Rab20 (RAB20, member RAS oncogene family) - Rat Genome Database

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Gene: Rab20 (RAB20, member RAS oncogene family) Rattus norvegicus
Analyze
Symbol: Rab20
Name: RAB20, member RAS oncogene family
RGD ID: 1593487
Description: Predicted to enable GTPase activity. Predicted to be involved in intracellular protein transport; phagosome acidification; and phagosome-lysosome fusion. Predicted to act upstream of or within cellular response to type II interferon. Predicted to be located in Golgi apparatus and phagocytic vesicle. Predicted to be active in endomembrane system. Orthologous to human RAB20 (RAB20, member RAS oncogene family); INTERACTS WITH 1,3-dinitrobenzene; 2,3,7,8-tetrachlorodibenzodioxine; 4-(ethoxymethylene)-2-phenyloxazol-5-one.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC689377; ras-related protein Rab-20; similar to Ras-related protein Rab-20
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81684,721,427 - 84,745,610 (+)NCBIGRCr8
mRatBN7.21678,019,337 - 78,043,529 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1678,019,337 - 78,043,529 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1683,299,781 - 83,323,965 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01686,752,438 - 86,776,630 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01681,994,065 - 82,018,501 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01683,358,116 - 83,382,326 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1683,358,116 - 83,382,326 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01682,824,911 - 82,848,168 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41682,871,002 - 82,895,146 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1675,818,103 - 75,841,942 (+)NCBICelera
Cytogenetic Map16q12.5NCBI
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
(-)-demecolcine  (ISO)
(1->4)-beta-D-glucan  (ISO)
1,2-dimethylhydrazine  (ISO)
1,3-dinitrobenzene  (EXP)
1-nitropyrene  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-butoxyethanol  (ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (EXP)
4-\{[(5,5,8,8-tetramethyl-5,6,7,8-tetrahydronaphthalen-2-yl)carbonyl]amino\}benzoic acid  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acrylamide  (EXP)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
amphetamine  (EXP)
antirheumatic drug  (ISO)
aristolochic acid A  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
carbamazepine  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
cobalt dichloride  (ISO)
copper(II) sulfate  (ISO)
Dibutyl phosphate  (ISO)
dibutyl phthalate  (EXP)
diethylstilbestrol  (ISO)
dioxygen  (ISO)
diuron  (EXP)
dorsomorphin  (ISO)
entinostat  (ISO)
ethyl methanesulfonate  (ISO)
etoposide  (ISO)
fluoranthene  (ISO)
formaldehyde  (ISO)
fulvestrant  (ISO)
furan  (EXP)
gentamycin  (EXP)
glycidyl methacrylate  (ISO)
iron dichloride  (ISO)
manganese(II) chloride  (EXP)
mercury dibromide  (ISO)
methapyrilene  (EXP)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
methylmercury chloride  (ISO)
mitomycin C  (ISO)
mono(2-ethylhexyl) phthalate  (EXP)
nickel atom  (ISO)
oxaliplatin  (EXP)
ozone  (ISO)
p-chloromercuribenzoic acid  (ISO)
panobinostat  (ISO)
paracetamol  (EXP,ISO)
perfluorooctane-1-sulfonic acid  (ISO)
phenylmercury acetate  (ISO)
pirinixic acid  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
T-2 toxin  (ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP,ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (EXP)
triphenyl phosphate  (ISO)
valproic acid  (ISO)
vincristine  (ISO)
vorinostat  (ISO)
zearalenone  (ISO)
zinc dichloride  (ISO)
zinc sulfate  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:19144319   PMID:21255211   PMID:29107708  


Genomics

Comparative Map Data
Rab20
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81684,721,427 - 84,745,610 (+)NCBIGRCr8
mRatBN7.21678,019,337 - 78,043,529 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1678,019,337 - 78,043,529 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1683,299,781 - 83,323,965 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01686,752,438 - 86,776,630 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01681,994,065 - 82,018,501 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01683,358,116 - 83,382,326 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1683,358,116 - 83,382,326 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01682,824,911 - 82,848,168 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41682,871,002 - 82,895,146 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1675,818,103 - 75,841,942 (+)NCBICelera
Cytogenetic Map16q12.5NCBI
RAB20
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3813110,523,066 - 110,561,722 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl13110,523,066 - 110,561,722 (-)EnsemblGRCh38hg38GRCh38
GRCh3713111,175,413 - 111,214,069 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3613109,973,414 - 110,012,072 (-)NCBINCBI36Build 36hg18NCBI36
Build 3413109,973,414 - 110,012,072NCBI
Celera1392,021,471 - 92,060,129 (-)NCBICelera
Cytogenetic Map13q34NCBI
HuRef1391,774,840 - 91,813,429 (-)NCBIHuRef
CHM1_113111,143,261 - 111,182,508 (-)NCBICHM1_1
T2T-CHM13v2.013109,753,501 - 109,792,327 (-)NCBIT2T-CHM13v2.0
Rab20
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39811,503,390 - 11,528,640 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl811,503,518 - 11,528,710 (-)EnsemblGRCm39 Ensembl
GRCm38811,453,390 - 11,478,640 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl811,453,518 - 11,478,710 (-)EnsemblGRCm38mm10GRCm38
MGSCv37811,453,977 - 11,478,499 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36811,453,949 - 11,478,471 (-)NCBIMGSCv36mm8
Celera811,628,822 - 11,653,857 (-)NCBICelera
Cytogenetic Map8A1.1NCBI
cM Map85.73NCBI
Rab20
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554042,087,580 - 2,088,545 (+)NCBIChiLan1.0ChiLan1.0
RAB20
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v214112,019,815 - 112,057,904 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan113110,703,541 - 110,741,624 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01391,660,142 - 91,698,215 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.113110,778,119 - 110,815,408 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl13110,778,119 - 110,815,408 (-)Ensemblpanpan1.1panPan2
RAB20
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12258,825,147 - 58,853,921 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2258,825,667 - 58,853,667 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2258,534,701 - 58,563,463 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02259,447,953 - 59,476,697 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2259,447,953 - 59,476,746 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12258,948,658 - 58,977,901 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02258,940,714 - 58,970,373 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02258,976,123 - 59,005,638 (-)NCBIUU_Cfam_GSD_1.0
Rab20
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945193,687,535 - 193,716,912 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364722,234,873 - 2,264,622 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364722,234,826 - 2,264,613 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RAB20
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1177,167,059 - 77,188,898 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11177,167,052 - 77,188,893 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21184,681,262 - 84,703,347 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RAB20
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1388,769,676 - 88,803,384 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl388,770,271 - 88,803,177 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604645,502,751 - 45,539,015 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rab20
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247932,180,419 - 2,198,962 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247932,180,803 - 2,199,420 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rab20
146 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:95
Count of miRNA genes:77
Interacting mature miRNAs:91
Transcripts:ENSRNOT00000031109
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163528887080288870Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)163775215682752156Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)163775215682752156Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164239634584729064Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165272646484729064Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165272646484729064Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165272646484729064Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)165571108783402471Rat

