Rab9a (RAB9A, member RAS oncogene family)

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Gene: Rab9a (RAB9A, member RAS oncogene family) Rattus norvegicus

Analyze

Symbol:

Rab9a

Name:

RAB9A, member RAS oncogene family

RGD ID:

619740

Description:

Predicted to have GTPase activity; identical protein binding activity; and purine ribonucleoside binding activity. Predicted to be involved in several processes, including negative regulation by host of symbiont molecular function; positive regulation of exocytosis; and retrograde transport, endosome to Golgi. Predicted to localize to cytoplasmic vesicle and lysosome. Orthologous to human RAB9A (RAB9A, member RAS oncogene family); PARTICIPATES IN measles pathway; INTERACTS WITH 3,3',4,4',5-pentachlorobiphenyl; ammonium chloride; benzene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

rab-9A; Rab9; RAB9, member RAS oncogene family; ras-related protein Rab-9A

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	RAB9A (RAB9A, member RAS oncogene family)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Rab9 (RAB9, member RAS oncogene family)	HGNC	Treefam, EggNOG, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Rab9a (RAB9A, member RAS oncogene family)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	RAB9A (RAB9A, member RAS oncogene family)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	RAB9A (RAB9A, member RAS oncogene family)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Rab9a (RAB9A, member RAS oncogene family)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	RAB9A (RAB9A, member RAS oncogene family)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	RAB9A (RAB9A, member RAS oncogene family)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Rab9a (RAB9A, member RAS oncogene family)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	RAB9A (RAB9A, member RAS oncogene family)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Rab9 (RAB9, member RAS oncogene family)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	rab9a (RAB9A, member RAS oncogene family)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	Rab9	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|PANTHER\|PhylomeDB\|TreeFam)

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	X	27,955,552 - 28,009,870 (+)	NCBI
Rnor_6.0 Ensembl	X	29,525,256 - 29,547,294 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	X	29,525,256 - 29,547,295 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	X	29,918,170 - 29,940,588 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	X	48,663,349 - 48,686,805 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	X	48,716,817 - 48,740,273 (+)	NCBI
Celera	X	28,350,514 - 28,373,237 (+)	NCBI		Celera
Cytogenetic Map	X	q13	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autistic disorder (ISO)

Neurodevelopmental Disorders (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

2,3,7,8-tetrachlorodibenzodioxine (ISO)

2-hydroxypropanoic acid (ISO)

3,3',4,4',5-pentachlorobiphenyl (EXP)

aflatoxin B1 (ISO)

ammonium chloride (EXP)

antirheumatic drug (ISO)

benzene (EXP)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

clofibrate (ISO)

cyclosporin A (ISO)

cylindrospermopsin (ISO)

dichloroacetic acid (ISO)

dicrotophos (ISO)

diuron (EXP)

finasteride (EXP)

folic acid (ISO)

homocysteine (ISO)

L-methionine (ISO)

leflunomide (ISO)

methylmercury(1+) (EXP)

nickel dichloride (ISO)

paracetamol (ISO)

perfluorohexanesulfonic acid (ISO)

perfluorononanoic acid (ISO)

perfluorooctane-1-sulfonic acid (EXP,ISO)

perfluorooctanoic acid (ISO)

phenobarbital (ISO)

phenol (ISO)

pirinixic acid (ISO)

rac-lactic acid (ISO)

resveratrol (ISO)

silicon dioxide (ISO)

Tesaglitazar (EXP)

tetrachloroethene (ISO)

trichloroethene (EXP,ISO)

triptonide (ISO)

tunicamycin (ISO)

vincristine (ISO)

zoledronic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

negative regulation by host of symbiont molecular function (ISO)

positive regulation of exocytosis (ISO)

protein transport (IEA)

Rab protein signal transduction (IEA)

regulation of protein localization (ISO)

retrograde transport, endosome to Golgi (IBA)

Cellular Component

cytoplasmic vesicle membrane (ISO)

cytosol (IEA)

endoplasmic reticulum membrane (IEA)

Golgi membrane (IEA)

late endosome (IBA,ISO)

lysosome (IBA,ISO)

melanosome (ISO,ISS)

phagocytic vesicle (IBA,ISO,ISS)

phagocytic vesicle membrane (IEA)

plasma membrane (IEA)

Molecular Function

GDP binding (ISO,ISS)

GTP binding (ISO,ISS,TAS)

GTPase activity (ISO,ISS,TAS)

identical protein binding (ISO)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

measles pathway (IEA)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	GOA data from the GO Consortium
3.	MGD data from the GO Consortium
4.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
5.	Pipeline to import KEGG annotations from KEGG into RGD
6.	RGD automated data pipeline
7.	RGD automated import pipeline for gene-chemical interactions
8.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
9.	Zhao H, etal., Biochem Biophys Res Commun 2002 May 10;293(3):1060-5.

