FB2022_02, released March 29, 2022

Gene: Dmel\onecut

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General Information
Symbol
Dmel\onecut
Species
D. melanogaster
Name
onecut
Annotation Symbol
CG1922
Feature Type
protein_coding_gene
FlyBase ID
FBgn0028996
Gene Model Status
Current
Stock Availability
10 publicly available
Gene Summary
onecut (onecut) encodes a transcription factor that binds two different DNA motifs (Cut and Hox). It is mainly expressed in mature neurons and maintains neuronal identity. [Date last reviewed: 2019-03-14] (FlyBase Gene Snapshot)
All Summaries
Key Links
Genomic Location
Cytogenetic map
Sequence location
Recombination map
4-0
RefSeq locus
NC_004353 REGION:598555..607649
Sequence
Get Decorated FASTA
Genomic Maps
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
NCBI
UCSC
Ensembl
Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (6 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
enables DNA-binding transcription activator activity, RNA polymerase II-specific
inferred from direct assay
(Nguyen et al., 2000)
Terms Based on Predictions or Assertions (2 terms)
CV Term
Evidence
References
enables DNA-binding transcription factor activity, RNA polymerase II-specific
inferred from biological aspect of ancestor with PANTHER:PTN001422142
(assigned by GO_Central )
(Gaudet et al., 2011)
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding
inferred from biological aspect of ancestor with PANTHER:PTN001422142
(assigned by GO_Central )
(Gaudet et al., 2011)
Biological Process (2 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
involved_in positive regulation of transcription by RNA polymerase II
inferred from direct assay
(Nguyen et al., 2000)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
involved_in regulation of transcription by RNA polymerase II
inferred from biological aspect of ancestor with PANTHER:PTN001422142
(assigned by GO_Central )
(Gaudet et al., 2011)
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
located_in nucleus
inferred from direct assay
(Nguyen et al., 2000)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
is_active_in nucleus
inferred from biological aspect of ancestor with PANTHER:PTN001422142
(assigned by GO_Central )
(Gaudet et al., 2011)
Gene Group (FlyBase)
Protein Family (UniProt)
Belongs to the CUT homeobox family. (Q9NJB5)
Protein Signatures (InterPro)
Summaries
Gene Snapshot
onecut (onecut) encodes a transcription factor that binds two different DNA motifs (Cut and Hox). It is mainly expressed in mature neurons and maintains neuronal identity. [Date last reviewed: 2019-03-14]
Gene Group (FlyBase)
CUT HOMEOBOX TRANSCRIPTION FACTORS -
CUT homeobox transcription factors are sequence-specific DNA binding proteins that regulate transcription. The CUT proteins have a homeodomain and one or more copies of the 75 amino acid DNA-binding CUT domain. (Adapted from FBrf0232555 and PMID:18797923).
Protein Function (UniProtKB)
Transcriptional regulator. Binds and recognize ATTG sites.
(UniProt, Q9NJB5)
Summary (Interactive Fly)

homeodomain and cut domain - regulates some aspects of neural differentiation or maintenance

Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
1

Please see the JBrowse view of Dmel\onecut 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 Q9NJB5)

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 5.43

Low-frequency RNA-Seq exon junction(s) not annotated.

Gene model reviewed during 5.47

Sequence Ontology: Class of Gene
nuclear_gene
protein_coding_gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
onecut-RA
FBtr0089104
NM_080103
6742
1081
onecut-RB
FBtr0310610
NM_001272136
6050
1081
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
onecut-PA
FBpp0088173
117.7
1081
5.02
NP_524842
AAF59330
onecut-PB
FBpp0302730
117.7
1081
5.02
NP_001259065
AGB96555
Polypeptides with Identical Sequences

