Rab4a (RAB4A, member RAS oncogene family) - Rat Genome Database
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Gene: Rab4a (RAB4A, member RAS oncogene family) Rattus norvegicus
Analyze
Symbol: Rab4a
Name: RAB4A, member RAS oncogene family
RGD ID: 3529
Description: Exhibits several functions, including ATPase binding activity; GTP binding activity; and ionotropic glutamate receptor binding activity. Involved in Rab protein signal transduction. Localizes to several cellular components, including cytoplasmic vesicle; cytosol; and plasma membrane. Orthologous to human RAB4A (RAB4A, member RAS oncogene family); PARTICIPATES IN insulin responsive facilitative sugar transporter mediated glucose transport pathway; platelet-derived growth factor signaling pathway; Rab family mediated signaling pathway; INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Rab4; ras-related protein Rab-4A; Ras-related small GTP binding protein 4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21951,795,613 - 51,822,706 (+)NCBI
Rnor_6.0 Ensembl1956,585,767 - 56,613,075 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01956,585,598 - 56,613,078 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01967,296,402 - 67,323,425 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41953,991,122 - 54,019,248 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11953,996,067 - 54,022,738 (+)NCBI
Celera1951,171,470 - 51,198,520 (+)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
1. Cormont M, etal., J Biol Chem. 1993 Sep 15;268(26):19491-7.
2. Cussac D, etal., Mol Cell Endocrinol. 1996 May 31;119(2):195-206.
3. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. GOA data from the GO Consortium
5. Han SY, etal., Biochem J 2000 Nov 15;352 Pt 1:165-73.
6. Hoogenraad CC, etal., PLoS Biol. 2010 Jan 19;8(1):e1000283. doi: 10.1371/journal.pbio.1000283.
7. Kaddai V, etal., Acta Physiol (Oxf). 2008 Jan;192(1):75-88.
8. Kuijl C, etal., EMBO J. 2013 Mar 6;32(5):713-27. doi: 10.1038/emboj.2013.10. Epub 2013 Feb 5.
9. Li L, etal., J Biol Chem. 2001 Feb 16;276(7):5265-73. Epub 2000 Nov 3.
10. Martinez-Turrillas R, etal., Biochem Biophys Res Commun. 2007 Feb 16;353(3):750-5. Epub 2006 Dec 19.
11. MGD data from the GO Consortium
12. NCBI rat LocusLink and RefSeq merged data July 26, 2002
13. Pavlos NJ, etal., J Neurosci. 2010 Oct 6;30(40):13441-53. doi: 10.1523/JNEUROSCI.0907-10.2010.
14. Pipeline to import KEGG annotations from KEGG into RGD
15. Pipeline to import Pathway Interaction Database annotations from NCI into RGD
16. RGD automated data pipeline
17. RGD automated import pipeline for gene-chemical interactions
18. Ricort JM, etal., FEBS Lett. 1994 Jun 20;347(1):42-4.
19. Schindler C, etal., Nat Cell Biol. 2015 May;17(5):639-50. doi: 10.1038/ncb3129. Epub 2015 Mar 23.
20. Sherman LA, etal., Endocrinology. 1996 Jan;137(1):266-73.
21. Shibata H, etal., J Biol Chem. 1997 Jun 6;272(23):14542-6.
22. Uphues I, etal., Biochem J 1995 Oct 1;311 ( Pt 1):161-6.
23. Uphues I, etal., Biochem J. 1994 Jul 1;301 ( Pt 1):177-82.
24. Verges M, etal., Proc Natl Acad Sci U S A. 1999 Aug 31;96(18):10146-51.
25. Watson RT and Pessin JE, Cell Signal. 2007 Nov;19(11):2209-17. Epub 2007 Jun 21.
26. Zahraoui A, etal., Nucleic Acids Res 1988 Feb 11;16(3):1204.
27. Zaid H, etal., Biochem J. 2008 Jul 15;413(2):201-15.
Additional References at PubMed
PMID:3317403   PMID:11172003   PMID:12477932   PMID:12703553   PMID:15128739   PMID:15326289   PMID:15907487   PMID:16034420   PMID:17494101   PMID:17562788   PMID:18656450   PMID:19590752  
PMID:19717423   PMID:20051515   PMID:20728450   PMID:22279005   PMID:22980744   PMID:26254426   PMID:28818525  


