Tbccd1 (TBCC domain containing 1) - Rat Genome Database

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Gene: Tbccd1 (TBCC domain containing 1) Rattus norvegicus
Analyze
Symbol: Tbccd1
Name: TBCC domain containing 1
RGD ID: 1309604
Description: Predicted to be involved in several processes, including maintenance of Golgi location; maintenance of centrosome location; and regulation of cell shape. Predicted to be located in centrosome; cytoplasm; and spindle pole. Predicted to be active in spindle pole centrosome. Orthologous to human TBCCD1 (TBCC domain containing 1); INTERACTS WITH 1,3-dinitrobenzene; acrylamide; bis(2-ethylhexyl) phthalate.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Crygs; crystallin, gamma S; LOC303830; MGC108782; TBCC domain-containing protein 1
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
GRCr81191,672,948 - 91,710,120 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1191,672,964 - 91,709,883 (+)EnsemblGRCr8
mRatBN7.21178,168,386 - 78,205,314 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1178,168,388 - 78,205,523 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1186,928,806 - 86,955,237 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01179,580,571 - 79,608,878 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01178,643,117 - 78,669,548 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01181,757,963 - 81,794,367 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1181,757,983 - 81,794,580 (+)Ensemblrn6Rnor6.0
Rnor_5.01184,845,805 - 84,882,196 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41180,387,000 - 80,415,192 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1177,049,125 - 77,073,928 (+)NCBICelera
RGSC_v3.11180,444,588 - 80,472,780 (+)NCBI
Cytogenetic Map11q23NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
centrosome  (IEA)
spindle pole  (IEA)
spindle pole centrosome  (IBA,IEA,ISO,ISS)

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:20168327  


Genomics

Comparative Map Data
Tbccd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81191,672,948 - 91,710,120 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1191,672,964 - 91,709,883 (+)EnsemblGRCr8
mRatBN7.21178,168,386 - 78,205,314 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1178,168,388 - 78,205,523 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1186,928,806 - 86,955,237 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01179,580,571 - 79,608,878 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01178,643,117 - 78,669,548 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01181,757,963 - 81,794,367 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1181,757,983 - 81,794,580 (+)Ensemblrn6Rnor6.0
Rnor_5.01184,845,805 - 84,882,196 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41180,387,000 - 80,415,192 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1177,049,125 - 77,073,928 (+)NCBICelera
RGSC_v3.11180,444,588 - 80,472,780 (+)NCBI
Cytogenetic Map11q23NCBI
TBCCD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383186,546,067 - 186,570,543 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3186,546,067 - 186,570,543 (-)Ensemblhg38GRCh38
GRCh373186,263,856 - 186,288,332 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 363187,746,824 - 187,767,806 (-)NCBIBuild 36Build 36hg18NCBI36
Celera3184,700,233 - 184,724,709 (-)NCBICelera
Cytogenetic Map3q27.3NCBI
HuRef3183,672,874 - 183,697,386 (-)NCBIHuRef
CHM1_13186,227,794 - 186,252,270 (-)NCBICHM1_1
T2T-CHM13v2.03189,361,789 - 189,386,265 (-)NCBIT2T-CHM13v2.0
Tbccd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391622,631,964 - 22,676,441 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1622,631,964 - 22,676,419 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381622,813,214 - 22,857,695 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1622,813,214 - 22,857,669 (-)Ensemblmm10GRCm38
MGSCv371622,813,288 - 22,857,642 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361622,728,548 - 22,759,977 (-)NCBIMGSCv36mm8
Celera1623,373,540 - 23,417,893 (-)NCBICelera
Cytogenetic Map16B1NCBI
cM Map1613.67NCBI
Tbccd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542021,115,228 - 21,135,704 (+)Ensembl
ChiLan1.0NW_00495542021,113,527 - 21,135,704 (+)NCBIChiLan1.0ChiLan1.0
TBCCD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22184,418,623 - 184,439,867 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan13184,422,931 - 184,447,855 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v03183,577,248 - 183,601,761 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.13192,045,208 - 192,069,701 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl3192,045,214 - 192,069,701 (-)EnsemblpanPan2panpan1.1
TBCCD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13419,165,290 - 19,185,020 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3419,166,025 - 19,184,786 (-)EnsemblcanFam3CanFam3.1
Tbccd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405602117,283,015 - 117,311,535 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365783,377,256 - 3,403,598 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365783,374,826 - 3,404,462 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TBCCD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13124,365,854 - 124,390,134 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.113124,357,614 - 124,388,387 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213133,749,155 - 133,779,383 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TBCCD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1152,858,291 - 2,882,014 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl152,858,511 - 2,882,336 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606311,606,629 - 11,630,307 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tbccd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473070,187,956 - 70,215,123 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462473070,187,482 - 70,215,876 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Tbccd1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v147,497,496 - 7,533,176 (-)NCBIRrattus_CSIRO_v1

miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:80
Count of miRNA genes:62
Interacting mature miRNAs:66
Transcripts:ENSRNOT00000038826
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70208Niddm22Non-insulin dependent diabetes mellitus QTL 223.61blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)117330848796070872Rat
1581565Pur10Proteinuria QTL 100.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)115827236396350770Rat
4889859Pur28Proteinuria QTL 2819.50.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)115892833699753367Rat
1549848Bvd6Brain ventricular dilatation QTL 63.10.0001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)117961851999753367Rat
10450831Scl80Serum cholesterol level QTL 804.70.01blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)119046178196556255Rat
10058954Gmadr7Adrenal mass QTL 72.490.0049adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)117385089499753367Rat
2298551Neuinf10Neuroinflammation QTL 103.7nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)115893182292356038Rat
1300135Rf19Renal function QTL 193.38blood creatinine amount (VT:0005328)creatinine clearance (CMO:0000765)115441539196071021Rat
1354656Bvd3Brain ventricular dilatation QTL 33.640.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)118295102896351019Rat
2312566Glom20Glomerulus QTL 203.60.001kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)115775483796071021Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112019354996351019Rat
724561Plsm4Polydactyly-luxate syndrome (PLS) morphotypes QTL 40.0003forelimb integrity trait (VT:0010562)front foot phalanges count (CMO:0001947)116796218499753367Rat
631506Bp104Blood pressure QTL 1042.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)117330831599753367Rat
4889521Gluco62Glucose level QTL 622.820.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)116859932196497754Rat
7411658Foco27Food consumption QTL 2716.20.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)116985594399753367Rat
1581572Uae35Urinary albumin excretion QTL 350.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)115827236396350770Rat
1300110Stl7Serum triglyceride level QTL 74.64blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)115107102196071021Rat

Markers in Region
BB165076  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21178,200,478 - 78,200,552 (+)MAPPERmRatBN7.2
Rnor_6.01181,790,068 - 81,790,141NCBIRnor6.0
Rnor_5.01184,877,897 - 84,877,970UniSTSRnor5.0
RGSC_v3.41180,409,132 - 80,409,205UniSTSRGSC3.4
Celera1177,071,118 - 77,071,191UniSTS
Cytogenetic Map11q23UniSTS


