Calcoco1 (calcium binding and coiled coil domain 1) - Rat Genome Database

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Gene: Calcoco1 (calcium binding and coiled coil domain 1) Rattus norvegicus
Analyze
Symbol: Calcoco1
Name: calcium binding and coiled coil domain 1
RGD ID: 619812
Description: Predicted to enable several functions, including armadillo repeat domain binding activity; beta-catenin binding activity; and nuclear receptor coactivator activity. Predicted to be involved in intracellular steroid hormone receptor signaling pathway; positive regulation of gene expression; and positive regulation of transcription by RNA polymerase II. Predicted to be located in chromatin; cytosol; and nucleus. Orthologous to human CALCOCO1 (calcium binding and coiled-coil domain 1); PARTICIPATES IN estrogen signaling pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,3',4,4',5-pentachlorobiphenyl; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: calcium-binding and coiled-coil domain-containing protein 1; calcium-binding and coiled-coil domain-containing protein 1-like; KIAA1536; LOC100912282; MGC93160
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
mRatBN7.27133,834,705 - 133,849,515 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7133,834,707 - 133,849,422 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7135,590,837 - 135,605,542 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.07137,820,202 - 137,834,906 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.07137,806,151 - 137,820,878 (-)NCBIRnor_WKY
Rnor_6.07144,307,562 - 144,322,253 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7144,307,509 - 144,322,240 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl7145,435,584 - 145,450,301 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07142,099,780 - 142,114,471 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47141,456,249 - 141,470,966 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera7130,261,950 - 130,276,675 (-)NCBICelera
Cytogenetic Map7q36NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
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. Coregulators in nuclear estrogen receptor action: from concept to therapeutic targeting. Hall JM and McDonnell DP, Mol Interv. 2005 Dec;5(6):343-57.
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
7. 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.
8. Cellular signaling mediated by calphoglin-induced activation of IPP and PGM. Takahashi K, etal., Biochem Biophys Res Commun 2004 Dec 3;325(1):203-14.
Additional References at PubMed
PMID:14690606   PMID:15383530   PMID:16344550   PMID:24245781   PMID:29476059  


Genomics

Comparative Map Data
Calcoco1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.27133,834,705 - 133,849,515 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7133,834,707 - 133,849,422 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx7135,590,837 - 135,605,542 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.07137,820,202 - 137,834,906 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.07137,806,151 - 137,820,878 (-)NCBIRnor_WKY
Rnor_6.07144,307,562 - 144,322,253 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7144,307,509 - 144,322,240 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl7145,435,584 - 145,450,301 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.07142,099,780 - 142,114,471 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.47141,456,249 - 141,470,966 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera7130,261,950 - 130,276,675 (-)NCBICelera
Cytogenetic Map7q36NCBI
CALCOCO1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381253,708,517 - 53,727,452 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1253,708,517 - 53,727,745 (-)EnsemblGRCh38hg38GRCh38
GRCh371254,102,301 - 54,121,236 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361252,391,169 - 52,407,486 (-)NCBINCBI36Build 36hg18NCBI36
Build 341252,391,169 - 52,407,486NCBI
Celera1253,754,817 - 53,771,222 (-)NCBICelera
Cytogenetic Map12q13.13NCBI
HuRef1251,142,897 - 51,159,310 (-)NCBIHuRef
CHM1_11254,071,838 - 54,088,243 (-)NCBICHM1_1
T2T-CHM13v2.01253,674,269 - 53,693,205 (-)NCBIT2T-CHM13v2.0
Calcoco1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3915102,615,212 - 102,630,616 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl15102,615,212 - 102,630,613 (-)EnsemblGRCm39 Ensembl
GRCm3815102,706,777 - 102,722,178 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl15102,706,777 - 102,722,178 (-)EnsemblGRCm38mm10GRCm38
MGSCv3715102,537,208 - 102,552,609 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3615102,534,813 - 102,550,103 (-)NCBIMGSCv36mm8
Celera15104,864,506 - 104,879,996 (-)NCBICelera
Cytogenetic Map15F3NCBI
Calcoco1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955458994,453 - 1,009,543 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955458994,511 - 1,009,430 (-)NCBIChiLan1.0ChiLan1.0
CALCOCO1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11235,814,629 - 35,831,191 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1235,814,629 - 35,831,191 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01235,027,491 - 35,044,039 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
CALCOCO1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1271,525,569 - 1,542,256 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl271,525,687 - 1,542,269 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2744,707,917 - 44,724,581 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0271,529,078 - 1,545,764 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl271,529,155 - 1,545,777 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1271,546,299 - 1,562,957 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0271,528,377 - 1,545,051 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02745,111,244 - 45,127,916 (-)NCBIUU_Cfam_GSD_1.0
Calcoco1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494562,200,417 - 62,217,004 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493651210,947,681 - 10,964,431 (-)EnsemblSpeTri2.0
SpeTri2.0NW_00493651210,947,826 - 10,964,372 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CALCOCO1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl518,910,700 - 18,930,321 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1518,910,698 - 18,930,402 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2519,356,276 - 19,375,989 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CALCOCO1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11149,816,546 - 49,833,655 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1149,814,007 - 49,833,632 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666037196,211,874 - 196,229,228 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Calcoco1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249041,790,587 - 1,809,277 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249041,792,861 - 1,809,265 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Calcoco1
43 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:527
Count of miRNA genes:237
Interacting mature miRNAs:280
Transcripts:ENSRNOT00000021523
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)783591953134666232Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)790482196135012528Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)791281130135012528Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)796670164135012528Rat
731174Uae23Urinary albumin excretion QTL 232.40.0042urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)7104603555135012528Rat
2306821Bp335Blood pressure QTL 3350.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7106571501135012528Rat
631663Bw6Body weight QTL 63.4body mass (VT:0001259)body weight (CMO:0000012)7111075573134976056Rat
1300112Bp183Blood pressure QTL 1833.51arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)7111182207135012528Rat
1354582Stl11Serum triglyceride level QTL 113.42blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)7119513385135012528Rat