Additional References at PubMed

PMID:15078902	PMID:15263003	PMID:15489334	PMID:18787122	PMID:19966785	PMID:20458337	PMID:20937701	PMID:21255211	PMID:21808068	PMID:23376485	PMID:25220469	PMID:26620560
PMID:29574782

Genomics

Comparative Map Data

Rab9a
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	X	27,955,552 - 28,009,870 (+)	NCBI
Rnor_6.0 Ensembl	X	29,525,256 - 29,547,294 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	X	29,525,256 - 29,547,295 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	X	29,918,170 - 29,940,588 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	X	48,663,349 - 48,686,805 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	X	48,716,817 - 48,740,273 (+)	NCBI
Celera	X	28,350,514 - 28,373,237 (+)	NCBI		Celera
Cytogenetic Map	X	q13	NCBI

RAB9A
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	X	13,689,128 - 13,710,504 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	X	13,689,128 - 13,710,504 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	X	13,707,247 - 13,728,623 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	X	13,617,262 - 13,637,685 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	X	13,466,997 - 13,487,419	NCBI
Celera	X	17,824,420 - 17,844,845 (+)	NCBI
Cytogenetic Map	X	p22.2	NCBI
HuRef	X	11,465,760 - 11,486,461 (+)	NCBI		HuRef
CHM1_1	X	13,738,054 - 13,758,769 (+)	NCBI		CHM1_1

Rab9
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	X	165,240,247 - 165,262,863 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	X	165,240,249 - 165,262,863 (-)	Ensembl
GRCm38	X	166,457,251 - 166,479,867 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	X	166,457,253 - 166,479,867 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	X	162,895,191 - 162,917,626 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	X	161,801,364 - 161,823,801 (-)	NCBI			mm8
Celera	X	149,637,081 - 149,659,269 (-)	NCBI		Celera
Cytogenetic Map	X	F5	NCBI

Rab9a
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955519	4,489,159 - 4,496,089 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955519	4,489,159 - 4,496,089 (-)	NCBI	ChiLan1.0	ChiLan1.0

RAB9A
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	X	13,564,061 - 13,605,532 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	X	13,604,454 - 13,605,059 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	X	6,296,483 - 6,317,826 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

RAB9A
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	X	10,072,764 - 10,124,620 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	X	10,102,387 - 10,124,620 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	X	10,076,908 - 10,099,141 (+)	NCBI
ROS_Cfam_1.0	X	10,030,636 - 10,082,741 (+)	NCBI
UMICH_Zoey_3.1	X	10,129,115 - 10,151,347 (+)	NCBI
UNSW_CanFamBas_1.0	X	10,120,485 - 10,142,705 (+)	NCBI
UU_Cfam_GSD_1.0	X	10,146,433 - 10,169,013 (+)	NCBI

Rab9a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	X	3,253,617 - 3,275,081 (+)	NCBI
SpeTri2.0	NW_004936470	3,253,631 - 3,275,078 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

RAB9A
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	X	10,293,757 - 10,349,387 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	X	10,328,085 - 10,349,399 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	X	11,281,830 - 11,303,135 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

RAB9A
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	X	12,181,447 - 12,202,778 (+)	NCBI
ChlSab1.1 Ensembl	X	12,201,049 - 12,201,651 (+)	Ensembl

Rab9a
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624882	435,877 - 489,691 (-)	NCBI

