FlyBase Gene Report: Dmel\fd96Ca

FORK HEAD BOX TRANSCRIPTION FACTORS -: The forkhead box family of transcription factors are sequence-specific DNA binding proteins that regulate transcription. They are characterized by approximately 110 amino acid DNA-binding domain known as the forkhead or winged helix. (Adapted from FBrf0173142).

Protein Function (UniProtKB)

Involved in development during embryogenesis.

(UniProt, P32028)

Gene Model and Products

Number of Transcripts

Number of Unique Polypeptides

Please see the JBrowse view of Dmel\fd96Ca 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

Protein 3D structure (Predicted by AlphaFold) (AlphaFold entry P32028)

If you don't see a structure in the viewer, 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.

Experimentally Determined Structures

Crossreferences

Comments on Gene Model

Gene model reviewed during 5.49

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Assoc. CDS (aa)

fd96Ca-RA

FBtr0084770

NM_079771

1702

372

fd96Ca-RB

FBtr0339246

NM_001300587

2195

372

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

UniProt

RefSeq ID

GenBank

fd96Ca-PA

FBpp0084145

41.7

372

7.01

FBpp0308353

41.7

372

7.01

P32028

NP_001287516

AHN57515

Polypeptides with Identical Sequences

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

372 aa isoforms: fd96Ca-PA, fd96Ca-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

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\fd96Ca 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

Testis-specificity index

The testis specificity index was calculated from modENCODE tissue expression data by Vedelek et al., 2018 to indicate the degree of testis enrichment compared to other tissues. Scores range from -2.52 (underrepresented) to 5.2 (very high testis bias).

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Transcript Expression

No Assay Recorded

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

sensory neuron

(Hacker et al., 1992)

head

(Hacker et al., 1992)

in situ

Stage

Tissue/Position (including subcellular localization)

Reference

embryonic stage

presumptive embryonic/larval peripheral nervous system

(Hacker et al., 1992)

neuroblast

(Hacker et al., 1992)

embryonic stage 1 -- 3

organism

Comment: maternally deposited

(Fisher et al., 2012)

embryonic stage 4 -- 6

organism | faint | ubiquitous

(Fisher et al., 2012)

embryonic stage 9 -- 10

central brain primordium

(Fisher et al., 2012)

gnathal primordium

Comment: reported as gnathal lobes anlage

(Fisher et al., 2012)

ventral nerve cord primordium

(Fisher et al., 2012)

embryonic stage 11

visceral trunk mesoderm

(Zhu et al., 2012)

embryonic stage 11 -- 12

maxillary sensory complex primordium

(Fisher et al., 2012)

procephalic neuroblast

(Fisher et al., 2012)

ventral nerve cord primordium

(Fisher et al., 2012)

embryonic stage 13 -- 16

embryonic brain

(Fisher et al., 2012)

embryonic maxillary sensory complex

(Fisher et al., 2012)

larval ventral nerve cord

(Fisher et al., 2012)

Additional Descriptive Data

fd96Ca transcripts are expressed in symmetrical pairs of 14 segmentally arranged neuroblasts along the longitudinal axis of the embryo. At the end of embryogenesis, transcripts are observed in a cluster of sensory neurons in the head. The transcripts are at low abundance.

(Hacker et al., 1992)

Marker for

Subcellular Localization

CV Term

Polypeptide Expression

Additional Descriptive Data

Marker for

Subcellular Localization

CV Term

Evidence

References

Expression Deduced from Reporters

High-Throughput Expression Data

Associated Tools

JBrowse - Visual display of RNA-Seq signals

View Dmel\fd96Ca in JBrowse

RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region

View exonic expression by developmental stage for Dmel\fd96Ca

View exonic expression by tissue for Dmel\fd96Ca

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

FBgn0004897

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

43010/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0004897

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0004897

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0004897

Flygut - An atlas of the Drosophila adult midgut

FBgn0004897

Images

FlyBase Wiki

Image Based Resources

Alleles, Insertions, Transgenic Constructs, and Aberrations

Classical and Insertion Alleles ( 2 )

For All Classical and Insertion Alleles Show

Other relevant insertions

Transgenic Constructs ( 6 )

For All Alleles Carried on Transgenic Constructs Show

Transgenic constructs containing/affecting coding region of fd96Ca

Transgenic constructs containing regulatory region of fd96Ca

Aberrations (Deficiencies and Duplications) ( 0 )

Inferred from experimentation ( 0 )

Inferred from location ( 7 )

Variants

Variant Molecular Consequences

Alleles Representing Disease-Implicated Variants

Phenotypes

For more details about a specific phenotype click on the relevant allele symbol.

