Human Gene CALCOCO1 (uc001sef.3) Description and Page Index
  Description: Homo sapiens calcium binding and coiled-coil domain 1 (CALCOCO1), transcript variant 1, mRNA.
Transcript (Including UTRs)
   Position: hg19 chr12:54,104,902-54,121,307 Size: 16,406 Total Exon Count: 15 Strand: -
Coding Region
   Position: hg19 chr12:54,105,728-54,119,026 Size: 13,299 Coding Exon Count: 14 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:54,104,902-54,121,307)mRNA (may differ from genome)Protein (691 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtPubMedStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: CACO1_HUMAN
DESCRIPTION: RecName: Full=Calcium-binding and coiled-coil domain-containing protein 1; AltName: Full=Calphoglin; AltName: Full=Coiled-coil coactivator protein; AltName: Full=Sarcoma antigen NY-SAR-3;
FUNCTION: Functions as a coactivator for aryl hydrocarbon and nuclear receptors (NR). Recruited to promoters through its contact with the N-terminal basic helix-loop-helix-Per-Arnt-Sim (PAS) domain of transcription factors or coactivators, such as NCOA2. During ER-activation acts synergistically in combination with other NCOA2-binding proteins, such as EP300, CREBBP and CARM1. Involved in the transcriptional activation of target genes in the Wnt/CTNNB1 pathway. Functions as a secondary coactivator in LEF1- mediated transcriptional activation via its interaction with CTNNB1. Coactivator function for nuclear receptors and LEF1/CTNNB1 involves differential utilization of two different activation regions (By similarity).
FUNCTION: Seems to enhance inorganic pyrphosphatase thus activating phosphogluomutase (PMG). Probably functions as component of the calphoglin complex, which is involved in linking cellular metabolism (phosphate and glucose metabolism) with other core functions including protein synthesis and degradation, calcium signaling and cell growth.
SUBUNIT: Part of a calphoglin complex consisting of CALCOCO1, PPA1 and PGM. Interacts with the bHLH-PAS domains of GRIP1, AHR and ARNT. Interacts with CTNNB1 via both its N- and C-terminal regions. Interacts with EP300 (By similarity).
SUBCELLULAR LOCATION: Cytoplasm. Nucleus. Note=Shuttles between nucleus and cytoplasm (By similarity).
DOMAIN: The C-terminal activation region (AD) is used for downstream signaling. Seems to be essential for coactivator function with nuclear receptors and with the aryl hydrocarbon receptor (By similarity).
DOMAIN: The N-terminal activation region (AD) is necessary and sufficient for synergistic activation of LEF1-mediated transcription by CTNNB1. Contains a EP3000 binding region which is important for synergistic cooperation (By similarity).
DOMAIN: Recruitment by nuclear receptors is accomplished by the interaction of the coiled-coiled domain with p160 coactivators (By similarity).
SIMILARITY: Belongs to the CALCOCO family.
SEQUENCE CAUTION: Sequence=BAA96060.1; Type=Erroneous initiation;

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): CALCOCO1
CDC HuGE Published Literature: CALCOCO1
Positive Disease Associations: Audiometry, Pure-Tone , Biliary Atresia , Cholesterol, HDL , Heart Failure , panic disorder , Suntan
Related Studies:
  1. Audiometry, Pure-Tone
    , , . [PubMed 0]
  2. Biliary Atresia
    , Genome-wide association study identifies a susceptibility locus for biliary atresia on 10q24.2., Human molecular genetics. [PubMed 20460270]
  3. Cholesterol, HDL
    Sekar Kathiresan et al. BMC medical genetics 2007, A genome-wide association study for blood lipid phenotypes in the Framingham Heart Study., BMC medical genetics. [PubMed 17903299]
    Using a 100K genome-wide scan, we have generated a set of putative associations for common sequence variants and lipid phenotypes. Validation of selected hypotheses in additional samples did not identify any new loci underlying variability in blood lipids. Lack of replication may be due to inadequate statistical power to detect modest quantitative trait locus effects (i.e., <1% of trait variance explained) or reduced genomic coverage of the 100K array. GWAS in FHS using a denser genome-wide genotyping platform and a better-powered replication strategy may identify novel loci underlying blood lipids.
           more ... click here to view the complete list

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 81.41 RPKM in Brain - Cerebellum
Total median expression: 2442.60 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -41.04144-0.285 Picture PostScript Text
3' UTR -235.87826-0.286 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR012852 - CoCoA

Pfam Domains:
PF07888 - Calcium binding and coiled-coil domain (CALCOCO1) like

ModBase Predicted Comparative 3D Structure on Q9P1Z2
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0001047 core promoter binding
GO:0003682 chromatin binding
GO:0003712 transcription cofactor activity
GO:0003713 transcription coactivator activity
GO:0005515 protein binding
GO:0008013 beta-catenin binding
GO:0008022 protein C-terminus binding
GO:0030374 ligand-dependent nuclear receptor transcription coactivator activity
GO:0043565 sequence-specific DNA binding
GO:0044212 transcription regulatory region DNA binding
GO:0070016 armadillo repeat domain binding

