Tubb3 (tubulin, beta 3 class III)

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Gene: Tubb3 (tubulin, beta 3 class III) Rattus norvegicus

Analyze

Symbol:

Tubb3

Name:

tubulin, beta 3 class III

RGD ID:

628595

Description:

Enables peptide binding activity. Involved in neuron differentiation. Located in axon. Human ortholog(s) of this gene implicated in complex cortical dysplasia with other brain malformations 1 and congenital fibrosis of the extraocular muscles 3A. Orthologous to human TUBB3 (tubulin beta 3 class III); PARTICIPATES IN phagocytosis pathway; INTERACTS WITH (+)-schisandrin B; 17alpha-ethynylestradiol; 2,3',4,4',5-Pentachlorobiphenyl.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

neuron-specific class III beta-tubulin; tubulin beta-3 chain; tubulin, beta 3

RGD Orthologs

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):	TUBB3 (tubulin beta 3 class III)	HGNC	Ensembl, HomoloGene, Inparanoid, NCBI, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Tubb3 (tubulin, beta 3 class III)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	TUBB3 (tubulin beta 3 class III)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Tubb3 (tubulin beta 3 class III)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Tubb3 (tubulin beta 3 class III)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	TUBB6 (tubulin beta 6 class V)	HGNC	OrthoDB
Homo sapiens (human):	TUBB2A (tubulin beta 2A class IIa)	HGNC	OrthoDB
Homo sapiens (human):	TUBB4A (tubulin beta 4A class IVa)	HGNC	OrthoDB
Homo sapiens (human):	TUBB4B (tubulin beta 4B class IVb)	HGNC	OrthoDB
Homo sapiens (human):	TUBB2B (tubulin beta 2B class IIb)	HGNC	OrthoDB
Homo sapiens (human):	FGF14 (fibroblast growth factor 14)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	TUBB3 (tubulin beta 3 class III)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Tubb3 (tubulin, beta 3 class III)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	TUB2	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	tbb-6	Alliance	DIOPT (Ensembl Compara\|PANTHER)
Caenorhabditis elegans (roundworm):	tbb-2	Alliance	DIOPT (Ensembl Compara\|PANTHER)
Xenopus tropicalis (tropical clawed frog):	tubb3	Alliance	DIOPT (OMA\|OrthoFinder\|PhylomeDB)

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	19	51,457,187 - 51,466,243 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	19	51,457,184 - 51,466,243 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	19	58,251,389 - 58,260,397 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	19	58,928,868 - 58,937,934 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	19	61,149,989 - 61,158,997 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	19	56,220,759 - 56,229,813 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	19	56,220,755 - 56,229,813 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	19	66,931,880 - 66,940,930 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	19	53,742,652 - 53,751,706 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	4	155,058,769 - 155,059,105 (+)	NCBI
Celera	19	50,689,724 - 50,698,713 (+)	NCBI		Celera
Cytogenetic Map	19	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

arrhythmogenic right ventricular dysplasia 8 (ISO)

autosomal recessive chronic granulomatous disease 4 (ISO)

Breast Neoplasms (ISO)

complex cortical dysplasia with other brain malformations 1 (ISO)

congenital fibrosis of the extraocular muscles (ISO,ISS)

congenital fibrosis of the extraocular muscles 3A (ISO)

Developmental Disease (ISO)

Fanconi anemia (ISO)

genetic disease (ISO)

lissencephaly (ISO)

Martsolf syndrome 1 (ISO)

MASA syndrome (ISO)

NEURODEVELOPMENTAL DISORDER WITH MICROCEPHALY, ARTHROGRYPOSIS, AND STRUCTURAL BRAIN ANOMALIES (ISO)

Ovarian Neoplasms (ISO)

primary ciliary dyskinesia 33 (ISO)

prostate cancer (ISO)

spastic ataxia (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

(-)-citrinin (ISO)

(-)-demecolcine (ISO)

(S)-amphetamine (ISO)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (EXP,ISO)

17beta-estradiol (ISO)

2,2',4,4',5,5'-hexachlorobiphenyl (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

2,3',4,4',5-Pentachlorobiphenyl (EXP)

