Pclo piccolo (presynaptic cytomatrix protein) [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Pcloprovided by RGD
Full Name: piccolo (presynaptic cytomatrix protein)provided by RGD
Primary source: RGD:69406
See related: EnsemblRapid:ENSRNOG00000005726 AllianceGenome:RGD:69406
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: aczonin
Summary: Enables calcium ion binding activity; calcium-dependent phospholipid binding activity; and transcription corepressor binding activity. Involved in several processes, including positive regulation of synaptic vesicle recycling; presynaptic active zone assembly; and regulation of endosome size. Located in several cellular components, including cytoplasmic vesicle; distal axon; and rod spherule. Is active in glutamatergic synapse; parallel fiber to Purkinje cell synapse; and presynaptic active zone cytoplasmic component. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia type 3. Orthologous to human PCLO (piccolo presynaptic cytomatrix protein). [provided by Alliance of Genome Resources, Apr 2022]
Annotation information: Note: This gene aligns across a gap in the Rnor_6.0 reference genome assembly, and therefore, the 5' end of this gene was annotated on NW_007905776.1 and the 3' end was annotated on NW_007905775.1 in NCBI's Rattus norvegicus Annotation Release 105. [15 Jun 2015]
Expression: Biased expression in Brain (RPKM 203.2), Adrenal (RPKM 24.4) and 1 other tissue See more
Orthologs: human mouse all
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Genomic context

Location:: 4q12

Exon count:: 26

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	4	NC_086022.1 (20646604..21005171, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	4	NC_051339.1 (19691439..20050015, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	4	NC_005103.4 (16454904..17058921, complement)

Chromosome 4 - NC_086022.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Loss of Piccolo Function in Rats Induces Cerebellar Network Dysfunction and Pontocerebellar Hypoplasia Type 3-like Phenotypes.
Title: Loss of Piccolo Function in Rats Induces Cerebellar Network Dysfunction and Pontocerebellar Hypoplasia Type 3-like Phenotypes.
Piccolo is critical for the recycling and maintenance of synaptic vesicles.
Title: Critical role for Piccolo in synaptic vesicle retrieval.
Piccolo organizes the readily releasable pool of synaptic vesicles at the calyx of Held.
Title: The presynaptic scaffolding protein Piccolo organizes the readily releasable pool at the calyx of Held.
The findings provide a mechanism for the presynaptic targeting of Trio and support a model in which Piccolo and Bassoon play a role in regulating neurotransmission through interactions with proteins, including Trio, that modulate the dynamic assembly of F-actin during cycles of synaptic vesicle exo- and endocytosis.
Title: Trio, a Rho Family GEF, Interacts with the Presynaptic Active Zone Proteins Piccolo and Bassoon.
Similar to Piccolo and Profilin, Daam1 loss of function impairs presynaptic-F-actin assembly in neurons.
Title: Piccolo Directs Activity Dependent F-Actin Assembly from Presynaptic Active Zones via Daam1.
CtBP1 is targeted and/or anchored to presynapses by direct interaction with the active zone scaffolding proteins Bassoon and piccolo.
Title: Synaptic activity controls localization and function of CtBP1 via binding to Bassoon and Piccolo.
a function of Piccolino at ribbon synapses of sensory neurons
Title: Identification and immunocytochemical characterization of Piccolino, a novel Piccolo splice variant selectively expressed at sensory ribbon synapses of the eye and ear.
a novel role for Bassoon and Piccolo as critical regulators of presynaptic ubiquitination and proteostasis.
Title: Bassoon and Piccolo maintain synapse integrity by regulating protein ubiquitination and degradation.
Data show that Bassoon colocalizes with Aczonin at conventional synapses, but in ribbon synapses, CAST, Munc13, and RIM are segregated from Aczonin, and Aczonin is positioned and may control the access of neurotransmitter vesicles to the fusion site.
Title: Molecular in situ topology of Aczonin/Piccolo and associated proteins at the mammalian neurotransmitter release site.
The total number of Bassoon and Piccolo clusters may contribute to the functional maturation associated with hearing onset.
Title: Targeted three-dimensional immunohistochemistry reveals localization of presynaptic proteins Bassoon and Piccolo in the rat calyx of Held before and after the onset of hearing.

