Cct4 (chaperonin containing TCP1 subunit 4) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Cct4 (chaperonin containing TCP1 subunit 4) Rattus norvegicus
Analyze
Symbol: Cct4
Name: chaperonin containing TCP1 subunit 4
RGD ID: 727937
Description: Predicted to enable protein folding chaperone and unfolded protein binding activity. Predicted to be involved in several processes, including positive regulation of DNA biosynthetic process; positive regulation of protein localization; and positive regulation of telomerase RNA localization to Cajal body. Predicted to act upstream of or within binding activity of sperm to zona pellucida and toxin transport. Predicted to be located in several cellular components, including cell body; microtubule cytoskeleton; and nucleoplasm. Predicted to be part of chaperonin-containing T-complex and zona pellucida receptor complex. Used to study hereditary sensory neuropathy. Orthologous to human CCT4 (chaperonin containing TCP1 subunit 4); INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: CCT-delta; chaperonin containing Tcp1, subunit 4 (delta); chaperonin subunit 4 (delta); T-complex protein 1 subunit delta; TCP-1-delta
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
mRatBN7.21496,991,853 - 97,004,732 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1496,991,859 - 97,005,267 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx14101,325,100 - 101,337,974 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.014102,567,399 - 102,580,273 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01499,039,002 - 99,051,876 (+)NCBIRnor_WKY
Rnor_6.014107,767,392 - 107,780,270 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14107,767,392 - 107,780,270 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.014107,843,411 - 107,856,260 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414103,675,110 - 103,687,893 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.114103,694,320 - 103,707,104 (+)NCBI
Celera1495,973,133 - 95,985,983 (+)NCBICelera
Cytogenetic Map14q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Normalization and subtraction: two approaches to facilitate gene discovery. Bonaldo MF, etal., Genome Res 1996 Sep;6(9):791-806.
2. 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.
3. Hereditary sensory neuropathy is caused by a mutation in the delta subunit of the cytosolic chaperonin-containing t-complex peptide-1 (Cct4 ) gene. Lee MJ, etal., Hum Mol Genet 2003 Aug 1;12(15):1917-25.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. NCBI rat LocusLink and RefSeq merged data October 15, 2003 NCBI rat LocusLink and RefSeq merged data October 15, 2003
6. GOA pipeline RGD automated data pipeline
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. 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:7828721   PMID:7953530   PMID:15193290   PMID:15489334   PMID:16854843   PMID:20080638   PMID:20193073   PMID:20458337   PMID:21525035   PMID:21880732   PMID:22658674   PMID:23011926  
PMID:23376485   PMID:23533145   PMID:23716698   PMID:24625528   PMID:25124038   PMID:25467444   PMID:26316108   PMID:29476059   PMID:32357304   PMID:33450132  


Genomics

Comparative Map Data
Cct4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21496,991,853 - 97,004,732 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1496,991,859 - 97,005,267 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx14101,325,100 - 101,337,974 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.014102,567,399 - 102,580,273 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01499,039,002 - 99,051,876 (+)NCBIRnor_WKY
Rnor_6.014107,767,392 - 107,780,270 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl14107,767,392 - 107,780,270 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.014107,843,411 - 107,856,260 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414103,675,110 - 103,687,893 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.114103,694,320 - 103,707,104 (+)NCBI
Celera1495,973,133 - 95,985,983 (+)NCBICelera
Cytogenetic Map14q22NCBI
CCT4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38261,868,085 - 61,888,671 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl261,868,085 - 61,888,671 (-)EnsemblGRCh38hg38GRCh38
GRCh37262,095,220 - 62,115,806 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36261,948,766 - 61,969,295 (-)NCBINCBI36Build 36hg18NCBI36
Build 34262,006,913 - 62,027,442NCBI
Celera261,940,173 - 61,960,736 (-)NCBICelera
Cytogenetic Map2p15NCBI
HuRef261,835,217 - 61,855,722 (-)NCBIHuRef
CHM1_1262,025,224 - 62,045,751 (-)NCBICHM1_1
T2T-CHM13v2.0261,874,246 - 61,894,829 (-)NCBIT2T-CHM13v2.0
Cct4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391122,940,593 - 22,953,336 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1122,940,519 - 22,953,780 (+)EnsemblGRCm39 Ensembl
GRCm381122,990,593 - 23,003,336 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1122,990,519 - 23,003,780 (+)EnsemblGRCm38mm10GRCm38
MGSCv371122,890,593 - 22,903,336 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361122,890,593 - 22,903,336 (+)NCBIMGSCv36mm8
Celera1125,126,226 - 25,138,969 (+)NCBICelera
Cytogenetic Map11A3.2NCBI
cM Map1114.25NCBI
Cct4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542422,088,949 - 22,108,514 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542422,088,949 - 22,108,514 (+)NCBIChiLan1.0ChiLan1.0
CCT4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A63,084,090 - 63,104,530 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A63,084,090 - 63,105,216 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A61,950,477 - 61,970,783 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
CCT4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11061,859,148 - 61,874,030 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1061,859,245 - 61,874,389 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1061,748,927 - 61,763,778 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01062,867,889 - 62,882,584 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1062,867,244 - 62,882,587 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11062,551,782 - 62,566,434 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01062,855,534 - 62,870,428 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01063,151,020 - 63,165,931 (-)NCBIUU_Cfam_GSD_1.0
Cct4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629221,330,016 - 21,346,300 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364917,224,692 - 7,241,358 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049364917,224,989 - 7,241,348 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CCT4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl379,924,507 - 79,946,207 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1379,924,338 - 79,941,926 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2383,760,065 - 83,777,463 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CCT4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11445,086,932 - 45,106,922 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1445,086,920 - 45,111,271 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604566,727,959 - 66,748,110 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cct4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462483346,076 - 62,665 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462483346,071 - 62,665 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cct4
54 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:28
Count of miRNA genes:25
Interacting mature miRNAs:26
Transcripts:ENSRNOT00000012847
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
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat
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
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