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

2,3,7,8-Tetrachlorodibenzofuran (EXP)

2,4,6-tribromophenol (ISO)

2,4,6-trinitrotoluene (EXP)

2,4-dibromophenyl 2,4,5-tribromophenyl ether (EXP)

3',5'-cyclic AMP (ISO)

3,3',5,5'-tetrabromobisphenol A (ISO)

3,4-methylenedioxymethamphetamine (ISO)

3-chloropropane-1,2-diol (EXP)

3-isobutyl-1-methyl-7H-xanthine (ISO)

3H-1,2-dithiole-3-thione (ISO)

4,4'-sulfonyldiphenol (ISO)

4-[3-(4-tert-butylphenyl)-2-methylpropyl]-2,6-dimethylmorpholine (ISO)

4-hydroxyphenyl retinamide (ISO)

4-phenylbutyric acid (ISO)

5-aza-2'-deoxycytidine (ISO)

5-fluorouracil (ISO)

6-propyl-2-thiouracil (EXP)

9-cis-retinoic acid (ISO)

abamectin (ISO)

acrylamide (ISO)

all-trans-retinoic acid (EXP,ISO)

aluminium atom (ISO)

aluminium(0) (ISO)

ammonium chloride (EXP)

amphetamine (EXP)

aristolochic acid A (ISO)

atorvastatin calcium (EXP)

atrazine (EXP,ISO)

Azaspiracid (ISO)

beauvericin (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bis(2-ethylhexyl) phthalate (EXP,ISO)

bisphenol A (EXP,ISO)

Bisphenol B (ISO)

bisphenol F (ISO)

butanal (ISO)

Butylbenzyl phthalate (EXP)

cadmium atom (ISO)

cadmium dichloride (ISO)

carbamazepine (ISO)

carbofuran (EXP)

carbon nanotube (ISO)

cefaloridine (EXP)

CGP 52608 (ISO)

CHIR 99021 (ISO)

chlordecone (ISO)

chloropicrin (ISO)

chlorpyrifos (ISO)

cisplatin (EXP)

cobalt dichloride (EXP,ISO)

colforsin daropate hydrochloride (ISO)

copper atom (ISO)

copper(0) (ISO)

copper(II) sulfate (ISO)

curcumin (EXP)

cyclosporin A (ISO)

cyhalothrin (EXP)

cypermethrin (ISO)

cytarabine (ISO)

DAPT (ISO)

decabromodiphenyl ether (ISO)

desferrioxamine B (ISO)

dexamethasone (ISO)

diallyl trisulfide (ISO)

dibutyl phthalate (EXP,ISO)

diclofenac (ISO)

diethyl phthalate (EXP)

diisobutyl phthalate (EXP)

diisononyl phthalate (EXP)

dimethyl sulfoxide (ISO)

dinophysistoxin 1 (ISO)

disulfiram (ISO)

Doramectin (ISO)

elemental selenium (ISO)

emodin (ISO)

endosulfan (EXP)

enniatin (ISO)

ethanol (EXP,ISO)

fenpropidin (ISO)

fluoxetine (ISO)

flusilazole (ISO)

folic acid (ISO)

fulvestrant (ISO)

fumonisin B1 (ISO)

gentamycin (EXP)

glutathione (ISO)

glyphosate (ISO)

heptachlor (EXP)

indometacin (ISO)

iohexol (ISO)

iopamidol (ISO)

ivermectin (ISO)

kaempferol (ISO)

L-ascorbic acid (ISO)

lead diacetate (EXP)

lead tetraacetate (ISO)

Licochalcone B (ISO)

manganese(II) chloride (ISO)

methylmercury chloride (ISO)

monocrotaline (EXP)

N-acetyl-L-cysteine (ISO)

N-methyl-4-phenylpyridinium (ISO)

N-nitrosodiethylamine (ISO)

ozone (ISO)

paracetamol (EXP,ISO)

paraquat (EXP)

PD123319 (EXP)

perfluorooctane-1-sulfonic acid (ISO)

phenethyl isothiocyanate (ISO)

phenol red (ISO)

pioglitazone (ISO)

pirinixic acid (ISO)

progesterone (EXP)

rotenone (ISO)

