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Gene: Dmel\ctrip

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General Information
Symbol
Dmel\ctrip
Species
D. melanogaster
Name
circadian trip
Annotation Symbol
CG42574
Feature Type
protein_coding_gene
FlyBase ID
FBgn0260794
Gene Model Status
Current
Stock Availability
17 publicly available
Gene Snapshot
Circadian trip (Ctrip) is a HECT ubiquitin ligase that regulates the levels and circadian oscillations of the Clk transcriptional activator. Ctrip plays a role in the control of rest-activity rhythms. [Date last reviewed: 2016-09-01]
Other Summaries
Key Links
Genomic Location
Cytogenetic map
82D5-82D5
Sequence location
3R:4,786,284..4,812,096 [-]
Recombination map
3-47.1
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI Genome Data Viewer
UCSC Genome Browser
Ensembl Genome Browser
PopFly Genome Browser
GO Summary Ribbons
Families, Domains and Molecular Function
Gene Group Membership (FlyBase)
Protein Family (UniProt, Sequence Similarities)
-
Protein Domains/Motifs
InterPro
HECT domain; WWE domain; Armadillo-like helical; Armadillo-type fold; WWE domain, subgroup; HECT, E3 ligase catalytic domain; WWE domain superfamily
Molecular Function (see GO section for details)
Experimental Evidence
-
Predictions / Assertions
ubiquitin-protein transferase activity; zinc ion binding
Summaries
Gene Group Membership
HECT UBIQUITIN LIGASES -
E3 (ubiquitin) ligases interact with both ubiquitin-E2 (ubiquitin-conjugating) enzymes and the target protein, transferring the ubiquitin from the E2 to the substrate. Members of the HECT family of E3 ubiquitin ligases are characterized by a C-terminal HECT domain. This catalytic domain forms an intermediate thioester bond with ubiquitin via a conserved Cys when transferring ubiquitin from the E2 to the target protein. (Adapted from FBrf0225009).
Gene Model and Products
Number of Transcripts
11
Number of Unique Polypeptides
9

Please see the GBrowse view of Dmel\ctrip or the JBrowse view of Dmel\ctrip 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 5.47
Annotated transcripts do not represent all possible combinations of alternative exons and/or alternative promoters.
Low-frequency RNA-Seq exon junction(s) not annotated.
Shares 5' UTR with upstream gene.
Gene model reviewed during 5.53
Sequence Ontology: Class of Gene
gene_with_edited_transcript
(Rodriguez et al., 2012, Graveley et al., 2011)
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
ctrip-RA
FBtr0301437
NM_141239
10589
3140
ctrip-RB
FBtr0303911
NM_001202241
10587
3140
ctrip-RC
FBtr0303912
NM_001202242
9366
2737
ctrip-RE
FBtr0303914
NM_001202244
9957
2930
ctrip-RF
FBtr0303915
NM_001202245
10759
3139
ctrip-RH
FBtr0303917
NM_001202247
9378
2737
ctrip-RI
FBtr0334902
NM_001202243
10136
2736
ctrip-RJ
FBtr0334903
NM_001202246
10831
2929
ctrip-RK
FBtr0344028
NM_001300232
10593
3111
ctrip-RL
FBtr0344029
NM_001300233
10631
2901
ctrip-RM
FBtr0344030
NM_001300234
9291
2708
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
ctrip-PA
FBpp0290652
336.6
3140
7.26
NP_649496
AAF52092
ctrip-PB
FBpp0292914
336.6
3140
7.26
NP_001189170
ADV37262
ctrip-PC
FBpp0292915
292.5
2737
6.72
NP_001189171
ADV37263
ctrip-PE
FBpp0292917
314.2
2930
6.99
NP_001189173
ADV37265
ctrip-PF
FBpp0292918
336.5
3139
7.26
NP_001189174
ADV37266
ctrip-PH
FBpp0292920
292.5
2737
6.72
NP_001189176
ADV37268
ctrip-PI
FBpp0306923
292.4
2736
6.72
NP_001189172
ADV37264
ctrip-PJ
FBpp0306924
314.1
2929
6.99
NP_001189175
ADV37267
ctrip-PK
FBpp0310477
333.7
3111
7.28
NP_001287161
AHN57160
ctrip-PL
FBpp0310478
311.3
2901
7.00
NP_001287162
AHN57161
ctrip-PM
FBpp0310479
289.6
2708
6.73
NP_001287163
AHN57162
Polypeptides with Identical Sequences

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

3140 aa isoforms: ctrip-PA, ctrip-PB
2737 aa isoforms: ctrip-PC, ctrip-PH
Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
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\ctrip using the Feature Mapper tool.