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

1081 aa isoforms: onecut-PA, onecut-PB
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\onecut 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
Polypeptide Expression
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\onecut 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 ( 5 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 11 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of onecut
Transgenic constructs containing regulatory region of onecut
Aberrations (Deficiencies and Duplications) ( 1 )
Inferred from experimentation ( 1 )
Gene partially disrupted in
Df(4)Ephx652
(Boyle et al., 2006)
Inferred from location ( 0 )
Alleles Representing Disease-Implicated Variants
Phenotypes
Orthologs
Downloads
Download All DIOPT Orthologs
Human Orthologs (via DIOPT v8.0)
Homo sapiens (Human) (5)
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\ONECUT1
10 of 15
Yes
Yes
Hsap\ONECUT2
9 of 15
No
Yes
Hsap\ONECUT3
6 of 15
No
Yes
Hsap\CUX1
1 of 15
No
No
1  
Hsap\CUX2
1 of 15
No
No
Model Organism Orthologs (via DIOPT v8.0)
Mus musculus (laboratory mouse) (5)
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\Onecut1
10 of 15
Yes
Yes
Mmus\Onecut2
9 of 15
No
Yes
Mmus\Onecut3
6 of 15
No
Yes
Mmus\Cux2
2 of 15
No
No
Mmus\Cux1
1 of 15
No
No
Rattus norvegicus (Norway rat) (4)
Rnor\Onecut1
5 of 13
Yes
Yes
Rnor\Cux2
1 of 13
No
No
Rnor\Onecut2
1 of 13
No
Yes
Rnor\Onecut3
1 of 13
No
Yes
Xenopus tropicalis (Western clawed frog) (6)
Xtro\onecut1.2
7 of 12
Yes
Yes
Xtro\onecut1
5 of 12
No
Yes
Xtro\cux1
1 of 12
No
No
Xtro\cux2
1 of 12
No
No
Xtro\onecut2
1 of 12
No
Yes
Xtro\onecut3
1 of 12
No
Yes
Danio rerio (Zebrafish) (9)
Drer\onecut1
11 of 15
Yes
Yes
Drer\onecut3b
8 of 15
No
Yes
Drer\onecutl
7 of 15
No
Yes
Drer\onecut3a
6 of 15
No
Yes
Drer\onecut2
5 of 15
No
Yes
Drer\cux2a
2 of 15
No
No
Drer\cux1a
1 of 15
No
No
Drer\cux1b
1 of 15
No
No
Drer\cux2b
1 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (7)
Cele\ceh-48
9 of 15
Yes
Yes
Cele\ceh-38
6 of 15
No
Yes
Cele\ceh-21
5 of 15
No
Yes
Cele\ceh-39
5 of 15
No
Yes
Cele\ceh-49
3 of 15
No
Yes
Cele\ceh-44
1 of 15
No
No
Cele\F41G3.6
1 of 15
No
Yes
Arabidopsis thaliana (thale-cress) (0)
No records found.
Saccharomyces cerevisiae (Brewer's yeast) (0)
No records found.
Schizosaccharomyces pombe (Fission yeast) (0)
No records found.
Other Organism Orthologs (via OrthoDB)
Paralogs
Downloads
Download All DIOPT Paralogs
Paralogs (via DIOPT v8.0)
Drosophila melanogaster (Fruit fly) (1)
Gene Symbol
Score
Source
Compara
eggNOG
Homologene
Inparanoid
Isobase
OrthoDB
OrthoFinder
orthoMCL
Panther
RoundUp
Alignment
ct
1 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?
    ONECUT1; one cut homeobox 1
    10 of 15
    604164
        ONECUT2; one cut homeobox 2
        9 of 15
        604894
            ONECUT3; one cut homeobox 3
            6 of 15
            611294
                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
                onecut - CG31955
                two hybrid array
                (Shokri et al., 2019)
                onecut - PolE4
                two hybrid array
                (Shokri et al., 2019)
                onecut - drm
                two hybrid array
                (Shokri et al., 2019)
                onecut - eg
                two hybrid array
                (Shokri et al., 2019)
                onecut - ftz-f1
                two hybrid array
                (Shokri et al., 2019)
                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
                DroID - A comprehensive database of gene and protein interactions.
                Pathways
                Signaling Pathways (FlyBase)
                Metabolic Pathways
                External Data
                Linkouts
                Genomic Location and Detailed Mapping Data
                Chromosome (arm)
                4
                Recombination map
                4-0
                Cytogenetic map
                102D1-102D1
                Sequence location
                FlyBase Computed Cytological Location
                Cytogenetic map
                Evidence for location
                102D1-102D1
                Experimentally Determined Cytological Location
                Cytogenetic map
                Notes
                References
                102C6-102C6
                (Nguyen, 1999.7.14)
                Experimentally Determined Recombination Data
                Location

                4-0

                (FlyBase, 2016)
                Left of (cM)
                Right of (cM)
                Notes
                Stocks and Reagents
                Stocks (10)
                Genomic Clones (14)
                 

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

                cDNA Clones (113)
                 

                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

                (Nguyen et al., 2000)
                Commercially Available Antibodies
                 
                Other Information
                Relationship to Other Genes
                Source for database identify of
                Source for database merge of

                Source for merge of: onecut CG1922

                (Bayraktaroglu, 2000.8.7)
                Additional comments
                Other Comments
                Origin and Etymology
                Discoverer
                Etymology
                Identification
                External Crossreferences and Linkouts ( 47 )
                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
                UniProt/TrEMBL - Automatically annotated and unreviewed 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
                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
                Interactive Fly - A cyberspace guide to Drosophila development and metazoan evolution
                Synonyms and Secondary IDs (5)
                Datasets (8)
                Study focus (0)
                Experimental Role
                Project
                Project Type
                Title
                Study result (8)
                Result
                Result Type
                Title
                scRNAseq_2020_Cattenoz_NI_seq_clustering
                Clustering analysis of hemocytes from non-infested third instar larvae
                scRNAseq_2020_Cattenoz_WI_seq_clustering
                Clustering analysis of hemocytes from wasp-infested third instar larvae
                scRNAseq_2020_Cho_NI72LG_seq_clustering
                Clustering analysis of lymph gland cells from non-infested larvae at 72 h after egg-laying
                scRNAseq_2020_Cho_NI96LG_seq_clustering
                Clustering analysis of lymph gland cells from non-infested larvae at 96 h after egg-laying
                scRNAseq_2020_Cho_NI120LG_seq_clustering
                Clustering analysis of lymph gland cells from non-infested larvae at 120 h after egg-laying
                scRNAseq_2020_Cho_WI96LG_seq_clustering
                Clustering analysis of lymph gland cells from wasp-infested larvae at 96 h after egg-laying
                scRNAseq_2020_Cho_NI96HL_seq_clustering
                Clustering analysis of circulating hemocytes from non-infested larvae at 96 h after egg-laying
                scRNAseq_2020_Cho_NI120HL_seq_clustering
                Clustering analysis of circulating hemocytes from non-infested larvae at 120 h after egg-laying
                References (52)