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 67 164 91 90 59 92 59 6 356 192 11 143 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000038826   ⟹   ENSRNOP00000036828
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1191,672,964 - 91,709,883 (+)Ensembl
mRatBN7.2 Ensembl1178,168,562 - 78,205,337 (+)Ensembl
Rnor_6.0 Ensembl1181,769,178 - 81,794,366 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000088503   ⟹   ENSRNOP00000072854
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1191,682,790 - 91,700,949 (+)Ensembl
mRatBN7.2 Ensembl1178,168,388 - 78,196,364 (+)Ensembl
Rnor_6.0 Ensembl1181,757,983 - 81,794,580 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000111940   ⟹   ENSRNOP00000088290
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1191,682,796 - 91,709,362 (+)Ensembl
mRatBN7.2 Ensembl1178,168,539 - 78,205,523 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000114309   ⟹   ENSRNOP00000081546
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1178,168,388 - 78,205,325 (+)Ensembl
RefSeq Acc Id: NM_001012016   ⟹   NP_001012016
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81191,682,932 - 91,709,363 (+)NCBI
mRatBN7.21178,178,346 - 78,204,778 (+)NCBI
Rnor_6.01181,767,936 - 81,794,367 (+)NCBI
Rnor_5.01184,845,805 - 84,882,196 (+)NCBI
RGSC_v3.41180,387,000 - 80,415,192 (+)RGD
Celera1177,049,125 - 77,073,928 (+)RGD
Sequence:
RefSeq Acc Id: XM_006248545   ⟹   XP_006248607
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81191,672,948 - 91,710,120 (+)NCBI
mRatBN7.21178,168,386 - 78,205,314 (+)NCBI
Rnor_6.01181,757,963 - 81,794,311 (+)NCBI
Rnor_5.01184,845,805 - 84,882,196 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039088289   ⟹   XP_038944217
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81191,684,345 - 91,710,120 (+)NCBI
mRatBN7.21178,179,769 - 78,205,314 (+)NCBI
RefSeq Acc Id: XM_039088290   ⟹   XP_038944218
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81191,672,970 - 91,710,120 (+)NCBI
mRatBN7.21178,168,386 - 78,205,314 (+)NCBI
RefSeq Acc Id: NP_001012016   ⟸   NM_001012016
- UniProtKB: Q5FVR8 (UniProtKB/Swiss-Prot),   A0A8I5ZT70 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006248607   ⟸   XM_006248545
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZT70 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000036828   ⟸   ENSRNOT00000038826
Ensembl Acc Id: ENSRNOP00000072854   ⟸   ENSRNOT00000088503
RefSeq Acc Id: XP_038944218   ⟸   XM_039088290
- Peptide Label: isoform X3
- UniProtKB: Q6AXX8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038944217   ⟸   XM_039088289
- Peptide Label: isoform X2
- UniProtKB: Q5FVR8 (UniProtKB/Swiss-Prot),   A0A8I5ZT70 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000088290   ⟸   ENSRNOT00000111940
Ensembl Acc Id: ENSRNOP00000081546   ⟸   ENSRNOT00000114309
Protein Domains
C-CAP/cofactor C-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5FVR8-F1-model_v2 AlphaFold Q5FVR8 1-569 view protein structure

Transcriptome

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

Promoters
RGD ID:13698252
Promoter ID:EPDNEW_R8777
Type:initiation region
Name:Tbccd1_1
Description:TBCC domain containing 1
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_6.01181,758,126 - 81,758,186EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309604 AgrOrtholog
BioCyc Gene G2FUF-20827 BioCyc
Ensembl Genes ENSRNOG00000026458 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000038826 ENTREZGENE
  ENSRNOT00000111940 ENTREZGENE
  ENSRNOT00000111940.1 UniProtKB/Swiss-Prot
Gene3D-CATH 2.160.20.70 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7133137 IMAGE-MGC_LOAD
  IMAGE:7134009 IMAGE-MGC_LOAD
InterPro C-CAP_CF_C-like UniProtKB/Swiss-Prot
  CAP/MinC_C UniProtKB/Swiss-Prot
  CARP_motif UniProtKB/Swiss-Prot
  TBCC1 UniProtKB/Swiss-Prot
  Tubulin-bd_cofactor_C_dom UniProtKB/Swiss-Prot
KEGG Report rno:303830 UniProtKB/Swiss-Prot
MGC_CLONE MGC:108782 IMAGE-MGC_LOAD
  MGC:94392 IMAGE-MGC_LOAD
NCBI Gene 303830 ENTREZGENE
PANTHER PTHR16052 UniProtKB/Swiss-Prot
  TBCC DOMAIN-CONTAINING PROTEIN 1 UniProtKB/Swiss-Prot
Pfam TBCC UniProtKB/Swiss-Prot
PhenoGen Tbccd1 PhenoGen
PROSITE C_CAP_COFACTOR_C UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000026458 RatGTEx
SMART CARP UniProtKB/Swiss-Prot
UniProt A0A8I5ZT70 ENTREZGENE
  A0A8L2QIV7_RAT UniProtKB/TrEMBL
  A0A8L2R6D3_RAT UniProtKB/TrEMBL
  Q5FVR8 ENTREZGENE
  Q6AXX8 ENTREZGENE, UniProtKB/TrEMBL
  TBCC1_RAT UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2007-10-02 Tbccd1  TBCC domain containing 1  Crygs  crystallin, gamma S  Symbol and Name updated to reflect Human and Mouse nomenclature 1299863 APPROVED
2005-12-06 Crygs  crystallin, gamma S  Crygs_predicted  crystallin, gamma S (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Crygs_predicted  crystallin, gamma S (predicted)      Symbol and Name status set to approved 70820 APPROVED