Markers in Region
RH143287  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21678,019,415 - 78,019,654 (+)MAPPERmRatBN7.2
Rnor_6.01683,358,195 - 83,358,433NCBIRnor6.0
Rnor_5.01682,824,990 - 82,825,228UniSTSRnor5.0
RGSC_v3.41682,871,081 - 82,871,319UniSTSRGSC3.4
Celera1675,818,182 - 75,818,420UniSTS
RH 3.4 Map16760.4UniSTS
Cytogenetic Map16q12.5UniSTS


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 2 43 6 4 11 4 4 6 31 19 11 4
Low 1 51 37 8 37 4 5 68 4 22 4
Below cutoff 6

Sequence


RefSeq Acc Id: ENSRNOT00000031109   ⟹   ENSRNOP00000033660
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1678,019,337 - 78,043,529 (+)Ensembl
Rnor_6.0 Ensembl1683,358,116 - 83,382,326 (+)Ensembl
RefSeq Acc Id: NM_001109535   ⟹   NP_001103005
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81684,721,427 - 84,745,610 (+)NCBI
mRatBN7.21678,019,337 - 78,043,529 (+)NCBI
Rnor_6.01683,358,116 - 83,382,326 (+)NCBI
Rnor_5.01682,824,911 - 82,848,168 (+)NCBI
RGSC_v3.41682,871,002 - 82,895,146 (+)RGD
Celera1675,818,103 - 75,841,942 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001103005 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM08822 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000033660
  ENSRNOP00000033660.2
RefSeq Acc Id: NP_001103005   ⟸   NM_001109535
- UniProtKB: D4AAE6 (UniProtKB/TrEMBL),   A6IWQ0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000033660   ⟸   ENSRNOT00000031109

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4AAE6-F1-model_v2 AlphaFold D4AAE6 1-232 view protein structure

Transcriptome

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

Promoters
RGD ID:13700246
Promoter ID:EPDNEW_R10769
Type:initiation region
Name:Rab20_1
Description:RAB20, member RAS oncogene family
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_6.01683,358,159 - 83,358,219EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1593487 AgrOrtholog
BioCyc Gene G2FUF-10653 BioCyc
Ensembl Genes ENSRNOG00000023991 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000031109 ENTREZGENE
  ENSRNOT00000031109.3 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
InterPro P-loop_NTPase UniProtKB/TrEMBL
  Rab20 UniProtKB/TrEMBL
  Ras_GTPase UniProtKB/TrEMBL
  Small_GTP-bd UniProtKB/TrEMBL
KEGG Report rno:689377 UniProtKB/TrEMBL
NCBI Gene 689377 ENTREZGENE
PANTHER DRAB5-RELATED UniProtKB/TrEMBL
  RAS-RELATED PROTEIN RAB-20 UniProtKB/TrEMBL
Pfam Ras UniProtKB/TrEMBL
PhenoGen Rab20 PhenoGen
PRINTS RASTRNSFRMNG UniProtKB/TrEMBL
PROSITE RAB UniProtKB/TrEMBL
RatGTEx ENSRNOG00000023991 RatGTEx
SMART RAB UniProtKB/TrEMBL
  RAS UniProtKB/TrEMBL
  RHO UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt A6IWQ0 ENTREZGENE, UniProtKB/TrEMBL
  D4AAE6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-17 Rab20  RAB20, member RAS oncogene family  LOC686866  similar to Ras-related protein Rab-20  Data merged from RGD:1592488 1643240 APPROVED
2008-03-06 Rab20  RAB20, member RAS oncogene family  LOC689377  similar to Ras-related protein Rab-20  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC689377  similar to Ras-related protein Rab-20      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 LOC686866  similar to Ras-related protein Rab-20      Symbol and Name status set to provisional 70820 PROVISIONAL