Rapgef4 (Rap guanine nucleotide exchange factor 4) - Rat Genome Database

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Gene: Rapgef4 (Rap guanine nucleotide exchange factor 4) Rattus norvegicus
Analyze
Symbol: Rapgef4
Name: Rap guanine nucleotide exchange factor 4
RGD ID: 621886
Description: Enables cAMP binding activity and guanyl-nucleotide exchange factor activity. Involved in several processes, including nervous system development; positive regulation of neuronal action potential; and regulation of protein localization. Located in several cellular components, including basolateral plasma membrane; brush border; and distal axon. Part of protein-containing complex. Is active in glutamatergic synapse; postsynaptic density; and presynapse. Human ortholog(s) of this gene implicated in autistic disorder. Orthologous to human RAPGEF4 (Rap guanine nucleotide exchange factor 4); INTERACTS WITH (+)-schisandrin B; 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: CAMP-GEFII; cAMP-regulated guanine nucleotide exchange factor II; CAMPS; Cgef2; epac 2; Epac2; exchange factor directly activated by cAMP 2; exchange protein directly activated by cAMP 2; Rap guanine nucleotide exchange factor (GEF) 4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: Rapgef4Tn(sb-T2/Bart3)2.314Mcwi  
Genetic Models: F344-Rapgef4Tn(sb-T2/Bart3)2.314Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8377,217,024 - 77,509,933 (+)NCBIGRCr8
mRatBN7.2356,809,388 - 57,101,332 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl356,809,270 - 57,102,316 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx360,204,514 - 60,496,004 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0368,788,153 - 69,079,646 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0366,553,199 - 66,844,692 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0358,632,338 - 58,925,127 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl358,632,476 - 58,924,038 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0365,122,705 - 65,409,814 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4354,396,312 - 54,717,148 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1354,578,917 - 54,613,517 (+)NCBI
Celera356,352,070 - 56,643,335 (+)NCBICelera
Cytogenetic Map3q23NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
17beta-estradiol  (EXP,ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-butan-2-yl-4-[4-[4-[4-[[2-(2,4-dichlorophenyl)-2-(1,2,4-triazol-1-ylmethyl)-1,3-dioxolan-4-yl]methoxy]phenyl]-1-piperazinyl]phenyl]-1,2,4-triazol-3-one  (ISO)
2-hydroxypropanoic acid  (ISO)
3,4-methylenedioxymethamphetamine  (ISO)
3H-1,2-dithiole-3-thione  (EXP)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
acrylamide  (EXP,ISO)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
anthra[1,9-cd]pyrazol-6(2H)-one  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
atrazine  (EXP)
benzene  (EXP)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
buspirone  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (EXP,ISO)
casticin  (ISO)
CGP 52608  (ISO)
chloroprene  (ISO)
ciguatoxin CTX1B  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP)
clorgyline  (ISO)
clozapine  (ISO)
cobalt dichloride  (EXP)
cocaine  (EXP)
copper(II) sulfate  (ISO)
corticosterone  (EXP)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
cyproconazole  (ISO)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (ISO)
doxorubicin  (ISO)
endosulfan  (EXP)
epoxiconazole  (ISO)
ethanol  (ISO)
folic acid  (ISO)
gentamycin  (EXP)
haloperidol  (ISO)
Heliotrine  (ISO)
inulin  (ISO)
isoprenaline  (ISO)
itraconazole  (ISO)
ketoconazole  (ISO)
levofloxacin  (EXP)
methapyrilene  (EXP,ISO)
