Tbc1d13 (TBC1 domain family, member 13) - Rat Genome Database

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Gene: Tbc1d13 (TBC1 domain family, member 13) Rattus norvegicus
Analyze
Symbol: Tbc1d13
Name: TBC1 domain family, member 13
RGD ID: 1591937
Description: Predicted to enable GTPase activator activity and small GTPase binding activity. Predicted to be involved in intracellular protein transport. Predicted to be located in cytosol and membrane. Predicted to be active in cytoplasm. Orthologous to human TBC1D13 (TBC1 domain family member 13); INTERACTS WITH 3-chloropropane-1,2-diol; bisphenol A; Soman.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC499768; similar to TBC1 domain family, member 13; TBC1 domain family member 13
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8333,806,772 - 33,823,346 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl333,795,746 - 33,823,345 (+)EnsemblGRCr8
mRatBN7.2313,408,944 - 13,425,524 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl313,408,920 - 13,425,517 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx316,480,974 - 16,497,485 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0325,065,940 - 25,082,451 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0323,319,360 - 23,335,883 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.038,701,849 - 8,718,400 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl38,701,855 - 8,717,515 (+)Ensemblrn6Rnor6.0
Rnor_5.0314,053,981 - 14,070,563 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.439,141,842 - 9,158,473 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera38,182,504 - 8,199,087 (+)NCBICelera
Cytogenetic Map3p12NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA,IEA)
cytosol  (ISO)
membrane  (IEA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:17646400   PMID:22762500  


Genomics

Comparative Map Data
Tbc1d13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8333,806,772 - 33,823,346 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl333,795,746 - 33,823,345 (+)EnsemblGRCr8
mRatBN7.2313,408,944 - 13,425,524 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl313,408,920 - 13,425,517 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx316,480,974 - 16,497,485 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0325,065,940 - 25,082,451 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0323,319,360 - 23,335,883 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.038,701,849 - 8,718,400 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl38,701,855 - 8,717,515 (+)Ensemblrn6Rnor6.0
Rnor_5.0314,053,981 - 14,070,563 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.439,141,842 - 9,158,473 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera38,182,504 - 8,199,087 (+)NCBICelera
Cytogenetic Map3p12NCBI
TBC1D13
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389128,787,253 - 128,810,430 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9128,787,233 - 128,810,432 (+)Ensemblhg38GRCh38
GRCh379131,549,532 - 131,572,709 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 369130,589,432 - 130,612,532 (+)NCBIBuild 36Build 36hg18NCBI36
Build 349128,629,164 - 128,652,264NCBI
Celera9102,200,284 - 102,223,500 (+)NCBICelera
Cytogenetic Map9q34.11NCBI
HuRef9101,158,509 - 101,181,851 (+)NCBIHuRef
CHM1_19131,700,471 - 131,723,717 (+)NCBICHM1_1
T2T-CHM13v2.09140,992,029 - 141,015,220 (+)NCBIT2T-CHM13v2.0
Tbc1d13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39230,023,742 - 30,042,024 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl230,023,758 - 30,042,025 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38230,133,730 - 30,152,014 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl230,133,746 - 30,152,013 (+)Ensemblmm10GRCm38
MGSCv37229,989,391 - 30,007,533 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36229,955,875 - 29,974,022 (+)NCBIMGSCv36mm8
Celera229,837,391 - 29,855,854 (+)NCBICelera
Cytogenetic Map2BNCBI
cM Map221.22NCBI
Tbc1d13
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555701,180,179 - 1,190,517 (+)Ensembl
ChiLan1.0NW_0049555701,180,154 - 1,192,525 (+)NCBIChiLan1.0ChiLan1.0
TBC1D13
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21110,540,526 - 10,563,712 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1910,542,873 - 10,566,037 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0999,910,685 - 99,933,856 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19128,576,097 - 128,600,523 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9128,576,246 - 128,597,979 (+)EnsemblpanPan2panpan1.1
TBC1D13
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1954,816,325 - 54,831,425 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl954,816,459 - 54,831,333 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha954,009,410 - 54,026,922 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0955,734,964 - 55,752,504 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl955,734,673 - 55,752,409 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1954,495,590 - 54,513,109 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0954,808,356 - 54,825,876 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0954,901,760 - 54,919,303 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tbc1d13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947196,470,619 - 196,509,907 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493648716,260,253 - 16,278,429 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493648716,260,319 - 16,278,434 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TBC1D13
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1269,134,160 - 269,152,284 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11269,134,532 - 269,153,056 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21303,149,248 - 303,168,334 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TBC1D13
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1129,333,341 - 9,362,817 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl129,333,685 - 9,362,675 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666096115,087 - 140,320 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tbc1d13
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247606,209,542 - 6,224,172 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247606,209,802 - 6,224,203 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Tbc1d13
(Rattus rattus - black rat)		 No map positions available.

