Tbc1d9 (TBC1 domain family, member 9) - Rat Genome Database
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Gene: Tbc1d9 (TBC1 domain family, member 9) Mus musculus
Analyze
Symbol: Tbc1d9
Name: TBC1 domain family, member 9
RGD ID: 1317871
MGI Page MGI
Description: Predicted to have GTPase activator activity and Rab GTPase binding activity. Predicted to be involved in activation of GTPase activity and intracellular protein transport. Orthologous to human TBC1D9 (TBC1 domain family member 9); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,4-methylenedioxymethamphetamine; chlordecone.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 4933431N12Rik; AI847101; AW490653; C76116; TBC1 domain family member 9
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39883,891,981 - 83,999,569 (+)NCBIGRCm39mm39
GRCm38883,165,352 - 83,272,940 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl883,165,352 - 83,272,934 (+)EnsemblGRCm38mm10GRCm38
MGSCv37885,689,251 - 85,796,839 (+)NCBIGRCm37mm9NCBIm37
MGSCv36886,055,457 - 86,162,527 (+)NCBImm8
Celera887,444,516 - 87,547,903 (+)NCBICelera
Cytogenetic Map8C2NCBI
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

Molecular Function

References

Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:10725249   PMID:11042159   PMID:11076861   PMID:12477932   PMID:14610273   PMID:15368895   PMID:15782199   PMID:16141072   PMID:16141073   PMID:21873635  
PMID:22442722   PMID:24154525   PMID:32325033  


Genomics

Comparative Map Data
Tbc1d9
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39883,891,981 - 83,999,569 (+)NCBIGRCm39mm39
GRCm38883,165,352 - 83,272,940 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl883,165,352 - 83,272,934 (+)EnsemblGRCm38mm10GRCm38
MGSCv37885,689,251 - 85,796,839 (+)NCBIGRCm37mm9NCBIm37
MGSCv36886,055,457 - 86,162,527 (+)NCBImm8
Celera887,444,516 - 87,547,903 (+)NCBICelera
Cytogenetic Map8C2NCBI
TBC1D9
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl4140,620,782 - 140,756,385 (-)EnsemblGRCh38hg38GRCh38
GRCh384140,620,782 - 140,756,385 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh374141,541,936 - 141,677,471 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 364141,761,386 - 141,896,921 (-)NCBINCBI36hg18NCBI36
Celera4138,871,921 - 139,007,760 (-)NCBI
Cytogenetic Map4q31.21NCBI
HuRef4137,272,361 - 137,407,474 (-)NCBIHuRef
CHM1_14141,519,260 - 141,654,776 (-)NCBICHM1_1
Tbc1d9
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.01924,328,381 - 24,429,908 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1924,329,023 - 24,429,909 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01935,298,430 - 35,408,204 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41926,571,531 - 26,672,475 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11926,577,642 - 26,677,302 (-)NCBI
Celera1924,378,762 - 24,479,282 (-)NCBICelera
Cytogenetic Map19q11NCBI
Tbc1d9
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554712,360,696 - 2,470,565 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554712,360,062 - 2,469,940 (+)NCBIChiLan1.0ChiLan1.0
TBC1D9
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.14144,291,723 - 144,426,643 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4144,293,141 - 144,426,374 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v04132,982,357 - 133,118,036 (-)NCBIMhudiblu_PPA_v0panPan3
Tbc1d9
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365357,168,756 - 7,230,911 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TBC1D9
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl886,402,837 - 86,517,784 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1886,402,745 - 86,518,182 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2891,902,294 - 91,946,118 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TBC1D9
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1787,553,136 - 87,691,254 (-)NCBI
ChlSab1.1 Ensembl787,552,715 - 87,690,438 (-)Ensembl
Tbc1d9
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462485336,571 - 151,871 (-)NCBI