Salidroside (ISO)

Salinomycin (ISO)

sarin (EXP)

selenium atom (ISO)

silicon dioxide (ISO)

SKF-96365 hydrochloride (EXP)

sodium arsenite (ISO)

sodium dichromate (ISO)

spiroxamine (ISO)

sterigmatocystin (EXP)

sunitinib (ISO)

tamibarotene (EXP)

tamoxifen (ISO)

tetrachloromethane (EXP)

thapsigargin (ISO)

thifluzamide (ISO)

thioacetamide (EXP)

titanium dioxide (ISO)

tributylstannane (ISO)

trichloroethene (EXP)

triclosan (ISO)

triphenyl phosphate (ISO)

tunicamycin (ISO)

urethane (ISO)

valproic acid (EXP,ISO)

valsartan (EXP)

vincristine (ISO)

vitamin E (ISO)

WIN 55212-2 (ISO)

XL147 (ISO)

zinc atom (EXP,ISO)

zinc(0) (EXP,ISO)

zoledronic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

axon guidance (IBA,ISO,ISS)

dorsal root ganglion development (ISO,ISS)

microtubule cytoskeleton organization (IBA,ISO,ISS)

mitotic cell cycle (IBA)

netrin-activated signaling pathway (ISO,ISS)

neuron differentiation (IMP)

Cellular Component

axon (IDA,ISO)

cell periphery (ISO)

cytoplasm (IBA,ISO)

dendrite (ISO,ISS)

filopodium (ISO,ISS)

growth cone (ISO,ISS)

intercellular bridge (IEA,ISO)

lamellipodium (ISO,ISS)

microtubule (IBA,ISO)

microtubule cytoskeleton (ISO,ISS)

mitotic spindle (IEA,ISO)

neuronal cell body (ISO)

Molecular Function

GTP binding (IBA,ISO,ISS)

GTPase activity (IEA)

metal ion binding (IEA)

netrin receptor binding (ISO)

peptide binding (IPI)

protein binding (IPI,ISO)

structural constituent of cytoskeleton (IBA,ISO,ISS,NAS)

Molecular Pathway Annotations Click to see Annotation Detail View

phagocytosis pathway (IEA)

References

References - curated

#	Reference Title	Reference Citation
1.	Cloning and characterization of the 5'-flanking region of the rat neuron-specific Class III beta-tubulin gene.	Dennis K, etal., Gene 2002 Jul 10;294(1-2):269-77.
2.	Peptide neuroprotection through specific interaction with brain tubulin.	Divinski I, etal., J Neurochem. 2006 Aug;98(3):973-84.
3.	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.
4.	Rat ISS GO annotations from GOA human gene data--August 2006	GOA data from the GO Consortium
5.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
6.	Synaptotagmin 11 interacts with components of the RNA-induced silencing complex RISC in clonal pancreatic beta-cells.	Milochau A, etal., FEBS Lett. 2014 Jun 27;588(14):2217-22. doi: 10.1016/j.febslet.2014.05.031. Epub 2014 May 29.
7.	Identification of a polymorphic, neuron-specific chromatin remodeling complex.	Olave I, etal., Genes Dev. 2002 Oct 1;16(19):2509-17.
8.	OMIM Disease Annotation Pipeline	OMIM Disease Annotation Pipeline
9.	KEGG Annotation Import Pipeline	Pipeline to import KEGG annotations from KEGG into RGD
10.	GOA pipeline	RGD automated data pipeline
11.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
12.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:8855335	PMID:12134159	PMID:12477932	PMID:15003631	PMID:15255972	PMID:15277470	PMID:15489334	PMID:16892058	PMID:17761882	PMID:18076286	PMID:18556119	PMID:18614158
PMID:19036983	PMID:19389377	PMID:20074521	PMID:21499258	PMID:21525035	PMID:21630459	PMID:21734264	PMID:21958528	PMID:22949634	PMID:23090999	PMID:23284756	PMID:23434913
PMID:23533145	PMID:24378336	PMID:24464040	PMID:25433207	PMID:26561800	PMID:28223217	PMID:28426968	PMID:28483977	PMID:29476059	PMID:31686426

