FB2021_01, released Feb 18, 2021

Gene: Dmel\Clbn

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General Information
Symbol
Dmel\Clbn
Species
D. melanogaster
Name
Caliban
Annotation Symbol
CG11847
Feature Type
protein_coding_gene
FlyBase ID
FBgn0259152
Gene Model Status
Current
Stock Availability
6 publicly available
Gene Snapshot
Contributions welcome
Other Summaries
Key Links
Genomic Location
Cytogenetic map
96C1-96C1
Sequence location
3R:25,127,502..25,131,155 [+]
Recombination map

3-87

RefSeq locus
NT_033777 REGION:25127502..25131155
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 (9 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables tRNA binding
inferred from direct assay
(assigned by UniProt )
(Wu et al., 2019)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables ribosomal large subunit binding
inferred from biological aspect of ancestor with PANTHER:PTN000391355
(assigned by GO_Central )
(Gaudet et al., 2011)
enables tRNA binding
inferred from biological aspect of ancestor with PANTHER:PTN000391355
(assigned by GO_Central )
(Gaudet et al., 2011)
Biological Process (5 terms)
Terms Based on Experimental Evidence (4 terms)
CV Term
Evidence
References
involved_in positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator
inferred from mutant phenotype
(Wang et al., 2013)
involved_in positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage
inferred from mutant phenotype
(Wang et al., 2013)
involved_in protein export from nucleus
inferred from mutant phenotype
(Bi et al., 2005)
involved_in rescue of stalled ribosome
inferred from direct assay
(assigned by UniProt )
(Dai et al., 2020)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
involved_in rescue of stalled ribosome
inferred from biological aspect of ancestor with PANTHER:PTN000391355
(assigned by GO_Central )
(Gaudet et al., 2011)
involved_in ribosome-associated ubiquitin-dependent protein catabolic process
inferred from biological aspect of ancestor with PANTHER:PTN000391357
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in cytoplasmic side of mitochondrial outer membrane
inferred from direct assay
(assigned by UniProt )
(Dai et al., 2020)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
part_of RQC complex
inferred from biological aspect of ancestor with PANTHER:PTN000391355
(assigned by GO_Central )
(Gaudet et al., 2011)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the NEMF family. (Q9VBX1)
Protein Signatures (InterPro)
Summaries
Protein Function (UniProtKB)
Component of the ribosome quality control complex (RQC), a ribosome-associated complex that mediates ubiquitination and extraction of incompletely synthesized nascent chains for proteasomal degradation. Clbn/NEMF is responsible for selective recognition of stalled 60S subunits by recognizing an exposed, nascent chain-conjugated tRNA moiety. Clbn/NEMF is important for the stable association of l(3)76BDr/LTN1 to the complex (By similarity). Plays a role in regulating nuclear transport possibly through directly binding to both emb and cargo proteins (PubMed:16103875).
(UniProt, Q9VBX1)
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\Clbn 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
Comments on Gene Model

Gene model reviewed during 5.49

Gene model reviewed during 5.55

Sequence Ontology: Class of Gene
gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
Clbn-RB
FBtr0301277
NM_001170250
3270
992
Clbn-RC
FBtr0301278
NM_143084
3258
992
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
Clbn-PB
FBpp0290492
112.6
992
7.17
NP_001163721
ACZ95015
Clbn-PC
FBpp0290493
112.6
992
7.17
NP_651341
AAF56406
Polypeptides with Identical Sequences

The group(s) of polypeptides indicated below share identical sequence to each other.

992 aa isoforms: Clbn-PB, Clbn-PC
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Component of the ribosome quality control complex (RQC), composed of at least the E3 ubiquitin ligase l(3)76BDr/LTN1 and Clbn/NEMF. The complex probably also contains TCF25 as well as TER94/VCP and its ubiquitin-binding cofactors. RQC forms a stable complex with 60S ribosomal subunits (By similarity). Interacts (via its C-terminus) with pros (via its homeobox) (PubMed:16103875). Interacts (via its N-terminus) with emb (PubMed:16103875).

