Gja1 (gap junction protein, alpha 1) - Rat Genome Database

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Gene: Gja1 (gap junction protein, alpha 1) Rattus norvegicus
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Symbol: Gja1
Name: gap junction protein, alpha 1
RGD ID: 2690
Description: Exhibits connexin binding activity; gap junction channel activity; and protein domain specific binding activity. Involved in several processes, including negative regulation of cell population proliferation; positive regulation of cell communication; and reproductive structure development. Localizes to several cellular components, including connexin complex; endosome; and fascia adherens. Used to study amnestic disorder; high grade glioma; and myocardial infarction. Biomarker of several diseases, including artery disease (multiple); autoimmune thyroiditis; borna disease; ischemia (multiple); and tongue squamous cell carcinoma. Human ortholog(s) of this gene implicated in several diseases, including autosomal recessive craniometaphyseal dysplasia; congenital heart disease (multiple); erythrokeratodermia variabilis (multiple); oculodentodigital dysplasia; and palmoplantar keratoderma and congenital alopecia 1. Orthologous to human GJA1 (gap junction protein alpha 1); PARTICIPATES IN connexin signaling pathway; N-cadherin signaling pathway; arrhythmogenic right ventricular cardiomyopathy pathway; INTERACTS WITH (+)-pilocarpine; (-)-antofine; (R)-lipoic acid.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: connexin 43; connexin k1; connexin-43; Cx43; Cxnk1; gap junction 43 kDa heart protein; gap junction alpha-1 protein; gap junction membrane channel protein alpha 1; gap junction protein alpha 1 43 kD; Gap junction protein alpha 1 43 kD (connexin 43); Gap junction protein, alpha 1, 43 kD (connexin 43); MGC93610
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22035,756,007 - 35,768,481 (+)NCBI
Rnor_6.0 Ensembl2037,876,650 - 37,889,089 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02037,876,650 - 37,889,097 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02039,612,080 - 39,624,555 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42035,409,815 - 35,422,262 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12035,423,614 - 35,436,057 (+)NCBI
Celera2037,095,121 - 37,107,568 (+)NCBICelera
Cytogenetic Map20q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
Acute Lung Injury  (IEP)
adenoma  (ISO)
amnestic disorder  (IMP)
arrhythmogenic right ventricular cardiomyopathy  (ISO)
atrial fibrillation  (IEP,ISO)
atrioventricular septal defect  (ISO)
Atrioventricular Septal Defect 3  (ISO)
autistic disorder  (ISO)
autoimmune thyroiditis  (IEP)
autosomal recessive craniometaphyseal dysplasia  (ISO)
Basaran Yilmaz Syndrome  (ISO)
borna disease  (IEP)
Brain Injuries  (IEP)
brain ischemia  (IEP)
Breast Neoplasms  (ISO)
Cardiac Arrhythmias  (IEP,ISO)
Cardiac Fibrosis  (IEP)
chronic kidney disease  (ISO)
Chylothorax  (ISO)
cleft lip  (ISO)
coronary aneurysm  (ISO)
Diabetic Foot  (ISO)
Diaphragmatic Hernia  (ISO)
dilated cardiomyopathy  (ISO)
Disease Progression  (ISO)
epilepsy  (ISO)
erythrokeratodermia variabilis  (ISO)
erythrokeratodermia variabilis et progressiva 3  (ISO)
Experimental Arthritis  (IMP)
Experimental Diabetes Mellitus  (IDA,IEP,ISO)
Experimental Liver Cirrhosis  (ISO)
genetic disease  (ISO)
Hearing Loss  (ISO)
Hemorrhagic Shock  (IEP)
hereditary lymphedema IA  (ISO)
high grade glioma  (IMP)
