Human Gene CNPY2 (uc001sku.1)
  Description: canopy 2 homolog
Transcript (Including UTRs)
   Position: hg18 chr12:54,990,484-54,996,387 Size: 5,904 Total Exon Count: 6 Strand: -
Coding Region
   Position: hg18 chr12:54,990,603-54,995,268 Size: 4,666 Coding Exon Count: 5 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsOther Names
Model InformationMethods
Data last updated at UCSC: 2009-03-03

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr12:54,990,484-54,996,387)mRNA (may differ from genome)Protein (182 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDMGIOMIM
PubMedTreefamUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CNPY2_HUMAN
DESCRIPTION: RecName: Full=Protein canopy homolog 2; AltName: Full=MIR-interacting saposin-like protein; AltName: Full=Putative secreted protein Zsig9; AltName: Full=Transmembrane protein 4; Flags: Precursor;
FUNCTION: Positive regulator of neurite outgrowth by stabilizing myosin regulatory light chain (MRLC). It prevents MIR-mediated MRLC ubiquitination and its subsequent proteasomal degradation.
SUBUNIT: Interacts with MYLIP/MIR.
SUBCELLULAR LOCATION: Endoplasmic reticulum (Potential).
TISSUE SPECIFICITY: Expressed in different tissues. Highest levels are detected in adult placenta, liver and pancreas.
SIMILARITY: Belongs to the canopy family.
SIMILARITY: Contains 1 saposin B-type domain.

-  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

-  Microarray Expression Data
 
Expression ratio colors:

GNF Expression Atlas 2 Data from U133A and GNF1H Chips

      
      
      
     
    
     
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Affymetrix All Exon Microarrays

           
Ratios

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -250.90541-0.464 Picture PostScript Text
3' UTR -24.40119-0.205 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
IPR021852 - DUF3456
IPR008139 - SaposinB

ModBase Predicted Comparative 3D Structure on Q9Y2B0
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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
Genome BrowserNo orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
MGI EnsemblFlyBaseWormBase 
Protein Sequence Protein SequenceProtein SequenceProtein Sequence 
Alignment AlignmentAlignmentAlignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding

Biological Process:
GO:0007167 enzyme linked receptor protein signaling pathway
GO:0009888 tissue development
GO:0010629 negative regulation of gene expression
GO:0010988 regulation of low-density lipoprotein particle clearance
GO:0045716 positive regulation of low-density lipoprotein particle receptor biosynthetic process

Cellular Component:
GO:0005783 endoplasmic reticulum
GO:0005887 integral component of plasma membrane


-  Descriptions from all associated GenBank mRNAs
  BC065015 - Homo sapiens canopy 2 homolog (zebrafish), mRNA (cDNA clone MGC:74660 IMAGE:6169229), complete cds.
AB015631 - Homo sapiens mRNA for type II membrane protein, complete cds, clone:HP10390.
AY359102 - Homo sapiens clone DNA93012 TMEM4 (UNQ1943) mRNA, complete cds.
AY032624 - Homo sapiens saposin-like protein mRNA, complete cds.
HQ448080 - Synthetic construct Homo sapiens clone IMAGE:100071460; CCSB012341_01 transmembrane protein 4 (CNPY2) gene, encodes complete protein.
AK312921 - Homo sapiens cDNA, FLJ93370, Homo sapiens transmembrane protein 4 (TMEM4), mRNA.
AL831869 - Homo sapiens mRNA; cDNA DKFZp547M0716 (from clone DKFZp547M0716).
BC001027 - Homo sapiens canopy 2 homolog (zebrafish), mRNA (cDNA clone IMAGE:3344788), complete cds.
AF186113 - Homo sapiens putative secreted protein ZSIG9 (ZSIG9) mRNA, complete cds.
JD431365 - Sequence 412389 from Patent EP1572962.
JD454964 - Sequence 435988 from Patent EP1572962.
JD510435 - Sequence 491459 from Patent EP1572962.
JD369040 - Sequence 350064 from Patent EP1572962.
JD442570 - Sequence 423594 from Patent EP1572962.
KJ893009 - Synthetic construct Homo sapiens clone ccsbBroadEn_02403 CNPY2 gene, encodes complete protein.
JD274025 - Sequence 255049 from Patent EP1572962.
JD060604 - Sequence 41628 from Patent EP1572962.
JD104282 - Sequence 85306 from Patent EP1572962.
JD192867 - Sequence 173891 from Patent EP1572962.
JD142327 - Sequence 123351 from Patent EP1572962.
JD211201 - Sequence 192225 from Patent EP1572962.
JD260570 - Sequence 241594 from Patent EP1572962.
JD132715 - Sequence 113739 from Patent EP1572962.
LF208957 - JP 2014500723-A/16460: Polycomb-Associated Non-Coding RNAs.
LF324479 - JP 2014500723-A/131982: Polycomb-Associated Non-Coding RNAs.
LF324478 - JP 2014500723-A/131981: Polycomb-Associated Non-Coding RNAs.
LF324475 - JP 2014500723-A/131978: Polycomb-Associated Non-Coding RNAs.
MA560056 - JP 2018138019-A/131982: Polycomb-Associated Non-Coding RNAs.
MA560055 - JP 2018138019-A/131981: Polycomb-Associated Non-Coding RNAs.
MA560052 - JP 2018138019-A/131978: Polycomb-Associated Non-Coding RNAs.
MA444534 - JP 2018138019-A/16460: Polycomb-Associated Non-Coding RNAs.

-  Other Names for This Gene
  Alternate Gene Symbols: CNPY2_HUMAN, MSAP, NM_014255, NP_055070, Q9UHE9, Q9Y2B0, TMEM4, UNQ1943/PRO4426, ZSIG9
UCSC ID: uc001sku.1
RefSeq Accession: NM_014255
Protein: Q9Y2B0 (aka CNPY2_HUMAN)
CCDS: CCDS8914.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014255.4
exon count: 6CDS single in 3' UTR: no RNA size: 1209
ORF size: 549CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 1298.00frame 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.