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FB2026_01
,
released March 12, 2026
transcription factor - homeodomain - paired domain - plays a decisive role in the progression of a regulatory hierarchy from pair-rule directed segmentation of the embryo to the subdivision carried out by segment polarity genes specifying positional information within segments - regulates accessory gland development and male fertility
Please see the JBrowse view of Dmel\prd for information on other features
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AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Some regions with low pLDDT may be unstructured in isolation.
Gene model reviewed during 5.51
Annotated transcripts do not represent all supported alternative splices within 5' UTR.
3.6, 2.5 (northern blot)
None of the polypeptides share 100% sequence identity.
613 (aa)
Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\prd using the Feature Mapper tool.
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).
Comment: reported as procephalic ectoderm anlage
Comment: reported as procephalic ectoderm anlage
Comment: reported as procephalic ectoderm anlage
Comment: reported as procephalic ectoderm anlage
Expression was examined at four phases of embryonic stage 5. prd is initially expressed in a nonperiodic gap-like pattern in the anterior, which begins to resolve into stripes in phase 2; however, the full 7-stripe pattern arises only during phase 3. The stripes emerge fully refined, with sharp, evenly spaced stripes.
prd expression is enriched in adult males.
Comment: rows E, F
prd protein is expressed in male accessory glands. It is initially expressed at high levels in all accessory gland cells, but protein levels decline with increasing age of virgin males. prd protein levels decline more rapidly in the main cells than in the secondary cells. In 10 day males, prd protein is detected only in scattered secondary cells in the distal region of the glands. Mating increases prd protein levels in both main and secondary cells throughout the glands.
prd protein is first detected in the anterior region of very early embryos and is subsequently restricted to a very narrow anterior stripe. During cellularization, bell-shaped stripes (stripes 3-7) are observed. The order of stripe appearance is 4 and 7, followed by 3 and 6, and finally stripe 5 emerges. At this point the anterior stripe splits into two. By mid-cellularization prd protein has reached equal levels in all stripes. At the same time, the preferential accumulation of prd protein at the posterior margins generates a gradient within each stripe. During the second half of cellularization, expression also occurs in a patch of cells at the anterior dorsal end of the embryo and in an eighth stripe. By the end of gastrulation, the number of stripes has doubled to 14 as a result of reduction of protein in the middle of the stripes accompanied by an increase of protein in the anterior region of the stripes. At the end of the germ band extended stage, the expression in the stripes has disappeared. prd protein is expressed in the head region, most strongly in the maxillary lobe, but also in the labial and mandibular lobes and in the clypeolabrum. prd protein is also detected in the developing CNS in 2-3 specific neurons per hemisegment.
JBrowse - Visual display of RNA-Seq signals
View Dmel\prd in JBrowse
Please Note FlyBase no longer curates genomic clone accessions so this list may not be complete
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.
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.
DNA-protein interactions: genome-wide binding profile assayed for prd protein in 2-3 hr embryos; see BDTNP1_TFBS_prd collection report.
prd is required for promoting cell proliferation during early accessory gland development.
In a sample of 79 genes with multiple introns, 33 showed significant heterogeneity in G+C content among introns of the same gene and significant positive correspondence between the intron and the third codon position G+C content within genes. These results are consistent with selection adding against preferred codons at the start of genes.
Ecol\CAT assays in culture cells reveal both the prd domain (PD) and the homeodomain (HD) can mediate transcriptional activation independently. PD binding sites are able to mimic the expression pattern of prd in vivo. In vivo expression of a PD reporter gene only requires prd to bind through its PD. Different C-terminal regions are involved in transactivation mediated by the HD or the PD.
Both the HD and the N-terminal subdomain of the PD (the PAI domain) are absolutely required within the same molecule for normal prd function. The conserved C-terminal subdomain of the PD (RED domain) appears to be dispensable. Inability to dimerize via the HD reduces but does not abolish the ability of the prd product to function. Deletion of the PRD repeat reduces but does not abolish the ability of the prd product to function. While prd can use its DNA-binding domains combinatorially in order to achieve different DNA-binding specificities, its principal binding mode requires a cooperative interaction between the PAI domain and the homeodomain.
prd regulates late even skipped expression through a composite binding site for the paired domain and the homeodomain. Mutagenesis of either binding site leads to significant reduction in the activity of the late element, indicating that both domains are required for regulation.