Submit: New GeneRIF Correction See all GeneRIFs (13)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH132306 (e-PCR)
- UniSTS:215589

d4rat150 (e-PCR)
- UniSTS:121969

BE121235 (e-PCR)
- UniSTS:248044

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calcium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables calcium-dependent phospholipid binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables profilin binding	IEA Inferred from Electronic Annotation more info
enables profilin binding	ISO Inferred from Sequence Orthology more info
enables profilin binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables structural constituent of presynaptic active zone	IBA Inferred from Biological aspect of Ancestor more info
enables structural constituent of presynaptic active zone	IEA Inferred from Electronic Annotation more info
enables structural constituent of presynaptic active zone	ISO Inferred from Sequence Orthology more info
enables transcription corepressor binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
acts_upstream_of_or_within cytoskeleton organization	ISO Inferred from Sequence Orthology more info
involved_in cytoskeleton organization	ISS Inferred from Sequence or Structural Similarity more info
involved_in insulin secretion	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within insulin secretion	ISO Inferred from Sequence Orthology more info
involved_in maintenance of presynaptic active zone structure	IEA Inferred from Electronic Annotation more info
involved_in modulation of excitatory postsynaptic potential	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of synaptic vesicle recycling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in presynapse to nucleus signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in presynaptic actin cytoskeleton organization	IEA Inferred from Electronic Annotation more info
involved_in presynaptic actin cytoskeleton organization	ISO Inferred from Sequence Orthology more info
involved_in presynaptic active zone assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in presynaptic active zone assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in protein localization to synapse	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein localization to synapse	IEA Inferred from Electronic Annotation more info
involved_in protein localization to synapse	ISO Inferred from Sequence Orthology more info
involved_in regulation of endosome size	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of exocytosis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within regulation of exocytosis	ISO Inferred from Sequence Orthology more info
involved_in regulation of ubiquitin protein ligase activity	IDA Inferred from Direct Assay more info	PubMed
involved_in synapse organization	IDA Inferred from Direct Assay more info	PubMed
involved_in synaptic vesicle clustering	IEA Inferred from Electronic Annotation more info
involved_in synaptic vesicle clustering	ISO Inferred from Sequence Orthology more info
involved_in synaptic vesicle targeting	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
is_active_in GABA-ergic synapse	IBA Inferred from Biological aspect of Ancestor more info
located_in Golgi-associated vesicle	IDA Inferred from Direct Assay more info	PubMed
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in axon	IDA Inferred from Direct Assay more info	PubMed
located_in cell projection	IEA Inferred from Electronic Annotation more info
located_in cone cell pedicle	IDA Inferred from Direct Assay more info	PubMed
is_active_in cytoskeleton of presynaptic active zone	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoskeleton of presynaptic active zone	IDA Inferred from Direct Assay more info	PubMed
located_in dendrite	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	IBA Inferred from Biological aspect of Ancestor more info
is_active_in glutamatergic synapse	IDA Inferred from Direct Assay more info	PubMed
located_in growth cone	IDA Inferred from Direct Assay more info	PubMed
located_in inhibitory synapse	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in neuromuscular junction	IDA Inferred from Direct Assay more info	PubMed
located_in neuronal cell body	IDA Inferred from Direct Assay more info	PubMed
located_in organelle	IEA Inferred from Electronic Annotation more info
is_active_in parallel fiber to Purkinje cell synapse	IDA Inferred from Direct Assay more info	PubMed
located_in perinuclear region of cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in postsynaptic density	IEA Inferred from Electronic Annotation more info
located_in postsynaptic density	ISO Inferred from Sequence Orthology more info
located_in presynaptic active zone	IDA Inferred from Direct Assay more info	PubMed
located_in presynaptic active zone	IEA Inferred from Electronic Annotation more info
is_active_in presynaptic active zone cytoplasmic component	IDA Inferred from Direct Assay more info	PubMed
located_in presynaptic active zone cytoplasmic component	ISO Inferred from Sequence Orthology more info
located_in ribbon synapse	IDA Inferred from Direct Assay more info	PubMed
located_in rod spherule	IDA Inferred from Direct Assay more info	PubMed
located_in synapse	IDA Inferred from Direct Assay more info	PubMed
located_in synapse	ISO Inferred from Sequence Orthology more info
located_in terminal bouton	IDA Inferred from Direct Assay more info	PubMed
located_in trans-Golgi network	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: protein piccolo

Names: multidomain presynaptic cytomatrix protein Piccolo; presynaptic cytomatrix protein; protein piccolo-like

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001110797.2 → NP_001104267.2 protein piccolo isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks several exons and its 3' terminal exon extends past a splice site that is used in variant 1. The encoded isoform (2) has a shorter and distinct C-terminus, compared to isoform 1.

