exd extradenticle [Drosophila melanogaster (fruit fly)] - Gene

Summary

Official Symbol: exdprovided by FlyBase
Official Full Name: extradenticleprovided by FlyBase
Primary source: FLYBASE:FBgn0000611
Locus tag: Dmel_CG8933
See related: AllianceGenome:FB:FBgn0000611
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Drosophila melanogaster
Lineage: Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota; Neoptera; Endopterygota; Diptera; Brachycera; Muscomorpha; Ephydroidea; Drosophilidae; Drosophila; Sophophora
Also known as: anon-EST:fe1H3; CG8933; DExd; Dm-EXD; Dmel\CG8933; Dpbx; Exd; EXD; l(1)IV; lincRNA.S9404; Pbx1; td48
Summary: Enables several functions, including DNA-binding transcription factor activity, RNA polymerase II-specific; protein heterodimerization activity; and transcription coactivator activity. Involved in several processes, including nervous system development; oenocyte development; and positive regulation of transcription by RNA polymerase II. Located in cytoplasm and nucleus. Part of RNA polymerase II transcription regulator complex and protein-DNA complex. Is expressed in several structures, including anlage in statu nascendi; embryonic/larval midgut primordium; head epidermis primordium; neuroblast NB5-6; and segmental subdivision of organ system. Human ortholog(s) of this gene implicated in congenital anomalies of kidney and urinary tract syndrome with or without hearing loss, abnormal ears, or developmental delay. Orthologous to several human genes including PBX1 (PBX homeobox 1) and PBX3 (PBX homeobox 3). [provided by Alliance of Genome Resources, Dec 2024]
Orthologs: all
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Genomic context

Location:: 14A5-14A5; 1-52 cM

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
Release 6.54	current	Release 6 plus ISO1 MT (GCF_000001215.4)	X	NC_004354.4 (15992468..15996509)
Release 5.57	previous assembly	Release 5 (GCF_000001215.2)	X	NC_004354.3 (15886501..15890542)

Chromosome X - NC_004354.4 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Novel Antennapedia and Ultrabithorax trimeric complexes with TBP and Exd regulate transcription.
Title: Novel Antennapedia and Ultrabithorax trimeric complexes with TBP and Exd regulate transcription.
Trimeric complexes of Antp-TBP with TFIIEbeta or Exd modulate transcriptional activity.
Title: Trimeric complexes of Antp-TBP with TFIIEβ or Exd modulate transcriptional activity.
Grh, AbdA, and Exd function together at multiple motifs on the apoptotic enhancer. Exd-Grh-Notch work with different Hox genes through region specific enhancers to pattern respective segments of larval central nervous system.
Title: Combinatorial action of Grainyhead, Extradenticle and Notch in regulating Hox mediated apoptosis in Drosophila larval CNS.
Hox protein Ultrabithorax (Ubx) in complex with its cofactor Extradenticle (Exd) bound specifically to clusters of very low affinity sites in enhancers of the shavenbaby gene of Drosophila. These low affinity sites conferred specificity for Ubx binding in vivo, but multiple clustered sites were required for robust expression when embryos developed in variable environments.
Title: Low affinity binding site clusters confer hox specificity and regulatory robustness.
Hth functions together with its co-factor Extradenticle to repress the R8-specific factor Senseless in dorsal rim area R8 cells, allowing expression of an ultraviolet-sensitive R7 Rhodopsin.
Title: Homothorax and Extradenticle alter the transcription factor network in Drosophila ommatidia at the dorsal rim of the retina.
cooperative binding sites for En, with the homeodomain-containing Hox cofactors Extradenticle (Exd) and Homothorax (Hth) was localized, within two CRMs that drive similar expression patterns
Title: Engrailed cooperates directly with Extradenticle and Homothorax on a distinct class of homeodomain binding sites to repress sloppy paired.
In the flight muscles, exd and hth are genetically upstream of another muscle identity gene, salm, and are direct transcriptional regulators of the signature flight muscle structural gene, Actin88F.
Title: Extradenticle and homothorax control adult muscle fiber identity in Drosophila.
Using computational platform, SELEX-seq, study shows that all eight Drosophila Hox proteins obtain novel recognition properties when they bind DNA with the dimeric cofactor Extradenticle-Homothorax.
Title: Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins.
Homothorax and extradenticle control dendritic and axonal targeting of olfactory projection neurons in the Drosophila brain.
Title: TALE-class homeodomain transcription factors, homothorax and extradenticle, control dendritic and axonal targeting of olfactory projection neurons in the Drosophila brain.
Selection of distinct Hox-Extradenticle interaction modes fine-tunes Hox protein activity.
Title: Selection of distinct Hox-Extradenticle interaction modes fine-tunes Hox protein activity.