Huntington's disease  (ISO)
Hyperalgesia  (IEP,IMP)
hypertension  (IEP,ISO)
hypoplastic left heart syndrome  (ISO)
Hypoplastic Left Heart Syndrome 1  (ISO)
impotence  (IEP)
intellectual disability  (ISO)
ischemia  (IEP)
Lung Neoplasms  (ISO)
Lymphatic Abnormalities  (ISO)
myocardial infarction  (IEP,IMP)
Myocardial Reperfusion Injury  (ISO)
myocarditis  (ISO)
Neuralgia  (ISO)
Nonsyndromic Sensorineural Hearing Loss  (ISO)
oculodentodigital dysplasia  (ISO)
Oculodentodigital Dysplasia, Autosomal Recessive  (ISO)
Overactive Urinary Bladder  (IEP)
palmoplantar keratoderma and congenital alopecia 1  (ISO)
palmoplantar keratosis  (ISO)
Parkinsonism  (IDA)
Prostatic Neoplasms  (ISO)
pulmonary hypertension  (IEP)
renovascular hypertension  (IEP)
Schwartz-Lelek Syndrome  (ISO)
Skin Neoplasms  (ISO)
Spinal Cord Injuries  (IEP,IMP)
Sudden Cardiac Death  (ISO)
syndactyly  (ISO)
syndactyly type 3  (ISO)
syndactyly type 5  (ISO)
tetralogy of Fallot  (ISO)
tongue squamous cell carcinoma  (IEP)
transient cerebral ischemia  (IEP,ISO)
type 2 diabetes mellitus  (IEP)
urethral obstruction  (IEP)
visual epilepsy  (IEP,ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-pilocarpine  (EXP)
(-)-antofine  (EXP)
(R)-lipoic acid  (EXP,ISO)
(S)-colchicine  (EXP)
1,3-dinitrobenzene  (EXP)
1-heptanol  (EXP)
1-naphthyl isothiocyanate  (EXP)
1-O-palmitoyl-2-O-(5-oxovaleryl)-sn-glycero-3-phosphocholine  (EXP)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (EXP,ISO)
2,2',4,4',5,5'-hexabromobiphenyl  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (EXP,ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (EXP)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-diaminotoluene  (ISO)
2,6-di-tert-butyl-4-methylphenol  (EXP,ISO)
2-acetamidofluorene  (EXP)
2-butoxyethanol  (ISO)
3,3',5-triiodo-L-thyronine  (EXP)
3,4-methylenedioxymethamphetamine  (EXP,ISO)
3,5-dibromo-4-hydroxybenzonitrile  (EXP)
3,5-diethoxycarbonyl-1,4-dihydrocollidine  (ISO)
3-\{1-[3-(dimethylamino)propyl]-1H-indol-3-yl\}-4-(1H-indol-3-yl)-1H-pyrrole-2,5-dione  (EXP)
3-methyladenine  (EXP)
3-methylcholanthrene  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-tert-Octylphenol  (EXP)
4-vinylcyclohexene dioxide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
5-azacytidine  (EXP,ISO)
5-fluorouracil  (ISO)
7,12-dimethyltetraphene  (EXP,ISO)
8-Br-cAMP  (ISO)
acetamide  (EXP)
acetylleucyl-leucyl-norleucinal  (ISO)
acetylsalicylic acid  (EXP)
acrylamide  (EXP)
afimoxifene  (ISO)
aflatoxin B1  (EXP,ISO)
aldehydo-D-glucose  (EXP,ISO)
all-trans-retinoic acid  (EXP,ISO)
all-trans-retinol  (EXP)
ametryn  (EXP)
amiodarone  (ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
anastrozole  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (EXP,ISO)
apocynin  (EXP)
Aroclor 1254  (ISO)
arotinoid acid  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
astaxanthin  (ISO)
atenolol  (EXP)
ATP  (ISO)
atrazine  (EXP)
benzene  (ISO)
benzo[a]pyrene  (EXP,ISO)
Benzoyl peroxide  (ISO)
beta-carotene  (EXP,ISO)
bis(2-chloroethyl) sulfide  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
BQ 123  (EXP)
bucladesine  (EXP)
butyric acid  (EXP)
cadmium atom  (EXP,ISO)
cadmium dichloride  (ISO)
caffeine  (EXP)
calcidiol  (EXP)
calciol  (EXP)
capsanthin  (EXP)
carbendazim  (EXP)
CARBENOXOLONE  (EXP)
carbon nanotube  (ISO)
carvedilol  (EXP,ISO)
chaetoglobosin A  (EXP)
chloral hydrate  (EXP)
chloropicrin  (ISO)
chloroprene  (ISO)
chloroquine  (EXP,ISO)
chlorothalonil  (ISO)
choline  (ISO)
chromium atom  (EXP)
