Rab40c (Rab40c, member RAS oncogene family) - Rat Genome Database

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Gene: Rab40c (Rab40c, member RAS oncogene family) Rattus norvegicus
Analyze
Symbol: Rab40c
Name: Rab40c, member RAS oncogene family
RGD ID: 727914
Description: Enables GDP binding activity and GTP binding activity. Predicted to be involved in cell migration; exocytosis; and lipid droplet formation. Predicted to act upstream of or within negative regulation of focal adhesion assembly; positive regulation of focal adhesion assembly; and proteasome-mediated ubiquitin-dependent protein catabolic process. Located in perinuclear region of cytoplasm. Orthologous to human RAB40C (RAB40C, member RAS oncogene family); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: ras-related protein Rab-40C
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81015,405,436 - 15,440,659 (-)NCBIGRCr8GRCr8GRCr8
mRatBN7.21014,900,926 - 14,936,153 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1014,900,929 - 14,936,557 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1019,641,467 - 19,675,115 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01019,130,345 - 19,163,990 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01014,630,680 - 14,664,091 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01015,247,913 - 15,283,111 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1015,247,914 - 15,282,951 (-)Ensemblrn6Rnor6.0
Rnor_5.01015,060,856 - 15,096,137 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41015,147,861 - 15,181,653 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1014,571,341 - 14,604,815 (-)NCBICelera
RGSC_v3.11015,147,860 - 15,181,653 (-)NCBI
Cytogenetic Map10q12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View
epilepsy  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

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. NCBI rat LocusLink and RefSeq merged data October 15, 2003 NCBI rat LocusLink and RefSeq merged data October 15, 2003
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Vesicle transport in oligodendrocytes: probable role of Rab40c protein. Rodriguez-Gabin AG, etal., J Neurosci Res 2004 Jun 15;76(6):758-70.
Additional References at PubMed
PMID:12477932  


Genomics

Comparative Map Data
Rab40c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81015,405,436 - 15,440,659 (-)NCBIGRCr8GRCr8GRCr8
mRatBN7.21014,900,926 - 14,936,153 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1014,900,929 - 14,936,557 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1019,641,467 - 19,675,115 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01019,130,345 - 19,163,990 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01014,630,680 - 14,664,091 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01015,247,913 - 15,283,111 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1015,247,914 - 15,282,951 (-)Ensemblrn6Rnor6.0
Rnor_5.01015,060,856 - 15,096,137 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41015,147,861 - 15,181,653 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1014,571,341 - 14,604,815 (-)NCBICelera
RGSC_v3.11015,147,860 - 15,181,653 (-)NCBI
Cytogenetic Map10q12NCBI
RAB40C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3816589,357 - 629,268 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl16589,007 - 629,273 (+)Ensemblhg38GRCh38
GRCh3716639,357 - 679,268 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3616580,177 - 619,273 (+)NCBIBuild 36Build 36hg18NCBI36
Build 3416580,179 - 619,272NCBI
Celera16840,134 - 879,407 (+)NCBICelera
Cytogenetic Map16p13.3NCBI
HuRef16561,196 - 600,572 (+)NCBIHuRef
CHM1_116639,212 - 679,111 (+)NCBICHM1_1
T2T-CHM13v2.016593,278 - 633,302 (+)NCBIT2T-CHM13v2.0
Rab40c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391726,101,088 - 26,138,688 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1726,101,088 - 26,138,701 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381725,882,114 - 25,919,714 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1725,882,114 - 25,919,727 (-)Ensemblmm10GRCm38
MGSCv371726,019,059 - 26,056,659 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361725,609,714 - 25,647,302 (-)NCBIMGSCv36mm8
Celera1726,415,170 - 26,452,734 (-)NCBICelera
Cytogenetic Map17A3.3NCBI
cM Map1712.97NCBI
Rab40c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544216,577,843 - 16,614,639 (-)Ensembl
ChiLan1.0NW_00495544216,577,843 - 16,614,132 (-)NCBIChiLan1.0ChiLan1.0
RAB40C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v218831,336 - 869,340 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1164,615,216 - 4,653,206 (+)NCBINHGRI_mPanPan1
PanPan1.116600,153 - 642,365 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl16606,023 - 640,714 (+)EnsemblpanPan2panpan1.1
RAB40C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1639,937,858 - 39,968,042 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl639,939,004 - 39,945,765 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha641,201,465 - 41,228,245 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0640,280,019 - 40,306,809 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl640,280,023 - 40,307,845 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1639,968,542 - 39,995,318 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0639,928,729 - 39,955,488 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0640,407,910 - 40,434,695 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Rab40c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344112,277,803 - 112,311,387 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936501373,859 - 409,267 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936501375,663 - 409,243 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RAB40C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl341,140,561 - 41,160,077 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1341,140,557 - 41,160,101 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2341,328,868 - 41,330,727 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RAB40C
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.15511,517 - 545,868 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl5511,660 - 544,225 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606830,589,408 - 30,648,400 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rab40c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249131,403,374 - 1,442,382 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046249131,402,655 - 1,441,509 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Rab40c
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v193,146,016 - 3,181,100 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Rab40c
209 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:490
Count of miRNA genes:250
Interacting mature miRNAs:299
Transcripts:ENSRNOT00000027266
Prediction methods:Microtar, Miranda, Rnahybrid
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
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10666111835509383Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10666092373950353Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10589381150893811Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10125055464349221Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10589381150893811Rat
2301967Cm73Cardiac mass QTL 734.55heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)101499153586964295Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014991535107713808Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)101465354159653541Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10687714251877142Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135730538Rat
7387235Uae41Urinary albumin excretion QTL 415.260.1874urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)10130004247Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10589381150893811Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10686461896620484Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1092219745922197Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014991535107556066Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)10210370847103708Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10589381150893811Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10117749933Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138832698Rat

