Human Gene PCLO (ENST00000333891.14_7) from GENCODE V47lift37
  Description: piccolo presynaptic cytomatrix protein, transcript variant 1 (from RefSeq NM_033026.6)
Gencode Transcript: ENST00000333891.14_7
Gencode Gene: ENSG00000186472.20_10
Transcript (Including UTRs)
   Position: hg19 chr7:82,383,328-82,792,200 Size: 408,873 Total Exon Count: 25 Strand: -
Coding Region
   Position: hg19 chr7:82,387,891-82,791,908 Size: 404,018 Coding Exon Count: 25 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr7:82,383,328-82,792,200)mRNA (may differ from genome)Protein (5142 aa)
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-  Comments and Description Text from UniProtKB
  ID: PCLO_HUMAN
DESCRIPTION: RecName: Full=Protein piccolo; AltName: Full=Aczonin;
FUNCTION: May act as a scaffolding protein involved in the organization of synaptic active zones and in synaptic vesicle trafficking (By similarity).
SUBUNIT: Interacts with RABAC1/PRA1, RIMS2 and profilin (By similarity).
SUBCELLULAR LOCATION: Cell junction, synapse (By similarity). Note=Concentrated at the presynaptic side of synaptic junctions (By similarity).
DOMAIN: C2 domain 1 is involved in binding calcium and phospholipids. Calcium binds with low affinity but with high specificity and induces a large conformational change.
SIMILARITY: Contains 2 C2 domains.
SIMILARITY: Contains 1 PDZ (DHR) domain.
SEQUENCE CAUTION: Sequence=AAB97937.1; Type=Erroneous gene model prediction; Sequence=AAD21789.2; Type=Erroneous gene model prediction;

-  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: PCLO
Diseases sorted by gene-association score: pontocerebellar hypoplasia, type 3* (1300), splenic flexure cancer (12), intracranial hypertension, idiopathic (11), vertebral artery insufficiency (11), descending colon cancer (11), corneal dystrophy, lisch epithelial (11), pontocerebellar hypoplasia (9), detrusor sphincter dyssynergia (9), transient global amnesia (6), papilledema (6), cerebral arterial disease (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  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: 13.67 RPKM in Brain - Cerebellum
Total median expression: 70.85 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 -150.30292-0.515 Picture PostScript Text
3' UTR -1037.904563-0.227 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
IPR020477 - C2_dom
IPR018029 - C2_membr_targeting
IPR001565 - Synaptotagmin
IPR011011 - Znf_FYVE_PHD
IPR008899 - Znf_piccolo
IPR013083 - Znf_RING/FYVE/PHD

Pfam Domains:
PF00168 - C2 domain
PF00595 - PDZ domain
PF05715 - Piccolo Zn-finger

SCOP Domains:
50156 - PDZ domain-like
49562 - C2 domain (Calcium/lipid-binding domain, CaLB)
57850 - RING/U-box
57903 - FYVE/PHD zinc finger

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1UJD - NMR


ModBase Predicted Comparative 3D Structure on Q9Y6V0
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:0005509 calcium ion binding
GO:0005522 profilin binding
GO:0005544 calcium-dependent phospholipid binding
GO:0046872 metal ion binding

Biological Process:
GO:0007010 cytoskeleton organization
GO:0007416 synapse assembly
GO:0016079 synaptic vesicle exocytosis
GO:0017157 regulation of exocytosis
GO:0019933 cAMP-mediated signaling
GO:0030073 insulin secretion
GO:0035418 protein localization to synapse
GO:0099526 presynapse to nucleus signaling pathway

Cellular Component:
GO:0005856 cytoskeleton
GO:0014069 postsynaptic density
GO:0030054 cell junction
GO:0045202 synapse
GO:0048786 presynaptic active zone
GO:0048788 cytoskeleton of presynaptic active zone
GO:0070062 extracellular exosome
GO:0098831 presynaptic active zone cytoplasmic component