cisplatin  (EXP,ISO)
clozapine  (EXP)
cobalt dichloride  (EXP,ISO)
copper atom  (EXP)
copper(0)  (EXP)
curcumin  (ISO)
cyclophosphamide  (EXP)
cylindrospermopsin  (ISO)
D-glucose  (EXP,ISO)
DDT  (EXP,ISO)
decabromodiphenyl ether  (ISO)
dexamethasone  (EXP)
diarsenic trioxide  (ISO)
dibenzo[a,l]pyrene  (ISO)
dibutyl phthalate  (EXP,ISO)
diclofenac  (ISO)
dieldrin  (EXP,ISO)
diethylstilbestrol  (ISO)
dimethyl sulfoxide  (EXP)
dimethylarsinous acid  (ISO)
dioxygen  (EXP,ISO)
diuron  (EXP)
doxorubicin  (EXP,ISO)
doxycycline  (ISO)
ebselen  (EXP)
endosulfan  (EXP,ISO)
ethanol  (ISO)
ethidium  (EXP)
etoposide  (ISO)
ferric oxide  (ISO)
fluoranthene  (ISO)
fluorene  (ISO)
fluoxetine  (EXP)
flutamide  (EXP,ISO)
folic acid  (ISO)
fucoxanthin  (ISO)
fulvestrant  (ISO)
furan  (EXP)
gamma-hexachlorocyclohexane  (EXP,ISO)
Gastrodin  (EXP)
genistein  (EXP,ISO)
glafenine  (EXP)
glucose  (EXP,ISO)
glutaraldehyde  (EXP)
gossypol  (EXP)
griseofulvin  (ISO)
haloperidol  (EXP)
heptachlor  (ISO)
Heptachlor epoxide  (EXP,ISO)
hydrogen peroxide  (EXP,ISO)
hydrogen sulfide  (ISO)
hydroxyflutamide  (EXP)
imidacloprid  (EXP)
indoxyl sulfate  (EXP)
ioxynil  (EXP)
iprodione  (EXP)
irinotecan  (EXP,ISO)
isocarbophos  (EXP)
isoprenaline  (EXP,ISO)
L-ascorbic acid  (EXP)
L-methionine  (ISO)
lactacystin  (ISO)
lead diacetate  (EXP)
lead(0)  (EXP)
lead(2+)  (EXP)
leflunomide  (EXP,ISO)
letrozole  (ISO)
leupeptin  (ISO)
lipoic acid  (EXP,ISO)
lipopolysaccharide  (ISO)
lithium atom  (EXP)
lithium chloride  (EXP)
lithium hydride  (EXP)
losartan  (EXP)
lycopene  (EXP,ISO)
lysophosphatidylcholine  (EXP)
manganese(II) chloride  (EXP)
medroxyprogesterone acetate  (ISO)
menadione  (ISO)
mercury dichloride  (ISO)
methoxychlor  (ISO)
methylseleninic acid  (ISO)
metoprolol  (EXP)
mifepristone  (ISO)
mono(2-ethylhexyl) phthalate  (EXP,ISO)
N-benzyloxycarbonyl-L-leucyl-L-leucyl-L-leucinal  (EXP,ISO)
N-ethyl-N-nitrosourea  (ISO)
N-methyl-4-phenylpyridinium  (EXP)
N-methyl-N'-nitro-N-nitrosoguanidine  (ISO)
N-nitrosodiethylamine  (EXP,ISO)
N-nitrosodimethylamine  (EXP)
nickel sulfate  (ISO)
nitric oxide  (EXP)
nitrofen  (EXP,ISO)
ochratoxin A  (EXP,ISO)
okadaic acid  (ISO)
oxaliplatin  (EXP)
p-cresol  (EXP)
p-tert-Amylphenol  (EXP)
paracetamol  (ISO)
paraquat  (ISO)
perfluorooctane-1-sulfonic acid  (EXP,ISO)
perfluorooctanoic acid  (ISO)
phenethyl isothiocyanate  (EXP,ISO)
phenobarbital  (ISO)
phenol  (EXP)
phenol red  (ISO)
phenylephrine  (EXP)
phorbol 13-acetate 12-myristate  (EXP,ISO)
piperonyl butoxide  (EXP)
pirinixic acid  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (EXP,ISO)
propranolol  (EXP)
quercetin  (EXP,ISO)
radicicol  (EXP)
reactive oxygen species  (ISO)
resveratrol  (EXP,ISO)
Ro 41-5253  (ISO)
rotenone  (EXP,ISO)
SB 203580  (EXP,ISO)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
simvastatin  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium dodecyl sulfate  (ISO)
sodium fluoride  (ISO)
sodium sulfide (anhydrous)  (ISO)
Soman  (EXP)
succimer  (ISO)
sulfur dioxide  (ISO)
tamoxifen  (EXP,ISO)
tert-butyl hydroperoxide  (ISO)
testosterone  (EXP)
tetrachloromethane  (EXP,ISO)
titanium dioxide  (EXP)
tolbutamide  (EXP)
toluene  (EXP)
topotecan  (EXP,ISO)
toxaphene  (ISO)
tributylstannane  (EXP)
trichloroethene  (EXP)
triclosan  (ISO)
Triptolide  (ISO)
triptonide  (ISO)
trovafloxacin  (ISO)
urethane  (ISO)
valdecoxib  (EXP)
valproic acid  (ISO)
vanadium atom  (EXP)
vanadium(0)  (EXP)
vinclozolin  (EXP)
vitamin E  (EXP)
WIN 55212-2  (ISO)