Markers in Region
BE118339  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21497,001,371 - 97,001,556 (+)MAPPERmRatBN7.2
Rnor_6.014107,776,910 - 107,777,094NCBIRnor6.0
Rnor_5.014107,852,903 - 107,853,087UniSTSRnor5.0
RGSC_v3.414103,684,664 - 103,684,848UniSTSRGSC3.4
Celera1495,982,642 - 95,982,826UniSTS
RH 3.4 Map14766.5UniSTS
Cytogenetic Map14q22UniSTS


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


Reference Sequences
RefSeq Acc Id: ENSRNOT00000012847   ⟹   ENSRNOP00000012847
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1496,991,859 - 97,005,267 (+)Ensembl
Rnor_6.0 Ensembl14107,767,392 - 107,780,270 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000109669   ⟹   ENSRNOP00000078161
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1496,991,859 - 97,005,267 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000116685   ⟹   ENSRNOP00000086401
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1496,993,448 - 97,005,267 (+)Ensembl
RefSeq Acc Id: NM_182814   ⟹   NP_877966
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21496,991,853 - 97,004,732 (+)NCBI
Rnor_6.014107,767,392 - 107,780,270 (+)NCBI
Rnor_5.014107,843,411 - 107,856,260 (+)NCBI
RGSC_v3.414103,675,110 - 103,687,893 (+)RGD
Celera1495,973,133 - 95,985,983 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_877966 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH79283 (Get FASTA)   NCBI Sequence Viewer  
  AAP46161 (Get FASTA)   NCBI Sequence Viewer  
  EDL97980 (Get FASTA)   NCBI Sequence Viewer  
  Q7TPB1 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_877966   ⟸   NM_182814
- UniProtKB: Q7TPB1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000012847   ⟸   ENSRNOT00000012847
RefSeq Acc Id: ENSRNOP00000078161   ⟸   ENSRNOT00000109669
RefSeq Acc Id: ENSRNOP00000086401   ⟸   ENSRNOT00000116685

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q7TPB1-F1-model_v2 AlphaFold Q7TPB1 1-539 view protein structure

Transcriptome

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

Promoters
RGD ID:13699519
Promoter ID:EPDNEW_R10043
Type:initiation region
Name:Cct4_1
Description:chaperonin containing TCP1 subunit 4
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_6.014107,767,398 - 107,767,458EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:727937 AgrOrtholog
BioCyc Gene G2FUF-14788 BioCyc
Ensembl Genes ENSRNOG00000009642 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000012847 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000078161.1 UniProtKB/TrEMBL
  ENSRNOP00000086401.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000012847 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000109669.1 UniProtKB/TrEMBL
  ENSRNOT00000116685.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.560.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.260.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.50.7.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7134210 IMAGE-MGC_LOAD
InterPro Chap_CCT_delta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chaperone_TCP-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Chaperonin_TCP-1_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Cpn60/GroEL/TCP-1 UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
  GroEL-like_apical_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  GROEL-like_equatorial_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TCP-1-like_intermed_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:29374 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94410 IMAGE-MGC_LOAD
NCBI Gene 29374 ENTREZGENE
PANTHER PTHR11353 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Cpn60_TCP1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Cct4 PhenoGen
PRINTS TCOMPLEXTCP1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE TCP1_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TCP1_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TCP1_3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48592 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF52029 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54849 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs chap_CCT_delta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I5YC75_RAT UniProtKB/TrEMBL
  A0A8I6A646_RAT UniProtKB/TrEMBL
  Q7TPB1 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-13 Cct4  chaperonin containing TCP1 subunit 4  Cct4  chaperonin containing Tcp1, subunit 4 (delta)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-29 Cct4  chaperonin containing Tcp1, subunit 4 (delta)  Cct4  chaperonin subunit 4 (delta)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-12-14 Cct4  chaperonin subunit 4 (delta)      Symbol and Name status set to approved 1299863 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_mutations_overexpression 1349G>A mutation causes hereditary sensory neuropathy 1299607