Human Gene CPNE1 (ENST00000397443.7_14) from GENCODE V47lift37

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Description: copine 1, transcript variant 5 (from RefSeq NM_152928.3)
Gencode Transcript: ENST00000397443.7_14
Gencode Gene: ENSG00000214078.13_20
Transcript (Including UTRs)
Position: hg19 chr20:34,213,966-34,252,822 Size: 38,857 Total Exon Count: 16 Strand: -
Coding Region
Position: hg19 chr20:34,214,163-34,220,845 Size: 6,683 Coding Exon Count: 15

Page Index	Sequence and Links	UniProtKB Comments	Primers	CTD	Gene Alleles
RNA-Seq Expression	Microarray Expression	RNA Structure	Protein Structure	Other Species	GO Annotations
mRNA Descriptions	Pathways	Other Names	Model Information	Methods

Data last updated at UCSC: 2024-08-22 23:36:26

Sequence and Links to Tools and Databases

Genomic Sequence (chr20:34,213,966-34,252,822)			mRNA (may differ from genome)		Protein (537 aa)
Gene Sorter	Genome Browser	Other Species FASTA	Gene interactions	Table Schema	AlphaFold
BioGPS	Ensembl	Entrez Gene	ExonPrimer	GeneCards	HGNC
MGI	OMIM	PubMed	Reactome	UniProtKB	Wikipedia
BioGrid CRISPR DB

Comments and Description Text from UniProtKB


	ID: CPNE1_HUMAN DESCRIPTION: RecName: Full=Copine-1; AltName: Full=Copine I; FUNCTION: May function in membrane trafficking. Exhibits calcium- dependent phospholipid binding properties. SUBUNIT: Interacts with CCDC22 (By similarity). SIMILARITY: Belongs to the copine family. SIMILARITY: Contains 2 C2 domains. SIMILARITY: Contains 1 VWFA 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 D014635 Valproic Acid D015123 7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide D001241 Aspirin D002922 Ciguatoxins D013467 Sulindac D019284 Thapsigargin D013806 Theophylline D014810 Vitamin E C018021 cobaltous chloride C008261 lead acetate C045463 leflunomide D020122 tert-Butylhydroperoxide C012589 trichostatin A

Common Gene Haplotype Alleles


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RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)


	Highest median expression: 91.30 RPKM in Spleen Total median expression: 2424.94 RPKM View in GTEx track of Genome Browser View at GTEx portal View GTEx Body Map

Microarray Expression Data


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mRNA Secondary Structure of 3' and 5' UTRs

Region	Fold Energy	Bases	Energy/Base	Display As
5' UTR	-64.80	141	-0.460	Picture	PostScript	Text
3' UTR	-39.10	197	-0.198	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
IPR000008 - C2_Ca-dep
IPR008973 - C2_Ca/lipid-bd_dom_CaLB
IPR018029 - C2_membr_targeting
IPR010734 - Copine
IPR002035 - VWF_A

Pfam Domains:
PF00168 - C2 domain
PF07002 - Copine

SCOP Domains:
69318 - Integrin alpha N-terminal domain
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
53300 - vWA-like

ModBase Predicted Comparative 3D Structure on Q99829


Front	Top	Side

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.

Mouse	Rat	Zebrafish	D. melanogaster	C. elegans	S. cerevisiae
No ortholog	No ortholog	No ortholog	No ortholog	No ortholog	No ortholog
Gene Details
Gene Sorter

Gene Ontology (GO) Annotations with Structured Vocabulary


	Molecular Function: GO:0001786 phosphatidylserine binding GO:0004175 endopeptidase activity GO:0005215 transporter activity GO:0005509 calcium ion binding GO:0005515 protein binding GO:0005544 calcium-dependent phospholipid binding GO:0042803 protein homodimerization activity GO:0051059 NF-kappaB binding Biological Process: GO:0006351 transcription, DNA-templated GO:0006355 regulation of transcription, DNA-templated GO:0006508 proteolysis GO:0006629 lipid metabolic process GO:0010629 negative regulation of gene expression GO:0016192 vesicle-mediated transport GO:0030154 cell differentiation GO:0043122 regulation of I-kappaB kinase/NF-kappaB signaling GO:0043312 neutrophil degranulation GO:0043392 negative regulation of DNA binding GO:0045666 positive regulation of neuron differentiation GO:0046474 glycerophospholipid biosynthetic process GO:0051897 positive regulation of protein kinase B signaling GO:0071277 cellular response to calcium ion GO:1901223 negative regulation of NIK/NF-kappaB signaling GO:1903265 positive regulation of tumor necrosis factor-mediated signaling pathway GO:1990138 neuron projection extension Cellular Component: GO:0005634 nucleus GO:0005654 nucleoplasm GO:0005737 cytoplasm GO:0005829 cytosol GO:0005886 plasma membrane GO:0016020 membrane GO:0031965 nuclear membrane GO:0035577 azurophil granule membrane GO:0070062 extracellular exosome