Variants

.
Variants in Tbc1d13
217 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:62
Count of miRNA genes:58
Interacting mature miRNAs:62
Transcripts:ENSRNOT00000021431
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)32267715050766390Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)32905627547904329Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
10450811Scl73Serum cholesterol level QTL 734.70.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3655634751556347Rat
10450808Scl72Serum cholesterol level QTL 724.40.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
10450806Scl71Serum cholesterol level QTL 715.80.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)32862533967641995Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)3612543751125437Rat
8693641Alc30Alcohol consumption QTL 3020.739drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)33083238444921701Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3136721849Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31141509147Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3655634751556347Rat
1558657Cm43Cardiac mass QTL 436.63e-08heart mass (VT:0007028)heart wet weight (CMO:0000069)32267715050766390Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)31527234860272348Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)32905627547904329Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35675975141509147Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3655634751556347Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 161 91 90 59 92 59 6 356 192 11 140 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000021431   ⟹   ENSRNOP00000021431
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl333,806,810 - 33,823,345 (+)Ensembl
mRatBN7.2 Ensembl313,408,920 - 13,425,517 (+)Ensembl
Rnor_6.0 Ensembl38,701,855 - 8,717,515 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000143123   ⟹   ENSRNOP00000108237
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl333,795,746 - 33,823,345 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000160657   ⟹   ENSRNOP00000099702
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl333,802,005 - 33,823,345 (+)Ensembl
RefSeq Acc Id: NM_001399454   ⟹   NP_001386383
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8333,806,772 - 33,823,346 (+)NCBI
mRatBN7.2313,408,944 - 13,425,524 (+)NCBI
RefSeq Acc Id: XM_039106775   ⟹   XP_038962703
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8333,806,868 - 33,823,343 (+)NCBI
mRatBN7.2313,409,035 - 13,425,524 (+)NCBI
RefSeq Acc Id: XM_039106776   ⟹   XP_038962704
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8333,812,259 - 33,823,343 (+)NCBI
mRatBN7.2313,414,440 - 13,425,524 (+)NCBI
RefSeq Acc Id: XM_063284345   ⟹   XP_063140415
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8333,806,789 - 33,817,921 (+)NCBI
Ensembl Acc Id: ENSRNOP00000021431   ⟸   ENSRNOT00000021431
RefSeq Acc Id: XP_038962703   ⟸   XM_039106775
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038962704   ⟸   XM_039106776
- Peptide Label: isoform X2
RefSeq Acc Id: NP_001386383   ⟸   NM_001399454
- UniProtKB: D4AEG7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063140415   ⟸   XM_063284345
- Peptide Label: isoform X3
Ensembl Acc Id: ENSRNOP00000108237   ⟸   ENSRNOT00000143123
Ensembl Acc Id: ENSRNOP00000099702   ⟸   ENSRNOT00000160657
Protein Domains
Rab-GAP TBC

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4AEG7-F1-model_v2 AlphaFold D4AEG7 1-400 view protein structure

Transcriptome

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

Promoters
RGD ID:13691963
Promoter ID:EPDNEW_R2476
Type:multiple initiation site
Name:Tbc1d13_1
Description:TBC1 domain family, member 13
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.038,701,923 - 8,701,983EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1591937 AgrOrtholog
BioCyc Gene G2FUF-50232 BioCyc
Ensembl Genes ENSRNOG00000015970 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021431 ENTREZGENE
  ENSRNOT00000021431.9 UniProtKB/TrEMBL
  ENSRNOT00000143123.1 UniProtKB/TrEMBL
  ENSRNOT00000160657.1 UniProtKB/TrEMBL
Gene3D-CATH 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 Rab-GTPase_TBC_sf UniProtKB/TrEMBL
  RabGAP_TBC UniProtKB/TrEMBL
NCBI Gene 499768 ENTREZGENE
PANTHER TBC1 DOMAIN FAMILY MEMBER 13 UniProtKB/TrEMBL
  TBC1 DOMAIN FAMILY MEMBER GTPASE-ACTIVATING PROTEIN UniProtKB/TrEMBL
Pfam TBC UniProtKB/TrEMBL
PhenoGen Tbc1d13 PhenoGen
PROSITE TBC_RABGAP UniProtKB/TrEMBL
RatGTEx ENSRNOG00000015970 RatGTEx
SMART TBC UniProtKB/TrEMBL
Superfamily-SCOP RabGAP_TBC UniProtKB/TrEMBL
UniProt A0ABK0LAM5_RAT UniProtKB/TrEMBL
  A0ABK0LZZ9_RAT UniProtKB/TrEMBL
  D4AEG7 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-05 Tbc1d13  TBC1 domain family, member 13  LOC499768  similar to TBC1 domain family, member 13  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-20 LOC499768  similar to TBC1 domain family, member 13      Symbol and Name status set to provisional 70820 PROVISIONAL