(UniProt, Q9VBX1)
Domain

The N-terminal domain contains a nuclear export signal. The C-terminal domain may interact with cargo proteins.

(UniProt, Q9VBX1)
Crossreferences
InterPro - A database of protein families, domains and functional sites
Linkouts
Sequences Consistent with the Gene Model
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\Clbn 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 expression data has been curated by FlyBase for that anatomical location. Colorless tiles indicate that there is no curated data for that location.
For complete stage-specific expression data, view the modENCODE Development RNA-Seq section under High-Throughput Expression below.
Transcript Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
mass spectroscopy
Stage
Tissue/Position (including subcellular localization)
Reference
adult stage
adult head
(Aradska et al., 2015)
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
located_in cytoplasmic side of mitochondrial outer membrane
inferred from direct assay
(assigned by UniProt )
(Dai et al., 2020)
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\Clbn 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
FLIGHT - Cell culture data for RNAi and other high-throughput technologies
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Flygut - An atlas of the Drosophila adult midgut
Images
FlyBase Wiki
Image Based Resources
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 5 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 5 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Clbn
Transgenic constructs containing regulatory region of Clbn
Aberrations (Deficiencies and Duplications) ( 0 )
Inferred from experimentation
Inferred from location
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (2)
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\NEMF
13 of 15
Yes
Yes
Hsap\ERMN
1 of 15
No
Yes
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (2)
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\Nemf
13 of 15
Yes
Yes
Mmus\Ermn
1 of 15
No
Yes
Rattus norvegicus (Norway rat) (2)
Rnor\Nemf
3 of 13
Yes
Yes
Rnor\Ermn
1 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\nemf
8 of 12
Yes
Yes
Danio rerio (Zebrafish) (2)
Drer\LOC108182745
4 of 15
Yes
Yes
Drer\zgc:153813
1 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\Y82E9BR.18
12 of 15
Yes
Yes
Arabidopsis thaliana (thale-cress) (1)
Atha\emb1441
8 of 9
Yes
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\RQC2
12 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\SPCC132.01c
10 of 12
Yes
Yes
Ortholog(s) in Drosophila Species (via OrthoDB v9.1) ( EOG0919037O )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00012576
Drosophila simulans
Dsim\GD21177
Drosophila sechellia
Dsec\GM17806
Drosophila erecta
Dere\GG11364
Drosophila yakuba
Dyak\GE23561
Drosophila ananassae
Dana\GF17891
Drosophila persimilis
Dper\GL21904
Drosophila willistoni
Dwil\GK13887
Drosophila virilis
Dvir\GJ23608
Drosophila mojavensis
Dmoj\GI23827
Drosophila grimshawi
Dgri\GH19576
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG0915016Q )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17011507
Glossina morsitans
Tsetse fly
Gmor\GMOY011494
Mayetiola destructor
Hessian fly
Mdes\Mdes011186
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL007639
Anopheles darlingi
American malaria mosquito
Adar\ADAC002240
Anopheles gambiae
Malaria mosquito
Agam\GPRNNA6
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ013434
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W0273 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA000753
Danaus plexippus
Monarch butterfly
Dple\DPOGS212811-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL008175
Apis florea
Little honeybee
Aflo\3346040228
Apis mellifera
Western honey bee
Amel\GB46751
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP10153
Bombus terrestris
Buff-tailed bumblebee
Bter\15216305
Linepithema humile
Argentine ant
Lhum\LH18302
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:000cc8
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG003047
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_05302
Tribolium castaneum
Red flour beetle
Tcas\TC009916
Pediculus humanus
Human body louse
Phum\PHUM452400
Pediculus humanus
Human body louse
Phum\PHUM622580
Rhodnius prolixus
Kissing bug
Rpro\RPRC003896
Cimex lectularius
Bed bug
Clec\CLEC006737
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI001375
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_01295
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X024H )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR013043
Ixodes scapularis
Black-legged tick
Isca\ISCW000678
Stegodyphus mimosarum
African social velvet spider
Smim\KFM68260.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur27g00100
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_305191
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G02MR )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Sdccag1
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-Sdccag1-2
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000000931
Gallus gallus
Domestic chicken
Ggal\GGA.42303
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (0)
No records found.
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?
    NEMF; nuclear export mediator factor
    13 of 15
    608378
      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
      Clbn - U4-U6-60K
      experimental knowledge based
      (Guruharsha et al., 2011)
      Clbn - p38b
      anti tag coimmunoprecipitation, peptide massfingerprinting, anti tag western blot
      (Belozerov et al., 2012)
      Clbn - pros
      two hybrid, pull down, autoradiography
      (Bi et al., 2005)
      RNA-protein
      Physical Interaction
      Assay
      References
      Clbn - tRNA:Ala-AGC-1-1
      clip, quantitative reverse transcription pcr
      (Wu et al., 2019)
      Summary of Genetic Interactions
      esyN Network Diagram
      esyN Network Key:
      Suppression
      Enhancement
      View in Interactions Browser
      Please look at the allele data for full details of the genetic interactions
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      Clbn
      suppressible
      hid
      (Wang et al., 2013)
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      tefu
      enhanceable
      Clbn
      (Wang et al., 2013)
      External Data
      Subunit Structure (UniProtKB)
      Component of the ribosome quality control complex (RQC), composed of at least the E3 ubiquitin ligase l(3)76BDr/LTN1 and Clbn/NEMF. The complex probably also contains TCF25 as well as TER94/VCP and its ubiquitin-binding cofactors. RQC forms a stable complex with 60S ribosomal subunits (By similarity). Interacts (via its C-terminus) with pros (via its homeobox) (PubMed:16103875). Interacts (via its N-terminus) with emb (PubMed:16103875).
      (UniProt, Q9VBX1 )
      Linkouts
      BioGRID - A database of protein and genetic interactions.
      DroID - A comprehensive database of gene and protein interactions.
      InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
      MIST (protein-protein) - An integrated Molecular Interaction Database
      Pathways
      Signaling Pathways (FlyBase)
      Metabolic Pathways
      External Data
      Linkouts
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      3R
      Recombination map

