Rab9b (RAB9B, member RAS oncogene family) - Rat Genome Database

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Gene: Rab9b (RAB9B, member RAS oncogene family) Rattus norvegicus
Analyze
Symbol: Rab9b
Name: RAB9B, member RAS oncogene family
RGD ID: 1562951
Description: Predicted to enable GDP binding activity and identical protein binding activity. Predicted to be involved in retrograde transport, endosome to Golgi. Predicted to be located in cytosol and phagocytic vesicle membrane. Predicted to be active in late endosome; lysosome; and phagocytic vesicle. Orthologous to human RAB9B (RAB9B, member RAS oncogene family); PARTICIPATES IN measles pathway; INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; bromobenzene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC367915; ras-related protein Rab-9B; RGD1562951; similar to RAB9B, member RAS oncogene family
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
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
GRCr8X105,013,178 - 105,023,872 (-)NCBIGRCr8
mRatBN7.2X100,220,897 - 100,231,591 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX100,220,894 - 100,231,701 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX102,351,081 - 102,361,775 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X105,849,755 - 105,860,445 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X103,418,926 - 103,429,616 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X107,531,404 - 107,542,510 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX107,531,404 - 107,542,510 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X107,414,930 - 107,426,468 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X124,525,742 - 124,528,535 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX101,055,137 - 101,065,806 (-)NCBICelera
Cytogenetic MapXq32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
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:20937701   PMID:21255211   PMID:25220469  


Genomics

Comparative Map Data
Rab9b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X105,013,178 - 105,023,872 (-)NCBIGRCr8
mRatBN7.2X100,220,897 - 100,231,591 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX100,220,894 - 100,231,701 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX102,351,081 - 102,361,775 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X105,849,755 - 105,860,445 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X103,418,926 - 103,429,616 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X107,531,404 - 107,542,510 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX107,531,404 - 107,542,510 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X107,414,930 - 107,426,468 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X124,525,742 - 124,528,535 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX101,055,137 - 101,065,806 (-)NCBICelera
Cytogenetic MapXq32NCBI
RAB9B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X103,776,324 - 103,832,257 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX103,822,327 - 103,832,257 (-)EnsemblGRCh38hg38GRCh38
GRCh37X103,031,252 - 103,087,187 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X102,966,607 - 102,973,814 (-)NCBINCBI36Build 36hg18NCBI36
Build 34X102,886,095 - 102,893,303NCBI
CeleraX103,516,271 - 103,526,228 (-)NCBICelera
Cytogenetic MapXq22.2NCBI
HuRefX92,732,783 - 92,742,676 (-)NCBIHuRef
CHM1_1X102,970,244 - 102,980,201 (-)NCBICHM1_1
T2T-CHM13v2.0X102,223,281 - 102,279,224 (-)NCBIT2T-CHM13v2.0
Rab9b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X135,758,896 - 135,769,305 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX135,758,896 - 135,769,504 (-)EnsemblGRCm39 Ensembl
GRCm38X136,858,147 - 136,868,556 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX136,858,147 - 136,868,755 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X133,392,690 - 133,403,079 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X132,204,515 - 132,214,904 (-)NCBIMGSCv36mm8
CeleraX120,140,142 - 120,150,492 (-)NCBICelera
Cytogenetic MapXF1NCBI
cM MapX59.1NCBI
Rab9b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_004955548825,208 - 829,815 (-)NCBIChiLan1.0ChiLan1.0
RAB9B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X103,443,483 - 103,453,503 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X103,447,084 - 103,457,100 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X93,060,899 - 93,070,911 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X103,442,543 - 103,451,813 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX103,444,776 - 103,445,381 (-)Ensemblpanpan1.1panPan2
RAB9B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X77,228,609 - 77,238,344 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX77,231,441 - 77,239,001 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX63,457,575 - 63,467,309 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X78,846,172 - 78,865,879 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX78,846,174 - 78,856,496 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X76,324,746 - 76,334,480 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X78,011,443 - 78,021,177 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X77,778,585 - 77,788,319 (-)NCBIUU_Cfam_GSD_1.0
Rab9b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X77,151,172 - 77,161,702 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649910,437,611 - 10,504,320 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493649910,501,837 - 10,506,793 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RAB9B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX84,721,274 - 84,732,990 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X84,721,269 - 84,733,000 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X98,599,279 - 98,610,984 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RAB9B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X91,716,741 - 91,727,167 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX91,719,610 - 91,720,212 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606516,582,249 - 16,667,935 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rab9b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462495497,988 - 102,617 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462495488,909 - 102,637 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rab9b
13 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:641
Count of miRNA genes:312
Interacting mature miRNAs:414
Transcripts:ENSRNOT00000074140
Prediction methods:Miranda, Pita
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
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X75294106120294106Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X93956491138956491Rat