Lethality

Allele

viable

fd96Ca^5nt

viable, with Dcr-2^UAS.cDa, Scer\GAL4^elav.PLu

fd96Ca^GD4345

viable, with Scer\GAL4^Mef2.PR

fd96Ca^GD4345

viable, with Scer\GAL4^pnr-MD237

fd96Ca^GD4345

viable, with Scer\GAL4^tin.CΔ4

fd96Ca^GD4345

Phenotype manifest in

Allele

sex comb tooth | decreased number

fd96Ca^5nt

sex comb tooth | decreased number, with Scer\GAL4^Dll-em212

Orthologs

Downloads

Download All DIOPT Orthologs

Human Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Homo sapiens (Human) (50)

Hsap\FOXB1

10 of 14

Yes

Hsap\FOXB2

10 of 14

Yes

3 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

Yes

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Model Organism Orthologs (via DIOPT v9.1)

Species\Gene Symbol

Score

Best Score

Best Reverse Score

Source

Alignment

Complementation?

Transgene?

Rattus norvegicus (Norway rat) (41)

Rnor\Foxb2

7 of 14

Yes

Rnor\Foxa3

3 of 14

Rnor\Foxb1

3 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Yes

Mus musculus (laboratory mouse) (40)

Mmus\Foxb1

10 of 14

Yes

Mmus\Foxb2

10 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Xenopus tropicalis (Western clawed frog) (43)

Xtro\foxb1

8 of 13

Yes

Xtro\foxb2

5 of 13

Yes

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

3 of 13

Yes

3 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

1 of 13

Yes

Xtro\gcdh

1 of 13

Xtro\nr2f6

1 of 13

Danio rerio (Zebrafish) (61)

Drer\foxb1a

11 of 14

Yes

Drer\foxb1b

11 of 14

Yes

Drer\foxb2

10 of 14

Yes

3 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

1 of 14

Drer\si:ch211-145o7.3

1 of 14

Drer\si:rp71-45k5.2

1 of 14

Drer\zgc:113424

1 of 14

Caenorhabditis elegans (Nematode, roundworm) (13)

Cele\lin-31

11 of 14

Yes

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

2 of 14

1 of 14

1 of 14

1 of 14

Anopheles gambiae (African malaria mosquito) (19)

Agam\AgaP_AGAP013297

10 of 12

Yes

Agam\AgaP_AGAP002460

6 of 12

Yes

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

2 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

1 of 12

Arabidopsis thaliana (thale-cress) (0)

Saccharomyces cerevisiae (Brewer's yeast) (4)

Scer\HCM1

5 of 13

Yes

Scer\FKH1

4 of 13

Scer\FKH2

3 of 13

Scer\FHL1

1 of 13

Schizosaccharomyces pombe (Fission yeast) (4)

Spom\mei4

5 of 12

Yes

Spom\fkh2

4 of 12

Spom\sep1

4 of 12

Spom\fhl1

3 of 12

Escherichia coli (enterobacterium) (0)

Other Organism Orthologs (via OrthoDB)

Data provided directly from OrthoDB:fd96Ca. Refer to their site for version information.

Paralogs

Downloads

Download All DIOPT Paralogs

Paralogs (via DIOPT v9.1)

Gene Symbol

Score

Source

Alignment

Drosophila melanogaster (Fruit fly) (16)

9 of 13

6 of 13

6 of 13

6 of 13

fkh

6 of 13

6 of 13

6 of 13

5 of 13

5 of 13

5 of 13

3 of 13

bin

2 of 13

2 of 13

2 of 13

2 of 13

2 of 13

Human Disease Associations

FlyBase Human Disease Model Reports

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 v9.1 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?

FOXB1; forkhead box B1

10 of 14

619961

FOXB2; forkhead box B2

10 of 14

619962

FOXA3; forkhead box A3

3 of 14

602295

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

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please see the Physical Interaction reports below for full details

protein-protein

Physical Interaction

Assay

References

fd96Ca - BuGZ

two hybrid array

(Shokri et al., 2019)

fd96Ca - CG4956

two hybrid array

(Shokri et al., 2019)

fd96Ca - D19A

two hybrid array

(Shokri et al., 2019)

fd96Ca - HP1b

two hybrid array

(Shokri et al., 2019)

fd96Ca - brk

two hybrid array

(Shokri et al., 2019)

Summary of Genetic Interactions

Interaction Browsers

View in FlyBase Interactions Browser View in MIST tool (external link)

Please look at the allele data for full details of the genetic interactions

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

fd96Ca

enhanceable

fd96Cb

(Ruiz-Losada et al., 2021)

Starting gene(s)

Interaction type

Interacting gene(s)

Reference

fd96Cb

enhanceable

fd96Ca

(Ruiz-Losada et al., 2021)

External Data

Linkouts

DroID - A comprehensive database of gene and protein interactions.

