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 nucleolus. 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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8227,745,985 - 27,800,624 (+)NCBIGRCr8
mRatBN7.2226,011,714 - 26,065,909 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl226,011,795 - 26,065,907 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx233,040,787 - 33,094,941 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0231,141,021 - 31,195,175 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0225,964,928 - 26,019,082 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0224,449,498 - 24,505,351 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl224,449,485 - 24,505,334 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0243,661,385 - 43,671,792 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera222,083,636 - 22,136,709 (+)NCBICelera
Cytogenetic Map2q12NCBI
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

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 (+)NCBIGRCr8
mRatBN7.2226,011,714 - 26,065,909 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl226,011,795 - 26,065,907 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx233,040,787 - 33,094,941 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0231,141,021 - 31,195,175 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0225,964,928 - 26,019,082 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0224,449,498 - 24,505,351 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl224,449,485 - 24,505,334 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0243,661,385 - 43,671,792 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
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 (-)EnsemblGRCh38hg38GRCh38
GRCh37576,986,991 - 77,072,163 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36577,022,751 - 77,107,941 (-)NCBINCBI36Build 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 Ensembl
GRCm381394,788,920 - 94,842,923 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1394,788,910 - 94,842,922 (+)EnsemblGRCm38mm10GRCm38
MGSCv371395,558,898 - 95,612,854 (+)NCBIGRCm37MGSCv37mm9NCBIm37
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 (+)EnsemblChiLan1.0
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 (+)Ensemblpanpan1.1panPan2
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 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha330,189,342 - 30,265,020 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0328,873,151 - 28,948,560 (+)NCBIROS_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_1.0
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 (-)EnsemblSpeTri2.0SpeTri2.0 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 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248692,153,427 - 2,228,166 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Tbca
142 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631682Bp115Blood pressure QTL 1154.30.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)2137410502Rat
738010Lnnr3Liver neoplastic nodule remodeling QTL 32.94liver integrity trait (VT:0010547)liver remodeling tumorous lesion number (CMO:0001461)2141244106Rat
61355Bp36Blood pressure QTL 362.9blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)25873687102844969Rat
1600379Mcs18Mammary carcinoma susceptibility QTL 182.6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)2788777242804738Rat
738012Anxrr3Anxiety related response QTL 33.8exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)2902351954023519Rat
10755430Coatc6Coat color QTL 60.02576coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)21159110056591100Rat
1578664Bmd9Bone mineral QTL density 95femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)21185206249003364Rat
731184Mamtr4Mammary tumor resistance QTL 40.0003mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)21649174061491740Rat
1357990Ael1Aortic elastin QTL 13.10.00091aorta elastin amount (VT:0003905)aortic elastin21907682564076825Rat
731167Glom4Glomerulus QTL 42.40.0082kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)22030467265304672Rat
2300168Bmd47Bone mineral density QTL 476.60.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)22066244865662448Rat
10402051Gdil2Gastrointestinal dilation QTL 2enteric ganglion morphology trait (VT:0001045)length of intestine affected by colonic aganglionosis to total length of colon ratio (CMO:0001836)22490385374786777Rat
1302794Stl27Serum triglyceride level QTL 274.40.0001blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)225413423143657569Rat
1358894Kidm24Kidney mass QTL 244.03kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358899Kidm23Kidney mass QTL 233.88kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358901Cm38Cardiac mass QTL 382heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358904Cm39Cardiac mass QTL 392.26heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423157142209Rat
1358910Kidm27Kidney mass QTL 275.77kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358911Kidm28Kidney mass QTL 285.42kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)225413423157142209Rat
1358913Cm41Cardiac mass QTL 412.73heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358917Cm42Cardiac mass QTL 422.82heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)225413423203928301Rat
1358887Bw50Body weight QTL 502.39body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat
1358908Bw49Body weight QTL 493.36body mass (VT:0001259)body weight (CMO:0000012)225413652157142078Rat


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 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


RefSeq Acc Id: ENSRNOT00000073688   ⟹   ENSRNOP00000067864
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl226,011,795 - 26,065,900 (+)Ensembl
Rnor_6.0 Ensembl224,449,485 - 24,505,334 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000099853   ⟹   ENSRNOP00000084980
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl226,011,809 - 26,065,783 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000101818   ⟹   ENSRNOP00000091156
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl226,039,457 - 26,065,907 (+)Ensembl
RefSeq 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:
RefSeq Acc Id: ENSRNOP00000067864   ⟸   ENSRNOT00000073688
RefSeq Acc Id: XP_038958744   ⟸   XM_039102816
- Peptide Label: isoform X3
RefSeq Acc Id: ENSRNOP00000091156   ⟸   ENSRNOT00000101818
RefSeq Acc Id: ENSRNOP00000083844   ⟸   ENSRNOT00000114175
RefSeq 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

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, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000073688 ENTREZGENE
  ENSRNOT00000073688.3 UniProtKB/Swiss-Prot
  ENSRNOT00000099853.1 UniProtKB/TrEMBL
  ENSRNOT00000101818.1 UniProtKB/TrEMBL
  ENSRNOT00000114175.1 UniProtKB/TrEMBL
Gene3D-CATH 1.20.58.90 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:6888541 IMAGE-MGC_LOAD
InterPro TBCA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TBCA_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:366995 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:72998 IMAGE-MGC_LOAD
NCBI Gene 366995 ENTREZGENE
PANTHER PTHR21500 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TUBULIN-SPECIFIC CHAPERONE A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam TBCA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Tbca PhenoGen
RatGTEx ENSRNOG00000048342 RatGTEx
Superfamily-SCOP SSF46988 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I5ZW23_RAT UniProtKB/TrEMBL
  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