Tbc1d4 (TBC1 domain family, member 4)

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Gene: Tbc1d4 (TBC1 domain family, member 4) Rattus norvegicus

Analyze

Symbol:

Tbc1d4

Name:

TBC1 domain family, member 4

RGD ID:

1561609

Description:

Predicted to enable GTPase activator activity. Involved in cellular response to insulin stimulus and negative regulation of vesicle fusion. Located in vesicle. Human ortholog(s) of this gene implicated in acanthosis nigricans. Orthologous to human TBC1D4 (TBC1 domain family member 4); PARTICIPATES IN altered insulin responsive facilitative sugar transporter mediated glucose transport pathway; insulin responsive facilitative sugar transporter mediated glucose transport pathway; phosphatidylinositol 3-kinase-Akt signaling pathway; INTERACTS WITH (S)-colchicine; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

LOC306117; RGD1561609; similar to TBC1 domain family member 4; similar to TBC1 domain family member 4 (Akt substrate of 160 kDa) (AS160); TBC1 domain family member 4

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):	TBC1D4 (TBC1 domain family member 4)	HGNC	EggNOG, Ensembl, HomoloGene, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Tbc1d4 (TBC1 domain family, member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Tbc1d4 (TBC1 domain family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	TBC1D4 (TBC1 domain family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	TBC1D4 (TBC1 domain family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Tbc1d4 (TBC1 domain family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	TBC1D4 (TBC1 domain family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	TBC1D4 (TBC1 domain family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Tbc1d4 (TBC1 domain family member 4)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	TMEM33 (transmembrane protein 33)	HGNC	OMA
Alliance orthologs ³
Homo sapiens (human):	TBC1D4 (TBC1 domain family member 4)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Tbc1d4 (TBC1 domain family, member 4)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	tbc1d4 (TBC1 domain family, member 4)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	GYP5	Alliance	DIOPT (Ensembl Compara\|OrthoInspector\|PANTHER)
Drosophila melanogaster (fruit fly):	plx	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	tbc1d4	Alliance	DIOPT (Ensembl Compara\|OMA\|OrthoFinder\|PANTHER\|PhylomeDB)

Allele / Splice:

Tbc1d4^em1

Genetic Models:

WI-Tbc1d4^em1Gdcz

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	15	78,256,030 - 78,434,168 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	15	78,257,121 - 78,434,265 (-)	Ensembl		mRatBN7.2 Ensembl
Rnor_6.0	15	85,927,978 - 86,105,829 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	15	85,930,044 - 86,105,273 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	15	89,695,614 - 89,871,879 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	15	85,359,159 - 85,561,229 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	15	77,452,014 - 77,628,396 (-)	NCBI		Celera
Cytogenetic Map	15	q21	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

acanthosis nigricans (ISO)

chromosome 13q14 deletion syndrome (ISO)

Congenital Hyperinsulinism (ISO)

genetic disease (ISO)

Insulin Resistance (ISO)

Type 2 Diabetes Mellitus 5 (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(-)-demecolcine (ISO)

(S)-colchicine (EXP)

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

1-chloro-2,4-dinitrobenzene (ISO)

17beta-hydroxy-5alpha-androstan-3-one (ISO)

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

2,2',5,5'-tetrachlorobiphenyl (ISO)

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

3,4-methylenedioxymethamphetamine (ISO)

4-hydroxyphenyl retinamide (ISO)

5-azacytidine (ISO)

6-propyl-2-thiouracil (EXP)

9-cis-retinoic acid (EXP)

aflatoxin B1 (EXP,ISO)

Aflatoxin B2 alpha (ISO)

AICA ribonucleotide (ISO)

aldehydo-D-glucose (ISO)

all-trans-retinoic acid (ISO)

aristolochic acid A (ISO)

arotinoid acid (EXP)

azoxystrobin (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

Benzo[ghi]perylene (ISO)

bis(2-ethylhexyl) phthalate (EXP)

bisphenol A (EXP,ISO)

caffeine (ISO)

carbon nanotube (ISO)

ciglitazone (EXP,ISO)

cisplatin (ISO)

cobalt dichloride (ISO)

copper atom (ISO)

copper(0) (ISO)

copper(II) sulfate (ISO)

coumarin (ISO)

