Caly calcyon neuron-specific vesicular protein [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Calyprovided by RGD
Official Full Name: calcyon neuron-specific vesicular proteinprovided by RGD
Primary source: RGD:621719
See related: Ensembl:ENSRNOG00000018337 AllianceGenome:RGD:621719
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: Drd1ip; Calcyon
Summary: Predicted to enable clathrin light chain binding activity. Involved in anterograde axonal transport; positive regulation of clathrin coat assembly; and positive regulation of retrograde axon cargo transport. Located in axon. Biomarker of attention deficit hyperactivity disorder. Human ortholog(s) of this gene implicated in attention deficit hyperactivity disorder. Orthologous to human CALY (calcyon neuron specific vesicular protein). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Restricted expression toward (RPKM 374.8) See more
Orthologs: human mouse all
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Genomic context

Location:: 1q41

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (204292317..204303506, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (194862671..194873861, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (212537851..212549040, complement)

Chromosome 1 - NC_086019.1 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
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?

Caly is a multifunctional scaffolding protein that regulates axonal transport of late endosomes and lysosome-related organelles by coordinately interacting with motor and vesicle coat proteins.
Title: Coupling of microtubule motors with AP-3 generated organelles in axons by NEEP21 family member calcyon.
endocytic and cargo sorting functions of Caly in neurons
Title: Dynein binds and stimulates axonal motility of the endosome adaptor and NEEP21 family member, calcyon.
Calcyon forms a novel ternary complex with dopamine D1 receptor through PSD-95 protein and plays a role in dopamine receptor internalization
Title: Calcyon forms a novel ternary complex with dopamine D1 receptor through PSD-95 protein and plays a role in dopamine receptor internalization.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables clathrin light chain binding	IBA Inferred from Biological aspect of Ancestor more info
enables clathrin light chain binding	ISO Inferred from Sequence Orthology more info
enables clathrin light chain binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein-containing complex binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in anterograde axonal transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in clathrin coat assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in clathrin coat assembly	ISO Inferred from Sequence Orthology more info
involved_in clathrin coat assembly	ISS Inferred from Sequence or Structural Similarity more info
involved_in dopamine receptor signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in endosomal transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of clathrin coat assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of endocytosis	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of endocytosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of retrograde axon cargo transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in postsynaptic neurotransmitter receptor internalization	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in axon	IDA Inferred from Direct Assay more info	PubMed
located_in axon cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasmic vesicle	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic vesicle	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasmic vesicle membrane	IEA Inferred from Electronic Annotation more info
is_active_in endosome	IBA Inferred from Biological aspect of Ancestor more info
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
is_active_in membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in postsynaptic endocytic zone	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: neuron-specific vesicular protein calcyon

Names: D1 dopamine receptor-interacting protein; calcyon; D1 dopamine receptor-interacting protein; dopamine receptor D1 interacting protein

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_001190399.1 → NP_001177328.1 neuron-specific vesicular protein calcyon

See identical proteins and their annotated locations for NP_001177328.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, compared to variant 1. Both variants 1 and 2 encode the same protein.

Source sequence(s)

AF303658, BC060543

UniProtKB/Swiss-Prot

P58821

UniProtKB/TrEMBL

A6HXF2

Conserved Domains (1) summary

pfam06387
Location:1 → 179

Calcyon; D1 dopamine receptor-interacting protein (calcyon)
NM_138915.1 → NP_620270.1 neuron-specific vesicular protein calcyon

See identical proteins and their annotated locations for NP_620270.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer variant. Both variants 1 and 2 encode the same protein.

Source sequence(s)

AF303658

UniProtKB/Swiss-Prot

P58821

UniProtKB/TrEMBL

A6HXF2

Related

ENSRNOP00000069564.1, ENSRNOT00000089729.2

Conserved Domains (1) summary

pfam06387
Location:1 → 179

Calcyon; D1 dopamine receptor-interacting protein (calcyon)