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 neurotransmitter receptor localization to postsynaptic specialization membrane. 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
Black 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: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8377,217,024 - 77,509,933 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl377,217,039 - 77,509,978 (+)EnsemblGRCr8
mRatBN7.2356,809,388 - 57,101,332 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl356,809,270 - 57,102,316 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx360,204,514 - 60,496,004 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0368,788,153 - 69,079,646 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0366,553,199 - 66,844,692 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0358,632,338 - 58,925,127 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl358,632,476 - 58,924,038 (+)Ensemblrn6Rnor6.0
Rnor_5.0365,122,705 - 65,409,814 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4354,396,312 - 54,717,148 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera356,352,070 - 56,643,335 (+)NCBICelera
RGSC_v3.1354,578,917 - 54,613,517 (+)NCBI
Cytogenetic Map3q23NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View
autistic disorder  (ISO)
Burns  (IDA)

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)
Azoxymethane  (ISO)
benzene  (EXP)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (EXP,ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
buspirone  (EXP)
Butylbenzyl phthalate  (ISO)
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)
genistein  (EXP)
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)
okadaic acid  (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 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl377,217,039 - 77,509,978 (+)EnsemblGRCr8
mRatBN7.2356,809,388 - 57,101,332 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl356,809,270 - 57,102,316 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx360,204,514 - 60,496,004 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0368,788,153 - 69,079,646 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0366,553,199 - 66,844,692 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0358,632,338 - 58,925,127 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl358,632,476 - 58,924,038 (+)Ensemblrn6Rnor6.0
Rnor_5.0365,122,705 - 65,409,814 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4354,396,312 - 54,717,148 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera356,352,070 - 56,643,335 (+)NCBICelera
RGSC_v3.1354,578,917 - 54,613,517 (+)NCBI
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 (+)Ensemblhg38GRCh38
GRCh372173,600,573 - 173,917,621 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362173,308,771 - 173,625,867 (+)NCBIBuild 36Build 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 EnsemblGRCm39
GRCm38271,981,215 - 72,257,474 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl271,981,240 - 72,257,474 (+)Ensemblmm10GRCm38
MGSCv37271,819,344 - 72,094,433 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
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 (-)Ensembl
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 (+)EnsemblpanPan2panpan1.1
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 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha3617,044,798 - 17,327,450 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.03617,166,818 - 17,450,241 (+)NCBIROS_Cfam_1.0ROS_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_1.0UU_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 (+)EnsemblSpeTri2.0 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 (+)EnsemblsusScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
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_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462478710,062,677 - 10,369,132 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Rapgef4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1549,281,236 - 49,569,224 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Rapgef4
1698 total Variants
miRNA Target Status (No longer updated)

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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300178Hrtrt4Heart rate QTL 43.74heart pumping trait (VT:2000009)heart rate (CMO:0000002)351490129111359995Rat
61377Edpm3Estrogen-dependent pituitary mass QTL 37.050.038pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)373592611110333156Rat
1358293Bw38Body weight QTL 3860.0000031body mass (VT:0001259)body weight (CMO:0000012)374364268119364268Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)373592512136118980Rat
1331795Rf30Renal function QTL 303.708urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)35986366387321459Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)373592512136118980Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)351581665184004958Rat
1354589Bw31Body weight QTL 313.3body mass (VT:0001259)body weight (CMO:0000012)35365182698651826Rat
2303593Gluco46Glucose level QTL 463blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)34887661993876619Rat
1354590Despr11Despair related QTL 110.000031locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)34887661993876619Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)33540319997383526Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)367641776167835660Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)358601291153936591Rat
631832Sach1Saccharin preference QTL 12.70.02consumption behavior trait (VT:0002069)calculated saccharin drink intake volume (CMO:0001600)34790417292904172Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)349872657138829559Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)373592512136118980Rat
1331777Bw24Body weight QTL 243.503body mass (VT:0001259)body weight (CMO:0000012)35986366387321459Rat
631647Bp122Blood pressure QTL 1226.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)35109256196092561Rat
1300169Bp177Blood pressure QTL 1772.96arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)33642511681425116Rat
9590286Uminl1Urine mineral level QTL 13.50.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)34865774493657744Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)370845569136091483Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)33779691982796919Rat
2302276Bw82Body weight QTL 824.32body mass (VT:0001259)body weight (CMO:0000012)35986366383358329Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)367641995130815812Rat
738019Anxrr10Anxiety related response QTL 103.9exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)358925062103925062Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)370311536115311536Rat
9590136Scort3Serum corticosterone level QTL 323.370.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)34865774493657744Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)35076614595766145Rat
61356Bp37Blood pressure QTL 373blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)35109256196092561Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)336721849110333156Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)35076614595766145Rat
8694196Abfw2Abdominal fat weight QTL 216.580.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)34865774493657744Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31141509147Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)342158111124558371Rat
1582249Bw77Body weight QTL 773.20.0025epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)37359251285062403Rat
2325840Bp345Blood pressure QTL 3450.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)33870893183708931Rat
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)34865774493657744Rat
631676Cm8Cardiac mass QTL 87.030.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)33736373482363734Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)33610140381101403Rat
8694386Bw159Body weight QTL 1594.520.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)34865774493657744Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)342158111124558371Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35675975141509147Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)367641995130815812Rat