Cuprizon (EXP)

cyclosporin A (ISO)

cytarabine (ISO)

D-glucose (ISO)

DDT (EXP)

dioxygen (ISO)

dorsomorphin (ISO)

endosulfan (EXP)

enzyme inhibitor (ISO)

epoxiconazole (ISO)

fenvalerate (EXP)

folic acid (ISO)

formaldehyde (ISO)

gentamycin (EXP)

ginsenoside Re (ISO)

glucose (ISO)

hexadecanoic acid (EXP,ISO)

hydrogen peroxide (ISO)

L-ascorbic acid (EXP)

lipopolysaccharide (ISO)

metformin (ISO)

methamphetamine (ISO)

mono(2-ethylhexyl) phthalate (EXP)

paracetamol (EXP)

PCB138 (ISO)

pirinixic acid (ISO)

quercetin (ISO)

S-(1,2-dichlorovinyl)-L-cysteine (ISO)

SB 431542 (ISO)

streptozocin (ISO)

succimer (ISO)

sunitinib (ISO)

temozolomide (ISO)

testosterone (ISO)

topotecan (ISO)

trichostatin A (ISO)

triptonide (ISO)

troglitazone (ISO)

valproic acid (ISO)

vincaleukoblastine (ISO)

vincristine (ISO)

vitamin E (EXP)

zoledronic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

activation of GTPase activity (IBA)

cellular response to insulin stimulus (IDA,ISO)

negative regulation of vesicle fusion (IMP)

vesicle-mediated transport (ISO)

Cellular Component

cytosol (IEA,ISO)

vesicle (IDA)

Molecular Function

GTPase activator activity (IBA)

protein binding (IPI,ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

altered insulin responsive facilitative sugar transporter mediated glucose transport pathway (ISO)

insulin responsive facilitative sugar transporter mediated glucose transport pathway (ISO)

phosphatidylinositol 3-kinase-Akt signaling pathway (ISO)

Rab family mediated signaling pathway (ISO)

Phenotype Annotations Click to see Annotation Detail View

Mammalian Phenotype

impaired glucose tolerance (IMP)

insulin resistance (IMP)

References

References - curated

#	Reference Title	Reference Citation
1.	Whole body glucoregulation and tissue-specific glucose uptake in a novel Akt substrate of 160 kDa knockout rat model.	Arias EB, etal., PLoS One. 2019 Apr 29;14(4):e0216236. doi: 10.1371/journal.pone.0216236. eCollection 2019.
2.	A truncation mutation in TBC1D4 in a family with acanthosis nigricans and postprandial hyperinsulinemia.	Dash S, etal., Proc Natl Acad Sci U S A. 2009 Jun 9;106(23):9350-5. doi: 10.1073/pnas.0900909106. Epub 2009 May 22.
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.	Rab proteins in endocytosis and Glut4 trafficking.	Kaddai V, etal., Acta Physiol (Oxf). 2008 Jan;192(1):75-88.
5.	AS160 phosphotyrosine-binding domain constructs inhibit insulin-stimulated GLUT4 vesicle fusion with the plasma membrane.	Koumanov F, etal., J Biol Chem. 2011 May 13;286(19):16574-82. doi: 10.1074/jbc.M111.226092. Epub 2011 Mar 17.
6.	The GLUT4 code.	Larance M, etal., Mol Endocrinol. 2008 Feb;22(2):226-33. Epub 2007 Aug 23.
7.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
9.	GLUT4 translocation: the last 200 nanometers.	Watson RT and Pessin JE, Cell Signal. 2007 Nov;19(11):2209-17. Epub 2007 Jun 21.
10.	Insulin action on glucose transporters through molecular switches, tracks and tethers.	Zaid H, etal., Biochem J. 2008 Jul 15;413(2):201-15.
11.	In vivo glucoregulation and tissue-specific glucose uptake in female Akt substrate 160 kDa knockout rats.	Zheng X, etal., PLoS One. 2020 Feb 13;15(2):e0223340. doi: 10.1371/journal.pone.0223340. eCollection 2020.