methoxychlor  (EXP)
methylseleninic acid  (ISO)
N,N-diethyl-m-toluamide  (EXP)
N-nitrosodiethylamine  (EXP)
nevirapine  (ISO)
nimesulide  (EXP)
ochratoxin A  (ISO)
olanzapine  (ISO)
ozone  (ISO)
paracetamol  (EXP,ISO)
pentachlorophenol  (ISO)
perfluorohexanesulfonic acid  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
perfluorooctanoic acid  (ISO)
permethrin  (EXP)
phenobarbital  (EXP,ISO)
phenylephrine  (EXP)
phenytoin  (EXP)
phorone  (EXP)
pirinixic acid  (EXP,ISO)
potassium chloride  (EXP)
potassium dichromate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
propiconazole  (ISO)
rac-lactic acid  (ISO)
rotenone  (EXP)
senecionine  (ISO)
Senkirkine  (ISO)
sevoflurane  (EXP)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
sulforaphane  (ISO)
sunitinib  (ISO)
tetrachloromethane  (EXP)
thioacetamide  (EXP)
titanium dioxide  (ISO)
triphenyl phosphate  (EXP)
valdecoxib  (EXP)
valproic acid  (ISO)
vinclozolin  (EXP)
zearalenone  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Screening of nine candidate genes for autism on chromosome 2q reveals rare nonsynonymous variants in the cAMP-GEFII gene. Bacchelli E, etal., Mol Psychiatry. 2003 Nov;8(11):916-24.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Phosphodiesterase (PDE) inhibitor torbafylline (HWA 448) attenuates burn-induced rat skeletal muscle proteolysis through the PDE4/cAMP/EPAC/PI3K/Akt pathway. Joshi R, etal., Mol Cell Endocrinol. 2014 Aug 5;393(1-2):152-63. doi: 10.1016/j.mce.2014.06.012. Epub 2014 Jun 25.
5. A family of cAMP-binding proteins that directly activate Rap1. Kawasaki H, etal., Science 1998 Dec 18;282(5397):2275-9.
6. Differential expression of proteins in rat plasma exposed to benzene. Lee HJ, etal., Proteomics. 2004 Nov;4(11):3498-504.
7. Renal expression of exchange protein directly activated by cAMP (Epac) 1 and 2. Li Y, etal., Am J Physiol Renal Physiol. 2008 Aug;295(2):F525-33. Epub 2008 May 21.
8. Exchange protein directly activated by cAMP (EPAC) interacts with the light chain (LC) 2 of MAP1A. Magiera MM, etal., Biochem J. 2004 Sep 15;382(Pt 3):803-10.
9. Cholangiocyte primary cilia are chemosensory organelles that detect biliary nucleotides via P2Y12 purinergic receptors. Masyuk AI, etal., Am J Physiol Gastrointest Liver Physiol. 2008 Oct;295(4):G725-34. doi: 10.1152/ajpgi.90265.2008. Epub 2008 Aug 7.
10. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
11. Epac mediates cyclic AMP-dependent axon growth, guidance and regeneration. Murray AJ and Shewan DA, Mol Cell Neurosci. 2008 Aug;38(4):578-88. doi: 10.1016/j.mcn.2008.05.006. Epub 2008 May 20.
12. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
13. GOA pipeline RGD automated data pipeline
14. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
15. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
16. Nerve growth factor mediates a switch in intracellular signaling for PGE2-induced sensitization of sensory neurons from protein kinase A to Epac. Vasko MR, etal., PLoS One. 2014 Aug 15;9(8):e104529. doi: 10.1371/journal.pone.0104529. eCollection 2014.
17. Differential distribution of exchange proteins directly activated by cyclic AMP within the adult rat retina. Whitaker CM and Cooper NG, Neuroscience. 2009 Oct 31.
18. Epac2 induces synapse remodeling and depression and its disease-associated forms alter spines. Woolfrey KM, etal., Nat Neurosci. 2009 Oct;12(10):1275-84. Epub 2009 Sep 6.
19. Prostaglandin E2-activated Epac promotes neointimal formation of the rat ductus arteriosus by a process distinct from that of cAMP-dependent protein kinase A. Yokoyama U, etal., J Biol Chem. 2008 Oct 17;283(42):28702-9. Epub 2008 Aug 11.