Markers in Region
WI-21742  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X100,221,582 - 100,221,847 (+)MAPPERmRatBN7.2
Rnor_6.0X107,532,090 - 107,532,354NCBIRnor6.0
Rnor_5.0X107,415,616 - 107,415,880UniSTSRnor5.0
RGSC_v3.4X124,526,428 - 124,526,692UniSTSRGSC3.4
CeleraX101,055,823 - 101,056,087UniSTS
Cytogenetic MapXq35UniSTS
BE106581  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X100,221,003 - 100,221,136 (+)MAPPERmRatBN7.2
Rnor_6.0X107,531,511 - 107,531,643NCBIRnor6.0
Rnor_5.0X107,415,037 - 107,415,169UniSTSRnor5.0
RGSC_v3.4X124,525,849 - 124,525,981UniSTSRGSC3.4
CeleraX101,055,244 - 101,055,376UniSTS
Cytogenetic MapXq35UniSTS


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 60
Low 1 10 22 6 17 6 2 2 12 19 10 9 2
Below cutoff 2 33 10 10 1 10 6 7 2 16 29 1 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000074140   ⟹   ENSRNOP00000066233
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX100,220,894 - 100,231,701 (-)Ensembl
Rnor_6.0 EnsemblX107,531,404 - 107,542,510 (-)Ensembl
RefSeq Acc Id: NM_001109018   ⟹   NP_001102488
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X105,013,178 - 105,023,872 (-)NCBI
mRatBN7.2X100,220,897 - 100,231,591 (-)NCBI
Rnor_6.0X107,531,404 - 107,542,510 (-)NCBI
Rnor_5.0X107,414,930 - 107,426,468 (-)NCBI
RGSC_v3.4X124,525,742 - 124,528,535 (-)RGD
CeleraX101,055,137 - 101,065,806 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102488 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL87990 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000066233
  ENSRNOP00000066233.1
Reference Protein Sequences
RefSeq Acc Id: NP_001102488   ⟸   NM_001109018
- UniProtKB: D3ZP15 (UniProtKB/TrEMBL),   A6KNU6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000066233   ⟸   ENSRNOT00000074140

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZP15-F1-model_v2 AlphaFold D3ZP15 1-201 view protein structure

Transcriptome

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

Promoters
RGD ID:13701947
Promoter ID:EPDNEW_R12470
Type:single initiation site
Name:Rab9b_1
Description:RAB9B, 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_6.0X107,542,557 - 107,542,617EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562951 AgrOrtholog
BioCyc Gene G2FUF-1604 BioCyc
Ensembl Genes ENSRNOG00000047960 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000074140 ENTREZGENE
  ENSRNOT00000074140.2 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
InterPro P-loop_NTPase UniProtKB/TrEMBL
  Rab9 UniProtKB/TrEMBL
  Small_GTP-bd_dom UniProtKB/TrEMBL
  Small_GTPase UniProtKB/TrEMBL
KEGG Report rno:367915 UniProtKB/TrEMBL
NCBI Gene 367915 ENTREZGENE
PANTHER RAB FAMILY UniProtKB/TrEMBL
  RAS-RELATED PROTEIN RAB-9B UniProtKB/TrEMBL
Pfam Ras UniProtKB/TrEMBL
PhenoGen Rab9b PhenoGen
PRINTS RASTRNSFRMNG UniProtKB/TrEMBL
PROSITE RAB UniProtKB/TrEMBL
  RAS UniProtKB/TrEMBL
  RHO UniProtKB/TrEMBL
RatGTEx ENSRNOG00000047960 RatGTEx
SMART RAB UniProtKB/TrEMBL
  RAN UniProtKB/TrEMBL
  RAS UniProtKB/TrEMBL
  RHO UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt A6KNU6 ENTREZGENE, UniProtKB/TrEMBL
  D3ZP15 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Rab9b  RAB9B, member RAS oncogene family   Rab9b_predicted  RAB9B, member RAS oncogene family (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Rab9b_predicted  RAB9B, member RAS oncogene family (predicted)  RGD1562951_predicted  similar to RAB9B, member RAS oncogene family (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1562951_predicted  similar to RAB9B, member RAS oncogene family (predicted)  LOC367915  similar to RAB9B, member RAS oncogene family  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC367915  similar to RAB9B, member RAS oncogene family      Symbol and Name status set to provisional 70820 PROVISIONAL