Position Markers
U27340  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38883,170,748 - 83,170,896UniSTSGRCm38
GRCm381060,302,386 - 60,302,534UniSTSGRCm38
MGSCv371059,765,134 - 59,765,282UniSTSGRCm37
MGSCv37885,694,647 - 85,694,795UniSTSGRCm37
Celera1061,399,243 - 61,399,391UniSTS
Cytogenetic Map10B4UniSTS
Cytogenetic Map10A3UniSTS
Cytogenetic Map8C3UniSTS
cM Map108.0UniSTS
cM Map1035.0UniSTS
Whitehead/MRC_RH10689.52UniSTS
D8Mit106  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38883,180,780 - 83,180,928UniSTSGRCm38
MGSCv37885,704,679 - 85,704,827UniSTSGRCm37
Celera875,414,875 - 75,414,992UniSTS
Cytogenetic Map8C3UniSTS
cM Map838.0UniSTS
Whitehead Genetic839.3UniSTS
Whitehead/MRC_RH8988.59UniSTS
Whitehead_YAC8 UniSTS
D8Mit265  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38883,223,760 - 83,223,860UniSTSGRCm38
MGSCv37885,747,659 - 85,747,759UniSTSGRCm37
Cytogenetic Map8C3UniSTS
cM Map838.0UniSTS
Whitehead Genetic839.3UniSTS
Whitehead_YAC8 UniSTS
UniSTS:235943  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38883,210,290 - 83,210,490UniSTSGRCm38
MGSCv37885,734,189 - 85,734,389UniSTSGRCm37
Celera887,488,827 - 87,489,027UniSTS
Cytogenetic Map8C3UniSTS
AI847101  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38883,272,629 - 83,272,746UniSTSGRCm38
MGSCv37885,796,528 - 85,796,645UniSTSGRCm37
Celera887,547,592 - 87,547,709UniSTS
Cytogenetic Map8C3UniSTS
Whitehead/MRC_RH8988.29UniSTS
Psap  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381060,302,388 - 60,302,533UniSTSGRCm38
GRCm38883,170,749 - 83,170,894UniSTSGRCm38
MGSCv371059,765,136 - 59,765,281UniSTSGRCm37
MGSCv37885,694,648 - 85,694,793UniSTSGRCm37
Celera1061,399,245 - 61,399,390UniSTS
Cytogenetic Map10A3UniSTS
Cytogenetic Map8C3UniSTS
Cytogenetic Map10B4UniSTS
cM Map1035.0UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301874Hdlq16_mHDL QTL 16 (mouse)Not determined875685348109685497Mouse
1301099Cbm2_mcerebellum weight 2 (mouse)Not determined878518613112518703Mouse
14747005Mancz7_mmandible centroid size 7 (mouse)85005330684053306Mouse
1301808Nhdlq1_mnon-HDL QTL 1 (mouse)Not determined875685348109685497Mouse
10755519Wbc1_mwhite blood cell count 1 (mouse)881619151115619151Mouse
27226754Femd6_mfemur midshaft diameter 6, 10 week (mouse)837400000109600000Mouse
12904012Cfq10_mconditioned fear QTL 10 (mouse)88006677589014359Mouse
1301872Cd4ts3_mCD4 T cell subset 3 (mouse)Not determined871396181105396393Mouse
1301952Im3_mimmunoregulatory 3 (mouse)Not determined85470661488706763Mouse
14700686Civq3_mcerebral infarct volume QTL 3 (mouse)85188219185882191Mouse
1357787Vtbt5_mvertebral trabecular bone trait 5 (mouse)Not determined86535776899357920Mouse
1357470Obq16_mobesity QTL 16 (mouse)Not determined875685348109685497Mouse
4142283Imraq2_mimmune response to AAV2 QTL 2 (mouse)Not determined870305375104305495Mouse
4141395Char2a_mP. chabaudi malaria resistance QTL 2a (mouse)Not determined7113678390202598Mouse
10412287Carg3_mCandida albicans resistance gene 3 (mouse)Not determined85554502889545028Mouse
14746987Manh64_mmandible shape 64 (mouse)85005330684053306Mouse
1558875Eae31_mexperimental allergic encephalomyelitis susceptibility 31 (mouse)Not determined834642776114837007Mouse
12904744Carcdq1_mcardiac collagen deposition QTL 1 (mouse)83970925694689598Mouse
4141797Skmw16_mskeletal muscle weight 16 (mouse)Not determined86393954797939696Mouse
1301767Fcsa2_mfemoral cross-sectional area 2 (mouse)Not determined870305375104305495Mouse
4142023W3q5_mweight 3 weeks QTL 5 (mouse)Not determined71287817123895615Mouse
10412234Nhdlq14_mnon-HDL QTL 14 (mouse)Not determined875685348109685497Mouse
1301581Char2_mP. chabaudi malaria resistance QTL 2 (mouse)Not determined879082178113082403Mouse
10043992Hbnr11_mHeligmosomoides bakeri nematode resistance 11 (mouse)Not determined86560020799600347Mouse
1357708Orq1_movulation rate QTL 1 (mouse)Not determined871287817123895615Mouse
10043975Obq31_mobesity QTL 31 (mouse)Not determined85840977692409776Mouse
1558780Idd22_minsulin dependent diabetes susceptibility 22 (mouse)Not determined871102903105103009Mouse
4141285Tgq18_mtriglyceride QTL 18 (mouse)Not determined6346010797460107Mouse
11353828Gf7_mgonadal fat pad weight 7 (mouse)85820147992201479Mouse
1301506Aevm1_mautoimmune extremity vasculitis in MRL mice 1 (mouse)Not determined85428781788287993Mouse
1301013Capsq4_mcapsaicin sensitivity related QTL 4 (mouse)Not determined83616300092728652Mouse
4140967Bmd39_mbone mineral density 39 (mouse)Not determined832016544117238700Mouse
1300920Pitm3_mprion incubation time 3 (mouse)Not determined873202495107202598Mouse
1558890Lith18_mlithogenic gene 18 (mouse)Not determined875675517109675623Mouse
10755530Wbc2_mwhite blood cell count 2 (mouse)881092664115092664Mouse
1301688Orch6_mautoimmune orchitis resistance 6 (mouse)Not determined86078685094786976Mouse
27095912Pglq14_mpelvic girdle length QTL 14, 16 week (mouse)873400000126100000Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:728
Count of miRNA genes:395
Interacting mature miRNAs:454
Transcripts:ENSMUST00000034145, ENSMUST00000093393, ENSMUST00000142673
Prediction methods: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.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000034145   ⟹   ENSMUSP00000034145
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl883,165,352 - 83,272,422 (+)Ensembl
RefSeq Acc Id: ENSMUST00000093393   ⟹   ENSMUSP00000091093
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl883,165,860 - 83,272,934 (+)Ensembl
RefSeq Acc Id: ENSMUST00000142673
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl883,259,259 - 83,270,950 (+)Ensembl
RefSeq Acc Id: NM_001111304   ⟹   NP_001104774
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39883,891,981 - 83,999,569 (+)NCBI
GRCm38883,165,352 - 83,272,940 (+)ENTREZGENE
MGSCv37885,689,251 - 85,796,839 (+)RGD
Celera887,444,516 - 87,547,903 (+)RGD
cM Map8 ENTREZGENE
Sequence:
RefSeq Acc Id: NM_027758   ⟹   NP_082034
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39883,891,981 - 83,999,569 (+)NCBI
GRCm38883,165,352 - 83,272,940 (+)ENTREZGENE
MGSCv37885,689,251 - 85,796,839 (+)RGD
Celera887,444,516 - 87,547,903 (+)RGD
cM Map8 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_030243771   ⟹   XP_030099631
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39883,927,070 - 83,999,569 (+)NCBI
GRCm38883,200,814 - 83,272,940 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_082034   ⟸   NM_027758
- Peptide Label: isoform 2
- UniProtKB: Q3UYK3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001104774   ⟸   NM_001111304
- Peptide Label: isoform 1
- UniProtKB: Q3UYK3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_030099631   ⟸   XM_030243771
- Peptide Label: isoform X1
RefSeq Acc Id: ENSMUSP00000034145   ⟸   ENSMUST00000034145
RefSeq Acc Id: ENSMUSP00000091093   ⟸   ENSMUST00000093393
Protein Domains
EF-hand   GRAM   Rab-GAP TBC