External Data
Crossreferences
Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
Linkouts
Gene Ontology (9 terms)
Molecular Function (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
ubiquitin-protein transferase activity
inferred from sequence or structural similarity with HGNC:12306
(FlyBase Curators, 2008--)
zinc ion binding
inferred from electronic annotation with InterPro:IPR018123
(assigned by InterPro )
(FlyBase Curators et al., 2004-)
Biological Process (5 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
positive regulation of circadian rhythm
inferred from mutant phenotype
(Lamaze et al., 2011)
positive regulation of protein catabolic process
inferred from mutant phenotype
(Lamaze et al., 2011)
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
cellular response to DNA damage stimulus
inferred from biological aspect of ancestor with PANTHER:PTN000134292
(assigned by GO_Central )
(Gaudet et al., 2011)
negative regulation of histone H2A K63-linked ubiquitination
inferred from biological aspect of ancestor with PANTHER:PTN000134292
(assigned by GO_Central )
(Gaudet et al., 2011)
ubiquitin-dependent protein catabolic process
inferred from biological aspect of ancestor with PANTHER:PTN000134292
(assigned by GO_Central )
(Gaudet et al., 2011)
inferred from sequence or structural similarity with HGNC:12306
(FlyBase Curators, 2008--)
Cellular Component (2 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
nuclear speck
inferred from biological aspect of ancestor with PANTHER:PTN000134292
(assigned by GO_Central )
(Gaudet et al., 2011)
nucleus
inferred from sequence or structural similarity with HGNC:12306
(FlyBase Curators, 2008--)
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
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
embryonic stage 1 -- 3
organism

Comment: maternally deposited

(Fisher et al., 2012)
embryonic stage 4 -- 6
organism
(Fisher et al., 2012)
embryonic stage 7 -- 8
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 9 -- 10
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 11 -- 12
organism | ubiquitous
(Fisher et al., 2012)
embryonic stage 13 -- 16
organism | ubiquitous
(Fisher et al., 2012)
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
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\ctrip 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
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, and Transgenic Constructs
Classical and Insertion Alleles ( 11 )
Transgenic Constructs ( 9 )
Deletions and Duplications ( 2 )
Disrupted in
Df(3R)Exel6142
(Ryder, 2004.4.26)
Partially disrupted in
DF(3R)1501
(Lamaze et al., 2011)
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Download All OrthoDB Orthologs
Human Orthologs (via DIOPT v7.1)
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\TRIP12
10 of 15
Yes
Yes
 