Pax proteins recognize different target genes in vivo through various combinations of their DNA binding domains, thus expanding their recognition repertoire. The prd protein can bind, in vitro, exclusively through its PAI domain, or through a dimer of its HD, or through cooperative interaction between the PAI domain and HD. However, prd function in vivo requires the synergistic action of both the PAI domain and the HD.
Both the paired domain and the homeodomain are required for in vivo function of the prd protein.
The paired domain of the prd protein has been crystallised and its structure solved. The structure reveals how a β turn can be used for minor groove recognition, provides new information about the docking of a helix turn helix units and provides a structural basis for the understanding of PAX developmental mutants.
The prd repeat is not required for the in vivo regulation of the target genes en and gsb. The prd repeat appears to be embedded within a Pro-rich transcriptional activation domain required for the regulation of these genes. Analysis of the prd domain indicates the N-terminal half, which is required for DNA binding in vitro, is also required for in vivo function, whereas the C-terminal half is dispensable for the regulation of en and gsb.
Transient expression assays using Ecol\CAT reporter gene constructs have been used to define the sequences responsible for the synergistic action of ftz and prd, these have been mapped to different regions of the two proteins. ftz protein has a synergistic effect on transcription of a target promoter in the presence of prd protein that is apparently entirely independent of binding of ftz protein to the promoter DNA. This synergism is dependent on the presence of homeodomain DNA binding sites in the promoter and does not occur at active promoters that are not regulated by homeodomain.
Expression of prd depends on activation by gap gene hb, Kr, kni and gt products. Primary pair rule gene products act primarily in subsequent modulation rather than activation of prd stripes. Factors activating prd expression in the pair rule mode interact with those activating it along the dorso-ventral axis.
wg expression is aberrantly activated and regulated in pair rule mutant embryos.
Homeo domain cooperative dimerization, binding site configuration and binding site sequence specificity allow for distinction between homeo domain proteins within the prd domain.
Expression of prd is repressed by ectopic expression of eve.
Mutant analysis shows that wild type prd function is required to set up expression of ac and sc in row B and D, respectively, of the embryonic proneural cluster.
Mutations in zygotic pair rule gene prd interact with RpII140wimp.
The paired box of prd encodes a DNA-binding activity, independent of the DNA-binding activity of the homeodomain and with a different sequence specificity.
prd RNA expression during early embryogenesis has been studied in wild-type and single double pair-rule mutant embryos. The regulation of prd expression is subject to a regulatory hierarchy among the pair-rule genes, and prd is at the bottom of this hierarchy, mediating the transition from pair-rule to segment-polarity genes. The transition of prd expression from the early 'pair-rule' pattern to the 'segment-polarity' pattern is regulated by the secondary pair-rule genes opa and odd.
A transient expression assay has been employed to investigate the potential of homeobox genes to function as transcriptional activators.
Genetic analysis demonstrates that prd is dispensable for efficient homeotic gene expression in the visceral mesoderm.
The wild-type allele of prd is required for normal segmentation in embryos and larvae. Mutant alleles and deficiencies show no maternal effect in homozygous germ-line cloness and are embryonic lethals with half the normal number of segmental units. In strong mutants, the anterior part of segments T1, T3, A2, A4, A6 and A8 and the posterior part of T2, A1, A3, A5 and A7 (i.e., odd-numbered parasegments) are deleted (Nusslein-Volhard, Kluding and Jurgens, 1985). Weak mutants such as prd2 show small and less regular segmental deletions. Structures missing in prd mutants include: derivatives of the mandibular segments, labial sense organs, anterior prothorax, posterior mesothorax, anterior metathorax and alternating posterior and anterior abdominal segments, including the telson and the posterior lateral sense organs (Nusslein-Volhard, Kluding and Jurgens, 1985). No head fold visible at gastrulation. Experiments with a temperature-sensitive mutant indicate that the TSP occurs during the cellular blastoderm stage (Nusslein-Volhard et al., 1985; Kilchherr et al., 1986).
Source for identity of: prd CG6716
