cep290 centrosomal protein 290 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: cep290provided by ZNC
Official Full Name: centrosomal protein 290provided by ZNC
Primary source: ZFIN:ZDB-GENE-041111-243
See related: Ensembl:ENSDARG00000062727 AllianceGenome:ZFIN:ZDB-GENE-041111-243
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: nphp6; im:7145703; im:7147820
Summary: Involved in animal organ development. Acts upstream of or within several processes, including cerebellum development; photoreceptor cell maintenance; and sensory organ development. Predicted to be located in centrosome and nucleus. Predicted to be active in centriolar satellite and ciliary transition zone. Is expressed in gut; nervous system; notochord; and post-vent region. Used to study ciliopathy. Human ortholog(s) of this gene implicated in Bardet-Biedl syndrome 14; Joubert syndrome 5; Leber congenital amaurosis 10; Meckel syndrome 4; and Senior-Loken syndrome. Orthologous to human CEP290 (centrosomal protein 290). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 25

Exon count:: 55

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	25	NC_007136.7 (17934427..18003018, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	25	NC_007136.6 (17838027..17906564, complement)

Chromosome 25 - NC_007136.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Genetic compensation for cilia defects in cep290 mutants by upregulation of cilia-associated small GTPases.
Title: Genetic compensation for cilia defects in cep290 mutants by upregulation of cilia-associated small GTPases.
Study data demonstrate a role for Cep290 in cone survival in zebrafish and indicate that the cep290fh297/fh297 mutant is a useful model to study the role of genetic modifiers on photoreceptor degeneration in zebrafish and to explore how progressive photoreceptor degeneration influences regeneration in adult zebrafish.
Title: Ciliary genes arl13b, ahi1 and cc2d2a differentially modify expression of visual acuity phenotypes but do not enhance retinal degeneration due to mutation of cep290 in zebrafish.
results provide a link between CEP290 and DNA replication stress and suggest CDK inhibition as a potential treatment strategy for a wide range of ciliopathy syndromes.
Title: DNA replication stress underlies renal phenotypes in CEP290-associated Joubert syndrome.
study proposes that Cep290 and Cep72 in centriolar satellites regulate the ciliary localization of BBS4, which in turn affects assembly and recruitment of the BBSome.
Title: The centriolar satellite proteins Cep72 and Cep290 interact and are required for recruitment of BBS proteins to the cilium.
Rkip prevents cilia formation and is associated with Cep290-mediated photoreceptor degeneration.
Title: Accumulation of the Raf-1 kinase inhibitory protein (Rkip) is associated with Cep290-mediated photoreceptor degeneration in ciliopathies.
the N-terminal region of the CEP290 protein is sufficient to restore visual function and this region may be a viable gene therapy target for Lebers disease patients with mutations in CEP290
Title: The N-terminal region of centrosomal protein 290 (CEP290) restores vision in a zebrafish model of human blindness.
The N-terminal domain of NPHP5 physically interacted with NPHP6.
Title: Genetic and physical interaction between the NPHP5 and NPHP6 gene products.

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General gene information

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Gene Ontology Provided by ZFIN

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA damage response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in camera-type eye development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within camera-type eye development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within cell projection organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cerebellum development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ciliary basal body-plasma membrane docking	IBA Inferred from Biological aspect of Ancestor more info
involved_in ciliary transition zone assembly	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within determination of heart left/right asymmetry	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within eye development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within eye photoreceptor cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within gastrulation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within head development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within inner ear development	IGI Inferred from Genetic Interaction more info	PubMed
involved_in kidney development	IBA Inferred from Biological aspect of Ancestor more info
involved_in non-motile cilium assembly	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within otic vesicle formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within otolith formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within otolith mineralization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within photoreceptor cell maintenance	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pronephros development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within pronephros development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of cilium assembly	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of retinal cell programmed cell death	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within retina layer formation	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in cell projection	IEA Inferred from Electronic Annotation more info
is_active_in centriolar satellite	IBA Inferred from Biological aspect of Ancestor more info
is_active_in ciliary transition zone	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: centrosomal protein of 290 kDa

