Tbc1d10a (TBC1 domain family, member 10a) - Rat Genome Database

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Gene: Tbc1d10a (TBC1 domain family, member 10a) Rattus norvegicus
Analyze
Symbol: Tbc1d10a
Name: TBC1 domain family, member 10a
RGD ID: 1311641
Description: Predicted to enable GTPase activator activity and PDZ domain binding activity. Predicted to be involved in positive regulation of proteolysis and retrograde transport, endosome to Golgi. Predicted to be located in plasma membrane. Orthologous to human TBC1D10A (TBC1 domain family member 10A); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; paracetamol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC360968; MGC105611; TBC1 domain family member 10A; TBC1 domain family, member 10; Tbc1d10
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81483,278,151 - 83,307,178 (+)NCBIGRCr8
mRatBN7.21479,051,822 - 79,083,603 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1479,055,432 - 79,083,600 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1483,496,159 - 83,523,867 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01484,736,238 - 84,763,946 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01481,182,137 - 81,209,845 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01484,417,320 - 84,445,034 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1484,417,320 - 84,445,034 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01485,098,646 - 85,127,054 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41484,810,214 - 84,837,928 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11484,829,295 - 84,857,428 (+)NCBI
Celera1477,966,529 - 77,994,243 (+)NCBICelera
Cytogenetic Map14q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytosol  (IEA)
plasma membrane  (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
5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:11285285   PMID:17562788   PMID:17646400   PMID:18387192   PMID:19056867   PMID:23533145   PMID:25468996  


Genomics

Comparative Map Data
Tbc1d10a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81483,278,151 - 83,307,178 (+)NCBIGRCr8
mRatBN7.21479,051,822 - 79,083,603 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1479,055,432 - 79,083,600 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1483,496,159 - 83,523,867 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01484,736,238 - 84,763,946 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01481,182,137 - 81,209,845 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01484,417,320 - 84,445,034 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1484,417,320 - 84,445,034 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01485,098,646 - 85,127,054 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41484,810,214 - 84,837,928 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11484,829,295 - 84,857,428 (+)NCBI
Celera1477,966,529 - 77,994,243 (+)NCBICelera
Cytogenetic Map14q21NCBI
TBC1D10A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382230,291,990 - 30,326,941 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2230,291,990 - 30,326,947 (-)EnsemblGRCh38hg38GRCh38
GRCh372230,687,979 - 30,722,930 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362229,017,979 - 29,052,894 (-)NCBINCBI36Build 36hg18NCBI36
Celera2214,487,683 - 14,522,588 (-)NCBICelera
Cytogenetic Map22q12.2NCBI
HuRef2213,649,780 - 13,684,744 (-)NCBIHuRef
CHM1_12230,647,114 - 30,682,078 (-)NCBICHM1_1
T2T-CHM13v2.02230,755,329 - 30,790,284 (-)NCBIT2T-CHM13v2.0
Tbc1d10a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39114,136,852 - 4,167,407 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl114,136,789 - 4,165,505 (+)EnsemblGRCm39 Ensembl
GRCm38114,186,833 - 4,215,507 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl114,186,789 - 4,215,505 (+)EnsemblGRCm38mm10GRCm38
MGSCv37114,086,836 - 4,115,508 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36114,086,836 - 4,115,508 (+)NCBIMGSCv36mm8
Celera114,683,776 - 4,712,449 (+)NCBICelera
Cytogenetic Map11A1NCBI
cM Map112.92NCBI
Tbc1d10a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554554,537,634 - 4,570,949 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554554,537,634 - 4,570,949 (-)NCBIChiLan1.0ChiLan1.0
TBC1D10A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22340,259,179 - 40,294,040 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12242,957,788 - 42,992,669 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02211,328,159 - 11,363,009 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12229,130,096 - 29,164,838 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2229,130,096 - 29,164,865 (-)Ensemblpanpan1.1panPan2
TBC1D10A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12623,446,251 - 23,478,287 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2623,446,607 - 23,478,317 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2623,317,434 - 23,349,461 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02623,830,218 - 23,862,484 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2623,830,243 - 23,862,523 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12623,531,901 - 23,563,925 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02623,794,735 - 23,826,752 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02623,855,089 - 23,887,117 (-)NCBIUU_Cfam_GSD_1.0
Tbc1d10a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118116,364,225 - 116,378,667 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936904357,634 - 369,652 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936904357,621 - 370,006 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TBC1D10A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1447,269,092 - 47,301,753 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11447,269,087 - 47,301,540 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21450,308,036 - 50,332,493 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TBC1D10A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11913,172,847 - 13,207,979 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1913,172,845 - 13,207,904 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666045112,938,151 - 112,973,593 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tbc1d10a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247476,607,448 - 6,643,734 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247476,607,085 - 6,643,745 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tbc1d10a
126 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:52
Count of miRNA genes:50
Interacting mature miRNAs:51
Transcripts:ENSRNOT00000008788
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.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
1300136Rf22Renal function QTL 223.9renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)144226252995023211Rat
1549834Scl45Serum cholesterol level QTL 455.8blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)145002321195023211Rat
2300197Scl59Serum cholesterol level QTL 59blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1455147478100147478Rat
9590294Uminl4Urine mineral level QTL 45.660.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)1455624247100624247Rat
9589034Epfw11Epididymal fat weight QTL 1160.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1455624247100624247Rat
2317879Alcrsp27Alcohol response QTL 273.30.63response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1456631369101631369Rat
634328Hc5Hypercalciuria QTL 52.3urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1458184885103184885Rat
70153Bp59Blood pressure QTL 593.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)146875779683368335Rat
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1470053989104886043Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1470053989104886043Rat
1582197Gluco27Glucose level QTL 273.40.0006blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)147341532392554092Rat
1582209Gluco20Glucose level QTL 203.80.0005blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582236Gluco22Glucose level QTL 223.30.0164blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532392554092Rat
1582255Gluco29Glucose level QTL 293.10.0025blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)147341532392554092Rat
1582250Gluco26Glucose level QTL 263.30.0009blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)147341532395876975Rat