Markers in Region
D17Jcs49  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21014,921,014 - 14,921,419 (+)MAPPERmRatBN7.2
Rnor_6.01015,267,978 - 15,268,381NCBIRnor6.0
Rnor_5.01015,080,953 - 15,081,356UniSTSRnor5.0
RGSC_v3.41015,166,447 - 15,166,850UniSTSRGSC3.4
Celera1014,589,882 - 14,590,285UniSTS
Cytogenetic Map10q12UniSTS
RH141016  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21014,901,050 - 14,901,231 (+)MAPPERmRatBN7.2
Rnor_6.01015,248,038 - 15,248,218NCBIRnor6.0
Rnor_5.01015,060,981 - 15,061,161UniSTSRnor5.0
RGSC_v3.41015,146,435 - 15,146,615UniSTSRGSC3.4
Celera1014,569,915 - 14,570,095UniSTS
RH 3.4 Map10156.7UniSTS
Cytogenetic Map10q12UniSTS


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
16 12 67 162 91 90 59 92 59 6 356 192 11 141 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000027266   ⟹   ENSRNOP00000027266
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1014,900,929 - 14,936,557 (-)Ensembl
Rnor_6.0 Ensembl1015,247,914 - 15,282,951 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000094273   ⟹   ENSRNOP00000082330
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1014,900,929 - 14,936,557 (-)Ensembl
RefSeq Acc Id: NM_182675   ⟹   NP_872616
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81015,405,436 - 15,440,659 (-)NCBI
mRatBN7.21014,900,926 - 14,936,153 (-)NCBI
Rnor_6.01015,249,464 - 15,282,910 (-)NCBI
Rnor_5.01015,060,856 - 15,096,137 (-)NCBI
RGSC_v3.41015,147,861 - 15,181,653 (-)RGD
Celera1014,571,341 - 14,604,815 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_872616 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI28721 (Get FASTA)   NCBI Sequence Viewer  
  AAO48789 (Get FASTA)   NCBI Sequence Viewer  
  EDM03982 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_872616   ⟸   NM_182675
- UniProtKB: Q6Y2E6 (UniProtKB/TrEMBL),   A2VCW4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000027266   ⟸   ENSRNOT00000027266
Ensembl Acc Id: ENSRNOP00000082330   ⟸   ENSRNOT00000094273
Protein Domains
SOCS box

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6Y2E6-F1-model_v2 AlphaFold Q6Y2E6 1-281 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:727914 AgrOrtholog
BioCyc Gene G2FUF-25743 BioCyc
Ensembl Genes ENSRNOG00000020067 Ensembl
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:8374477 IMAGE-MGC_LOAD
InterPro P-loop_NTPase UniProtKB/TrEMBL
  Ras_GTPase UniProtKB/TrEMBL
  Small_GTP_bd UniProtKB/TrEMBL
  Small_GTPase_Rab UniProtKB/TrEMBL
  SOCS_box_dom_like UniProtKB/TrEMBL
  SOCS_C UniProtKB/TrEMBL
KEGG Report rno:359728 UniProtKB/TrEMBL
MGC_CLONE MGC:156560 IMAGE-MGC_LOAD
NCBI Gene 359728 ENTREZGENE
PANTHER LD44762P UniProtKB/TrEMBL
Pfam Ras UniProtKB/TrEMBL
  SOCS_box UniProtKB/TrEMBL
PhenoGen Rab40c PhenoGen
PRINTS RASTRNSFRMNG UniProtKB/TrEMBL
PROSITE RAB UniProtKB/TrEMBL
  RAS UniProtKB/TrEMBL
  SOCS UniProtKB/TrEMBL
RatGTEx ENSRNOG00000020067 RatGTEx
SMART RAB UniProtKB/TrEMBL
  RAN UniProtKB/TrEMBL
  RAS UniProtKB/TrEMBL
  RHO UniProtKB/TrEMBL
  SOCS UniProtKB/TrEMBL
  SOCS_box UniProtKB/TrEMBL
Superfamily-SCOP SSF158235 UniProtKB/TrEMBL
  SSF52540 UniProtKB/TrEMBL
UniProt A2VCW4 ENTREZGENE, UniProtKB/TrEMBL
  Q6Y2E6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Rab40c  Rab40c, member RAS oncogene family      Symbol and Name status set to approved 1299863 APPROVED