      3-87

      Cytogenetic map
      96C1-96C1
      Sequence location
      3R:25,127,502..25,131,155 [+]
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      96C1-96C1
      Limits computationally determined from genome sequence between P{lacW}OstStt3j2D9 and P{PZ}Aats-gln05461
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      Experimentally Determined Recombination Data
      Location

      3-87

      (FlyBase, 2016)

      3-85.6

      (Comeron et al., 2012)
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (6)
      Genomic Clones (26)
      cDNA Clones (12)
       

      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
         

        polyclonal

        (Song et al., 2018, Wang et al., 2013)
        Commercially Available Antibodies
         
        Other Information
        Relationship to Other Genes
        Source for database identify of
        Source for database merge of

        Source for merge of: Clbn CG11847

        (Bi et al., 2005)
        Additional comments
        Other Comments

        Clbn facilitates both p53-dependent and p53-independent DNA damage-induced apoptosis. It has proapoptotic activity.

        (Wang et al., 2013)
        Origin and Etymology
        Discoverer
        Etymology
        Identification
        External Crossreferences and Linkouts ( 29 )
        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/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
        Other crossreferences
        BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
        Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
        Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
        Flygut - An atlas of the Drosophila adult midgut
        FlyMine - An integrated database for Drosophila genomics
        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.
        modMine - A data warehouse for the modENCODE project
        Linkouts
        BioGRID - A database of protein and genetic interactions.
        DroID - A comprehensive database of gene and protein interactions.
        DRSC - Results frm RNAi screens
        FLIGHT - Cell culture data for RNAi and other high-throughput technologies
        FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
        FlyCyc Genes - Genes from a BioCyc PGDB for Dmel
        InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
        MIST (protein-protein) - An integrated Molecular Interaction Database
        Synonyms and Secondary IDs (4)
        Datasets (0)
        Study focus (0)
        Experimental Role
        Project
        Project Type
        Title
        References (39)