Tbca (tubulin folding cofactor A) - Rat Genome Database

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Gene: Tbca (tubulin folding cofactor A) Rattus norvegicus
Analyze
Symbol: Tbca
Name: tubulin folding cofactor A
RGD ID: 1311538
Description: Predicted to enable tubulin binding activity. Predicted to be involved in protein folding and tubulin complex assembly. Predicted to be located in cytoplasm and microtubule. Predicted to be active in microtubule cytoskeleton. Orthologous to human TBCA (tubulin folding cofactor A); INTERACTS WITH bisphenol A; Brodifacoum; cadmium dichloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: CFA; LOC366995; TCP1-chaperonin cofactor A; tubulin cofactor a; tubulin-folding cofactor A; tubulin-specific chaperone A
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
GRCr8227,745,985 - 27,800,624 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl227,746,268 - 27,800,641 (+)EnsemblGRCr8
mRatBN7.2226,011,714 - 26,065,909 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl226,011,795 - 26,065,907 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx233,040,787 - 33,094,941 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0231,141,021 - 31,195,175 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0225,964,928 - 26,019,082 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0224,449,498 - 24,505,351 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl224,449,485 - 24,505,334 (+)Ensemblrn6Rnor6.0
Rnor_5.0243,661,385 - 43,671,792 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera222,083,636 - 22,136,709 (+)NCBICelera
Cytogenetic Map2q12NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

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 GOA human gene data--August 2006 GOA data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
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:22681889   PMID:23376485  


Genomics

Comparative Map Data
Tbca
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8227,745,985 - 27,800,624 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl227,746,268 - 27,800,641 (+)EnsemblGRCr8
mRatBN7.2226,011,714 - 26,065,909 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl226,011,795 - 26,065,907 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx233,040,787 - 33,094,941 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0231,141,021 - 31,195,175 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0225,964,928 - 26,019,082 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0224,449,498 - 24,505,351 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl224,449,485 - 24,505,334 (+)Ensemblrn6Rnor6.0
Rnor_5.0243,661,385 - 43,671,792 (+)NCBIRnor_5.0Rnor_5.0rn5
Celera222,083,636 - 22,136,709 (+)NCBICelera
Cytogenetic Map2q12NCBI
TBCA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38577,691,166 - 77,776,339 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl577,691,166 - 77,868,780 (-)Ensemblhg38GRCh38
GRCh37576,986,991 - 77,072,163 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36577,022,751 - 77,107,941 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34577,022,828 - 77,107,886NCBI
Celera572,881,651 - 72,966,197 (-)NCBICelera
Cytogenetic Map5q14.1NCBI
HuRef572,194,090 - 72,279,072 (-)NCBIHuRef
CHM1_1576,421,166 - 76,506,343 (-)NCBICHM1_1
T2T-CHM13v2.0578,173,750 - 78,258,323 (-)NCBIT2T-CHM13v2.0
Tbca
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391394,925,428 - 94,979,431 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1394,925,418 - 94,979,430 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381394,788,920 - 94,842,923 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1394,788,910 - 94,842,922 (+)Ensemblmm10GRCm38
MGSCv371395,558,898 - 95,612,854 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361395,889,642 - 95,943,598 (+)NCBIMGSCv36mm8
Celera1398,402,227 - 98,458,103 (+)NCBICelera
Cytogenetic Map13C3NCBI
cM Map1349.22NCBI
Tbca
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542523,300,480 - 23,313,497 (+)Ensembl
ChiLan1.0NW_00495542523,301,457 - 23,312,740 (+)NCBIChiLan1.0ChiLan1.0
TBCA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2437,527,521 - 37,611,910 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1535,681,134 - 35,765,561 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0537,530,924 - 37,615,330 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1538,060,299 - 38,144,457 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl538,060,398 - 38,144,457 (+)EnsemblpanPan2panpan1.1
TBCA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1328,972,469 - 29,027,436 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl328,910,025 - 29,025,297 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha330,189,342 - 30,265,020 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0328,873,151 - 28,948,560 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl328,873,170 - 28,954,090 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1328,807,711 - 28,882,941 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0328,785,816 - 28,861,651 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0329,116,567 - 29,192,256 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tbca
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213185,112,177 - 185,176,324 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365495,682,630 - 5,746,777 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365495,682,558 - 5,746,784 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TBCA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl286,579,835 - 86,665,163 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1286,581,603 - 86,664,994 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2288,189,131 - 88,273,262 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TBCA
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1471,921,187 - 72,004,619 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604920,759,981 - 20,843,497 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tbca
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248692,153,570 - 2,228,543 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248692,153,427 - 2,228,166 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Tbca
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v13201,523,704 - 201,577,436 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tbca
344 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:53
Count of miRNA genes:37
Interacting mature miRNAs:41
Transcripts:ENSRNOT00000021543, ENSRNOT00000073688
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21332504158325041Rat
7387318Stl32Serum triglyceride level QTL 323.20.0003blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)22411781369117813Rat
10755499Bp389Blood pressure QTL 3892.61arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)220695736231474293Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2142977529Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)227148328206613235Rat
9590080Insglur4Insulin/glucose ratio QTL 428.70.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)2615276751152767Rat
1579916Bp270Blood pressure QTL 2700.003arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)21605188361051883Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22203804467038044Rat
731166Mamtr2Mammary tumor resistance QTL 20.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2962358154623581Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)227148328206613235Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)227148328145807373Rat
1331764Bp205Blood pressure QTL 2053.476arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)21436870759368707Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)227148328159440891Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2962358144538110Rat
1331760Bp206Blood pressure QTL 2063.62454arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)24265106205135428Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)227148328159440891Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)227148557159440760Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)227148328159440891Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)27605533104774005Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)227148328159440891Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)227148328159440891Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)2573632550736325Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)227148557159440760Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)227148328159440891Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21822713763227137Rat