Additional References at PubMed
PMID:11056535   PMID:11598134   PMID:12401793   PMID:15334074   PMID:16076873   PMID:17725712   PMID:18660803   PMID:21700703   PMID:22076955   PMID:23080165   PMID:24586073   PMID:25904804  
PMID:26854595   PMID:28216156   PMID:28546426   PMID:30225708   PMID:31199033   PMID:38985989  


Genomics

Comparative Map Data
Rapgef4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8377,217,024 - 77,509,933 (+)NCBIGRCr8
mRatBN7.2356,809,388 - 57,101,332 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl356,809,270 - 57,102,316 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx360,204,514 - 60,496,004 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0368,788,153 - 69,079,646 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0366,553,199 - 66,844,692 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0358,632,338 - 58,925,127 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl358,632,476 - 58,924,038 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0365,122,705 - 65,409,814 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4354,396,312 - 54,717,148 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1354,578,917 - 54,613,517 (+)NCBI
Celera356,352,070 - 56,643,335 (+)NCBICelera
Cytogenetic Map3q23NCBI
RAPGEF4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382172,735,318 - 173,052,893 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2172,735,274 - 173,052,893 (+)EnsemblGRCh38hg38GRCh38
GRCh372173,600,573 - 173,917,621 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362173,308,771 - 173,625,867 (+)NCBINCBI36Build 36hg18NCBI36
Build 342173,426,113 - 173,743,122NCBI
Celera2167,213,920 - 167,531,026 (+)NCBICelera
Cytogenetic Map2q31.1NCBI
HuRef2165,478,909 - 165,797,009 (+)NCBIHuRef
CHM1_12173,607,657 - 173,924,727 (+)NCBICHM1_1
T2T-CHM13v2.02173,221,758 - 173,539,439 (+)NCBIT2T-CHM13v2.0
Rapgef4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39271,811,559 - 72,087,818 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl271,811,584 - 72,087,818 (+)EnsemblGRCm39 Ensembl
GRCm38271,981,215 - 72,257,474 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl271,981,240 - 72,257,474 (+)EnsemblGRCm38mm10GRCm38
MGSCv37271,819,344 - 72,094,433 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36271,782,126 - 72,057,215 (+)NCBIMGSCv36mm8
Celera273,684,323 - 73,945,757 (+)NCBICelera
Cytogenetic Map2C3NCBI
cM Map242.9NCBI
Rapgef4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554492,171,924 - 2,462,451 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554492,172,354 - 2,453,367 (-)NCBIChiLan1.0ChiLan1.0
RAPGEF4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21375,410,092 - 75,727,470 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B75,425,073 - 75,742,443 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B60,022,738 - 60,339,981 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B177,485,404 - 177,794,769 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B177,655,733 - 177,793,644 (+)Ensemblpanpan1.1panPan2
RAPGEF4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13617,087,488 - 17,323,504 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3617,087,488 - 17,323,220 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3617,044,798 - 17,327,450 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03617,166,818 - 17,450,241 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3617,166,807 - 17,450,214 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13617,247,410 - 17,530,838 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03617,246,048 - 17,529,604 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03617,349,948 - 17,632,781 (+)NCBIUU_Cfam_GSD_1.0
Rapgef4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303134,168,378 - 134,452,112 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365092,722,428 - 3,005,288 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365092,722,279 - 3,006,436 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RAPGEF4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1578,773,266 - 79,095,040 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11578,773,270 - 79,094,490 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21588,093,533 - 88,416,683 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RAPGEF4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11058,233,503 - 58,549,337 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1058,233,654 - 58,549,331 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666040141,024,710 - 141,334,996 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rapgef4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462478710,062,717 - 10,369,632 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462478710,062,677 - 10,369,132 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rapgef4