Source sequence(s)

JAXUCZ010000004

UniProtKB/TrEMBL

F1M7V4

Conserved Domains (8) summary

PTZ00121
Location:1080 → 1637

PTZ00121; MAEBL; Provisional

cd04031
Location:4639 → 4771

C2A_RIM1alpha; C2 domain first repeat contained in Rab3-interacting molecule (RIM) proteins

PHA03247
Location:64 → 516

PHA03247; large tegument protein UL36; Provisional

PRK01741
Location:3789 → 3931

PRK01741; cell division protein ZipA; Provisional

PRK10263
Location:3367 → 3911

PRK10263; DNA translocase FtsK; Provisional

cd00992
Location:4442 → 4533

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

cd15774
Location:522 → 583

FYVE1_PCLO; FYVE-related domain 1 found in protein piccolo

cd15776
Location:1011 → 1072

FYVE2_PCLO; FYVE-related domain 2 found in protein piccolo
NM_020098.2 → NP_064483.2 protein piccolo isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

JAXUCZ010000004

UniProtKB/Swiss-Prot

Q9JKS6, Q9JLT1

UniProtKB/TrEMBL

D3Z9C7

Related

ENSRNOP00000008637.8, ENSRNOT00000008637.10

Conserved Domains (9) summary

PTZ00121
Location:1080 → 1637

PTZ00121; MAEBL; Provisional

cd04031
Location:4639 → 4771

C2A_RIM1alpha; C2 domain first repeat contained in Rab3-interacting molecule (RIM) proteins

PHA03247
Location:64 → 516

PHA03247; large tegument protein UL36; Provisional

PRK01741
Location:3789 → 3931

PRK01741; cell division protein ZipA; Provisional

PRK10263
Location:3367 → 3911

PRK10263; DNA translocase FtsK; Provisional

cd00992
Location:4442 → 4533

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

cd15774
Location:522 → 583

FYVE1_PCLO; FYVE-related domain 1 found in protein piccolo

cd15776
Location:1011 → 1072

FYVE2_PCLO; FYVE-related domain 2 found in protein piccolo

cl14603
Location:4952 → 5077

C2; C2 domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086022.1 Reference GRCr8

Range

20646604..21005171 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039108295.2 → XP_038964223.1 protein piccolo isoform X8

UniProtKB/Swiss-Prot

Q9JKS6, Q9JLT1

Conserved Domains (8) summary

PTZ00121
Location:1080 → 1637

PTZ00121; MAEBL; Provisional

cd04031
Location:4494 → 4626

C2A_RIM1alpha; C2 domain first repeat contained in Rab3-interacting molecule (RIM) proteins

PHA03247
Location:64 → 516

PHA03247; large tegument protein UL36; Provisional

PRK01741
Location:3630 → 3772

PRK01741; cell division protein ZipA; Provisional

cd00992
Location:4296 → 4387

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

cd15774
Location:522 → 583

FYVE1_PCLO; FYVE-related domain 1 found in protein piccolo

pfam00168
Location:4848 → 4957

C2; C2 domain

pfam05715
Location:1009 → 1067

zf-piccolo; Piccolo Zn-finger
XM_063286636.1 → XP_063142706.1 protein piccolo isoform X3

UniProtKB/Swiss-Prot

Q9JKS6, Q9JLT1
XM_039108291.2 → XP_038964219.1 protein piccolo isoform X6

UniProtKB/Swiss-Prot

Q9JKS6, Q9JLT1

Conserved Domains (9) summary

PTZ00121
Location:1080 → 1637

PTZ00121; MAEBL; Provisional

cd04031
Location:4640 → 4772

C2A_RIM1alpha; C2 domain first repeat contained in Rab3-interacting molecule (RIM) proteins