Biological Process:
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0007165 signal transduction
GO:0010628 positive regulation of gene expression
GO:0016055 Wnt signaling pathway
GO:0030518 intracellular steroid hormone receptor signaling pathway
GO:0045893 positive regulation of transcription, DNA-templated
GO:0045944 positive regulation of transcription from RNA polymerase II promoter

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0043231 intracellular membrane-bounded organelle


-  Descriptions from all associated GenBank mRNAs
  LF210473 - JP 2014500723-A/17976: Polycomb-Associated Non-Coding RNAs.
BX538208 - Homo sapiens mRNA; cDNA DKFZp686A11272 (from clone DKFZp686A11272).
AY358397 - Homo sapiens clone DNA44675 EESP2436 (UNQ2436) mRNA, complete cds.
AL136895 - Homo sapiens mRNA; cDNA DKFZp434P097 (from clone DKFZp434P097).
AB040969 - Homo sapiens mRNA for KIAA1536 protein, partial cds.
AK122773 - Homo sapiens cDNA FLJ16315 fis, clone SPLEN2032112, highly similar to Homo sapiens calcium binding and coiled-coil domain 1 (CALCOCO1), mRNA.
AK092788 - Homo sapiens cDNA FLJ35469 fis, clone SMINT2006205, highly similar to Homo sapiens calcium binding and coiled-coil domain 1 (CALCOCO1), mRNA.
AX747731 - Sequence 1256 from Patent EP1308459.
AK027881 - Homo sapiens cDNA FLJ14975 fis, clone THYRO1001405, weakly similar to PLECTIN.
JD312946 - Sequence 293970 from Patent EP1572962.
JD067349 - Sequence 48373 from Patent EP1572962.
AY563137 - Homo sapiens calphoglin mRNA, complete cds.
BC003177 - Homo sapiens calcium binding and coiled-coil domain 1, mRNA (cDNA clone MGC:4414 IMAGE:2957946), complete cds.
AK222646 - Homo sapiens mRNA, coiled-coil transcriptional coactivator variant, clone: CBL04472.
AF370415 - Homo sapiens PP13275 mRNA, complete cds.
JD150509 - Sequence 131533 from Patent EP1572962.
JD298450 - Sequence 279474 from Patent EP1572962.
JD234832 - Sequence 215856 from Patent EP1572962.
JD418963 - Sequence 399987 from Patent EP1572962.
JD255901 - Sequence 236925 from Patent EP1572962.
JD136840 - Sequence 117864 from Patent EP1572962.
JD254283 - Sequence 235307 from Patent EP1572962.
CR533567 - Homo sapiens full open reading frame cDNA clone RZPDo834E1221D for gene KIAA1536, KIAA1536 protein; complete cds, incl. stopcodon.
JD288468 - Sequence 269492 from Patent EP1572962.
JD050410 - Sequence 31434 from Patent EP1572962.
JD417269 - Sequence 398293 from Patent EP1572962.
JD429275 - Sequence 410299 from Patent EP1572962.
JD266923 - Sequence 247947 from Patent EP1572962.
AK315578 - Homo sapiens cDNA, FLJ96654.
AB463455 - Synthetic construct DNA, clone: pF1KB8294, Homo sapiens CALCOCO1 gene for calcium binding and coiled-coil domain 1, without stop codon, in Flexi system.
AM393253 - Synthetic construct Homo sapiens clone IMAGE:100001643 for hypothetical protein (CALCOCO1 gene).
AK294424 - Homo sapiens cDNA FLJ59620 complete cds, highly similar to Homo sapiens calcium binding and coiled-coil domain 1 (CALCOCO1), mRNA.
LF338145 - JP 2014500723-A/145648: Polycomb-Associated Non-Coding RNAs.
AY211909 - Homo sapiens sarcoma antigen NY-SAR-3 mRNA, partial cds.
AK296497 - Homo sapiens cDNA FLJ54085 complete cds, highly similar to Homo sapiens calcium binding and coiled-coil domain 1 (CALCOCO1), mRNA.
AK309199 - Homo sapiens cDNA, FLJ99240.
LF338146 - JP 2014500723-A/145649: Polycomb-Associated Non-Coding RNAs.
LF338147 - JP 2014500723-A/145650: Polycomb-Associated Non-Coding RNAs.
MA446050 - JP 2018138019-A/17976: Polycomb-Associated Non-Coding RNAs.
MA573722 - JP 2018138019-A/145648: Polycomb-Associated Non-Coding RNAs.
MA573723 - JP 2018138019-A/145649: Polycomb-Associated Non-Coding RNAs.
MA573724 - JP 2018138019-A/145650: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: B3KVA8, CACO1_HUMAN, KIAA1536, NM_020898, NP_065949, PP13275, Q6FI59, Q71RC3, Q86WF8, Q96JU3, Q9H090, Q9P1Z2, UNQ2436/PRO4996
UCSC ID: uc001sef.3
RefSeq Accession: NM_020898
Protein: Q9P1Z2 (aka CACO1_HUMAN)
CCDS: CCDS8864.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_020898.2
exon count: 15CDS single in 3' UTR: no RNA size: 3046
ORF size: 2076CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4349.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.