Markers in Region
RH129938  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21479,083,380 - 79,083,593 (+)MAPPERmRatBN7.2
Rnor_6.01484,445,167 - 84,445,379NCBIRnor6.0
Rnor_5.01485,126,832 - 85,127,044UniSTSRnor5.0
RGSC_v3.41484,838,061 - 84,838,273UniSTSRGSC3.4
Celera1477,994,376 - 77,994,588UniSTS
RH 3.4 Map14550.49UniSTS
Cytogenetic Map14q21UniSTS
D19343  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21479,083,439 - 79,083,597 (+)MAPPERmRatBN7.2
Rnor_6.01484,445,226 - 84,445,383NCBIRnor6.0
Rnor_5.01485,126,891 - 85,127,048UniSTSRnor5.0
RGSC_v3.41484,838,120 - 84,838,277UniSTSRGSC3.4
Celera1477,994,435 - 77,994,592UniSTS
Cytogenetic Map14q21UniSTS


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 10 12 4 19 4 69 35 40 11
Low 33 45 37 37 8 11 5 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008788   ⟹   ENSRNOP00000008788
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1479,055,432 - 79,083,600 (+)Ensembl
Rnor_6.0 Ensembl1484,417,320 - 84,445,034 (+)Ensembl
RefSeq Acc Id: NM_001015022   ⟹   NP_001015022
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81483,279,071 - 83,307,178 (+)NCBI
mRatBN7.21479,055,495 - 79,083,603 (+)NCBI
Rnor_6.01484,417,320 - 84,445,034 (+)NCBI
Rnor_5.01485,098,646 - 85,127,054 (+)NCBI
RGSC_v3.41484,810,214 - 84,837,928 (+)RGD
Celera1477,966,529 - 77,994,243 (+)RGD
Sequence:
RefSeq Acc Id: XM_039092211   ⟹   XP_038948139
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81483,278,151 - 83,307,178 (+)NCBI
mRatBN7.21479,051,822 - 79,083,603 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001015022 (Get FASTA)   NCBI Sequence Viewer  
  XP_038948139 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH93603 (Get FASTA)   NCBI Sequence Viewer  
  BAD95469 (Get FASTA)   NCBI Sequence Viewer  
  EDM00217 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000008788
  ENSRNOP00000008788.5
Reference Protein Sequences
RefSeq Acc Id: NP_001015022   ⟸   NM_001015022
- UniProtKB: Q587K3 (UniProtKB/TrEMBL),   Q566D9 (UniProtKB/TrEMBL),   F7EVS3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000008788   ⟸   ENSRNOT00000008788
RefSeq Acc Id: XP_038948139   ⟸   XM_039092211
- Peptide Label: isoform X1
Protein Domains
Rab-GAP TBC

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q587K3-F1-model_v2 AlphaFold Q587K3 1-505 view protein structure

Transcriptome

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

Promoters
RGD ID:13699442
Promoter ID:EPDNEW_R9966
Type:initiation region
Name:Tbc1d10a_1
Description:TBC1 domain family, member 10a
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_6.01484,417,282 - 84,417,342EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311641 AgrOrtholog
BioCyc Gene G2FUF-15182 BioCyc
Ensembl Genes ENSRNOG00000006394 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008788 ENTREZGENE
  ENSRNOT00000008788.8 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 1 UniProtKB/TrEMBL
  Ypt/Rab-GAP domain of gyp1p, domain 3 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7316341 IMAGE-MGC_LOAD
InterPro Rab-GTPase_TBC_sf UniProtKB/TrEMBL
  RabGAP_TBC UniProtKB/TrEMBL
KEGG Report rno:360968 UniProtKB/TrEMBL
MGC_CLONE MGC:105611 IMAGE-MGC_LOAD
NCBI Gene 360968 ENTREZGENE
PANTHER RAB GTPASE-ACTIVATING PROTEIN 1-LIKE UniProtKB/TrEMBL
  TBC1 DOMAIN FAMILY MEMBER 10B UniProtKB/TrEMBL
Pfam TBC UniProtKB/TrEMBL
PhenoGen Tbc1d10a PhenoGen
PROSITE TBC_RABGAP UniProtKB/TrEMBL
RatGTEx ENSRNOG00000006394 RatGTEx
SMART TBC UniProtKB/TrEMBL
Superfamily-SCOP RabGAP_TBC UniProtKB/TrEMBL
UniProt F7EVS3 ENTREZGENE, UniProtKB/TrEMBL
  Q566D9 ENTREZGENE, UniProtKB/TrEMBL
  Q587K3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Tbc1d10a  TBC1 domain family, member 10a  Tbc1d10  TBC1 domain family, member 10  Symbol and Name updated 1299863 APPROVED
2005-12-06 Tbc1d10  TBC1 domain family, member 10  Tbc1d10_predicted  TBC1 domain family, member 10 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Tbc1d10_predicted  TBC1 domain family, member 10 (predicted)      Symbol and Name status set to approved 70820 APPROVED