Human Gene CBY1 (ENST00000216029.8_3) from GENCODE V47lift37
  Description: chibby family member 1, beta catenin antagonist, transcript variant 1 (from RefSeq NM_015373.4)
Gencode Transcript: ENST00000216029.8_3
Gencode Gene: ENSG00000100211.12_9
Transcript (Including UTRs)
   Position: hg19 chr22:39,052,643-39,069,855 Size: 17,213 Total Exon Count: 5 Strand: +
Coding Region
   Position: hg19 chr22:39,064,060-39,069,241 Size: 5,182 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr22:39,052,643-39,069,855)mRNA (may differ from genome)Protein (126 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CBY1_HUMAN
DESCRIPTION: RecName: Full=Protein chibby homolog 1; AltName: Full=ARPP-binding protein; AltName: Full=Cytosolic leucine-rich protein; AltName: Full=PIGEA-14; AltName: Full=PKD2 interactor, Golgi and endoplasmic reticulum-associated 1;
FUNCTION: Inhibits the Wnt/Wingless pathway by binding to beta- catenin and inhibiting beta-catenin-mediated transcriptional activation through competition with TCF/LEF transcription factors. Has also been shown to play a role in regulating the intracellular trafficking of polycystin-2/PKD2 and possibly of other intracellular proteins. Promotes adipocyte and cardiomyocyte differentiation.
SUBUNIT: Homodimer. Interacts with polycystin-2/PKD2 and GM130. Interacts with the C-terminal region of beta-catenin.
SUBCELLULAR LOCATION: Nucleus speckle. Golgi apparatus, trans- Golgi network. Note=Nuclear, in a punctate manner. Also found in the trans-Golgi.
TISSUE SPECIFICITY: Widely expressed. Expressed at higher levels in heart, skeletal muscle, kidney and placenta. Also found in brain, lung, liver and testis. Significantly down-regulated in thyroid and metastatic uterine tumors.
MISCELLANEOUS: 'Chibby' is Japanese for 'small'; the gene was so named for the RNAi phenotype seen in flies.
SIMILARITY: Belongs to the chibby family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  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: 26.44 RPKM in Colon - Sigmoid
Total median expression: 790.94 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 -60.80151-0.403 Picture PostScript Text
3' UTR -196.00614-0.319 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
  Pfam Domains:
PF14645 - Chibby family

SCOP Domains:
46689 - Homeodomain-like

ModBase Predicted Comparative 3D Structure on Q9Y3M2
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 DetailsGene Details    
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008013 beta-catenin binding
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity

Biological Process:
GO:0008104 protein localization
GO:0030030 cell projection organization
GO:0030154 cell differentiation
GO:0030178 negative regulation of Wnt signaling pathway
GO:0045444 fat cell differentiation
GO:0045892 negative regulation of transcription, DNA-templated
GO:0051289 protein homotetramerization
GO:0055007 cardiac muscle cell differentiation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0005814 centriole
GO:0005829 cytosol
GO:0005856 cytoskeleton
GO:0016607 nuclear speck
GO:0042995 cell projection


-  Descriptions from all associated GenBank mRNAs
  AK307265 - Homo sapiens cDNA, FLJ97213.
AK311928 - Homo sapiens cDNA, FLJ92195.
LF385056 - JP 2014500723-A/192559: Polycomb-Associated Non-Coding RNAs.
AL136686 - Homo sapiens mRNA; cDNA DKFZp564F1978 (from clone DKFZp564F1978).
AL050345 - Novel human gene mapping to chomosome 22.
BC016139 - Homo sapiens chibby homolog 1 (Drosophila), mRNA (cDNA clone MGC:8970 IMAGE:3922707), complete cds.
AF331041 - Homo sapiens cytosolic leucine-rich protein mRNA, complete cds.
MA620633 - JP 2018138019-A/192559: Polycomb-Associated Non-Coding RNAs.
JD362241 - Sequence 343265 from Patent EP1572962.
JD440622 - Sequence 421646 from Patent EP1572962.
CR456410 - Homo sapiens C22orf2 full length open reading frame (ORF) cDNA clone (cDNA clone C22ORF:pGEM.C22orf2).
AB111855 - Homo sapiens arb1 mRNA for ARPP-binding protein, complete cds.
AB462979 - Synthetic construct DNA, clone: pF1KB8442, Homo sapiens CBY1 gene for chibby homolog 1, without stop codon, in Flexi system.
CU013258 - Homo sapiens PGEA1, mRNA (cDNA clone IMAGE:100000036), complete cds, without stop codon, in Gateway system.
HQ258005 - Synthetic construct Homo sapiens clone IMAGE:100072314 chibby homolog 1 (Drosophila) (CBY1), transcript variant 2 (CBY1) gene, encodes complete protein.
KJ893456 - Synthetic construct Homo sapiens clone ccsbBroadEn_02850 CBY1 gene, encodes complete protein.
CU012970 - Homo sapiens PGEA1, mRNA (cDNA clone IMAGE:100000132), complete cds, with stop codon, in Gateway system.
LF337342 - JP 2014500723-A/144845: Polycomb-Associated Non-Coding RNAs.
AB015347 - Homo sapiens HRIHFB2025 mRNA, partial cds.
LF337343 - JP 2014500723-A/144846: Polycomb-Associated Non-Coding RNAs.
JD532966 - Sequence 513990 from Patent EP1572962.
JD182759 - Sequence 163783 from Patent EP1572962.
LF337344 - JP 2014500723-A/144847: Polycomb-Associated Non-Coding RNAs.
JD307767 - Sequence 288791 from Patent EP1572962.
JD382252 - Sequence 363276 from Patent EP1572962.
JD561808 - Sequence 542832 from Patent EP1572962.
JD502800 - Sequence 483824 from Patent EP1572962.
JD131401 - Sequence 112425 from Patent EP1572962.
JD372195 - Sequence 353219 from Patent EP1572962.
JD049287 - Sequence 30311 from Patent EP1572962.
MA572919 - JP 2018138019-A/144845: Polycomb-Associated Non-Coding RNAs.
MA572920 - JP 2018138019-A/144846: Polycomb-Associated Non-Coding RNAs.
MA572921 - JP 2018138019-A/144847: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9Y3M2 (Reactome details) participates in the following event(s):

R-HSA-3769383 CBY1 binds beta-catenin
R-HSA-3769394 AKT phosphorylates CBY1
R-HSA-3769393 YWHAZ binds p-CBY:CTNNB1
R-HSA-3769391 XPO1 binds the beta-catenin:CBY complex
R-HSA-3769402 Deactivation of the beta-catenin transactivating complex
R-HSA-201681 TCF dependent signaling in response to WNT
R-HSA-195721 Signaling by WNT
R-HSA-162582 Signal Transduction

-  Other Names for This Gene
  Alternate Gene Symbols: ARB1, B2R4S2, C22orf2, CBY, CBY1_HUMAN, ENST00000216029.1, ENST00000216029.2, ENST00000216029.3, ENST00000216029.4, ENST00000216029.5, ENST00000216029.6, ENST00000216029.7, HRIHFB2025, NM_015373, PGEA1, Q66GT6, Q9UIK9, Q9Y3M2, uc317cnt.1, uc317cnt.2
UCSC ID: ENST00000216029.8_3
RefSeq Accession: NM_015373.4
Protein: Q9Y3M2 (aka CBY1_HUMAN)

-  Gene Model Information
  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.