PHA03247
Location:64 → 516

PHA03247; large tegument protein UL36; Provisional

PRK01741
Location:3789 → 3931

PRK01741; cell division protein ZipA; Provisional

PRK10263
Location:3367 → 3911

PRK10263; DNA translocase FtsK; Provisional

cd00992
Location:4442 → 4533

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

cd15774
Location:522 → 583

FYVE1_PCLO; FYVE-related domain 1 found in protein piccolo

pfam00168
Location:4969 → 5078

C2; C2 domain

pfam05715
Location:1009 → 1067

zf-piccolo; Piccolo Zn-finger
XM_063286639.1 → XP_063142709.1 protein piccolo isoform X5

UniProtKB/Swiss-Prot

Q9JKS6, Q9JLT1
XM_063286638.1 → XP_063142708.1 protein piccolo isoform X4

UniProtKB/Swiss-Prot

Q9JKS6, Q9JLT1
XM_039108290.2 → XP_038964218.1 protein piccolo isoform X2

UniProtKB/Swiss-Prot

Q9JKS6, Q9JLT1

Related

ENSRNOP00000007608.9, ENSRNOT00000007608.9

Conserved Domains (9) summary

PTZ00121
Location:1080 → 1637

PTZ00121; MAEBL; Provisional

cd04031
Location:4652 → 4784

C2A_RIM1alpha; C2 domain first repeat contained in Rab3-interacting molecule (RIM) proteins

PHA03247
Location:64 → 516

PHA03247; large tegument protein UL36; Provisional

PRK01741
Location:3789 → 3931

PRK01741; cell division protein ZipA; Provisional

PRK10263
Location:3367 → 3911

PRK10263; DNA translocase FtsK; Provisional

cd00992
Location:4455 → 4546

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

cd15774
Location:522 → 583

FYVE1_PCLO; FYVE-related domain 1 found in protein piccolo

pfam00168
Location:5006 → 5115

C2; C2 domain

pfam05715
Location:1009 → 1067

zf-piccolo; Piccolo Zn-finger
XM_039108294.2 → XP_038964222.1 protein piccolo isoform X7

UniProtKB/TrEMBL

F1M7V4

Conserved Domains (9) summary

PTZ00121
Location:1080 → 1637

PTZ00121; MAEBL; Provisional

cd04031
Location:4653 → 4785

C2A_RIM1alpha; C2 domain first repeat contained in Rab3-interacting molecule (RIM) proteins

PHA03247
Location:64 → 516

PHA03247; large tegument protein UL36; Provisional

PRK01741
Location:3789 → 3931

PRK01741; cell division protein ZipA; Provisional

PRK10263
Location:3367 → 3911

PRK10263; DNA translocase FtsK; Provisional

cd00992
Location:4455 → 4546

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

cd15774
Location:522 → 583

FYVE1_PCLO; FYVE-related domain 1 found in protein piccolo

pfam00168
Location:4912 → 5021

C2; C2 domain

pfam05715
Location:1009 → 1067

zf-piccolo; Piccolo Zn-finger
XM_039108289.2 → XP_038964217.1 protein piccolo isoform X1

UniProtKB/Swiss-Prot

Q9JKS6, Q9JLT1

Conserved Domains (9) summary

PTZ00121
Location:1080 → 1637

PTZ00121; MAEBL; Provisional

cd04031
Location:4653 → 4785

C2A_RIM1alpha; C2 domain first repeat contained in Rab3-interacting molecule (RIM) proteins

PHA03247
Location:64 → 516

PHA03247; large tegument protein UL36; Provisional

PRK01741
Location:3789 → 3931

PRK01741; cell division protein ZipA; Provisional

PRK10263
Location:3367 → 3911

PRK10263; DNA translocase FtsK; Provisional

cd00992
Location:4455 → 4546

PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

cd15774
Location:522 → 583

FYVE1_PCLO; FYVE-related domain 1 found in protein piccolo

pfam00168
Location:5007 → 5116

C2; C2 domain

pfam05715
Location:1009 → 1067

zf-piccolo; Piccolo Zn-finger
XM_063286640.1 → XP_063142710.1 protein piccolo isoform X9

UniProtKB/TrEMBL

F1M7V4
XM_063286641.1 → XP_063142711.1 protein piccolo isoform X10

UniProtKB/TrEMBL

F1M7V4
XM_063286642.1 → XP_063142712.1 protein piccolo isoform X10

UniProtKB/TrEMBL

F1M7V4