Additional References at PubMed

PMID:18701652	PMID:19249902	PMID:19435856	PMID:19724017	PMID:22908308	PMID:23376485	PMID:27041232	PMID:27482072	PMID:27714805	PMID:31505169	PMID:31573845	PMID:34753801
PMID:36634338

Genomics

Comparative Map Data

Tbc1d4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	15	78,256,030 - 78,434,168 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	15	78,257,121 - 78,434,265 (-)	Ensembl		mRatBN7.2 Ensembl
Rnor_6.0	15	85,927,978 - 86,105,829 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	15	85,930,044 - 86,105,273 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	15	89,695,614 - 89,871,879 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	15	85,359,159 - 85,561,229 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	15	77,452,014 - 77,628,396 (-)	NCBI		Celera
Cytogenetic Map	15	q21	NCBI

TBC1D4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	13	75,283,503 - 75,482,169 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p13 Ensembl	13	75,283,503 - 75,482,169 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	13	75,857,639 - 76,056,305 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	13	74,756,810 - 74,954,251 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	13	74,757,253 - 74,954,251	NCBI
Celera	13	56,756,694 - 56,954,119 (-)	NCBI		Celera
Cytogenetic Map	13	q22.2	NCBI
HuRef	13	56,556,159 - 56,753,666 (-)	NCBI		HuRef
CHM1_1	13	75,826,535 - 76,023,986 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	13	74,507,182 - 74,705,799 (-)	NCBI		T2T-CHM13v2.0

Tbc1d4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	14	101,679,800 - 101,846,717 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	14	101,679,796 - 101,846,627 (-)	Ensembl		GRCm39 Ensembl
GRCm38	14	101,442,360 - 101,609,281 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	14	101,442,360 - 101,609,191 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	14	101,841,577 - 102,008,408 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	14	100,325,233 - 100,494,965 (-)	NCBI		MGSCv36	mm8
Celera	14	100,079,886 - 100,248,354 (-)	NCBI		Celera
Cytogenetic Map	14	E2.3	NCBI

Tbc1d4
(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_004955404	31,622,102 - 31,691,517 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955404	31,516,727 - 31,691,414 (+)	NCBI	ChiLan1.0	ChiLan1.0

TBC1D4
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1	13	75,457,938 - 75,656,273 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	13	56,513,065 - 56,706,491 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	13	75,282,441 - 75,480,138 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	13	75,282,441 - 75,361,729 (-)	Ensembl	panpan1.1		panPan2

TBC1D4
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	22	29,109,079 - 29,175,357 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	22	29,110,201 - 29,290,154 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	22	28,971,148 - 29,151,992 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	22	29,444,745 - 29,625,974 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	22	29,445,331 - 29,625,959 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	22	29,095,512 - 29,277,006 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	22	29,139,459 - 29,320,685 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	22	29,208,132 - 29,388,931 (-)	NCBI		UU_Cfam_GSD_1.0

Tbc1d4
(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_024404945	130,255,477 - 130,441,705 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936511	5,673,368 - 5,856,631 (+)	Ensembl	SpeTri2.0
SpeTri2.0	NW_004936511	5,789,683 - 5,858,930 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

TBC1D4
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	11	47,543,815 - 47,828,208 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	11	47,543,808 - 47,760,928 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	11	52,161,139 - 52,187,164 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

TBC1D4
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	3	54,384,597 - 54,588,842 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	3	54,386,342 - 54,464,531 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666046	10,524,400 - 10,732,251 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Tbc1d4
(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_female_1.0 Ensembl	NW_004624751	24,999,386 - 25,181,702 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624751	24,999,301 - 25,183,905 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Tbc1d4
1326 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	298
Count of miRNA genes:	180
Interacting mature miRNAs:	204
Transcripts:	ENSRNOT00000012600, ENSRNOT00000064942, ENSRNOT00000073961
Prediction methods:	Microtar, Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