wortmannin  (EXP)
zardaverine  (EXP)
zinc atom  (EXP)
zinc sulfate  (EXP)
zinc(0)  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
adult heart development  (ISO)
apoptotic process  (IMP)
ATP transport  (IMP)
atrial ventricular junction remodeling  (ISO)
blood vessel morphogenesis  (ISO)
bone development  (ISO,ISS)
bone remodeling  (ISO,ISS)
cardiac conduction  (ISO)
cell communication  (IMP)
cell communication by chemical coupling  (ISO)
cell communication by electrical coupling  (ISO)
cell-cell junction organization  (ISO)
cell-cell signaling  (IBA,IDA,ISO)
cellular protein localization  (ISO)
cellular response to amyloid-beta  (ISO)
cellular response to mechanical stimulus  (IEP)
cellular response to parathyroid hormone stimulus  (IEP)
cellular response to pH  (ISO)
cellular response to platelet-derived growth factor stimulus  (ISO)
chronic inflammatory response  (IMP)
decidualization  (IEP)
embryonic digit morphogenesis  (ISO)
embryonic heart tube development  (ISO)
endothelium development  (IEP)
epididymis development  (IEP)
epithelial cell maturation  (ISO)
establishment of mitotic spindle orientation  (ISO)
export across plasma membrane  (ISO)
gap junction assembly  (TAS)
glutamate secretion  (ISO)
glutathione transmembrane transport  (IEA)
heart development  (IEP,ISO)
heart looping  (ISO)
in utero embryonic development  (ISO)
ion transmembrane transport  (ISO)
lens development in camera-type eye  (ISO)
maintenance of protein localization in endoplasmic reticulum  (IDA)
male gonad development  (ISO)
microtubule-based transport  (ISO,ISS)
milk ejection reflex  (ISO)
negative regulation of cardiac muscle cell proliferation  (IMP)
negative regulation of cell growth  (IMP,ISO)
negative regulation of cell population proliferation  (IDA)
negative regulation of DNA biosynthetic process  (IDA)
negative regulation of endothelial cell proliferation  (IMP)
negative regulation of gene expression  (ISO)
negative regulation of gonadotropin secretion  (ISO)
negative regulation of trophoblast cell migration  (ISO)
negative regulation of wound healing  (IMP)
neuron migration  (ISO)
neuron projection morphogenesis  (IMP)
osteoblast differentiation  (ISO)
positive regulation of behavioral fear response  (IMP)
positive regulation of cell communication by chemical coupling  (IMP)
positive regulation of cold-induced thermogenesis  (ISO,ISS)
positive regulation of cytosolic calcium ion concentration  (IMP)
positive regulation of gene expression  (ISO)
positive regulation of glomerular filtration  (IMP)
positive regulation of I-kappaB kinase/NF-kappaB signaling  (ISO)
positive regulation of insulin secretion  (IMP)
positive regulation of mesodermal cell differentiation  (ISO)
positive regulation of morphogenesis of an epithelium  (ISO)
positive regulation of protein catabolic process  (IDA)
positive regulation of smooth muscle cell chemotaxis  (ISO)
positive regulation of stem cell proliferation  (ISO)
positive regulation of striated muscle tissue development  (ISO)
positive regulation of vascular associated smooth muscle cell proliferation  (ISO)
positive regulation of vasoconstriction  (IMP)
regulation of apoptotic process  (IMP)
regulation of atrial cardiac muscle cell membrane depolarization  (ISO)
regulation of bicellular tight junction assembly  (IMP)
regulation of bone mineralization  (ISO)
regulation of bone remodeling  (ISO)
regulation of calcium ion transport  (IMP)
regulation of cell communication by electrical coupling  (IDA)
