FB2022_03, released June 9, 2022

Gene: Dmel\CSN1b

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General Information
Symbol
Dmel\CSN1b
Species
D. melanogaster
Name
COP9 signalosome subunit 1b
Annotation Symbol
CG3889
Feature Type
protein_coding_gene
FlyBase ID
FBgn0027057
Gene Model Status
Current
Stock Availability
5 publicly available
Gene Summary
COP9 signalosome subunit 1b (CSN1b) encodes the subunit 1 of the COP9 signalosome (CSN) and is essential for the stability of the complex. The CSN plays a central role in the regulation of E3-cullin RING ubiquitin ligases. [Date last reviewed: 2019-03-07] (FlyBase Gene Snapshot)
All Summaries
Also Known As

CSN1, DCH1-2

Key Links
Genomic Location
Cytogenetic map
75E4-75E4
Sequence location
Recombination map
3-45
RefSeq locus
NT_037436 REGION:18903057..18904930
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
PopFly
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (7 terms)
Molecular Function (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (6 terms)
Terms Based on Experimental Evidence (5 terms)
CV Term
Evidence
References
involved_in female germ-line stem cell population maintenance
inferred from mutant phenotype
(Pan et al., 2014)
involved_in germ cell development
inferred from mutant phenotype
(Qian et al., 2015)
involved_in germarium-derived cystoblast division
inferred from mutant phenotype
(Pan et al., 2014)
involved_in male germ-line cyst encapsulation
inferred from mutant phenotype
(Qian et al., 2015)
involved_in protein stabilization
inferred from mutant phenotype
(Ullah et al., 2007)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in protein deneddylation
inferred from sequence or structural similarity with HGNC:454
(FlyBase Curators, 2008-)
Cellular Component (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
part_of COP9 signalosome
inferred from biological aspect of ancestor with PANTHER:PTN000365417
(assigned by GO_Central )
(Gaudet et al., 2011)
inferred from sequence or structural similarity with MGI:MGI:2384801
(Freilich et al., 1999)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the CSN1 family. (Q9VVU5)
Protein Signatures (InterPro)
Summaries
Gene Snapshot
COP9 signalosome subunit 1b (CSN1b) encodes the subunit 1 of the COP9 signalosome (CSN) and is essential for the stability of the complex. The CSN plays a central role in the regulation of E3-cullin RING ubiquitin ligases. [Date last reviewed: 2019-03-07]
Gene Group (FlyBase)
COP9 SIGNALOSOME -
The COP9 signalosome is an eight-subunit complex that is structurally and evolutionarily related to the 19S lid of the 26S proteasome. The COP9 signalosome plays a central role in the regulation of the E3-cullin RING ubiquitin ligases, deNEDDylating the cullin subunit via the isopeptidase activity of the CNS5 subunit. (Adapted from FBrf0225508 and FBrf0225509).
Protein Function (UniProtKB)
Essential component of the COP9 signalosome complex (CSN), a complex involved in various cellular and developmental processes. The CSN complex is an essential regulator of the ubiquitin (Ubl) conjugation pathway by mediating the deneddylation of the cullin subunits of the SCF-type E3 ligase complexes, leading to decrease the Ubl ligase activity of SCF. The CSN complex plays an essential role in oogenesis and embryogenesis and is required for proper photoreceptor R cell differentiation and promote lamina glial cell migration or axon targeting. It also promotes Ubl-dependent degradation of cyclin E (CycE) during early oogenesis.
(UniProt, Q9VVU5)
Gene Model and Products
Number of Transcripts
1
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\CSN1b for information on other features

To submit a correction to a gene model please use the Contact FlyBase form

Protein Domains (via Pfam)
Isoform displayed:
Pfam protein domains
InterPro name
classification
start
end
Protein Domains (via SMART)
Isoform displayed:
SMART protein domains
InterPro name
classification
start
end
Structure New Section
Protein 3D structure   (Predicted by AlphaFold)   (AlphaFold entry Q9VVU5)

If you don't see the viewer to the right, refresh your browser.
Model Confidence:
  • Very high (pLDDT > 90)
  • Confident (90 > pLDDT > 70)
  • Low (70 > pLDDT > 50)
  • Very low (pLDDT < 50)

AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.