1976 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:103
Count of miRNA genes:89
Interacting mature miRNAs:96
Transcripts:ENSRNOT00000010630
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)353184593115665732Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)31500542276927699Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)353184593115665732Rat
1581568Rf53Renal function QTL 53urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
9590286Uminl1Urine mineral level QTL 13.50.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)32824968773249687Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)350437504115638231Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
731180Bp152Blood pressure QTL 1520.03arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35378111291609953Rat
61356Bp37Blood pressure QTL 373blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)33068464275684642Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
8694196Abfw2Abdominal fat weight QTL 216.580.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)32824968773249687Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
1582249Bw77Body weight QTL 773.20.0025epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)35318459364655484Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
12879868Am6Aortic mass QTL 60.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)33142640370668733Rat
11565451Bw177Body weight QTL 1770.002body mass (VT:0001259)body weight (CMO:0000012)33142640370668733Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
11565452Kidm57Kidney mass QTL 570.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)33142640370668733Rat
12879866Cm94Cardiac mass QTL 940.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)33142640370668733Rat
12879867Cm95Cardiac mass QTL 950.047heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)33142640370668733Rat
1300178Hrtrt4Heart rate QTL 43.74heart pumping trait (VT:2000009)heart rate (CMO:0000002)34382736490905114Rat
61377Edpm3Estrogen-dependent pituitary mass QTL 37.050.038pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)35318469289878207Rat
2302055Pia30Pristane induced arthritis QTL 303.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)32793691972936919Rat
1331795Rf30Renal function QTL 303.708urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)33945463789115240Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
1354589Bw31Body weight QTL 313.3body mass (VT:0001259)body weight (CMO:0000012)33370334778196190Rat
2303593Gluco46Glucose level QTL 463blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)32846857173468571Rat
1354590Despr11Despair related QTL 110.000031locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)32846857173468571Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1331777Bw24Body weight QTL 243.503body mass (VT:0001259)body weight (CMO:0000012)33945463789115240Rat
631647Bp122Blood pressure QTL 1226.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)33068464275684642Rat
1300169Bp177Blood pressure QTL 1772.96arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)33370334761017857Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2302276Bw82Body weight QTL 824.32body mass (VT:0001259)body weight (CMO:0000012)33945463762951183Rat
738019Anxrr10Anxiety related response QTL 103.9exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)33851780383517803Rat
9590136Scort3Serum corticosterone level QTL 323.370.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)32824968773249687Rat
10450804Scl70Serum cholesterol level QTL 704.70.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32071409065714090Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)33035677398535386Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)341874578104104347Rat
8552950Pigfal12Plasma insulin-like growth factor 1 level QTL 127.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)32824968773249687Rat
631676Cm8Cardiac mass QTL 87.030.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)31695470861954708Rat
10450794Scl69Serum cholesterol level QTL 696.30.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32071409065714090Rat
8694386Bw159Body weight QTL 1594.520.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)32824968773249687Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)333703347104104347Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)350437042119183768Rat
