Rab40b (Rab40b, member RAS oncogene family) - Rat Genome Database

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Gene: Rab40b (Rab40b, member RAS oncogene family) Rattus norvegicus
Analyze
Symbol: Rab40b
Name: Rab40b, member RAS oncogene family
RGD ID: 1305663
Description: Predicted to enable GTPase activity. Predicted to be involved in protein localization to plasma membrane and toxin transport. Predicted to be located in nuclear envelope and perinuclear region of cytoplasm. Predicted to be active in endosome; plasma membrane; and synaptic vesicle. Orthologous to several human genes including RAB40B (RAB40B, member RAS oncogene family); INTERACTS WITH (+)-schisandrin B; 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC303754; ras-related protein Rab-40B
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr810107,129,801 - 107,157,375 (-)NCBIGRCr8
mRatBN7.210106,631,514 - 106,659,090 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl10106,631,514 - 106,659,090 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx10111,733,874 - 111,761,463 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.010111,196,923 - 111,224,513 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.010106,551,924 - 106,579,498 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.010110,557,798 - 110,585,424 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10110,557,729 - 110,585,376 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010110,143,366 - 110,171,085 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410110,590,703 - 110,618,223 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.110110,605,202 - 110,632,641 (-)NCBI
Celera10105,169,974 - 105,197,417 (-)NCBICelera
Cytogenetic Map10q32.3NCBI
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
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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:22042847  


Genomics

Comparative Map Data
Rab40b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr810107,129,801 - 107,157,375 (-)NCBIGRCr8
mRatBN7.210106,631,514 - 106,659,090 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl10106,631,514 - 106,659,090 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx10111,733,874 - 111,761,463 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.010111,196,923 - 111,224,513 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.010106,551,924 - 106,579,498 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.010110,557,798 - 110,585,424 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10110,557,729 - 110,585,376 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.010110,143,366 - 110,171,085 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410110,590,703 - 110,618,223 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.110110,605,202 - 110,632,641 (-)NCBI
Celera10105,169,974 - 105,197,417 (-)NCBICelera
Cytogenetic Map10q32.3NCBI
RAB40B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381782,654,973 - 82,698,698 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1782,654,973 - 82,698,698 (-)EnsemblGRCh38hg38GRCh38
GRCh371780,612,849 - 80,656,574 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361778,208,238 - 78,249,802 (-)NCBINCBI36Build 36hg18NCBI36
Build 341778,208,237 - 78,249,802NCBI
Celera1777,209,247 - 77,250,771 (-)NCBICelera
Cytogenetic Map17q25.3NCBI
HuRef1776,014,951 - 76,056,442 (-)NCBIHuRef
CHM1_11780,701,145 - 80,742,977 (-)NCBICHM1_1
T2T-CHM13v2.01783,529,323 - 83,573,130 (-)NCBIT2T-CHM13v2.0
Rab40b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911121,246,951 - 121,279,080 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl11121,246,951 - 121,279,077 (-)EnsemblGRCm39 Ensembl
GRCm3811121,356,121 - 121,388,251 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11121,356,125 - 121,388,251 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711121,217,435 - 121,249,565 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3611121,172,215 - 121,204,335 (-)NCBIMGSCv36mm8
Celera11133,093,587 - 133,125,778 (-)NCBICelera
Cytogenetic Map11E2NCBI
cM Map1185.28NCBI
Rab40b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955506479,516 - 512,362 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955506480,236 - 509,038 (+)NCBIChiLan1.0ChiLan1.0
RAB40B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21999,196,529 - 99,241,990 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan117104,100,556 - 104,145,357 (-)NCBINHGRI_mPanPan1
PanPan1.1 Ensembl1782,872,403 - 82,902,803 (-)Ensemblpanpan1.1panPan2
RAB40B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha9359,952 - 379,474 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.09351,762 - 371,277 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl9351,795 - 371,277 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.19345,847 - 365,366 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.09507,101 - 526,608 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.09582,386 - 601,900 (+)NCBIUU_Cfam_GSD_1.0
RAB40B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl12493,315 - 516,962 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.112492,298 - 516,965 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.212221,054 - 245,023 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RAB40B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11674,558,970 - 74,595,967 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1674,559,763 - 74,595,841 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607746,199,797 - 46,237,650 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rab40b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462480111,363,537 - 11,389,183 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462480111,363,539 - 11,389,201 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rab40b
187 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:512
Count of miRNA genes:258
Interacting mature miRNAs:318
Transcripts:ENSRNOT00000054917
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
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014487011107057807Rat
1331791Cm31Cardiac mass QTL 313.84606heart mass (VT:0007028)heart wet weight (CMO:0000069)1029299504107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1051770177107211142Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1051770177107211142Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1053797385107211142Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062057807107057807Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062057807107057807Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063221094107211142Rat
2317029Aia19Adjuvant induced arthritis QTL 192.98joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)1066978955107211142Rat
2317039Aia6Adjuvant induced arthritis QTL 64.31joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)1066978955107211142Rat
10450498Bp384Blood pressure QTL 3840.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1067750049107211142Rat
1642980Bp300Blood pressure QTL 300arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068383129107211142Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068420376107211142Rat
2300172Bmd57Bone mineral density QTL 579.80.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)1069738412107211142Rat
2293646Bss25Bone structure and strength QTL 2510.960.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1069738412107211142Rat
2293663Bss33Bone structure and strength QTL 339.340.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1069738412107211142Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070199100107211142Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072224939107211142Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1072224939107211142Rat
2292438Bp311Blood pressure QTL 311arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1076246085107211142Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076452683107211142Rat
4889492Pancm2Pancreatic morphology QTL 23.2pancreatic beta cell morphology trait (VT:0005217)ratio of insulin-positive cell area to total area of splenic region of pancreas (CMO:0001814)1076748906107211142Rat
2303589Bw87Body weight QTL 872body mass (VT:0001259)body weight (CMO:0000012)1081285008107211142Rat
2317754Glom25Glomerulus QTL 253.5urine protein amount (VT:0005160)urine protein level (CMO:0000591)1082685200107211142Rat
631538Oia5Oil induced arthritis QTL 5joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087055121107211142Rat
61363Oia3Oil induced arthritis QTL 30.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087307617107211142Rat
634320Niddm49Non-insulin dependent diabetes mellitus QTL 494.41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1088539139107211142Rat
12880395Cm109Cardiac mass QTL 1090.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1090404397107211142Rat
12880396Am13Aortic mass QTL 130.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1090404397107211142Rat
12880398Kidm67Kidney mass QTL 670.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1090404397107211142Rat
12880384Cm107Cardiac mass QTL 1070.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)90404397107211142Rat
12880385Cm108Cardiac mass QTL 1080.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)90404397107211142Rat
1579915Bp280Blood pressure QTL 2800.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090404397107211142Rat
1300137Bp186Blood pressure QTL 1863.57arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1090627439107057807Rat
724530Bp149Blood pressure QTL 1490.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1090627439107211142Rat
1354641Bvd2Brain ventricular dilatation QTL 26.360.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)1093223816107057807Rat
10450493Bp382Blood pressure QTL 3820.002arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1094759759107211142Rat
2292436Bp310Blood pressure QTL 310arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1094759759107211142Rat
1578663Bss18Bone structure and strength QTL 183.6femur width (VT:1000666)femoral neck width (CMO:0001695)1096703043107057807Rat
1578672Bmd16Bone mineral density QTL 166.2femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)1096703043107057807Rat