regulation of heart contraction  (ISO)
regulation of transmembrane transporter activity  (IMP)
regulation of ventricular cardiac muscle cell membrane depolarization  (ISO)
regulation of ventricular cardiac muscle cell membrane repolarization  (ISO)
response to estradiol  (IEP)
response to fluid shear stress  (IEP)
response to glucose  (IEP)
response to ischemia  (IEP,ISO)
response to lipopolysaccharide  (IEP)
response to peptide hormone  (IEP)
response to pH  (IDA)
response to retinoic acid  (IEP)
response to wounding  (ISO)
signal transduction  (ISO)
skeletal muscle tissue regeneration  (ISO)
spermatogenesis  (ISO,ISS)
T cell activation  (ISO)
T cell proliferation  (ISO)
transmembrane transport  (IDA)
vascular transport  (IMP)
vasodilation  (IMP)
xenobiotic transport  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
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Genomics

Comparative Map Data
Gja1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22035,756,007 - 35,768,481 (+)NCBI
Rnor_6.0 Ensembl2037,876,650 - 37,889,089 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02037,876,650 - 37,889,097 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02039,612,080 - 39,624,555 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42035,409,815 - 35,422,262 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12035,423,614 - 35,436,057 (+)NCBI
Celera2037,095,121 - 37,107,568 (+)NCBICelera
Cytogenetic Map20q11NCBI
GJA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6121,435,595 - 121,449,727 (+)EnsemblGRCh38hg38GRCh38
GRCh386121,435,646 - 121,449,727 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh376121,756,792 - 121,770,873 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366121,798,444 - 121,812,572 (+)NCBINCBI36hg18NCBI36
Build 346121,798,486 - 121,812,571NCBI
Celera6122,501,175 - 122,515,303 (+)NCBI
Cytogenetic Map6q22.31NCBI
HuRef6119,340,180 - 119,354,307 (+)NCBIHuRef
CHM1_16122,020,528 - 122,034,696 (+)NCBICHM1_1
Gja1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391056,253,297 - 56,266,519 (+)NCBIGRCm39mm39
GRCm39 Ensembl1056,253,426 - 56,278,609 (+)Ensembl
GRCm381056,377,300 - 56,390,419 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1056,377,330 - 56,402,513 (+)EnsemblGRCm38mm10GRCm38
MGSCv371056,097,106 - 56,110,225 (+)NCBIGRCm37mm9NCBIm37
MGSCv361056,065,762 - 56,078,833 (+)NCBImm8
Celera1057,194,935 - 57,208,041 (+)NCBICelera
Cytogenetic Map10B4NCBI
cM Map1028.64NCBI
Gja1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554363,612,533 - 3,618,095 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554363,612,533 - 3,618,095 (+)NCBIChiLan1.0ChiLan1.0
GJA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.16123,348,744 - 123,360,887 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v06119,213,513 - 119,227,617 (+)NCBIMhudiblu_PPA_v0panPan3
GJA1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1160,941,772 - 60,944,694 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl160,929,097 - 60,942,936 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha161,750,272 - 61,753,194 (+)NCBI
ROS_Cfam_1.0161,130,176 - 61,143,784 (+)NCBI
UMICH_Zoey_3.1161,052,769 - 61,055,708 (+)NCBI
UNSW_CanFamBas_1.0160,868,101 - 60,871,024 (+)NCBI
UU_Cfam_GSD_1.0161,515,138 - 61,518,103 (+)NCBI
Gja1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946111,813,180 - 111,826,131 (+)NCBI
SpeTri2.0NW_0049366583,920,043 - 3,932,987 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