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

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

QTLs in Region (mRatBN7.2)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
61424	Scl1	Serum cholesterol level QTL 1	7.7	0.001	blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	15	16725528	80672115	Rat
1578646	Bmd18	Bone mineral density QTL 18	5.2		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	15	22806240	98288169	Rat
1578647	Bmd17	Bone mineral density QTL 17	4		femur mineral mass (VT:0010011)	total volumetric bone mineral density (CMO:0001728)	15	22806240	98288169	Rat
1578660	Bss19	Bone structure and strength QTL 19	4.3		femur morphology trait (VT:0000559)	bone trabecular cross-sectional area (CMO:0002311)	15	22806240	98288169	Rat
1582214	Stl21	Serum triglyceride level QTL 21	3.1	0.022	blood triglyceride amount (VT:0002644)	serum triglyceride level (CMO:0000360)	15	28030665	82262678	Rat
1582227	Gluco30	Glucose level QTL 30	3.6	0.0003	blood glucose amount (VT:0000188)	absolute change in blood glucose level area under curve (CMO:0002034)	15	28030665	82262678	Rat
1582228	Epfw3	Epididymal fat weight QTL 3	4.1	0.0002	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	15	28030665	82262678	Rat
1582242	Gluco28	Glucose level QTL 28	3.3	0.0008	blood glucose amount (VT:0000188)	blood glucose level area under curve (AUC) (CMO:0000350)	15	28030665	82262678	Rat
1582244	Bw79	Body weight QTL 79	4	0.0002	epididymal fat pad mass (VT:0010421)	epididymal fat pad weight to body weight ratio (CMO:0000658)	15	28030665	82262678	Rat
1598828	Glom14	Glomerulus QTL 14	2.5		kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	15	34054139	79054139	Rat
1300144	Rf23	Renal function QTL 23	3.61		renal blood flow trait (VT:2000006)	absolute change in renal vascular resistance (CMO:0001900)	15	40631268	98288169	Rat
1576315	Schws6	Schwannoma susceptibility QTL 6		0.0069	nervous system integrity trait (VT:0010566)	post-insult time of death (CMO:0002005)	15	53806152	98806152	Rat
61477	Aia4	Adjuvant induced arthritis QTL 4	3		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	15	55596089	91365858	Rat
631516	Gluco31	Glucose level QTL 31	7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	15	55596089	95018120	Rat
631655	Bp126	Blood pressure QTL 126	4		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	15	58156477	101769107	Rat
731177	Uae26	Urinary albumin excretion QTL 26	2.4	0.025	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	15	67588667	101769107	Rat
2300326	Plaw1	Placental weight QTL 1	15	0.005	placenta mass (VT:0004257)	placenta wet weight (CMO:0002088)	15	68327165	100062518	Rat
1331724	Bp223	Blood pressure QTL 223	3.53715		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	15	73690518	95018228	Rat
1641889	Colcr6	Colorectal carcinoma resistance QTL 6	2.9	0.0126	intestine integrity trait (VT:0010554)	benign colorectal tumor surface area measurement (CMO:0001799)	15	73690518	99794247	Rat
70182	BpQTLcluster12	Blood pressure QTL cluster 12	3.53		arterial blood pressure trait (VT:2000000)	absolute change in mean arterial blood pressure (CMO:0000533)	15	73690657	95018120	Rat
2317055	Aia10	Adjuvant induced arthritis QTL 10	3.41		joint integrity trait (VT:0010548)	left rear ankle joint diameter (CMO:0002149)	15	75788062	101769107	Rat
1549844	Bss7	Bone structure and strength QTL 7	6.4		femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	15	75788062	101769107	Rat
1581555	Eae19	Experimental allergic encephalomyelitis QTL 19	4.7		nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis severity score (CMO:0001419)	15	76306099	90088744	Rat
70155	Gcs1	Gastric cancer susceptibility QTL1	3.8		stomach morphology trait (VT:0000470)	stomach tumor susceptibility score (CMO:0002043)	15	76306099	101769107	Rat

Markers in Region

D15Rat71

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	15	78,329,942 - 78,330,139 (+)	MAPPER	mRatBN7.2
Rnor_6.0	15	86,001,834 - 86,002,030	NCBI	Rnor6.0
Rnor_5.0	15	89,768,256 - 89,768,452	UniSTS	Rnor5.0
RGSC_v3.4	15	85,456,316 - 85,456,512	UniSTS	RGSC3.4
RGSC_v3.4	15	85,456,315 - 85,456,512	RGD	RGSC3.4
RGSC_v3.1	15	85,472,096 - 85,472,292	RGD
Celera	15	77,523,991 - 77,524,187	UniSTS
RH 3.4 Map	15	541.3	RGD
RH 3.4 Map	15	541.3	UniSTS
RH 2.0 Map	15	419.4	RGD
SHRSP x BN Map	15	50.5798	RGD
FHH x ACI Map	15	63.69	RGD
Cytogenetic Map	15	q21	UniSTS