Submit: New GeneRIF Correction See all GeneRIFs (20)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

NCBI Orthologs

Orthologs from OrthoDB

Gene Ontology Provided by FlyBase

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
contributes_to DNA-binding transcription factor activity, RNA polymerase II-specific	IPI Inferred from Physical Interaction more info	PubMed
enables DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables protein heterodimerization activity	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription coactivator activity	IDA Inferred from Direct Assay more info	PubMed
enables transcription coregulator activity	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in animal organ morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
involved_in brain development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in embryonic organ development	IBA Inferred from Biological aspect of Ancestor more info
involved_in eye development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron development	IBA Inferred from Biological aspect of Ancestor more info
involved_in oenocyte development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in peripheral nervous system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in regulation of cell fate specification	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in salivary gland boundary specification	TAS Traceable Author Statement more info	PubMed
involved_in somatic muscle development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of RNA polymerase II transcription regulator complex	IPI Inferred from Physical Interaction more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of protein-DNA complex	IDA Inferred from Direct Assay more info	PubMed
part_of transcription regulator complex	IDA Inferred from Direct Assay more info	PubMed
part_of transcription regulator complex	IPI Inferred from Physical Interaction more info	PubMed

General protein information

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Preferred Names: extradenticle

Names: CG8933-PA; CG8933-PB; CG8933-PD; CG8933-PE; Pbx1-oncogene-like; anon-fast-evolving-1H3; exd-PA; exd-PB; exd-PD; exd-PE

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_004354.4 Reference assembly

Range

15992468..15996509

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_078636.5 → NP_523360.1 extradenticle, isoform A [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_523360.1

Status: REVIEWED

UniProtKB/Swiss-Prot

A4V4K5, P40427, Q0KHS1, Q9V3S2

UniProtKB/TrEMBL

M9PHV1

Related

FBpp0073940

Conserved Domains (2) summary

cd00086
Location:239 → 299

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam03792
Location:41 → 237

PBC; PBC domain
NM_001272663.2 → NP_001259592.1 extradenticle, isoform D [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001259592.1

Status: REVIEWED

UniProtKB/Swiss-Prot

A4V4K5, P40427, Q0KHS1, Q9V3S2

UniProtKB/TrEMBL

M9PHV1

Conserved Domains (2) summary

cd00086
Location:239 → 299

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam03792
Location:41 → 237

PBC; PBC domain
NM_167478.3 → NP_727923.1 extradenticle, isoform B [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_727923.1

Status: REVIEWED

UniProtKB/Swiss-Prot

A4V4K5, P40427, Q0KHS1, Q9V3S2

UniProtKB/TrEMBL

M9PHV1

Related

FBpp0073942

Conserved Domains (2) summary

cd00086
Location:239 → 299

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam03792
Location:41 → 237

PBC; PBC domain
NM_001272664.1 → NP_001259593.1 extradenticle, isoform E [Drosophila melanogaster]

See identical proteins and their annotated locations for NP_001259593.1

Status: REVIEWED

UniProtKB/Swiss-Prot

A4V4K5, P40427, Q0KHS1, Q9V3S2

UniProtKB/TrEMBL

M9PHV1

Conserved Domains (2) summary

cd00086
Location:239 → 299

homeodomain; Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.

pfam03792
Location:41 → 237

PBC; PBC domain