Descriptions from all associated GenBank mRNAs


	JD126870 - Sequence 107894 from Patent EP1572962. AF314092 - Homo sapiens copine I (CPNE1) mRNA, partial cds. U83246 - Homo sapiens copine I mRNA, complete cds. BC001142 - Homo sapiens copine I, mRNA (cDNA clone MGC:1142 IMAGE:3502122), complete cds. AB209827 - Homo sapiens mRNA for copine I variant protein. JD114618 - Sequence 95642 from Patent EP1572962. JD496918 - Sequence 477942 from Patent EP1572962. JD107251 - Sequence 88275 from Patent EP1572962. KJ892652 - Synthetic construct Homo sapiens clone ccsbBroadEn_02046 CPNE1 gene, encodes complete protein. CR456790 - Homo sapiens full open reading frame cDNA clone RZPDo834H014D for gene CPNE1, copine I; complete cds, incl. stopcodon. BC021010 - Homo sapiens copine I, mRNA (cDNA clone IMAGE:4074508). AK308795 - Homo sapiens cDNA, FLJ98836. CU674576 - Synthetic construct Homo sapiens gateway clone IMAGE:100017693 5' read CPNE1 mRNA. JD026259 - Sequence 7283 from Patent EP1572962. DQ655943 - Homo sapiens clone UGL2a06, mRNA sequence. DQ655944 - Homo sapiens clone UGL2c06, mRNA sequence. DQ655945 - Homo sapiens clone UGL2d06, mRNA sequence. DQ655946 - Homo sapiens clone UGL2e06, mRNA sequence. DQ656050 - Homo sapiens clone UGL055-A-E5, mRNA sequence. JD028002 - Sequence 9026 from Patent EP1572962. JD022947 - Sequence 3971 from Patent EP1572962. JD020283 - Sequence 1307 from Patent EP1572962. JD034214 - Sequence 15238 from Patent EP1572962. JD025422 - Sequence 6446 from Patent EP1572962. JD027238 - Sequence 8262 from Patent EP1572962. JD033490 - Sequence 14514 from Patent EP1572962. JD024641 - Sequence 5665 from Patent EP1572962. JD021600 - Sequence 2624 from Patent EP1572962. JD024454 - Sequence 5478 from Patent EP1572962. JD026364 - Sequence 7388 from Patent EP1572962. JD025409 - Sequence 6433 from Patent EP1572962. JD305131 - Sequence 286155 from Patent EP1572962. AB018308 - Homo sapiens KIAA0765 mRNA for KIAA0765 protein. AF345332 - Homo sapiens SWAN mRNA, complete cds. AF393214 - Homo sapiens swan mRNA, complete cds; alternatively spliced. AK092239 - Homo sapiens cDNA FLJ34920 fis, clone NT2RP7002802, highly similar to RNA-binding protein 12. BC012787 - Homo sapiens RNA binding motif protein 12, mRNA (cDNA clone MGC:16487 IMAGE:3956772), complete cds. BC013981 - Homo sapiens RNA binding motif protein 12, mRNA (cDNA clone MGC:19528 IMAGE:3845090), complete cds. AK299371 - Homo sapiens cDNA FLJ58274 complete cds, highly similar to RNA-binding protein 12. JD028864 - Sequence 9888 from Patent EP1572962. JD142383 - Sequence 123407 from Patent EP1572962. JD407186 - Sequence 388210 from Patent EP1572962. JD462583 - Sequence 443607 from Patent EP1572962.

Biochemical and Signaling Pathways


	Reactome (by CSHL, EBI, and GO) Protein Q99829 (Reactome details) participates in the following event(s): R-HSA-5333678 CPNEs bind PL R-HSA-6798739 Exocytosis of azurophil granule membrane proteins R-HSA-1483206 Glycerophospholipid biosynthesis R-HSA-6798695 Neutrophil degranulation R-HSA-1483257 Phospholipid metabolism R-HSA-168249 Innate Immune System R-HSA-556833 Metabolism of lipids R-HSA-168256 Immune System R-HSA-1430728 Metabolism

Other Names for This Gene


	Alternate Gene Symbols: CPN1, CPNE1 , CPNE1_HUMAN, E1P5Q4, ENST00000397443.1, ENST00000397443.2, ENST00000397443.3, ENST00000397443.4, ENST00000397443.5, ENST00000397443.6, NM_152928, Q6IBL3, Q99829, Q9H243, Q9NTZ7, uc318zai.1, uc318zai.2 UCSC ID: ENST00000397443.7_14 RefSeq Accession: NM_152925.3 Protein: Q99829 (aka CPNE1_HUMAN or CNE1_HUMAN)

Gene Model Information


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Methods, Credits, and Use Restrictions


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