GJA1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl140,988,515 - 41,002,137 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1140,988,818 - 41,002,129 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2145,543,880 - 45,557,193 (-)NCBISscrofa10.2Sscrofa10.2susScr3
GJA1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11352,397,291 - 52,410,341 (-)NCBI
Gja1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247989,358,996 - 9,364,413 (-)NCBI

Position Markers
D18Wox12  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01862,570,290 - 62,570,429NCBIRnor6.0
Rnor_5.01861,757,051 - 61,757,190UniSTSRnor5.0
RGSC_v3.41862,660,084 - 62,660,224RGDRGSC3.4
RGSC_v3.41862,660,085 - 62,660,224UniSTSRGSC3.4
RGSC_v3.11862,733,285 - 62,733,425RGD
Celera1858,484,925 - 58,485,064UniSTS
Cytogenetic Map20q11UniSTS
D18Wox13  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01862,570,265 - 62,570,427NCBIRnor6.0
Rnor_5.01861,757,026 - 61,757,188UniSTSRnor5.0
Celera1858,484,900 - 58,485,062UniSTS
RH 3.4 Map18610.4UniSTS
RH 3.4 Map18610.4RGD
RH 2.0 Map18301.2RGD
Cytogenetic Map20q11UniSTS
RH128006  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02037,888,716 - 37,888,922NCBIRnor6.0
Rnor_5.02039,624,174 - 39,624,380UniSTSRnor5.0
RGSC_v3.42035,421,881 - 35,422,087UniSTSRGSC3.4
Celera2037,107,187 - 37,107,393UniSTS
RH 3.4 Map20375.01UniSTS
Cytogenetic Map20q11UniSTS
RH135241  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02037,888,716 - 37,888,923NCBIRnor6.0
Rnor_5.02039,624,174 - 39,624,381UniSTSRnor5.0
RGSC_v3.42035,421,881 - 35,422,088UniSTSRGSC3.4
Celera2037,107,187 - 37,107,394UniSTS
RH 3.4 Map20372.51UniSTS
Cytogenetic Map20q11UniSTS
PMC151788P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02037,886,965 - 37,887,297NCBIRnor6.0
Rnor_5.02039,622,423 - 39,622,755UniSTSRnor5.0
RGSC_v3.42035,420,130 - 35,420,462UniSTSRGSC3.4
Celera2037,105,436 - 37,105,768UniSTS
Cytogenetic Map20q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201383430956205956Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201383430956205956Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201782709656205956Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201887215049108956Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)202085847056205956Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202660884356205956Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202660884356205956Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202660884356205956Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202671232356205956Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)203091348156205956Rat
70158Bp60Blood pressure QTL 603arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)203335478345719230Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:215
Count of miRNA genes:137
Interacting mature miRNAs:174
Transcripts:ENSRNOT00000001054
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 18 8 13 8 1 2 74 24 39 11 1
Low 39 33 6 33 7 9 11 2 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001054   ⟹   ENSRNOP00000001054
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2037,876,650 - 37,889,089 (+)Ensembl
RefSeq Acc Id: NM_012567   ⟹   NP_036699
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22035,756,035 - 35,768,481 (+)NCBI
Rnor_6.02037,876,650 - 37,889,097 (+)NCBI
Rnor_5.02039,612,080 - 39,624,555 (+)NCBI
RGSC_v3.42035,409,815 - 35,422,262 (+)RGD
Celera2037,095,121 - 37,107,568 (+)RGD
Sequence:
RefSeq Acc Id: XM_039098413   ⟹   XP_038954341
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22035,756,007 - 35,768,481 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_036699   ⟸   NM_012567
- UniProtKB: P08050 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000001054   ⟸   ENSRNOT00000001054
RefSeq Acc Id: XP_038954341   ⟸   XM_039098413
- Peptide Label: isoform X1
Protein Domains
CNX   Connexin_CCC

Transcriptome

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

Promoters
RGD ID:13701633
Promoter ID:EPDNEW_R12157
Type:multiple initiation site
Name:Gja1_1
Description:gap junction protein, alpha 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_6.02037,876,642 - 37,876,702EPDNEW

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


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 35419326 35419327 G C snv FHL/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2690 AgrOrtholog
Ensembl Genes ENSRNOG00000000805 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000001054 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000001054 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.1440.80 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  1.20.5.1130 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7105924 IMAGE-MGC_LOAD
InterPro Alpha_helix_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Connexin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Connexin43 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Connexin43_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Connexin_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Connexin_CCC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Connexin_CS UniProtKB/Swiss-Prot
  Connexin_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Connexin_N_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24392 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:93610 IMAGE-MGC_LOAD
NCBI Gene 24392 ENTREZGENE
PANTHER PTHR11984 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11984:SF33 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Connexin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Connexin43 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB GJA1 RGD
PhenoGen Gja1 PhenoGen
PRINTS CONNEXIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CONNEXINA1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE CONNEXINS_1 UniProtKB/Swiss-Prot
  CONNEXINS_2 UniProtKB/Swiss-Prot
SMART CNX UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Connexin_CCC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF118220 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC230392
UniProt A0A654ICE6_RAT UniProtKB/TrEMBL
  CXA1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q53ZE1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-11 Gja1  gap junction protein, alpha 1  Gja1  gap junction membrane channel protein alpha 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-11-06 Gja1  gap junction membrane channel protein alpha 1    Gap junction protein, alpha 1, 43 kD (connexin 43)  Name updated 625702 APPROVED
2002-06-10 Gja1  Gap junction protein, alpha 1, 43 kD (connexin 43)      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease decreased expression is assocaited with impaired cell-cell communication in heart failure 728855
gene_expression expressed in adult epididymis 628541
gene_physical_interaction forms gap junctions between principal and basal cells but not between adjacent principal cells 628541