Markers in Region
BF387379  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27133,835,696 - 133,835,863 (+)MAPPERmRatBN7.2
Rnor_6.07144,308,554 - 144,308,720NCBIRnor6.0
Rnor_6.07145,436,576 - 145,436,742NCBIRnor6.0
Rnor_5.07143,219,493 - 143,219,659UniSTSRnor5.0
Rnor_5.07142,100,772 - 142,100,938UniSTSRnor5.0
RGSC_v3.47141,457,241 - 141,457,407UniSTSRGSC3.4
Celera7130,262,942 - 130,263,108UniSTS
RH 3.4 Map71053.5UniSTS
Cytogenetic Map7q36UniSTS
AI010402  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.27133,834,759 - 133,835,016 (+)MAPPERmRatBN7.2
Rnor_6.07144,307,617 - 144,307,873NCBIRnor6.0
Rnor_6.07145,435,639 - 145,435,895NCBIRnor6.0
Rnor_5.07143,218,556 - 143,218,812UniSTSRnor5.0
Rnor_5.07142,099,835 - 142,100,091UniSTSRnor5.0
RGSC_v3.47141,456,304 - 141,456,560UniSTSRGSC3.4
Celera7130,262,005 - 130,262,261UniSTS
RH 3.4 Map71062.9UniSTS
Cytogenetic Map7q36UniSTS


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
Low 1
Below cutoff 2 5 14 3 15 3 2 5 23 11 16 10 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000021523   ⟹   ENSRNOP00000021522
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7133,834,707 - 133,849,422 (-)Ensembl
Rnor_6.0 Ensembl7145,435,584 - 145,450,301 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000070855   ⟹   ENSRNOP00000064554
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7133,834,707 - 133,849,422 (-)Ensembl
Rnor_6.0 Ensembl7144,308,345 - 144,319,804 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000089290   ⟹   ENSRNOP00000071559
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl7133,834,716 - 133,849,390 (-)Ensembl
Rnor_6.0 Ensembl7144,307,509 - 144,322,240 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000092974   ⟹   ENSRNOP00000075971
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl7145,447,362 - 145,450,233 (-)Ensembl
RefSeq Acc Id: NM_139190   ⟹   NP_631929
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27133,834,705 - 133,849,422 (-)NCBI
Rnor_6.07144,307,562 - 144,322,253 (-)NCBI
Rnor_5.07142,099,780 - 142,114,471 (-)NCBI
RGSC_v3.47141,456,249 - 141,470,966 (-)RGD
Celera7130,261,950 - 130,276,675 (-)RGD
Sequence:
RefSeq Acc Id: XM_039078406   ⟹   XP_038934334
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27133,834,705 - 133,849,515 (-)NCBI
RefSeq Acc Id: XM_039078407   ⟹   XP_038934335
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.27133,834,705 - 133,849,349 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_631929   ⟸   NM_139190
- UniProtKB: Q8R443 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000064554   ⟸   ENSRNOT00000070855
RefSeq Acc Id: ENSRNOP00000071559   ⟸   ENSRNOT00000089290
RefSeq Acc Id: XP_038934334   ⟸   XM_039078406
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K0S1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038934335   ⟸   XM_039078407
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K0S1 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSRNOP00000075971   ⟸   ENSRNOT00000092974
RefSeq Acc Id: ENSRNOP00000021522   ⟸   ENSRNOT00000021523
Protein Domains
UBZ1-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q66HR5-F1-model_v2 AlphaFold Q66HR5 1-691 view protein structure

Transcriptome

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

Promoters
RGD ID:13695709
Promoter ID:EPDNEW_R6232
Type:initiation region
Name:Calcoco1_1
Description:calcium binding and coiled coil domain 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_6.07144,322,242 - 144,322,302EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619812 AgrOrtholog
BioCyc Gene G2FUF-31926 BioCyc
Ensembl Genes ENSRNOG00000015447 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSRNOG00000048982 Ensembl
Ensembl Protein ENSRNOP00000021522 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000064554.2 UniProtKB/TrEMBL
  ENSRNOP00000071559 ENTREZGENE
  ENSRNOP00000071559.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021523 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000070855.2 UniProtKB/TrEMBL
  ENSRNOT00000089290 ENTREZGENE
  ENSRNOT00000089290.2 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7124320 IMAGE-MGC_LOAD
InterPro CALCOCO1-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  CALCOCO1/2_Zn-C2H2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SKICH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:246047 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93160 IMAGE-MGC_LOAD
NCBI Gene 246047 ENTREZGENE
Pfam CALCOCO1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SKICH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Zn-C2H2_12 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Calcoco1 PhenoGen
PROSITE ZF_UBZ1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K0S1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8L2QVZ6_RAT UniProtKB/TrEMBL
  CACO1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q8R443 ENTREZGENE
UniProt Secondary Q8R443 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Calcoco1  calcium binding and coiled coil domain 1  LOC100912282  calcium-binding and coiled-coil domain-containing protein 1-like  Data Merged 737654 PROVISIONAL
2012-07-05 LOC100912282  calcium-binding and coiled-coil domain-containing protein 1-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-03-30 Calcoco1  calcium binding and coiled coil domain 1  KIAA1536  KIAA1536 protein  Symbol and Name updated 1299863 APPROVED
2002-08-07 KIAA1536  KIAA1536 protein      Symbol and Name status set to provisional 70820 PROVISIONAL