Hsap\HECTD1
1 of 15
No
No
Model Organism Orthologs (via DIOPT v7.1)
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\Trip12
9 of 15
Yes
Yes
Mmus\Hectd1
1 of 15
No
No
Rattus norvegicus (Norway rat) (1)
Rnor\Trip12
6 of 13
Yes
Yes
Xenopus tropicalis (Western clawed frog) (1)
Xtro\trip12
7 of 12
Yes
Yes
Danio rerio (Zebrafish) (2)
Drer\trip12
8 of 15
Yes
Yes
Drer\hectd1
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (1)
Cele\hecd-1
1 of 15
Yes
No
Arabidopsis thaliana (thale-cress) (2)
Atha\KAK
5 of 9
Yes
Yes
Atha\UPL4
4 of 9
No
Yes
Saccharomyces cerevisiae (Brewer's yeast) (1)
Scer\UFD4
9 of 15
Yes
Yes
Schizosaccharomyces pombe (Fission yeast) (1)
Spom\SPAC12B10.01c
8 of 12
Yes
Yes
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190093 )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Dmel\ctrip
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00008599
Drosophila suzukii
Spotted wing Drosophila
Dsuz\DS10_00008600
Drosophila simulans
Dsim\GD19654
Drosophila sechellia
Dsec\GM10679
Drosophila erecta
Dere\GG11366
Drosophila yakuba
Dyak\GE25331
Drosophila ananassae
Dana\GF16088
Drosophila pseudoobscura pseudoobscura
Dpse\GA30193
Drosophila persimilis
Dper\GL22220
Drosophila willistoni
Dwil\GK14424
Drosophila virilis
Dvir\GJ10115
Drosophila mojavensis
Dmoj\GI22511
Drosophila grimshawi
Dgri\GH17429
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091500B5 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Mdoa\17011537
Glossina morsitans
Tsetse fly
Gmor\GMOY002668
Lucilia cuprina
Australian sheep blowfly
Lcup\FF38_12445
Mayetiola destructor
Hessian fly
Mdes\Mdes010120
Aedes aegypti
Yellow fever mosquito
Aaeg\AAEL017357
Anopheles darlingi
American malaria mosquito
Adar\ADAC009382
Anopheles gambiae
Malaria mosquito
Agam\AGAP001296
Culex quinquefasciatus
Southern house mosquito
Cqui\CPIJ012812
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W00A8 )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bmor\BGIBMGA007539
Danaus plexippus
Monarch butterfly
Dple\DPOGS204268-PA
Heliconius melpomene
Postman butterfly
Hmel\HMEL015203
Apis florea
Little honeybee
Aflo\2247287108
Apis mellifera
Western honey bee
Amel\LOC409382
Bombus impatiens
Common eastern bumble bee
Bimp\BIMP25193
Bombus terrestris
Buff-tailed bumblebee
Bter\15216278
Linepithema humile
Argentine ant
Lhum\LH11940
Megachile rotundata
Alfalfa leafcutting bee
Mrot\MROTU:001c97
Nasonia vitripennis
Parasitic wasp
Nvit\Nasvi2EG006926
Dendroctonus ponderosae
Mountain pine beetle
Dpod\YQE_02693
Tribolium castaneum
Red flour beetle
Tcas\TC010408
Pediculus humanus
Human body louse
Phum\PHUM075960
Rhodnius prolixus
Kissing bug
Rpro\RPRC011284
Rhodnius prolixus
Kissing bug
Rpro\RPRC014638
Rhodnius prolixus
Kissing bug
Rpro\RPRC008389
Rhodnius prolixus
Kissing bug
Rpro\ctrip
Cimex lectularius
Bed bug
Clec\CLEC009803
Acyrthosiphon pisum
Pea aphid
Apim\ACYPI009777
Zootermopsis nevadensis
Nevada dampwood termite
Znev\Znev_09932
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X00AI )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Smar\SMAR005156
Stegodyphus mimosarum
African social velvet spider
Smim\KFM71329.1
Stegodyphus mimosarum
African social velvet spider
Smim\KFM64798.1
Tetranychus urticae
Two-spotted spider mite
Turt\tetur02g01880
Tetranychus urticae
Two-spotted spider mite
Turt\tetur02g01900
Tetranychus urticae
Two-spotted spider mite
Turt\tetur02g01940
Tetranychus urticae
Two-spotted spider mite
Turt\tetur02g01920
Daphnia pulex
Water flea
Dpux\DAPPUDRAFT_50916
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G00GQ )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Spur\Sp-trip12
Strongylocentrotus purpuratus
Purple sea urchin
Spur\SPU_016715gn
Ciona intestinalis
Vase tunicate
Cint\ENSCING00000022256
Ciona intestinalis
Vase tunicate
Cint\LOC100181389
Gallus gallus
Domestic chicken
Ggal\TRIP12
Human Disease Model Data
FlyBase Human Disease Model Reports
    Alleles Reported to Model Human Disease (Disease Ontology)
    Download
    Models ( 0 )
    Allele
    Disease
    Evidence
    References
    Interactions ( 0 )
    Allele
    Disease
    Interaction
    References
    Comments ( 0 )
     
    Human Orthologs (via DIOPT v7.1)
    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
    Complementation?
    Transgene?
    TRIP12; thyroid hormone receptor interactor 12
    10 of 15
    604506
     
    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
    Interactions Browser
    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
    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.
    Pathways
    Gene Group - Pathway Membership (FlyBase)
    External Data
    Linkouts
    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    3R
    Recombination map
    3-47.1
    Cytogenetic map
    82D5-82D5
    Sequence location
    3R:4,786,284..4,812,096 [-]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    82D5-82D5
    Limits computationally determined from genome sequence between P{PZ}l(3)0273302733 and P{EP}EP974
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    Experimentally Determined Recombination Data
    Location
    3-47.1
    (FlyBase, 2016)
    3-44.1
    (Comeron et al., 2012)
    Left of (cM)
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (17)
    Genomic Clones (20)
    cDNA Clones (97)
     

    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 sequences
    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
    Source for merge of: CG17735 CG14656
    (FlyBase Genome Annotators, 2008)
    Additional comments
    Annotations CG17735 and CG14656 merged as CG42574 in release 5.16 of the genome annotation.
    (FlyBase Genome Annotators, 2008)
    Other Comments
    Origin and Etymology
    Discoverer
    Etymology
    Source for identity of: ctrip CG42574
    (Lamaze et al., 2011)
    Identification
    External Crossreferences and Linkouts ( 70 )
    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/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information
    Other crossreferences
    BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
    InterPro - A database of protein families, domains and functional sites
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    Drosophila Genomics Resource Center - Drosophila Genomics Resource Center cDNA clones
    DroID - A comprehensive database of gene and protein interactions.
    DRSC - Results frm RNAi screens
    Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
    FLIGHT - Cell culture data for RNAi and other high-throughput technologies
    Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
    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)
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    KEGG Genes - Molecular building blocks of life in the genomic space.
    KEGG Pathways - Wiring diagrams of molecular interactions, reactions and relations.
    modMine - A data warehouse for the modENCODE project
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    Synonyms and Secondary IDs (7)
    Datasets (0)
    Study focus (0)
    Experimental Role
    Project
    Project Type
    Title
    References (61)