2301400Cm68Cardiac mass QTL 680.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)33142640370668733Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat

Markers in Region
D3Mco27  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2356,920,851 - 56,921,009 (+)MAPPERmRatBN7.2
Rnor_6.0358,741,026 - 58,741,183NCBIRnor6.0
Rnor_5.0365,229,425 - 65,229,582UniSTSRnor5.0
RGSC_v3.4354,509,096 - 54,509,254RGDRGSC3.4
RGSC_v3.4354,509,097 - 54,509,254UniSTSRGSC3.4
RGSC_v3.1354,405,468 - 54,405,626RGD
Celera356,463,310 - 56,463,467UniSTS
Cytogenetic Map3q22UniSTS
D3Got218  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2357,038,087 - 57,038,192 (+)MAPPERmRatBN7.2
Rnor_6.0358,860,718 - 58,860,822NCBIRnor6.0
Rnor_5.0365,345,817 - 65,345,921UniSTSRnor5.0
RGSC_v3.4354,652,558 - 54,652,662UniSTSRGSC3.4
Celera356,579,151 - 56,579,255UniSTS
Cytogenetic Map3q22UniSTS
D3Got295  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2356,876,073 - 56,876,217 (+)MAPPERmRatBN7.2
Rnor_6.0358,695,292 - 58,695,437NCBIRnor6.0
Rnor_5.0365,185,425 - 65,185,570UniSTSRnor5.0
RGSC_v3.4354,464,315 - 54,464,460UniSTSRGSC3.4
Celera356,418,298 - 56,418,443UniSTS
Cytogenetic Map3q22UniSTS
D3Got217  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2357,058,033 - 57,058,201 (+)MAPPERmRatBN7.2
Rnor_6.0358,880,719 - 58,880,886NCBIRnor6.0
Rnor_5.0365,365,818 - 65,365,985UniSTSRnor5.0
RGSC_v3.4354,672,585 - 54,672,752UniSTSRGSC3.4
Celera356,598,941 - 56,599,108UniSTS
Cytogenetic Map3q22UniSTS
RH144457  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2357,018,396 - 57,018,562 (+)MAPPERmRatBN7.2
Rnor_6.0358,839,594 - 58,839,759NCBIRnor6.0
Rnor_5.0365,326,022 - 65,326,187UniSTSRnor5.0
RGSC_v3.4354,632,726 - 54,632,891UniSTSRGSC3.4
Celera356,560,285 - 56,560,450UniSTS
RH 3.4 Map4401.94UniSTS
Cytogenetic Map3q22UniSTS


Genetic Models
This gene Rapgef4 is modified in the following models/strains:
F344-Rapgef4Tn(sb-T2/Bart3)2.314Mcwi    


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000010630   ⟹   ENSRNOP00000010630
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl356,809,270 - 57,101,332 (+)Ensembl
Rnor_6.0 Ensembl358,632,476 - 58,924,038 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000094770   ⟹   ENSRNOP00000086379
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl356,897,560 - 57,102,316 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000100000   ⟹   ENSRNOP00000095541
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl356,809,270 - 57,101,332 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000116465   ⟹   ENSRNOP00000096055
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl356,874,255 - 57,102,316 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000119235   ⟹   ENSRNOP00000087630
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl356,809,270 - 57,101,332 (+)Ensembl
RefSeq Acc Id: NM_001100642   ⟹   NP_001094112
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8377,217,047 - 77,508,945 (+)NCBI
mRatBN7.2356,809,411 - 57,101,332 (+)NCBI
RefSeq Acc Id: XM_039104344   ⟹   XP_038960272
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8377,217,024 - 77,509,933 (+)NCBI
mRatBN7.2356,809,388 - 57,101,234 (+)NCBI
RefSeq Acc Id: XM_039104345   ⟹   XP_038960273
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8377,297,588 - 77,509,933 (+)NCBI
mRatBN7.2356,897,114 - 57,101,234 (+)NCBI
RefSeq Acc Id: XM_039104346   ⟹   XP_038960274
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8377,297,588 - 77,509,933 (+)NCBI
mRatBN7.2356,897,114 - 57,101,234 (+)NCBI
RefSeq Acc Id: XM_063283144   ⟹   XP_063139214
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8377,388,863 - 77,509,933 (+)NCBI
RefSeq Acc Id: XM_063283145   ⟹   XP_063139215
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8377,396,715 - 77,509,933 (+)NCBI
RefSeq Acc Id: XM_063283146   ⟹   XP_063139216
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8377,408,603 - 77,509,933 (+)NCBI
RefSeq Acc Id: XM_063283147   ⟹   XP_063139217
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8377,410,981 - 77,509,933 (+)NCBI
Ensembl Acc Id: ENSRNOP00000010630   ⟸   ENSRNOT00000010630
RefSeq Acc Id: XP_038960272   ⟸   XM_039104344
- Peptide Label: isoform X1
- UniProtKB: A0A8I6A857 (UniProtKB/TrEMBL),   A0A8I6B2Y4 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001094112   ⟸   NM_001100642
- UniProtKB: F1LQ26 (UniProtKB/TrEMBL),   D3KR63 (UniProtKB/TrEMBL),   A0A8I6B2Y4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038960273   ⟸   XM_039104345
- Peptide Label: isoform X2
- UniProtKB: A0A8I6GEV8 (UniProtKB/TrEMBL),   A0A8I6GLW9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038960274   ⟸   XM_039104346
