NM_001033955
- Peptide Label: isoform Cgrp preproprotein
- UniProtKB: P01256 (UniProtKB/Swiss-Prot),   A0A0G2JSX2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_001029128   ⟸   NM_001033956
- Peptide Label: isoform Cgrp preproprotein
- UniProtKB: P01256 (UniProtKB/Swiss-Prot),   A0A0G2JSX2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: NP_059034   ⟸   NM_017338
- Peptide Label: isoform Calca preproprotein
- UniProtKB: P01257 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008757898   ⟸   XM_008759676
- Peptide Label: isoform X1
- UniProtKB: P01257 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000051997   ⟸   ENSRNOT00000055124
RefSeq Acc Id: ENSRNOP00000014948   ⟸   ENSRNOT00000014948
Protein Domains
CALCITONIN

Transcriptome

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

Promoters
RGD ID:13690332
Promoter ID:EPDNEW_R857
Type:single initiation site
Name:Calca_1
Description:calcitonin-related polypeptide alpha
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_6.01184,188,910 - 184,188,970EPDNEW
RGD ID:6849988
Promoter ID:EP29003
Type:single initiation site
Name:RN_CAL1
Description:Calcitonin/calcitonin gene-related peptide, CALCA or CALC gene.
SO ACC ID:SO:0000170
Source:EPD (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Notes:homology_group=Homology group 156; Mammalian calcitonin gene
Experiment Methods:Nuclease protection; Sequencing of a full-length cDNA; Primer extension; transfected or transformed cells
Regulation:thyroid C (repressed by or weakly expressed in) cells, CNS
Position:No map positions available.

Strain Variation

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2254 AgrOrtholog
Ensembl Genes ENSRNOG00000011130 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000014948 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000051997 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000014948 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000055124 ENTREZGENE, UniProtKB/TrEMBL
InterPro Calcitonin UniProtKB/Swiss-Prot
  Calcitonin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Calcitonin/adrenomedullin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Calcitonin_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Calcitonin_gene-rel_peptide UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Calcitonin_peptide-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24241 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 24241 ENTREZGENE
PANTHER PTHR10505 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Calc_CGRP_IAPP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB CALCA RGD
PhenoGen Calca PhenoGen
PRINTS CALCITONINA UniProtKB/Swiss-Prot
  CALCITONINB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CALCITONIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART CALCITONIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC219251
UniProt A0A0G2JSX2 ENTREZGENE, UniProtKB/TrEMBL
  CALC_RAT UniProtKB/Swiss-Prot
  CALCA_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  P01257 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2009-11-05 Calca  calcitonin-related polypeptide alpha  Calca  calcitonin/calcitonin-related polypeptide, alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Calca  calcitonin/calcitonin-related polypeptide, alpha      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_cellular_localization secreted by C cells of the thyroid 628360
gene_drugs antiestrogen ICI 182,780 blocks the decrease in mRNA levels due to estrogen treatment; anti-progestin RU 486 lowers mRNA levels 628360
gene_expression highest level of expression in diestrus and the lowest in proestrus evening during estrus cycle 628360
gene_process dilates peripheral arteries, decreasing blood pressure 68890
gene_process indicator for bacterial infection and sepsis 625748
gene_process exhibits selective and potent inhibition of prolactin biosynthesis, secretion and lactotroph cell proliferation 628360
gene_process may be involved in negative regulation of lactotroph function in anterior pituitary gland; interplay of ovarian hormones modulate calcitonin secretion thay may affect lactotroph function 628360
gene_protein procalcitonin (PCT), the precursor for calcitonin, is a 110-amino acid polypeptide 628360
gene_regulation regulated by serum Ca2+ concentrations 628360
gene_regulation lipopolysaccharide increases mRNA in the pituitary and is associated with significant elevations of the immunoreactive calcitonin (iCT) levels in the serum 628360
gene_regulation tightly regulated by ovarian hormones; estrogen downregulates transcription while progesterone produces marked increase in estrogen-primed pituitary gland 628360
gene_regulation mature calcitonin is produced by posttranslational processing from procalcitonin and carboxy-terminus amidation 628360