Genomics

Comparative Map Data

Tubb3
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	19	51,457,187 - 51,466,243 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	19	51,457,184 - 51,466,243 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	19	58,251,389 - 58,260,397 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	19	58,928,868 - 58,937,934 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	19	61,149,989 - 61,158,997 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	19	56,220,759 - 56,229,813 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	19	56,220,755 - 56,229,813 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	19	66,931,880 - 66,940,930 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	19	53,742,652 - 53,751,706 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	4	155,058,769 - 155,059,105 (+)	NCBI
Celera	19	50,689,724 - 50,698,713 (+)	NCBI		Celera
Cytogenetic Map	19	q12	NCBI

TUBB3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	16	89,921,925 - 89,936,097 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	16	89,921,392 - 89,938,761 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	16	89,988,333 - 90,002,505 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	16	88,517,246 - 88,530,006 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	16	88,517,245 - 88,530,006	NCBI
Celera	16	75,054,835 - 75,067,595 (+)	NCBI		Celera
Cytogenetic Map	16	q24.3	NCBI
HuRef	16	75,681,526 - 75,695,522 (+)	NCBI		HuRef
CHM1_1	16	91,400,537 - 91,414,621 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	16	96,008,170 - 96,022,338 (+)	NCBI		T2T-CHM13v2.0

Tubb3
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	8	124,138,292 - 124,148,754 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	8	124,138,163 - 124,148,754 (+)	Ensembl		GRCm39 Ensembl
GRCm38	8	123,411,553 - 123,422,015 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	8	123,411,424 - 123,422,015 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	8	125,935,464 - 125,945,910 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	8	126,297,654 - 126,308,100 (+)	NCBI		MGSCv36	mm8
Celera	8	127,654,088 - 127,664,534 (+)	NCBI		Celera
Cytogenetic Map	8	E1	NCBI
cM Map	8	72.1	NCBI

TUBB3
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	5	63,681,765 - 63,690,898 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	5	63,681,752 - 63,729,684 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	5	63,694,960 - 63,704,093 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	5	63,909,742 - 63,918,874 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	5	63,909,745 - 63,919,020 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	5	63,930,270 - 63,939,401 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	5	63,767,793 - 63,776,934 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	5	64,174,159 - 64,183,292 (-)	NCBI		UU_Cfam_GSD_1.0

Tubb3
(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	NW_024409349	24,431,189 - 24,440,321 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936641	184,765 - 193,819 (-)	Ensembl	SpeTri2.0
SpeTri2.0	NW_004936641	184,736 - 193,835 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

Tubb3
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624746	124,014 - 130,476 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Tubb3
46 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	52
Count of miRNA genes:	46
Interacting mature miRNAs:	50
Transcripts:	ENSRNOT00000023452
Prediction methods:	Miranda, Rnahybrid
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
724566	Uae12	Urinary albumin excretion QTL 12	5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	19	2187927	56457239	Rat
1331737	Uae29	Urinary albumin excretion QTL 29	5.5		urine albumin amount (VT:0002871)	urine albumin level (CMO:0000130)	19	4096155	55283277	Rat
7411549	Bw130	Body weight QTL 130	5	0.001	body mass (VT:0001259)	body weight gain (CMO:0000420)	19	15455860	57337602	Rat
1578764	Stresp19	Stress response QTL 19	3.6	0.001	blood renin amount (VT:0003349)	plasma renin activity level (CMO:0000116)	19	15630201	57337602	Rat
2298478	Eau8	Experimental allergic uveoretinitis QTL 8		0.0163	uvea integrity trait (VT:0010551)	experimental autoimmune uveitis score (CMO:0001504)	19	17154433	57337602	Rat
61350	Bp32	Blood pressure QTL 32		0.012	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	19	20483575	57337602	Rat
724546	Kidm3	Kidney mass QTL 3	3.1		kidney mass (VT:0002707)	calculated kidney weight (CMO:0000160)	19	29322490	57337602	Rat
1358200	Insglur2	Insulin/glucose ratio QTL 2	4.1		blood glucose amount (VT:0000188)	serum insulin level (CMO:0000358)	19	33838214	55283146	Rat
1358200	Insglur2	Insulin/glucose ratio QTL 2	4.1		blood glucose amount (VT:0000188)	serum glucose level (CMO:0000543)	19	33838214	55283146	Rat
5135224	Leukc1	Leukocyte quantity QTL 1			eosinophil quantity (VT:0002602)	blood eosinophil count (CMO:0000033)	19	44340214	55283277	Rat
2313395	Anxrr26	Anxiety related response QTL 26			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	19	49976481	53225766	Rat

