Human Gene CNP (ENST00000393892.8_9) from GENCODE V47lift37
  Description: 2',3'-cyclic nucleotide 3' phosphodiesterase, transcript variant 1 (from RefSeq NM_033133.5)
Gencode Transcript: ENST00000393892.8_9
Gencode Gene: ENSG00000173786.17_15
Transcript (Including UTRs)
   Position: hg19 chr17:40,118,813-40,129,758 Size: 10,946 Total Exon Count: 4 Strand: +
Coding Region
   Position: hg19 chr17:40,118,903-40,125,942 Size: 7,040 Coding Exon Count: 4 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:40,118,813-40,129,758)mRNA (may differ from genome)Protein (421 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCHuman Cortex Gene ExpressionMalacardsMGIOMIMPubMed
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CN37_HUMAN
DESCRIPTION: RecName: Full=2',3'-cyclic-nucleotide 3'-phosphodiesterase; Short=CNP; Short=CNPase; EC=3.1.4.37;
FUNCTION: May participate in RNA metabolism in the myelinating cell, CNP is the third most abundant protein in central nervous system myelin (By similarity).
CATALYTIC ACTIVITY: Nucleoside 2',3'-cyclic phosphate + H(2)O = nucleoside 2'-phosphate.
SUBUNIT: Exists as monomers and homodimers (By similarity).
SUBCELLULAR LOCATION: Membrane; Lipid-anchor. Melanosome. Note=Firmly bound to membrane structures of brain white matter. Identified by mass spectrometry in melanosome fractions from stage I to stage IV.
SIMILARITY: Belongs to the cyclic nucleotide phosphodiesterase 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


-  MalaCards Disease Associations
  MalaCards Gene Search: CNP
Diseases sorted by gene-association score: niemann-pick disease, type a (3), multiple sclerosis, disease progression, modifier of (3), oligodendroglioma (2), mannosidosis, beta (2), hyperphenylalaninemia (2), hair disease (2), schizophrenia (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D003993 Dibutyl Phthalate
  • D013749 Tetrachlorodibenzodioxin
  • C111118 2',3,3',4',5-pentachloro-4-hydroxybiphenyl
  • C029790 2,2',3',4,4',5-hexachlorobiphenyl
  • C012267 2,4-D n-butyl ester
  • D015084 2,4-Dichlorophenoxyacetic Acid
  • C030370 2-methoxy-5-(2',3',4'-trimethoxyphenyl)tropone
  • D000324 Adrenocorticotropic Hormone
  • D000638 Amiodarone
  • D000643 Ammonium Chloride
          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: 229.65 RPKM in Brain - Spinal cord (cervical c-1)
Total median expression: 1277.08 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 -40.0090-0.444 Picture PostScript Text
3' UTR -1395.203816-0.366 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
IPR008431 - CNPase
IPR009097 - RNA_ligase/cNuc_Pdiesterase

Pfam Domains:
PF05881 - 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNP or CNPase)
PF13671 - AAA domain

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases
53795 - PEP carboxykinase-like
55144 - LigT-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1WOJ - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P09543
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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 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003723 RNA binding
GO:0004113 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity
GO:0016787 hydrolase activity
GO:0030551 cyclic nucleotide binding

Biological Process:
GO:0000226 microtubule cytoskeleton organization
GO:0007268 chemical synaptic transmission
GO:0007409 axonogenesis
GO:0007568 aging
GO:0008344 adult locomotory behavior
GO:0009214 cyclic nucleotide catabolic process
GO:0009636 response to toxic substance
GO:0021762 substantia nigra development
GO:0030900 forebrain development
GO:0032496 response to lipopolysaccharide
GO:0046902 regulation of mitochondrial membrane permeability
GO:0048709 oligodendrocyte differentiation