-  Descriptions from all associated GenBank mRNAs
  AB587523 - Synthetic construct DNA, clone: pF1KE0299, Homo sapiens PCLO gene for piccolo, without stop codon, in Flexi system.
BX649041 - Homo sapiens mRNA; cDNA DKFZp779L0262 (from clone DKFZp779L0262).
CR749552 - Homo sapiens mRNA; cDNA DKFZp779G1236 (from clone DKFZp779G1236).
AK125999 - Homo sapiens cDNA FLJ44011 fis, clone TESTI4024420, highly similar to Rattus norvegicus presynaptic cytomatrix protein (Pclo).
AB011131 - Homo sapiens mRNA for KIAA0559 protein, partial cds.
BC108289 - Homo sapiens piccolo (presynaptic cytomatrix protein), mRNA (cDNA clone IMAGE:6157434), partial cds.
BC001304 - Homo sapiens piccolo (presynaptic cytomatrix protein), mRNA (cDNA clone IMAGE:3452412), complete cds.
KJ902473 - Synthetic construct Homo sapiens clone ccsbBroadEn_11867 PCLO gene, encodes complete protein.
JD419284 - Sequence 400308 from Patent EP1572962.
JD022863 - Sequence 3887 from Patent EP1572962.
JD031450 - Sequence 12474 from Patent EP1572962.
JD035484 - Sequence 16508 from Patent EP1572962.
JD023089 - Sequence 4113 from Patent EP1572962.
JD020380 - Sequence 1404 from Patent EP1572962.
JD029331 - Sequence 10355 from Patent EP1572962.
JD031317 - Sequence 12341 from Patent EP1572962.
AK297315 - Homo sapiens cDNA FLJ54500 partial cds, highly similar to Protein piccolo.
Y19188 - Homo sapiens mRNA for partial aczonin (acz gene).
JD036915 - Sequence 17939 from Patent EP1572962.
JD248989 - Sequence 230013 from Patent EP1572962.
JD323627 - Sequence 304651 from Patent EP1572962.
JD188648 - Sequence 169672 from Patent EP1572962.
JD353454 - Sequence 334478 from Patent EP1572962.
JD260309 - Sequence 241333 from Patent EP1572962.
JD335877 - Sequence 316901 from Patent EP1572962.
JD380971 - Sequence 361995 from Patent EP1572962.
JD129968 - Sequence 110992 from Patent EP1572962.
JD354677 - Sequence 335701 from Patent EP1572962.
JD500366 - Sequence 481390 from Patent EP1572962.
BC122565 - Homo sapiens piccolo (presynaptic cytomatrix protein), mRNA (cDNA clone IMAGE:40033500), partial cds.
BC125271 - Homo sapiens piccolo (presynaptic cytomatrix protein), mRNA (cDNA clone IMAGE:40033499), partial cds.
JD564114 - Sequence 545138 from Patent EP1572962.
JD301751 - Sequence 282775 from Patent EP1572962.
JD373486 - Sequence 354510 from Patent EP1572962.
JD363202 - Sequence 344226 from Patent EP1572962.
JD394988 - Sequence 376012 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  BioCarta from NCI Cancer Genome Anatomy Project
h_PDZsPathway - Synaptic Proteins at the Synaptic Junction

-  Other Names for This Gene
  Alternate Gene Symbols: A4D1A7, A6NNX9, ACZ , ENST00000333891.1, ENST00000333891.10, ENST00000333891.11, ENST00000333891.12, ENST00000333891.13, ENST00000333891.2, ENST00000333891.3, ENST00000333891.4, ENST00000333891.5, ENST00000333891.6, ENST00000333891.7, ENST00000333891.8, ENST00000333891.9, KIAA0559, NM_033026, O43373, O60305, PCLO , PCLO_HUMAN, Q08E72, Q9BVC8, Q9UIV2, Q9Y6U9, Q9Y6V0, uc317ttw.1, uc317ttw.2
UCSC ID: ENST00000333891.14_7
RefSeq Accession: NM_033026.6
Protein: Q9Y6V0 (aka PCLO_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.