Markers in Region
D3Mco27  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8377,328,474 - 77,328,632 (+)Marker Load Pipeline
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
Celera356,463,310 - 56,463,467UniSTS
RGSC_v3.1354,405,468 - 54,405,626RGD
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
GRCr8377,283,699 - 77,283,845 (+)Marker Load Pipeline
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
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
15 12 67 161 91 90 59 60 59 6 317 160 11 139 75 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000010630   ⟹   ENSRNOP00000010630
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl377,217,056 - 77,509,978 (+)Ensembl
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
GRCr8 Ensembl377,305,251 - 77,509,927 (+)Ensembl
mRatBN7.2 Ensembl356,897,560 - 57,102,316 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000100000   ⟹   ENSRNOP00000095541
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl377,217,039 - 77,509,978 (+)Ensembl
mRatBN7.2 Ensembl356,809,270 - 57,101,332 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000116465   ⟹   ENSRNOP00000096055
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl377,281,737 - 77,509,978 (+)Ensembl
mRatBN7.2 Ensembl356,874,255 - 57,102,316 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000119235   ⟹   ENSRNOP00000087630
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl377,217,039 - 77,509,978 (+)Ensembl
mRatBN7.2 Ensembl356,809,270 - 57,101,332 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000162637   ⟹   ENSRNOP00000109712
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl377,217,060 - 77,509,927 (+)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
- UniProtKB: A0A8I6GLW9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063139215   ⟸   XM_063283145
- Peptide Label: isoform X5
- UniProtKB: A0A8I6GLW9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063139216   ⟸   XM_063283146
- Peptide Label: isoform X5
- UniProtKB: A0A8I6GLW9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063139217   ⟸   XM_063283147
- Peptide Label: isoform X5
- UniProtKB: A0A8I6GLW9 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000109712   ⟸   ENSRNOT00000162637
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, ENTREZGENE
Ensembl Transcript ENSRNOT00000010630 ENTREZGENE
  ENSRNOT00000094770 ENTREZGENE
  ENSRNOT00000116465 ENTREZGENE
  ENSRNOT00000119235 ENTREZGENE
Gene3D-CATH 1.10.840.10 UniProtKB/Swiss-Prot
  Phosphatidylinositol 3-kinase Catalytic Subunit, Chain A, domain 1 UniProtKB/Swiss-Prot
  Son of sevenless (SoS) protein Chain: S domain 1 UniProtKB/Swiss-Prot
InterPro Ras-like_GEF UniProtKB/Swiss-Prot
  Ras-like_Gua-exchang_fac_N UniProtKB/Swiss-Prot
  Ras_G-nucl-exch_fac_CS UniProtKB/Swiss-Prot
  Ras_GEF_dom_sf UniProtKB/Swiss-Prot
  RASGEF_cat_dom UniProtKB/Swiss-Prot
  RASGEF_cat_dom_sf UniProtKB/Swiss-Prot
  Ubiquitin-like_domsf UniProtKB/Swiss-Prot
NCBI Gene 252857 ENTREZGENE
PANTHER PTHR23113 UniProtKB/Swiss-Prot
  RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR 4 UniProtKB/Swiss-Prot
Pfam RasGEF UniProtKB/Swiss-Prot
PharmGKB RAPGEF4 RGD
PhenoGen Rapgef4 PhenoGen
PROSITE RASGEF UniProtKB/Swiss-Prot
  RASGEF_CAT UniProtKB/Swiss-Prot
  RASGEF_NTER UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000001516 RatGTEx
SMART RasGEF UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48366 UniProtKB/Swiss-Prot
  SSF54236 UniProtKB/Swiss-Prot
UniProt A0A8I6A857 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6B2Y4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GEV8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GLW9 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0LW86_RAT UniProtKB/TrEMBL
  A6HM69_RAT UniProtKB/TrEMBL
  A6HM70_RAT UniProtKB/TrEMBL
  D3KR63 ENTREZGENE, UniProtKB/TrEMBL
  F1LQ26 ENTREZGENE
  Q9Z1C7 ENTREZGENE, UniProtKB/Swiss-Prot


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