Names: nephrocystin-6

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_001168267.1 → NP_001161739.1 centrosomal protein of 290 kDa

See identical proteins and their annotated locations for NP_001161739.1

Status: VALIDATED

Source sequence(s)

CR759966

UniProtKB/Swiss-Prot

P85001

UniProtKB/TrEMBL

A0A8M1NU93, F8W5U5

Related

ENSDARP00000141028.1, ENSDART00000158688.2

Conserved Domains (4) summary

COG1196
Location:131 → 997

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

TIGR02168
Location:1118 → 1985

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam16574
Location:1272 → 1399

CEP209_CC5; Coiled-coil region of centrosome protein CE290

cl19219
Location:77 → 185

DUF342; Protein of unknown function (DUF342)

RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007136.7 Reference GRCz11 Primary Assembly

Range

17934427..18003018 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005163020.4 → XP_005163077.1 centrosomal protein of 290 kDa isoform X2

UniProtKB/Swiss-Prot

P85001

UniProtKB/TrEMBL

A0A8M2BA16

Conserved Domains (4) summary

COG1196
Location:113 → 997

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

TIGR02168
Location:1118 → 1985

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam16574
Location:1272 → 1399

CEP209_CC5; Coiled-coil region of centrosome protein CE290

cl19219
Location:77 → 204

DUF342; Protein of unknown function (DUF342)
XM_009297907.3 → XP_009296182.1 centrosomal protein of 290 kDa isoform X5

See identical proteins and their annotated locations for XP_009296182.1

UniProtKB/Swiss-Prot

P85001

UniProtKB/TrEMBL

A0A8M1NU93, F8W5U5

Related

ENSDARP00000124972.1, ENSDART00000149696.3

Conserved Domains (4) summary

COG1196
Location:131 → 997

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

TIGR02168
Location:1118 → 1985

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam16574
Location:1272 → 1399

CEP209_CC5; Coiled-coil region of centrosome protein CE290

cl19219
Location:77 → 185

DUF342; Protein of unknown function (DUF342)
XM_009297905.3 → XP_009296180.1 centrosomal protein of 290 kDa isoform X3

UniProtKB/Swiss-Prot

P85001

UniProtKB/TrEMBL

A0A8M3AWH7

Conserved Domains (4) summary

COG1196
Location:131 → 997

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

TIGR02168
Location:1118 → 1985

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam16574
Location:1272 → 1399

CEP209_CC5; Coiled-coil region of centrosome protein CE290

cl19219
Location:77 → 185

DUF342; Protein of unknown function (DUF342)
XM_009297906.3 → XP_009296181.1 centrosomal protein of 290 kDa isoform X4

UniProtKB/Swiss-Prot

P85001

UniProtKB/TrEMBL

A0A8M3AP13

Conserved Domains (4) summary

COG1196
Location:131 → 1004

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

TIGR02168
Location:1125 → 1992

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam16574
Location:1279 → 1406

CEP209_CC5; Coiled-coil region of centrosome protein CE290

cl19219
Location:77 → 185

DUF342; Protein of unknown function (DUF342)
XM_009297904.3 → XP_009296179.1 centrosomal protein of 290 kDa isoform X1

UniProtKB/Swiss-Prot

P85001

UniProtKB/TrEMBL

A0A8M3AZL6

Conserved Domains (4) summary

COG1196
Location:131 → 1004

Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]

TIGR02168
Location:1125 → 1992

SMC_prok_B; chromosome segregation protein SMC, common bacterial type

pfam16574
Location:1279 → 1406

CEP209_CC5; Coiled-coil region of centrosome protein CE290

cl19219
Location:77 → 185

DUF342; Protein of unknown function (DUF342)