FBgn0004897

Pathways

Signaling Pathways (FlyBase)

Metabolic Pathways

FlyBase

External Links

External Data

Linkouts

Class of Gene

nuclear_gene

protein_coding_gene

Genomic Location and Detailed Mapping Data

Chromosome (arm)

Recombination map

3-86

Cytogenetic map

96B20-96B20

Sequence location

3R:25,082,684..25,084,878 [+]

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

96B20-96B20

Limits computationally determined from genome sequence between P{lacW}OstStt3^j2D9 and P{PZ}Aats-gln⁰⁵⁴⁶¹

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

96C-96C

(determined by in situ hybridisation)

(Hacker et al., 1992)

Experimentally Determined Recombination Data

Location

3-86

(FlyBase, 2016)

3-85.6

(Comeron et al., 2012)

Left of (cM)

Right of (cM)

Notes

Stocks and Reagents

Stocks (5)

Aberrations including deletions of this gene Aberrations including duplications of this gene

Bloomington

83379

y¹ w^*; P{fd96Ca-GFP.FPTB}attP40

79887

y¹ sc^* v¹ sev²¹; P{TOE.GS02123}attP40

57262

y¹ sc^* v¹ sev²¹; P{TRiP.HMC04655}attP40

VDRC

v100261

P{KK107313}VIE-260B

v13719

w¹¹¹⁸; P{GD4345}v13719

Genomic Clones (15)

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

cDNA Clones (1)

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 JBrowse for alignment of the cDNAs and ESTs to the gene model.

cDNA clones, fully sequenced

BDGP DGC clones

Other clones

RT01156

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.

FBgn0004897

cDNA Clones, End Sequenced (ESTs)

BDGP DGC clones

Other clones

RNAi and Array Information

Linkouts

DRSC - Results frm RNAi screens

FBgn0004897

Antibody Information

Laboratory Generated Antibodies

Commercially Available Antibodies

Cell Line Information

Publicly Available Cell Lines

Other Stable Cell Lines

Other Comments

Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5.

(Clark et al., 1993)

One of seven genes identified on basis of sequence similarity to forkhead domain that is conserved in the rodent hepatocyte enriched nuclear transcription factor.

(Hacker et al., 1992)

Relationship to Other Genes

Source for database merge of

Additional comments

Nomenclature History

Source for database identify of

Nomenclature comments

Etymology

Synonyms and Secondary IDs (8)

Reported As

Symbol Synonym

CG11921

(Neuert et al., 2017, Ni et al., 2010.12.1, Keleman et al., 2009.8.5, Klebes et al., 2005)

Dm-FoxB1

(Heingård et al., 2019)

Dmfd4

(Mazet et al., 2003)

FD4

(Lee and Frasch, 2004, Kaufmann and Knoechel, 1996, Häcker, 1992.9.29, Hacker et al., 1992)

FoxB

(Janssen et al., 2022)

fd4

(Ruiz-Losada et al., 2021, Mazet et al., 2006)

fd96Ca

(Drake et al., 2025, Schomburg et al., 2022, Spierer et al., 2021, Shokri et al., 2019, Neuert et al., 2017, Transgenic RNAi Project members, 2017-, model organism Encyclopedia of Regulatory Network (modERN) Project, 2015-, Archbold et al., 2014, Zhu et al., 2012, Mazet et al., 2006, Copley, 2005, Hoskins et al., 2005, Lee and Frasch, 2004)

Name Synonyms

forkhead domain 96Ca

Secondary FlyBase IDs

Datasets (0)

Study focus (0)

Experimental Role

Project

Project Type

Title

Study result (0)

Result

Result Type

Title

External Crossreferences and Linkouts ( 36 )

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.

43010

GenBank Nucleotide - A collection of sequences from several sources, including GenBank, RefSeq, TPA, and PDB.

M96443

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.

P32028

UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information

P32028

UniProt/TrEMBL - Automatically annotated and unreviewed records of protein sequence and functional information

A0A0B4LHW8

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.

P32028

BDGP expression data - Patterns of gene expression in Drosophila embryogenesis

FBgn0004897

DRscDB - A single-cell RNA-seq resource for data mining and data comparison across species

43010/tissue=All

EMBL-EBI Single Cell Expression Atlas - Single cell expression across species

FBgn0004897

FlyAtlas2 - A Drosophila melanogaster expression atlas with RNA-Seq, miRNA-Seq and sex-specific data

FBgn0004897

FlyMine - An integrated database for Drosophila genomics

FBgn0004897

InterPro - A database of protein families, domains and functional sites

KEGG Genes - Molecular building blocks of life in the genomic space.

dme:Dmel_CG11921

MARRVEL_MODEL - MARRVEL (model organism gene)

43010

Linkouts

Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones

FBgn0004897

DroID - A comprehensive database of gene and protein interactions.

FBgn0004897

DRSC - Results frm RNAi screens

FBgn0004897

Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

FBgn0004897

FlyCyc Genes - Genes from a BioCyc PGDB for Dmel

FBGN0004897

Flygut - An atlas of the Drosophila adult midgut

FBgn0004897

iBeetle-Base - RNAi phenotypes in the red flour beetle (Tribolium castaneum)

References (40)

The following external sites may use different assemblies or annotations than FlyBase.

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