Comments on Gene Model

Gene model reviewed during 5.41

Gene model reviewed during 5.46

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
CSN1b-RA
FBtr0075074
NM_079428
1802
525
Additional Transcript Data and Comments
Reported size (kB)

1.754 (longest cDNA)

(Freilich et al., 1999)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
UniProt
RefSeq ID
GenBank
CSN1b-PA
FBpp0074841
58.2
525
6.82
Q9VVU5
NP_524152
AAF49212
Polypeptides with Identical Sequences

There is only one protein coding transcript and one polypeptide associated with this gene

Additional Polypeptide Data and Comments
Reported size (kDa)

525 (aa)

(Freilich et al., 1999)
Comments
External Data
Subunit Structure (UniProtKB)

Component of the CSN complex, probably composed of CSN1b, alien/CSN2, CSN3, CSN4, CSN5, CSN6, CSN7 and CSN8.

(UniProt, Q9VVU5)
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
UniProt
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\CSN1b using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Expression Data
Expression Summary Ribbons
Colored tiles in ribbon indicate that the Fly Cell Atlas project found the gene expressed in that cell type. Darker colors mean that more cells of that cell type express the gene:
 low
high 
Colorless tiles indicate that there is no scRNAseq data for the gene in that cell type.
Colored tiles in ribbon indicate that expression data (RNA and/or protein) has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
Colored tiles in the ribbon indicate the average RNA expression level of the gene at the indicated stages:
 low
high 
as determined by RNA-seq (RPKM) using whole organism samples modENCODE, Brown et al., 2014. For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\CSN1b in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
Bulk Downloads
RNA-Seq RPKM values for all genes
Reference
See Gelbart and Emmert, 2013 for analysis details and data files for all genes.
Developmental Proteome: Life Cycle
Developmental Proteome: Embryogenesis
External Data and Images
Linkouts
BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 3 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 7 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of CSN1b
Transgenic constructs containing regulatory region of CSN1b
Aberrations (Deficiencies and Duplications) ( 0 )
Inferred from experimentation ( 0 )
Inferred from location ( 0 )
    Alleles Representing Disease-Implicated Variants
    Phenotypes
    For more details about a specific phenotype click on the relevant allele symbol.
    Lethality
    Allele
    lethal
    lethal - all die during P-stage, with Scer\GAL4Mef2.PR
    partially lethal - majority die, with Scer\GAL4pnr-MD237
    viable
    viable, with Dcr-2UAS.cDa, Scer\GAL4elav.PLu
    viable, with Scer\GAL4tin.CΔ4
    Sterility
    Allele
    fertile
    Other Phenotypes
    Allele
    abnormal neuroanatomy | larval stage
    some die during pupal stage, with Scer\GAL4pnr-MD237
    visible, with Scer\GAL4Dll-md23
    visible, with Scer\GAL4pnr-MD237
    visible | adult stage | somatic clone
    Phenotype manifest in
    Allele
    arista, with Scer\GAL4Dll-md23
    chaeta | increased number, with Scer\GAL4pnr-MD237
    cyst cell of testis, with Scer\GAL4A3.eya
    cyst cell of testis, with Scer\GAL4c784
    cyst cell of testis, with Scer\GAL4NP1624
    embryonic/larval fat body | third instar larval stage, with Scer\GAL4SPARC-MI00329-GAL4
    extracellular matrix | third instar larval stage, with Scer\GAL4SPARC-MI00329-GAL4
    eye disc | somatic clone | third instar larval stage
    female germline stem cell | somatic clone, with Scer\GAL4VP16.nos.-FRT
    ganglion mother cell | larval stage
    larval neuroblast | larval stage
    leg, with Scer\GAL4Dll-md23
    mesothoracic tergum, with Scer\GAL4pnr-MD237
    sex comb, with Scer\GAL4Dll-md23
    testis, with Scer\GAL4A3.eya
    testis, with Scer\GAL4c784
    testis, with Scer\GAL4NP1624
    trichogen cell, with Scer\GAL4pnr-MD237
    trichogen cell | increased number, with Scer\GAL4pnr-MD237
    wing, with Scer\GAL4Dll-md23
    wing vein | somatic clone
    Orthologs
    Downloads
    Download All DIOPT Orthologs
    Human Orthologs (via DIOPT v8.0)
    Homo sapiens (Human) (1)
    Species\Gene Symbol
    Score
    Best Score
    Best Reverse Score
    Source
    Compara
    eggNOG
    Hieranoid
    Homologene
    Inparanoid
    Isobase
    OMA
    OrthoDB
    OrthoFinder
    OrthoInspector
    orthoMCL
    Panther
    Phylome
    RoundUp
    TreeFam
    ZFIN
    Alignment
    Complementation?
    Transgene?
    Hsap\GPS1
    14 of 15
    Yes
    Yes
    Model Organism Orthologs (via DIOPT v8.0)