Promoters
RGD ID:8667587
Promoter ID:EPDNEW_M11825
Type:initiation region
Name:Tbc1d9_1
Description:Mus musculus TBC1 domain family, member 9 , transcript variant2, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M11826  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38883,165,354 - 83,165,414EPDNEW
RGD ID:8667589
Promoter ID:EPDNEW_M11826
Type:initiation region
Name:Tbc1d9_2
Description:Mus musculus TBC1 domain family, member 9 , transcript variant2, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M11825  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38883,165,510 - 83,165,570EPDNEW
RGD ID:6843789
Promoter ID:MM_KWN:54989
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Lung,   MEF_B4,   MEF_B6
Transcripts:NM_001111304,   NM_027758
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36885,689,191 - 85,689,691 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1918560 AgrOrtholog
Ensembl Genes ENSMUSG00000031709 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSMUSP00000034145 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000091093 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000034145 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000093393 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.30.29.30 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro EF-hand-dom_pair UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF_hand_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GRAM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PH-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Rab-GTPase-TBC_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Rab-GTPase_TBC_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TCB1D9/TCB1D9B_PH-GRAM1 UniProtKB/Swiss-Prot
  TCB1D9/TCB1D9B_PH-GRAM2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:71310 UniProtKB/Swiss-Prot
MGD MGI:1918560 ENTREZGENE
NCBI Gene 71310 ENTREZGENE
Pfam GRAM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RabGAP-TBC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tbc1d9 PhenoGen
PROSITE EF_HAND_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TBC_RABGAP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART GRAM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TBC UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF47923 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Mm.24031 ENTREZGENE
UniProt Q3UYK3 ENTREZGENE
  Q6PGG9_MOUSE UniProtKB/TrEMBL
  TBCD9_MOUSE UniProtKB/Swiss-Prot
UniProt Secondary Q69ZW8 UniProtKB/Swiss-Prot
  Q8BIJ5 UniProtKB/Swiss-Prot
  Q8BVP3 UniProtKB/Swiss-Prot
  Q9CUB3 UniProtKB/Swiss-Prot