Genomics

Comparative Map Data
Rab4a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21951,795,613 - 51,822,706 (+)NCBI
Rnor_6.0 Ensembl1956,585,767 - 56,613,075 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01956,585,598 - 56,613,078 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01967,296,402 - 67,323,425 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41953,991,122 - 54,019,248 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11953,996,067 - 54,022,738 (+)NCBI
Celera1951,171,470 - 51,198,520 (+)NCBICelera
Cytogenetic Map19q12NCBI
RAB4A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1229,271,062 - 229,305,894 (+)EnsemblGRCh38hg38GRCh38
GRCh381229,271,111 - 229,305,894 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371229,406,858 - 229,441,641 (+)NCBIGRCh37GRCh37hg19GRCh37
GRCh371229,406,809 - 229,441,641 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361227,473,502 - 227,507,141 (+)NCBINCBI36hg18NCBI36
Build 341225,713,613 - 225,747,252NCBI
Celera1202,675,200 - 202,708,836 (+)NCBI
Cytogenetic Map1q42.13NCBI
HuRef1199,897,464 - 199,932,284 (+)NCBIHuRef
CHM1_11230,679,139 - 230,713,964 (+)NCBICHM1_1
Rab4a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398124,532,583 - 124,562,030 (+)NCBIGRCm39mm39
GRCm388123,805,846 - 123,835,291 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8123,805,985 - 123,835,287 (+)EnsemblGRCm38mm10GRCm38
MGSCv378126,329,896 - 126,359,191 (+)NCBIGRCm37mm9NCBIm37
MGSCv368126,692,115 - 126,721,377 (+)NCBImm8
Celera8128,073,037 - 128,102,572 (+)NCBICelera
Cytogenetic Map8E2NCBI
cM Map872.19NCBI
Rab4a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554928,713,968 - 8,743,434 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554928,715,252 - 8,743,432 (-)NCBIChiLan1.0ChiLan1.0
RAB4A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11209,848,620 - 209,883,305 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1209,848,620 - 209,883,305 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01204,818,445 - 204,849,775 (+)NCBIMhudiblu_PPA_v0panPan3
RAB4A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl49,916,235 - 9,965,469 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.149,914,681 - 9,965,468 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Rab4a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_00493648420,281,495 - 20,301,906 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RAB4A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1460,478,235 - 60,529,095 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11460,481,484 - 60,528,549 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21465,322,929 - 65,370,292 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RAB4A
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12566,540,462 - 66,574,729 (+)NCBI
ChlSab1.1 Ensembl2566,540,549 - 66,572,173 (+)Ensembl
Rab4a
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477519,738,220 - 19,762,351 (-)NCBI

Position Markers
RH127889  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.01956,612,844 - 56,613,023NCBIRnor6.0
Rnor_5.01967,323,191 - 67,323,370UniSTSRnor5.0
RGSC_v3.41954,019,013 - 54,019,193UniSTSRGSC3.4
Celera1951,198,286 - 51,198,465UniSTS
RH 3.4 Map19739.2UniSTS
Cytogenetic Map19q12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191899398262275575Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191917749562275575Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)192140778762275575Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192481825762275575Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)193299439262275575Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193791679960220451Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193791679960220451Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194883071260220581Rat
2313395Anxrr26Anxiety related response QTL 26aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)195473521758072143Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:364
Count of miRNA genes:204
Interacting mature miRNAs:232
Transcripts:ENSRNOT00000049337
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.


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 3 39 33 21 13 21 8 11 74 35 31 11 8
Low 4 24 20 6 20 10
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000049337   ⟹   ENSRNOP00000048878
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1956,585,767 - 56,613,075 (+)Ensembl
RefSeq Acc Id: NM_013019   ⟹   NP_037151
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21951,795,613 - 51,822,706 (+)NCBI
Rnor_6.01956,585,767 - 56,613,078 (+)NCBI
Rnor_5.01967,296,402 - 67,323,425 (+)NCBI
RGSC_v3.41953,991,122 - 54,019,248 (+)RGD
Celera1951,171,470 - 51,198,520 (+)RGD
Sequence:
RefSeq Acc Id: XM_008772600   ⟹   XP_008770822
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01956,585,598 - 56,613,078 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_037151 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH62016 (Get FASTA)   NCBI Sequence Viewer  
  CAA30006 (Get FASTA)   NCBI Sequence Viewer  
  EDL96711 (Get FASTA)   NCBI Sequence Viewer  
  P05714 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_037151   ⟸   NM_013019
- UniProtKB: P05714 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008770822   ⟸   XM_008772600
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000048878   ⟸   ENSRNOT00000049337

Transcriptome

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

Promoters
RGD ID:13701229
Promoter ID:EPDNEW_R11753
Type:multiple initiation site
Name:Rab4a_1
Description:RAB4A, 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_6.01956,585,768 - 56,585,828EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3529 AgrOrtholog
Ensembl Genes ENSRNOG00000017467 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000048878 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000049337 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:5621494 IMAGE-MGC_LOAD
InterPro P-loop_NTPase UniProtKB/Swiss-Prot
  Rab4 UniProtKB/Swiss-Prot
  Small_GTP-bd_dom UniProtKB/Swiss-Prot
  Small_GTPase UniProtKB/Swiss-Prot
KEGG Report rno:25532 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72520 IMAGE-MGC_LOAD
NCBI Gene 25532 ENTREZGENE
Pfam Ras UniProtKB/Swiss-Prot
PhenoGen Rab4a PhenoGen
PROSITE RAB UniProtKB/Swiss-Prot
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot
TIGRFAMs small_GTP UniProtKB/Swiss-Prot
UniProt P05714 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q6P6U4 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2003-04-09 Rab4a  RAB4A, member RAS oncogene family  Rab4  Ras-related small GTP binding protein 4  Symbol and Name updated 629477 APPROVED
2002-06-10 Rab4  Ras-related small GTP binding protein 4      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_regulation displays increased localization to the cytosol from the plasma membrane in response to insulin 735238