D15Got221

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	15	78,330,022 - 78,330,193 (+)	MAPPER	mRatBN7.2
Rnor_6.0	15	86,001,914 - 86,002,084	NCBI	Rnor6.0
Rnor_5.0	15	89,768,336 - 89,768,506	UniSTS	Rnor5.0
RGSC_v3.4	15	85,456,396 - 85,456,566	UniSTS	RGSC3.4
Celera	15	77,524,071 - 77,524,241	UniSTS
Cytogenetic Map	15	q21	UniSTS

TBC1D4

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	15	78,264,296 - 78,264,433 (+)	MAPPER	mRatBN7.2
Rnor_6.0	15	85,936,244 - 85,936,380	NCBI	Rnor6.0
Rnor_5.0	15	89,703,880 - 89,704,016	UniSTS	Rnor5.0
RGSC_v3.4	15	85,365,533 - 85,365,669	UniSTS	RGSC3.4
Celera	15	77,460,281 - 77,460,417	UniSTS
Cytogenetic Map	15	q21	UniSTS

Genetic Models

This gene Tbc1d4 is modified in the following models/strains

WI-Tbc1d4^em1Gdcz

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		42	16		19		8	11	8	28	11	10	8
Low	3	1	41	41		41			66	7	30	1
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_003752837	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006222048	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017599918	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017604953	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017604954	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017604955	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017604956	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017604957	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017604958	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039093968	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039093969	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039093970	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039093971	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	FQ227467	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000272	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000012600 ⟹ ENSRNOP00000012600

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	15	78,257,121 - 78,434,265 (-)	Ensembl
Rnor_6.0 Ensembl	15	85,930,044 - 86,105,273 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000064942 ⟹ ENSRNOP00000062670

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	15	78,257,121 - 78,434,265 (-)	Ensembl
Rnor_6.0 Ensembl	15	85,930,044 - 86,105,273 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000109400 ⟹ ENSRNOP00000089194

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	15	78,257,121 - 78,434,265 (-)	Ensembl

RefSeq Acc Id:

ENSRNOT00000120033 ⟹ ENSRNOP00000096754

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	15	78,257,121 - 78,434,265 (-)	Ensembl

RefSeq Acc Id:

XM_039093968 ⟹ XP_038949896

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	15	78,256,030 - 78,434,167 (-)	NCBI

RefSeq Acc Id:

XM_039093969 ⟹ XP_038949897

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	15	78,256,030 - 78,434,168 (-)	NCBI

RefSeq Acc Id:

XM_039093970 ⟹ XP_038949898

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	15	78,256,030 - 78,434,166 (-)	NCBI

RefSeq Acc Id:

XM_039093971 ⟹ XP_038949899

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	15	78,256,030 - 78,327,627 (-)	NCBI

Protein Sequences


Protein RefSeqs	XP_038949896	(Get FASTA)	NCBI Sequence Viewer
	XP_038949897	(Get FASTA)	NCBI Sequence Viewer
	XP_038949898	(Get FASTA)	NCBI Sequence Viewer
	XP_038949899	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

ENSRNOP00000012600 ⟸ ENSRNOT00000012600

RefSeq Acc Id:

ENSRNOP00000062670 ⟸ ENSRNOT00000064942

RefSeq Acc Id:	XP_038949897 ⟸ XM_039093969
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038949896 ⟸ XM_039093968
- Peptide Label:	isoform X1
- UniProtKB:	A0A8I6AT49 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_038949898 ⟸ XM_039093970
- Peptide Label:	isoform X3
- UniProtKB:	D3Z881 (UniProtKB/TrEMBL)

RefSeq Acc Id:	XP_038949899 ⟸ XM_039093971
- Peptide Label:	isoform X4

RefSeq Acc Id:

ENSRNOP00000096754 ⟸ ENSRNOT00000120033

RefSeq Acc Id:

ENSRNOP00000089194 ⟸ ENSRNOT00000109400

Protein Domains

PID Rab-GAP TBC

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-D3ZGN0-F1-model_v2	AlphaFold	D3ZGN0	1-1309	view protein structure

Transcriptome

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1561609	AgrOrtholog
BioCyc Gene	G2FUF-12753	BioCyc
Ensembl Genes	ENSRNOG00000009431	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000012600.8	UniProtKB/TrEMBL
	ENSRNOP00000062670	ENTREZGENE
	ENSRNOP00000062670.4	UniProtKB/TrEMBL
	ENSRNOP00000089194.1	UniProtKB/TrEMBL
	ENSRNOP00000096754	ENTREZGENE
	ENSRNOP00000096754.1	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000012600.9	UniProtKB/TrEMBL
	ENSRNOT00000064942	ENTREZGENE
	ENSRNOT00000064942.5	UniProtKB/TrEMBL
	ENSRNOT00000109400.1	UniProtKB/TrEMBL
	ENSRNOT00000120033	ENTREZGENE
	ENSRNOT00000120033.1	UniProtKB/TrEMBL
Gene3D-CATH	1.10.10.2750	UniProtKB/TrEMBL
	2.30.29.30	UniProtKB/TrEMBL
	putative rabgap domain of human tbc1 domain family member 14 like domains	UniProtKB/TrEMBL
	Ypt/Rab-GAP domain of gyp1p, domain 3	UniProtKB/TrEMBL
InterPro	DUF3350	UniProtKB/TrEMBL
	PH_like_dom	UniProtKB/TrEMBL
	PTyr_interaction_dom	UniProtKB/TrEMBL
	Rab-GTPase-TBC_dom	UniProtKB/TrEMBL
	Rab-GTPase_TBC_sf	UniProtKB/TrEMBL
NCBI Gene	306117	ENTREZGENE
PANTHER	RAB GTPASE-ACTIVATING PROTEIN 1-LIKE	UniProtKB/TrEMBL
	TBC1 DOMAIN FAMILY MEMBER 1	UniProtKB/TrEMBL
Pfam	DUF3350	UniProtKB/TrEMBL
	PID	UniProtKB/TrEMBL
	RabGAP-TBC	UniProtKB/TrEMBL
PhenoGen	Tbc1d4	PhenoGen
PROSITE	PID	UniProtKB/TrEMBL
	TBC_RABGAP	UniProtKB/TrEMBL
SMART	PTB	UniProtKB/TrEMBL
	TBC	UniProtKB/TrEMBL
Superfamily-SCOP	PH domain-like	UniProtKB/TrEMBL
	RabGAP_TBC	UniProtKB/TrEMBL
UniProt	A0A8I6ABF1_RAT	UniProtKB/TrEMBL
	A0A8I6AT49	ENTREZGENE, UniProtKB/TrEMBL
	D3Z881	ENTREZGENE, UniProtKB/TrEMBL
	D3ZGN0_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2013-08-06	Tbc1d4	TBC1 domain family, member 4	RGD1561609	similar to TBC1 domain family member 4	Name and Symbol changed	629549	APPROVED
2013-05-24	RGD1561609	similar to TBC1 domain family member 4	LOC686547	similar to TBC1 domain family member 4 (Akt substrate of 160 kDa) (AS160)	Data Merged	1643240	APPROVED
2008-04-30	RGD1561609	similar to TBC1 domain family member 4	RGD1561609_predicted	similar to TBC1 domain family member 4 (predicted)	'predicted' is removed	2292626	APPROVED
2006-11-20	LOC686547	similar to TBC1 domain family member 4 (Akt substrate of 160 kDa) (AS160)			Symbol and Name status set to provisional	70820	PROVISIONAL
2006-03-07	RGD1561609_predicted	similar to TBC1 domain family member 4 (predicted)	LOC306117	similar to TBC1 domain family member 4	Symbol and Name status set to approved	1299863	APPROVED
2006-02-09	LOC306117	similar to TBC1 domain family member 4			Symbol and Name status set to provisional	70820	PROVISIONAL

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 - OMIM

RGD Manual Annotations

Imported Annotations - PID (archival)

Mammalian Phenotype

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Imported Disease Annotations - ClinVar

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Imported Annotations - PID (archival)

Mammalian Phenotype