    Mus musculus (laboratory mouse) (1)
    Species\Gene Symbol
    Score
    Best Score
    Best Reverse Score
    Source
    Compara
    eggNOG
    Hieranoid
    Homologene
    Inparanoid
    Isobase
    OMA
    OrthoDB
    OrthoFinder
    OrthoInspector
    orthoMCL
    Panther
    Phylome
    RoundUp
    TreeFam
    ZFIN
    Alignment
    Complementation?
    Transgene?
    Mmus\Gps1
    13 of 15
    Yes
    Yes
    Rattus norvegicus (Norway rat) (1)
    Rnor\Gps1
    11 of 13
    Yes
    Yes
    Xenopus tropicalis (Western clawed frog) (1)
    Xtro\gps1
    10 of 12
    Yes
    Yes
    Danio rerio (Zebrafish) (1)
    Drer\gps1
    10 of 15
    Yes
    Yes
    Caenorhabditis elegans (Nematode, roundworm) (1)
    Cele\csn-1
    11 of 15
    Yes
    Yes
    Arabidopsis thaliana (thale-cress) (2)
    Atha\FUS6
    9 of 9
    Yes
    Yes
    Atha\AT3G12850
    1 of 9
    No
    Yes
    Saccharomyces cerevisiae (Brewer's yeast) (1)
    Scer\PCI8
    1 of 15
    Yes
    Yes
    Schizosaccharomyces pombe (Fission yeast) (1)
    Spom\csn1
    9 of 12
    Yes
    Yes
    Other Organism Orthologs (via OrthoDB)
    Paralogs
    Downloads
    Download All DIOPT Paralogs
    Paralogs (via DIOPT v8.0)
    Drosophila melanogaster (Fruit fly) (2)
    Gene Symbol
    Score
    Source
    Compara
    eggNOG
    Homologene
    Inparanoid
    Isobase
    OrthoDB
    OrthoFinder
    orthoMCL
    Panther
    RoundUp
    Alignment
    CSN1a
    6 of 10
    Rpn7
    2 of 10
    Human Disease Associations
    FlyBase Human Disease Model Reports
      Disease Model Summary Ribbon
      Disease Ontology (DO) Annotations
      Models Based on Experimental Evidence ( 0 )
      Allele
      Disease
      Evidence
      References
      Potential Models Based on Orthology ( 0 )
      Human Ortholog
      Disease
      Evidence
      References
      Modifiers Based on Experimental Evidence ( 0 )
      Allele
      Disease
      Interaction
      References
      Disease Associations of Human Orthologs (via DIOPT v8.0 and OMIM)
      Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
      Homo sapiens (Human)
      Gene name
      Score
      OMIM
      OMIM Phenotype
      DO term
      Complementation?
      Transgene?
      GPS1; G protein pathway suppressor 1
      14 of 15
      601934
          Functional Complementation Data
          Functional complementation data is computed by FlyBase using a combination of the orthology data obtained from DIOPT and OrthoDB and the allele-level genetic interaction data curated from the literature.
          Interactions
          Summary of Physical Interactions
          esyN Network Diagram
          Show neighbor-neighbor interactions:
          Select Layout:
          Legend:
          Protein
          RNA
          Selected Interactor(s)
          Interactions Browser
          View in Interactions Browser
          Please see the Physical Interaction reports below for full details
          protein-protein
          Physical Interaction
          Assay
          References
          CSN1b - cic
          anti tag coimmunoprecipitation, anti tag western blot
          (Suisse et al., 2017)
          Summary of Genetic Interactions
          esyN Network Diagram
          Starting gene(s)
          Interaction type
          Interacting gene(s)
          Reference
          Starting gene(s)
          Interaction type
          Interacting gene(s)
          Reference
          External Data
          Subunit Structure (UniProtKB)
          Component of the CSN complex, probably composed of CSN1b, alien/CSN2, CSN3, CSN4, CSN5, CSN6, CSN7 and CSN8.
          (UniProt, Q9VVU5 )
          Linkouts
          DroID - A comprehensive database of gene and protein interactions.
          Pathways
          Signaling Pathways (FlyBase)
          Metabolic Pathways
          FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
          External Data
          Linkouts
          Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
          Genomic Location and Detailed Mapping Data
          Chromosome (arm)
          3L
          Recombination map
          3-45
          Cytogenetic map
          75E4-75E4
          Sequence location
          FlyBase Computed Cytological Location
          Cytogenetic map
          Evidence for location
          75E4-75E4
          Limits computationally determined from genome sequence between P{lacW}l(3)j4E6j4E6 and P{EP}MESR6EP3142
          Experimentally Determined Cytological Location
          Cytogenetic map
          Notes
          References
          Experimentally Determined Recombination Data
          Location