Cellular Component:
GO:0005615 extracellular space
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005741 mitochondrial outer membrane
GO:0005743 mitochondrial inner membrane
GO:0005829 cytosol
GO:0005874 microtubule
GO:0005886 plasma membrane
GO:0005902 microvillus
GO:0016020 membrane
GO:0031143 pseudopodium
GO:0035748 myelin sheath abaxonal region
GO:0035749 myelin sheath adaxonal region
GO:0042470 melanosome
GO:0042995 cell projection
GO:0043209 myelin sheath
GO:0048471 perinuclear region of cytoplasm
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  BC028040 - Homo sapiens 2',3'-cyclic nucleotide 3' phosphodiesterase, mRNA (cDNA clone MGC:40095 IMAGE:5248370), complete cds.
BC006392 - Homo sapiens 2',3'-cyclic nucleotide 3' phosphodiesterase, mRNA (cDNA clone MGC:12818 IMAGE:4126696), complete cds.
AK295351 - Homo sapiens cDNA FLJ52954 complete cds, highly similar to 2',3'-cyclic-nucleotide 3'-phosphodiesterase(EC 3.1.4.37).
AK294179 - Homo sapiens cDNA FLJ59866 complete cds, highly similar to 2',3'-cyclic-nucleotide 3'-phosphodiesterase (EC 3.1.4.37).
AK097833 - Homo sapiens cDNA FLJ40514 fis, clone TESTI2046535, highly similar to 2',3'-CYCLIC NUCLEOTIDE 3'-PHOSPHODIESTERASE (EC 3.1.4.37).
AK098384 - Homo sapiens cDNA FLJ25518 fis, clone CBR06704, highly similar to 2',3'-CYCLIC NUCLEOTIDE 3'-PHOSPHODIESTERASE (EC 3.1.4.37).
AK026876 - Homo sapiens cDNA: FLJ23223 fis, clone ADSU02123, highly similar to HUMCNPDEA Human 2'3'-cyclic nucleotide 3'-phosphodiesterase mRNA.
JD539974 - Sequence 520998 from Patent EP1572962.
BC001362 - Homo sapiens 2',3'-cyclic nucleotide 3' phosphodiesterase, mRNA (cDNA clone MGC:2262 IMAGE:3051112), complete cds.
BC011046 - Homo sapiens 2',3'-cyclic nucleotide 3' phosphodiesterase, mRNA (cDNA clone MGC:17217 IMAGE:4179083), complete cds.
JD076411 - Sequence 57435 from Patent EP1572962.
AK308696 - Homo sapiens cDNA, FLJ98737.
CU675383 - Synthetic construct Homo sapiens gateway clone IMAGE:100017233 5' read CNP mRNA.
CU674668 - Synthetic construct Homo sapiens gateway clone IMAGE:100017232 5' read CNP mRNA.
DQ892575 - Synthetic construct clone IMAGE:100005205; FLH187687.01X; RZPDo839C01150D 2',3'-cyclic nucleotide 3' phosphodiesterase (CNP) gene, encodes complete protein.
DQ895791 - Synthetic construct Homo sapiens clone IMAGE:100010251; FLH187683.01L; RZPDo839C01149D 2',3'-cyclic nucleotide 3' phosphodiesterase (CNP) gene, encodes complete protein.
KJ905717 - Synthetic construct Homo sapiens clone ccsbBroadEn_15387 CNP gene, encodes complete protein.
KJ896622 - Synthetic construct Homo sapiens clone ccsbBroadEn_06016 CNP gene, encodes complete protein.
D28445 - Homo sapiens mRNA for 2',3'-cyclic nucleotide 3'-phosphodiesterase, 5'UTR region.
M19650 - Human 2',3'-cyclic nucleotide 3'-phosphodiesterase mRNA, complete cds.
DQ581677 - Homo sapiens piRNA piR-49789, complete sequence.
JD270797 - Sequence 251821 from Patent EP1572962.
JD145529 - Sequence 126553 from Patent EP1572962.
JD077123 - Sequence 58147 from Patent EP1572962.
JD313132 - Sequence 294156 from Patent EP1572962.
JD153910 - Sequence 134934 from Patent EP1572962.
JD253583 - Sequence 234607 from Patent EP1572962.
JD483368 - Sequence 464392 from Patent EP1572962.
JD453238 - Sequence 434262 from Patent EP1572962.
JD074511 - Sequence 55535 from Patent EP1572962.
JD466413 - Sequence 447437 from Patent EP1572962.
JD104437 - Sequence 85461 from Patent EP1572962.
JD104438 - Sequence 85462 from Patent EP1572962.
JD387361 - Sequence 368385 from Patent EP1572962.
JD456946 - Sequence 437970 from Patent EP1572962.
JD104343 - Sequence 85367 from Patent EP1572962.
JD456850 - Sequence 437874 from Patent EP1572962.
JD441062 - Sequence 422086 from Patent EP1572962.
JD198244 - Sequence 179268 from Patent EP1572962.
BC148241 - Homo sapiens cDNA clone IMAGE:40131460.
JD423460 - Sequence 404484 from Patent EP1572962.
JD538825 - Sequence 519849 from Patent EP1572962.
JD297538 - Sequence 278562 from Patent EP1572962.
JD546438 - Sequence 527462 from Patent EP1572962.
JD151190 - Sequence 132214 from Patent EP1572962.
JD062690 - Sequence 43714 from Patent EP1572962.
JD109412 - Sequence 90436 from Patent EP1572962.
JD476553 - Sequence 457577 from Patent EP1572962.
JD465809 - Sequence 446833 from Patent EP1572962.
JD449973 - Sequence 430997 from Patent EP1572962.
JD216327 - Sequence 197351 from Patent EP1572962.
JD423749 - Sequence 404773 from Patent EP1572962.
JD271908 - Sequence 252932 from Patent EP1572962.
JD460114 - Sequence 441138 from Patent EP1572962.
JD077432 - Sequence 58456 from Patent EP1572962.
JD427259 - Sequence 408283 from Patent EP1572962.
JD283490 - Sequence 264514 from Patent EP1572962.
JD135235 - Sequence 116259 from Patent EP1572962.
JD490022 - Sequence 471046 from Patent EP1572962.
BC045561 - Homo sapiens 2',3'-cyclic nucleotide 3' phosphodiesterase, mRNA (cDNA clone IMAGE:4814196).
AK124861 - Homo sapiens cDNA FLJ42871 fis, clone BRHIP2024146.
AK098048 - Homo sapiens cDNA FLJ40729 fis, clone TKIDN2000246.
CU678527 - Synthetic construct Homo sapiens gateway clone IMAGE:100022474 3' read DNAJC7 mRNA.
CU689735 - Synthetic construct Homo sapiens gateway clone IMAGE:100019617 3' read DNAJC7 mRNA.
CU680077 - Synthetic construct Homo sapiens gateway clone IMAGE:100019667 3' read DNAJC7 mRNA.
JD024725 - Sequence 5749 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: CN37_HUMAN, CNP , ENST00000393892.1, ENST00000393892.2, ENST00000393892.3, ENST00000393892.4, ENST00000393892.5, ENST00000393892.6, ENST00000393892.7, NM_033133, P09543, uc318wfb.1, uc318wfb.2
UCSC ID: ENST00000393892.8_9
RefSeq Accession: NM_033133.5
Protein: P09543 (aka CN37_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.