Position Markers

px-37e4

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	X	27,999,733 - 27,999,995 (+)	MAPPER
Rnor_6.0	X	29,546,555 - 29,546,816	NCBI	Rnor6.0
Rnor_5.0	X	29,939,848 - 29,940,109	UniSTS	Rnor5.0
RGSC_v3.4	X	48,686,065 - 48,686,326	UniSTS	RGSC3.4
Celera	X	28,372,497 - 28,372,758	UniSTS
Cytogenetic Map	X	q21	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
731181	Uae27	Urinary albumin excretion QTL 27	2.7	0.0059	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	X	1	44092703	Rat
70165	Bp64	Blood pressure QTL 64	5.2		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	X	1662609	33443848	Rat
1298071	Edpm12	Estrogen-dependent pituitary mass QTL 12	3.2		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	X	4282140	49282140	Rat
631666	Iddm5	Insulin dependent diabetes mellitus QTL 5			blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	X	5954078	50954078	Rat
61430	Cia18	Collagen induced arthritis QTL 18	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	X	15688119	127888215	Rat
71116	Niddm16	Non-insulin dependent diabetes mellitus QTL 16	7.81		blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	X	18153352	63153352	Rat
1598873	Memor2	Memory QTL 2	2.5		exploratory behavior trait (VT:0010471)	average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)	X	21592623	44320739	Rat
2290375	Gluco34	Glucose level QTL 34	2.75		blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	X	21592623	44468300	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	112
Count of miRNA genes:	90
Interacting mature miRNAs:	106
Transcripts:	ENSRNOT00000050018
Prediction methods:	Miranda, Pita, 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	33	57	41	19	41	2	4	74	35	34	11	2
Low		10					6	7			7		6
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_053458	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039100118	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039100119	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039100120	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005498075	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC130009	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF325692	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC070502	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474014	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ212962	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ222207	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000383	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000050018 ⟹ ENSRNOP00000050986

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	X	29,525,256 - 29,547,294 (+)	Ensembl

RefSeq Acc Id:

NM_053458 ⟹ NP_445910

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	X	27,978,435 - 28,000,474 (+)	NCBI
Rnor_6.0	X	29,525,256 - 29,547,295 (+)	NCBI
Rnor_5.0	X	29,918,170 - 29,940,588 (+)	NCBI
RGSC_v3.4	X	48,663,349 - 48,686,805 (+)	RGD
Celera	X	28,350,514 - 28,373,237 (+)	RGD

Sequence:

show sequence

CTTCTGCCCAAGTCGCTCCCTGCTGGAAGTGCTCTCGACATTCCCGACTCTCTGGCCCTCTTTC
TGCCCTGGTTGTACCCAGGTGTGTTGGCGAATAGCTCCCAGGACGTCCTGTGTGTGTCTGCAAG
ATAATGATGTTTGAACTGAACTACTAAGGATTCTGAAATCAAAACTTACACTATTAATCATGGC
AGGAAAATCGTCTCTTTTTAAAATAATTCTCCTTGGAGATGGTGGAGTTGGCAAGAGTTCTCTT
ATGAACAGATATGTAGCCAATAAATTTGATTCCCAGCTCTTCCACACAATAGGTGTGGAATTTT
TAAATAAAGATTTGGAGGTGGATGGACATTTTGTTACCATGCAGATTTGGGACACAGCTGGTCA
AGAACGATTCCGAAGCCTGAGGACACCATTTTACCGAGGTTCTGACTGTTGCCTGCTTACATTT
AGTGTCGATGATTCACAAAGCTTCCAGAATCTGAGCAACTGGAAGAAAGAGTTCATATATTATG
CAGATGTGAAAGAGCCTGAAAGCTTTCCTTTTGTGATTTTGGGCAACAAGACTGACATAAAAGA
ACGGCAGGTATCTACAGAAGAAGCCCAAGCCTGGTGCAAGGACAACGGCGACTATCCTTACTTC
GAAACAAGTGCAAAAGATTCCACCAATGTTGCTGCTGCCTTTGAGGAGGCAGTTCGAAGAATTC
TGGCTACAGAAGATAGGTCAGATCACCTGATTCAAACAGACACAGTCAATCTGCACCGAAAGCC
CAAGCCAAACTCTTCTTGCTGTTGATGGCATTAAAGGGATAGCTGGTGCATTTTAACCAACCAA
CACACACACACACACACACACACACACACACACACACACACACAGACACACGAATGAGAGTGGA
GAACAAATTAGTATGCAGAAGAGTTCATCTACTAATAAAATTCAATTAACGCATATTGTTGCCT
CATTAGTCCATGGAAGAAGGGACCACTCACTCTGAAGGAATCTATTTACTCAGTAATGGCACAT
TACATTTATAAACTGTAATGGTTGTCTATTGTTTCTTAAAATTAAAACATTAGTGCTAATAAGA
TGACCAAGAATTGACTTAATTGTAATTCAGACATAAATCTTGACTATTCTTAGATTGTTTTGCC
CCACAAGAAAATGGAGAATTACTTTTATATGTGTATATTTTTATGTAATGAGCATTCTATTCTT
GGTCCAGGAAAGTAAATTCCTACAGCAATACTATTAAAGATTAAAATCTAATGCAAAAAAAAAA
AAAAAA

hide sequence

RefSeq Acc Id:

XM_039100118 ⟹ XP_038956046

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	X	27,955,552 - 28,000,482 (+)	NCBI

RefSeq Acc Id:

XM_039100119 ⟹ XP_038956047

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	X	27,978,404 - 28,000,482 (+)	NCBI

RefSeq Acc Id:

XM_039100120 ⟹ XP_038956048

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	X	27,982,478 - 28,000,482 (+)	NCBI

RefSeq Acc Id:

XR_005498075

RefSeq Status:

Type:

NON-CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	X	27,978,404 - 28,009,870 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_445910	(Get FASTA)	NCBI Sequence Viewer
	XP_038956046	(Get FASTA)	NCBI Sequence Viewer
	XP_038956047	(Get FASTA)	NCBI Sequence Viewer
	XP_038956048	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAG49586	(Get FASTA)	NCBI Sequence Viewer
	AAH70502	(Get FASTA)	NCBI Sequence Viewer
	EDL90552	(Get FASTA)	NCBI Sequence Viewer
	EDL90553	(Get FASTA)	NCBI Sequence Viewer
	EDL90554	(Get FASTA)	NCBI Sequence Viewer
	Q99P75	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_445910 ⟸ NM_053458

- Sequence:

show sequence

MAGKSSLFKIILLGDGGVGKSSLMNRYVANKFDSQLFHTIGVEFLNKDLEVDGHFVTMQIWDTA
GQERFRSLRTPFYRGSDCCLLTFSVDDSQSFQNLSNWKKEFIYYADVKEPESFPFVILGNKTDI
KERQVSTEEAQAWCKDNGDYPYFETSAKDSTNVAAAFEEAVRRILATEDRSDHLIQTDTVNLHR
KPKPNSSCC

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RefSeq Acc Id:

ENSRNOP00000050986 ⟸ ENSRNOT00000050018

RefSeq Acc Id:	XP_038956046 ⟸ XM_039100118
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038956047 ⟸ XM_039100119
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_038956048 ⟸ XM_039100120
- Peptide Label:	isoform X1

Transcriptome

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

Promoters

RGD ID:

13701788

Promoter ID:

EPDNEW_R12312

Type:

initiation region

Name:

Rab9a_1

Description:

RAB9A, 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 Assembly	Chr	Position (strand)	Source
Rnor_6.0	X	29,525,255 - 29,525,315	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (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)

ACI/EurMcwi (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

ACI/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

BBDP/Wor (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

BN/SsN (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

Buf/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

COP/CrCrl (MCW & UW)

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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)

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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

F344/NRrrc (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

FHH/EurMcwi (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)

FHH/EurMcwi (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

FHL/EurMcwi (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)

FHL/EurMcwi (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

GH/OmrMcwi (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)

GK/Ox (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

LE/Stm (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

LEW/Crl (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

LEW/NCrlBR (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

LH/MavRrrc (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

LL/MavRrrc (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

LN/MavRrrc (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

M520/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

MHS/Gib (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

MNS/Gib (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

MR/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

SBH/Ygl (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:	SBH/Ygl sequenced by MCW

SBH/Ygl (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

SBN/Ygl (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:	SBN/Ygl sequenced by MCW

SBN/Ygl (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

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

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:619740	AgrOrtholog
Ensembl Genes	ENSRNOG00000030443	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000050986	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000050018	ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7096737	IMAGE-MGC_LOAD
InterPro	P-loop_NTPase	UniProtKB/Swiss-Prot
	Rab9	UniProtKB/Swiss-Prot
	Small_GTP-bd_dom	UniProtKB/Swiss-Prot
	Small_GTPase	UniProtKB/Swiss-Prot
KEGG Report	rno:84589	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:91579	IMAGE-MGC_LOAD
NCBI Gene	84589	ENTREZGENE
Pfam	Ras	UniProtKB/Swiss-Prot
PhenoGen	Rab9a	PhenoGen
PROSITE	RAB	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF52540	UniProtKB/Swiss-Prot
TIGRFAMs	small_GTP	UniProtKB/Swiss-Prot
UniProt	Q99P75	ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary	Q6NS34	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-09-24	Rab9a	RAB9A, member RAS oncogene family	Rab9	RAB9, member RAS oncogene family	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-01-20	Rab9	RAB9, member RAS oncogene family			Symbol and Name status set to approved	1299863	APPROVED
2002-08-07	Rab9	RAB9, member RAS oncogene family			Symbol and Name status set to provisional	70820	PROVISIONAL

RGD Curation Notes

Note Type	Note	Reference

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Annotations - KEGG (archival)