          3-45

          (FlyBase, 2016)

          3-42.0

          (Comeron et al., 2012)
          Left of (cM)
          Right of (cM)
          Notes
          Stocks and Reagents
          Stocks (5)
          Genomic Clones (12)
           

          Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete

          cDNA Clones (289)
           

          Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.

          cDNA clones, fully sequenced
          BDGP DGC clones
          Other clones
            Drosophila Genomics Resource Center cDNA clones

            For each fully sequenced cDNA the DGRC maintains various forms of the cDNA (e.g tagged or untagged) in several different host vectors for subsequent cloning and expression in Drosophila and Drosophila cell lines.

            cDNA Clones, End Sequenced (ESTs)
            BDGP DGC clones
            Other clones
            RNAi and Array Information
            Linkouts
            DRSC - Results frm RNAi screens
            GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
            Antibody Information
            Laboratory Generated Antibodies
             
            Commercially Available Antibodies
             
            Other Information
            Relationship to Other Genes
            Source for database identify of
            Source for database merge of
            Additional comments
            Other Comments

            S2 cells are treated with dsRNA made from templates generated with primers directed against this gene to assess effect on degradation of dup and geminin genes.

            (Higa et al., 2003)

            CSN1b blocks degradation of dup protein after γ-irradiation.

            (Higa et al., 2003)

            Area matching Drosophila COP 9 complex homolog subunit 1-2 gene. Acc. No. AF129080.

            (Davies, 2001.3.15)

            COP9 signalosome is essential for development.

            (Freilich et al., 1999)
            Origin and Etymology
            Discoverer
            Etymology
            Identification
            External Crossreferences and Linkouts ( 43 )
            Sequence Crossreferences
            NCBI Gene - Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
            GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.
            GenBank Protein - A collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB.
            RefSeq - A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein.
            UniProt/GCRP - The gene-centric reference proteome (GCRP) provides a 1:1 mapping between genes and UniProt accessions in which a single 'canonical' isoform represents the product(s) of each protein-coding gene.
            UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
            Other crossreferences
            AlphaFold DB - AlphaFold provides open access to protein structure predictions for the human proteome and other key proteins of interest, to accelerate scientific research.
            BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
            Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
            DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species
            EMBL-EBI Single Cell Expression Atlas - Single cell expression across species
            Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
            FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
            FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data
            Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
            Flygut - An atlas of the Drosophila adult midgut
            FlyMet - A comprehensive tissue-specific metabolomics resource for Drosophila.
            GenomeRNAi - A database for cell-based and in vivo RNAi phenotypes and reagents
            iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)
            InterPro - A database of protein families, domains and functional sites
            KEGG Genes - Molecular building blocks of life in the genomic space.
            MARRVEL_MODEL - MARRVEL (model organism gene)
            modMine - A data warehouse for the modENCODE project
            Linkouts
            DroID - A comprehensive database of gene and protein interactions.
            DRSC - Results frm RNAi screens
            FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
            FlyMine - An integrated database for Drosophila genomics
            Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
            Synonyms and Secondary IDs (16)
            Datasets (0)
            Study focus (0)
            Experimental Role
            Project
            Project Type
            Title
            Study result (0)
            Result
            Result Type
            Title
            References (65)