- Peptide Label: isoform X4
- UniProtKB: A0A8I6GLW9 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000086379   ⟸   ENSRNOT00000094770
Ensembl Acc Id: ENSRNOP00000087630   ⟸   ENSRNOT00000119235
Ensembl Acc Id: ENSRNOP00000096055   ⟸   ENSRNOT00000116465
Ensembl Acc Id: ENSRNOP00000095541   ⟸   ENSRNOT00000100000
RefSeq Acc Id: XP_063139214   ⟸   XM_063283144
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063139215   ⟸   XM_063283145
- Peptide Label: isoform X5
RefSeq Acc Id: XP_063139216   ⟸   XM_063283146
- Peptide Label: isoform X5
RefSeq Acc Id: XP_063139217   ⟸   XM_063283147
- Peptide Label: isoform X5
Protein Domains
Cyclic nucleotide-binding   DEP   N-terminal Ras-GEF   Ras-GEF

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9Z1C7-F1-model_v2 AlphaFold Q9Z1C7 1-436 view protein structure

Transcriptome

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

Promoters
RGD ID:13692145
Promoter ID:EPDNEW_R2664
Type:single initiation site
Name:Rapgef4_1
Description:Rap guanine nucleotide exchange factor 4
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_6.0358,632,456 - 58,632,516EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621886 AgrOrtholog
BioCyc Gene G2FUF-49444 BioCyc
Ensembl Genes ENSRNOG00000001516 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000010630.8 UniProtKB/TrEMBL
  ENSRNOT00000094770.1 UniProtKB/TrEMBL
  ENSRNOT00000100000.1 UniProtKB/TrEMBL
  ENSRNOT00000116465.1 UniProtKB/TrEMBL
  ENSRNOT00000119235.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.10.10 UniProtKB/TrEMBL
  1.10.8.1240 UniProtKB/TrEMBL
  1.10.840.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.60.120.10 UniProtKB/TrEMBL
  Son of sevenless (SoS) protein Chain: S domain 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro CNBD1/2 UniProtKB/TrEMBL
  cNMP-bd-like UniProtKB/TrEMBL
  cNMP-bd_dom UniProtKB/TrEMBL
  DEP_dom UniProtKB/TrEMBL
  Ras-like_GEF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ras-like_Gua-exchang_fac_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ras_G-nucl-exch_fac_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Ras_GEF_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RASGEF_cat_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RASGEF_cat_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RmlC-like_jellyroll UniProtKB/TrEMBL
  Ubiquitin-like_domsf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WH-like_DNA-bd_sf UniProtKB/TrEMBL
  WH_DNA-bd_sf UniProtKB/TrEMBL
NCBI Gene 252857 ENTREZGENE
PANTHER CYCLIC NUCLEOTIDE-BINDING DOMAIN-CONTAINING PROTEIN 1 UniProtKB/TrEMBL
  PTHR23113 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR (GEF) 4 UniProtKB/TrEMBL
  RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR 4 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  UNCHARACTERIZED UniProtKB/TrEMBL
Pfam cNMP_binding UniProtKB/TrEMBL
  DEP UniProtKB/TrEMBL
  RasGEF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RasGEF_N UniProtKB/TrEMBL
PharmGKB RAPGEF4 RGD
PhenoGen Rapgef4 PhenoGen
PRINTS CAMPKINASE UniProtKB/TrEMBL
PROSITE CNMP_BINDING_3 UniProtKB/TrEMBL
  DEP UniProtKB/TrEMBL
  RASGEF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RASGEF_CAT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RASGEF_NTER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000001516 RatGTEx
SMART cNMP UniProtKB/TrEMBL
  DEP UniProtKB/TrEMBL
  RasGEF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RasGEFN UniProtKB/TrEMBL
Superfamily-SCOP cNMP_binding UniProtKB/TrEMBL
  SSF46785 UniProtKB/TrEMBL
  SSF48366 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54236 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6A857 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6B2Y4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GEV8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GLW9 ENTREZGENE, UniProtKB/TrEMBL
  A6HM69_RAT UniProtKB/TrEMBL
  A6HM70_RAT UniProtKB/TrEMBL
  D3KR63 ENTREZGENE, UniProtKB/TrEMBL
  F1LQ26 ENTREZGENE
  Q9Z1C7 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary F1LQ26 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-11-17 Rapgef4  Rap guanine nucleotide exchange factor (GEF) 4    cAMP-regulated guanine nucleotide exchange factor II  Name updated 1299863 APPROVED
2004-09-10 Rapgef4  cAMP-regulated guanine nucleotide exchange factor II  Cgef2    Symbol and Name updated 1299863 APPROVED
2002-08-07 Cgef2  cAMP-regulated guanine nucleotide exchange factor II      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_domains contains cAMP-binding and guanine nucleotide exchange factor (GEF) domains 632397