Copa coatomer protein complex subunit alpha [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Copaprovided by MGI
Official Full Name: coatomer protein complex subunit alphaprovided by MGI
Primary source: MGI:MGI:1334462
See related: Ensembl:ENSMUSG00000026553 AllianceGenome:MGI:1334462
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: xenin
Summary: Enables mRNA binding activity. Acts upstream of or within protein localization to axon and protein localization to cell leading edge. Located in COPI-coated vesicle; Golgi apparatus; and growth cone. Is expressed in several structures, including brain; jaw bone; and thoracic segment skeleton. Used to study autoimmune interstitial lung, joint, and kidney disease. Human ortholog(s) of this gene implicated in autoimmune interstitial lung, joint, and kidney disease. Orthologous to human COPA (COPI coat complex subunit alpha). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in limb E14.5 (RPKM 46.2), placenta adult (RPKM 40.1) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 1 H3; 1 79.54 cM

Exon count:: 34

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	1	NC_000067.7 (171909885..171949899)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	1	NC_000067.6 (172082529..172122332)

Chromosome 1 - NC_000067.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Individual and combined effects of GIP and xenin on differentiation, glucose uptake and lipolysis in 3T3-L1 adipocytes.
Title: Individual and combined effects of GIP and xenin on differentiation, glucose uptake and lipolysis in 3T3-L1 adipocytes.
Interaction between alpha-COP and SMN ameliorates disease phenotype in a mouse model of spinal muscular atrophy.
Title: Interaction between alpha-COP and SMN ameliorates disease phenotype in a mouse model of spinal muscular atrophy.
Remarkably, an improvement of the memory impairments was also observed. Importantly, human genetic association studies of different AD cohorts led to the identification of 12 SNPs and 24 mutations located in COPI genes linked to an increased AD risk.
Title: Relevance of the COPI complex for Alzheimer's disease progression in vivo.
The novel function of Copa in inter-compartmental trafficking of RNA.
Title: COPI transport complexes bind to specific RNAs in neuronal cells.
SMN directly binds to COPI and moves with survival motor neuron within axons.
Title: The COPI vesicle complex binds and moves with survival motor neuron within axons.
In a a large-scale functional screening of mesothelioma cells, the COPA protein was highly expressed in some mesothelioma cell lines but not in a pleural mesothelial cell line.
Title: Knockdown of COPA, identified by loss-of-function screen, induces apoptosis and suppresses tumor growth in mesothelioma mouse model.

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Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Targeted (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH126904 (e-PCR)
- UniSTS:209425

D1S2004E (e-PCR)
- UniSTS:151313

Copa (e-PCR), detects polymorphism
- UniSTS:141375

Copa (e-PCR), detects polymorphism
- UniSTS:141376

G42032 (e-PCR)
- UniSTS:105057

AU040324 (e-PCR)
- UniSTS:158888

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables hormone activity	IEA Inferred from Electronic Annotation more info
enables mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables structural molecule activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in endoplasmic reticulum to Golgi vesicle-mediated transport	IEA Inferred from Electronic Annotation more info
involved_in intra-Golgi vesicle-mediated transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in intracellular protein transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in intracellular protein transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within pancreatic juice secretion	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within protein localization to axon	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within protein localization to cell leading edge	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum	IBA Inferred from Biological aspect of Ancestor more info
involved_in signal transduction	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of COPI vesicle coat	IBA Inferred from Biological aspect of Ancestor more info
part_of COPI vesicle coat	ISO Inferred from Sequence Orthology more info
located_in COPI-coated vesicle	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi apparatus	ISO Inferred from Sequence Orthology more info	PubMed
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
located_in axon	ISO Inferred from Sequence Orthology more info	PubMed
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in extracellular space	ISO Inferred from Sequence Orthology more info
located_in growth cone	IDA Inferred from Direct Assay more info	PubMed
located_in growth cone	ISO Inferred from Sequence Orthology more info	PubMed
located_in neuronal cell body	ISO Inferred from Sequence Orthology more info	PubMed

General protein information

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Preferred Names: coatomer subunit alpha

Names: alpha-COP; alpha-coat 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_009938.4 → NP_034068.3 coatomer subunit alpha

See identical proteins and their annotated locations for NP_034068.3

Status: VALIDATED

Source sequence(s)

AC158930, AK043479, AW537456, CF734857

Consensus CDS

CCDS35780.1

UniProtKB/Swiss-Prot

E9Q075, Q8CIE6

UniProtKB/TrEMBL

Q8BTF0

Related

ENSMUSP00000118179.2, ENSMUST00000135192.8

Conserved Domains (5) summary

COG2319
Location:99 → 504

WD40; WD40 repeat [General function prediction only]

cd00200
Location:9 → 318

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

pfam04053
Location:339 → 767

Coatomer_WDAD; Coatomer WD associated region

pfam06957
Location:816 → 1218

COPI_C; Coatomer (COPI) alpha subunit C-terminus

sd00039
Location:15 → 49

7WD40; WD40 repeat [structural motif]

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000067.7 Reference GRCm39 C57BL/6J

Range

171909885..171949899

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036157379.1 → XP_036013272.1 coatomer subunit alpha isoform X1

UniProtKB/TrEMBL

F8WHL2, Q8BTF0

Related

ENSMUSP00000027833.6, ENSMUST00000027833.12

Conserved Domains (4) summary

cd00200
Location:9 → 318

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

sd00039
Location:15 → 49

7WD40; WD40 repeat [structural motif]

pfam04053
Location:338 → 776

Coatomer_WDAD; Coatomer WD associated region

pfam06957
Location:825 → 1227

COPI_C; Coatomer (COPI) alpha subunit C-terminus
XM_036157391.1 → XP_036013284.1 coatomer subunit alpha isoform X2

Conserved Domains (2) summary

pfam04053
Location:24 → 437

Coatomer_WDAD; Coatomer WD associated region

pfam06957
Location:486 → 888

COPI_C; Coatomer (COPI) alpha subunit C-terminus
XM_030245513.2 → XP_030101373.1 coatomer subunit alpha isoform X3

Conserved Domains (2) summary

pfam04053
Location:24 → 428

Coatomer_WDAD; Coatomer WD associated region

pfam06957
Location:477 → 879

COPI_C; Coatomer (COPI) alpha subunit C-terminus