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 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000073688   ⟹   ENSRNOP00000067864
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl227,774,413 - 27,800,641 (+)Ensembl
mRatBN7.2 Ensembl226,011,795 - 26,065,900 (+)Ensembl
Rnor_6.0 Ensembl224,449,485 - 24,505,334 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000099853   ⟹   ENSRNOP00000084980
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl227,756,539 - 27,800,641 (+)Ensembl
mRatBN7.2 Ensembl226,011,809 - 26,065,783 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000101818   ⟹   ENSRNOP00000091156
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl227,746,268 - 27,800,641 (+)Ensembl
mRatBN7.2 Ensembl226,039,457 - 26,065,907 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000114175   ⟹   ENSRNOP00000083844
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl226,020,825 - 26,065,907 (+)Ensembl
RefSeq Acc Id: NM_001013245   ⟹   NP_001013263
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8227,746,533 - 27,800,624 (+)NCBI
mRatBN7.2226,011,795 - 26,065,890 (+)NCBI
Rnor_6.0224,449,537 - 24,505,351 (+)NCBI
Rnor_5.0243,661,385 - 43,671,792 (+)NCBI
Celera222,083,636 - 22,136,709 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039102816   ⟹   XP_038958744
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8227,745,985 - 27,795,035 (+)NCBI
mRatBN7.2226,011,714 - 26,060,207 (+)NCBI
RefSeq Acc Id: XM_063282310   ⟹   XP_063138380
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8227,756,524 - 27,800,624 (+)NCBI
RefSeq Acc Id: XM_063282311   ⟹   XP_063138381
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8227,745,985 - 27,798,546 (+)NCBI
RefSeq Acc Id: XM_063282312   ⟹   XP_063138382
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8227,745,985 - 27,795,035 (+)NCBI
RefSeq Acc Id: NP_001013263   ⟸   NM_001013245
- UniProtKB: Q6PEC1 (UniProtKB/Swiss-Prot),   A6I4X1 (UniProtKB/TrEMBL),   A0A8I6APW4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000067864   ⟸   ENSRNOT00000073688
RefSeq Acc Id: XP_038958744   ⟸   XM_039102816
- Peptide Label: isoform X3
Ensembl Acc Id: ENSRNOP00000091156   ⟸   ENSRNOT00000101818
Ensembl Acc Id: ENSRNOP00000083844   ⟸   ENSRNOT00000114175
Ensembl Acc Id: ENSRNOP00000084980   ⟸   ENSRNOT00000099853
RefSeq Acc Id: XP_063138381   ⟸   XM_063282311
- Peptide Label: isoform X2
RefSeq Acc Id: XP_063138382   ⟸   XM_063282312
- Peptide Label: isoform X4
RefSeq Acc Id: XP_063138380   ⟸   XM_063282310
- Peptide Label: isoform X1
- UniProtKB: A0A8I5ZW23 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6PEC1-F1-model_v2 AlphaFold Q6PEC1 1-108 view protein structure

Transcriptome

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

Promoters
RGD ID:13691073
Promoter ID:EPDNEW_R1598
Type:multiple initiation site
Name:Tbca_1
Description:tubulin folding cofactor A
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_6.0224,449,524 - 24,449,584EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1311538 AgrOrtholog
BioCyc Gene G2FUF-54827 BioCyc
Ensembl Genes ENSRNOG00000048342 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000073688.3 UniProtKB/Swiss-Prot
  ENSRNOT00000099853 ENTREZGENE
Gene3D-CATH 1.20.58.90 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:6888541 IMAGE-MGC_LOAD
InterPro TBCA UniProtKB/Swiss-Prot
  TBCA_sf UniProtKB/Swiss-Prot
KEGG Report rno:366995 UniProtKB/Swiss-Prot
MGC_CLONE MGC:72998 IMAGE-MGC_LOAD
NCBI Gene 366995 ENTREZGENE
PANTHER PTHR21500 UniProtKB/Swiss-Prot
  TUBULIN-SPECIFIC CHAPERONE A UniProtKB/Swiss-Prot
Pfam TBCA UniProtKB/Swiss-Prot
PhenoGen Tbca PhenoGen
RatGTEx ENSRNOG00000048342 RatGTEx
Superfamily-SCOP SSF46988 UniProtKB/Swiss-Prot
UniProt A0A8I5ZW23 ENTREZGENE
  A0A8I6APW4 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6GCC1_RAT UniProtKB/TrEMBL
  A6I4X1 ENTREZGENE, UniProtKB/TrEMBL
  Q6PEC1 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-23 Tbca  tubulin folding cofactor A  Tbca  tubulin cofactor a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Tbca  tubulin cofactor a  Tbca_predicted  tubulin cofactor a (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Tbca_predicted  tubulin cofactor a (predicted)      Symbol and Name status set to approved 70820 APPROVED