Markers in Region

BE108480

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	19	51,467,365 - 51,467,573 (+)	MAPPER	mRatBN7.2
Rnor_6.0	19	56,230,936 - 56,231,143	NCBI	Rnor6.0
Rnor_5.0	19	66,942,053 - 66,942,260	UniSTS	Rnor5.0
RGSC_v3.4	19	53,752,829 - 53,753,036	UniSTS	RGSC3.4
Celera	19	50,699,836 - 50,700,043	UniSTS
RH 3.4 Map	19	716.7	UniSTS
Cytogenetic Map	19	q12	UniSTS

MARC_24021-24022:1029778648:1

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	19	51,465,188 - 51,465,794 (+)	MAPPER	mRatBN7.2
mRatBN7.2	9	1,918,543 - 1,919,149 (-)	MAPPER	mRatBN7.2
Rnor_6.0	9	9,967,112 - 9,967,717	NCBI	Rnor6.0
Rnor_6.0	19	56,228,759 - 56,229,364	NCBI	Rnor6.0
Rnor_5.0	9	8,966,864 - 8,967,469	UniSTS	Rnor5.0
Rnor_5.0	19	66,939,876 - 66,940,481	UniSTS	Rnor5.0
RGSC_v3.4	19	53,750,652 - 53,751,257	UniSTS	RGSC3.4
Celera	19	50,697,659 - 50,698,264	UniSTS
Celera	9	6,598,574 - 6,599,179	UniSTS
Cytogenetic Map	19	q12	UniSTS

UniSTS:498328

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	19	51,465,873 - 51,466,083 (+)	MAPPER	mRatBN7.2
Rnor_6.0	19	56,229,444 - 56,229,653	NCBI	Rnor6.0
Rnor_5.0	19	66,940,561 - 66,940,770	UniSTS	Rnor5.0
RGSC_v3.4	19	53,751,337 - 53,751,546	UniSTS	RGSC3.4
Celera	19	50,698,344 - 50,698,553	UniSTS
Cytogenetic Map	19	q12	UniSTS

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									43
Medium	2		5		1				31		29
Low	1	43	43	32	18	32	8	11		24	12	11	8
Below cutoff			9	9		9				9

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_139254	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC132057	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AF458477	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC097281	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CF976541	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473972	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000313	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000023452 ⟹ ENSRNOP00000023452

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	19	51,457,184 - 51,466,243 (+)	Ensembl
Rnor_6.0 Ensembl	19	56,220,755 - 56,229,813 (+)	Ensembl

RefSeq Acc Id:

NM_139254 ⟹ NP_640347

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	19	51,457,187 - 51,466,243 (+)	NCBI
Rnor_6.0	19	56,220,759 - 56,229,813 (+)	NCBI
Rnor_5.0	19	66,931,880 - 66,940,930 (+)	NCBI
RGSC_v3.4	19	53,742,652 - 53,751,706 (+)	RGD
Celera	19	50,689,724 - 50,698,713 (+)	RGD

Sequence:

show sequence

GCAGCCCGCTGTCCGCCTGCCTCTTCGTCTCTAGCCGAGTGAAGTCAGCATGAGGGAGATCGTG
CACATCCAGGCCGGCCAGTGCGGCAACCAGATAGGGGCCAAGTTCTGGGAGGTCATCAGTGACG
AGCATGGCATAGACCCCAGCGGCAACTATGTGGGGGACTCGGACCTGCAGCTGGAACGCATCAG
TGTCTACTACAATGAGGCCTCCTCTCACAAGTATGTGCCCAGAGCCATTCTGGTGGACCTGGAG
CCTGGAACCATGGACAGCGTTCGGTCTGGGGCCTTTGGACACCTATTCAGGCCTGACAACTTTA
TCTTCGGTCAGAGTGGTGCTGGCAACAACTGGGCCAAAGGGCACTATACAGAGGGCGCCGAGCT
GGTGGACTCAGTCCTGGATGTCGTGAGGAAAGAATGTGAGAATTGTGACTGCCTGCAGGGCTTC
CAGCTCACTCACTCACTGGGTGGGGGCACGGGCTCAGGCATGGGCACACTGCTCATCAGCAAAG
TGCGTGAGGAGTACCCTGACCGCATCATGAACACCTTCAGCGTGGTGCCCTCACCCAAAGTGTC
AGACACCGTGGTAGAGCCCTACAACGCCACCCTGTCCATCCACCAGCTAGTGGAGAACACGGAT
GAGACCTACTGCATCGACAATGAAGCCCTCTACGACATCTGCTTCCGCACCCTCAAGCTGGCTA
CACCCACCTACGGGGACCTCAACCACCTTGTGTCTGCTACCATGAGCGGAGTCACCACCTCCCT
TCGATTCCCTGGTCAGCTCAATGCCGACCTCCGCAAGCTAGCTGTCAACATGGTGCCCTTCCCC
CGCTTGCATTTCTTCATGCCCGGCTTTGCCCCACTAACAGCCCGGGGCAGCCAACAGTACCGTG
CCCTGACGGTGCCTGAGCTCACCCAGCAGATGTTCGACGCCAAGAACATGATGGCTGCCTGTGA
CCCACGCCACGGCCGCTACCTGACCGTGGCCACCGTCTTCCGTGGGCGCATGTCCATGAAGGAG
GTGGATGAGCAGATGCTGGCCATTCAGAGTAAGAACAGTAGTTACTTCGTGGAGTGGATCCCCA
ACAACGTCAAGGTAGCGGTGTGTGACATCCCGCCCCGAGGGCTCAAGATGTCGTCCACCTTCAT
CGGCAACAGCACGGCCATCCAGGAGCTGTTCAAGCGCATCTCCGAGCAGTTTACGGCCATGTTC
CGGCGCAAGGCCTTCCTCCACTGGTACACGGGCGAAGGCATGGATGAGATGGAGTTCACCGAGG
CCGAGAGCAACATGAACGACCTGGTGTCTGAGTACCAGCAGTACCAGGACGCCACTGCCGAGGA
GGAGGGGGAGATGTATGAAGATGACGACGAGGAGTCGGAAGCCCAGGGGCCCAAGTGAAGTTGC
TTGCAGCTGGGGTGTGGGGCCAAGTGGCAGCCAGGGCCAAGACAAGCAGCATCTGTCCCCCAGA
GCCATCTAGCTACTGACACTGCCCCCAGCTTACCTTCCTACCAGCTCTTCAGGGCACCCTAGGG
CTCCCGGGTTAAAGTCCTTCAGTATTTATGGCCATCCCCCACCCCACGTGAGTCCACTTGGCTC
TGTCCTCCCCGTTTTAGCCACCTTTGTATTTATGTTGCTTTTGTGTCTGTTTTATTATGGCTCC
AGGCCTGATGTTTTATGTTTTTTTTTTTTTTTAAAAACTGGGTTGTGTTTATATTTGGAGGGGG
GTCTACTTAATAAAGTCACTGCTGTCTGTCACATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_640347	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH97281	(Get FASTA)	NCBI Sequence Viewer
	AAM28680	(Get FASTA)	NCBI Sequence Viewer
	EDL92810	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000023452
GenBank Protein	Q4QRB4	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

NP_640347 ⟸ NM_139254

- UniProtKB:

Q6P9T8 (UniProtKB/Swiss-Prot), Q8K5B6 (UniProtKB/Swiss-Prot), Q4QRB4 (UniProtKB/Swiss-Prot), A6IZY2 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MREIVHIQAGQCGNQIGAKFWEVISDEHGIDPSGNYVGDSDLQLERISVYYNEASSHKYVPRAI
LVDLEPGTMDSVRSGAFGHLFRPDNFIFGQSGAGNNWAKGHYTEGAELVDSVLDVVRKECENCD
CLQGFQLTHSLGGGTGSGMGTLLISKVREEYPDRIMNTFSVVPSPKVSDTVVEPYNATLSIHQL
VENTDETYCIDNEALYDICFRTLKLATPTYGDLNHLVSATMSGVTTSLRFPGQLNADLRKLAVN
MVPFPRLHFFMPGFAPLTARGSQQYRALTVPELTQQMFDAKNMMAACDPRHGRYLTVATVFRGR
MSMKEVDEQMLAIQSKNSSYFVEWIPNNVKVAVCDIPPRGLKMSSTFIGNSTAIQELFKRISEQ
FTAMFRRKAFLHWYTGEGMDEMEFTEAESNMNDLVSEYQQYQDATAEEEGEMYEDDDEESEAQG
PK

hide sequence

RefSeq Acc Id:

ENSRNOP00000023452 ⟸ ENSRNOT00000023452

Protein Domains

Tubulin/FtsZ 2-layer sandwich Tubulin/FtsZ GTPase

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-Q4QRB4-F1-model_v2	AlphaFold	Q4QRB4	1-450	view protein structure

Transcriptome

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

Promoters

RGD ID:

13701226

Promoter ID:

EPDNEW_R11750

Type:

single initiation site

Name:

Tubb3_1

Description:

tubulin, beta 3 class III

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	19	56,220,755 - 56,220,815	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:628595	AgrOrtholog
BioCyc Gene	G2FUF-5325	BioCyc
Ensembl Genes	ENSRNOG00000017209	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000023452	ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH	1.10.287.600	UniProtKB/Swiss-Prot
	3.30.1330.20	UniProtKB/Swiss-Prot
	3.40.50.1440	UniProtKB/Swiss-Prot
	Helix hairpin bin	UniProtKB/TrEMBL
	Tubulin/FtsZ, C-terminal domain	UniProtKB/TrEMBL
	Tubulin/FtsZ, GTPase domain	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7461390	IMAGE-MGC_LOAD
InterPro	Beta-tubulin_BS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Beta_tubulin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Tub_FtsZ_C	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Tubulin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Tubulin/FtsZ-like_C	UniProtKB/TrEMBL
	Tubulin/FtsZ_2-layer-sand-dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Tubulin/FtsZ_C_sf	UniProtKB/Swiss-Prot
	Tubulin/FtsZ_GTPase_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Tubulin_C	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Tubulin_CS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Tubulin_FtsZ_GTPase	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:246118	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:114260	IMAGE-MGC_LOAD
NCBI Gene	246118	ENTREZGENE
PANTHER	PTHR11588	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	TUBULIN BETA-3 CHAIN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Tubulin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Tubulin_C	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Tubb3	PhenoGen
PRINTS	BETATUBULIN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	TUBULIN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	TUBULIN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	TUBULIN_B_AUTOREG	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000017209	RatGTEx
SMART	Tubulin	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Tubulin_C	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF52490	UniProtKB/Swiss-Prot
	SSF55307	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Tubulin nucleotide-binding domain-like	UniProtKB/TrEMBL
UniProt	A6IZY2	ENTREZGENE, UniProtKB/TrEMBL
	Q4QRB4	ENTREZGENE
	Q6P9T8	ENTREZGENE
	Q8K5B6	ENTREZGENE
	TBB3_RAT	UniProtKB/Swiss-Prot
UniProt Secondary	Q8K5B6	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2011-10-19	Tubb3	tubulin, beta 3 class III	Tubb3	tubulin, beta 3	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2011-10-12	Tubb3	tubulin, beta 3	Tubb3	tubulin, beta 3 class III	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2011-10-10	Tubb3	tubulin, beta 3 class III	Tubb3	tubulin, beta 3	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2004-09-10	Tubb3	tubulin, beta 3			Symbol and Name status set to approved	1299863	APPROVED
2003-02-27	Tubb3	tubulin, beta 3			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 Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - MGI

Imported Disease Annotations - OMIM

Imported Annotations - KEGG (archival)