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 4 7 25 2 4
Low 3 43 57 41 19 41 4 4 49 33 39 11 4
Below cutoff 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000054917   ⟹   ENSRNOP00000051800
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl10106,631,514 - 106,659,090 (-)Ensembl
Rnor_6.0 Ensembl10110,557,729 - 110,585,376 (-)Ensembl
RefSeq Acc Id: NM_001107076   ⟹   NP_001100546
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr810107,129,801 - 107,157,375 (-)NCBI
mRatBN7.210106,631,514 - 106,659,090 (-)NCBI
Rnor_6.010110,557,798 - 110,585,424 (-)NCBI
Rnor_5.010110,143,366 - 110,171,085 (-)NCBI
RGSC_v3.410110,590,703 - 110,618,223 (-)RGD
Celera10105,169,974 - 105,197,417 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001100546 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI68956 (Get FASTA)   NCBI Sequence Viewer  
  EDM06950 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000051800
  ENSRNOP00000051800.2
Reference Protein Sequences
RefSeq Acc Id: NP_001100546   ⟸   NM_001107076
- UniProtKB: B5DF78 (UniProtKB/TrEMBL),   F7F5I6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000051800   ⟸   ENSRNOT00000054917
Protein Domains
SOCS box

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B5DF78-F1-model_v2 AlphaFold B5DF78 1-279 view protein structure

Transcriptome

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

Promoters
RGD ID:13697993
Promoter ID:EPDNEW_R8518
Type:multiple initiation site
Name:Rab40b_1
Description:Rab40b, 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_6.010110,585,428 - 110,585,488EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305663 AgrOrtholog
BioCyc Gene G2FUF-22356 BioCyc
Ensembl Genes ENSRNOG00000036661 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000054917 ENTREZGENE
  ENSRNOT00000054917.4 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
InterPro P-loop_NTPase UniProtKB/TrEMBL
  Ras_GTPase UniProtKB/TrEMBL
  Small_GTP_bd UniProtKB/TrEMBL
  SOCS_box_dom_like UniProtKB/TrEMBL
  SOCS_C UniProtKB/TrEMBL
KEGG Report rno:303754 UniProtKB/TrEMBL
NCBI Gene 303754 ENTREZGENE
PANTHER LD44762P UniProtKB/TrEMBL
  RAS-RELATED PROTEIN RAB-40B UniProtKB/TrEMBL
Pfam Ras UniProtKB/TrEMBL
  SOCS_box UniProtKB/TrEMBL
PhenoGen Rab40b PhenoGen
PRINTS RASTRNSFRMNG UniProtKB/TrEMBL
PROSITE RAB UniProtKB/TrEMBL
  RAS UniProtKB/TrEMBL
  SOCS UniProtKB/TrEMBL
RatGTEx ENSRNOG00000036661 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 B5DF78 ENTREZGENE, UniProtKB/TrEMBL
  F7F5I6 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Rab40b  Rab40b, member RAS oncogene family   Rab40b_predicted  Rab40b, member RAS oncogene family (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Rab40b_predicted  Rab40b, member RAS oncogene family (predicted)      Symbol and Name status set to approved 70820 APPROVED