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General Information
Symbol
Dmel\prd
Species
D. melanogaster
Name
paired
Annotation Symbol
CG6716
Feature Type
FlyBase ID
FBgn0003145
Gene Model Status
Stock Availability
Gene Snapshot
paired (prd) is a paired-rule gene that encodes a transcription factor with two independent DNA binding domains, a paired domain and a homeodomain. Its roles include embryonic segmentation, accessory gland development and male fertility. [Date last reviewed: 2019-03-14]
Key Links
Genomic Location
Cytogenetic map
Sequence location
2L:12,082,995..12,085,827 [-]
Recombination map
2-46
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Protein Family (UniProt)
Belongs to the paired homeobox family. (P06601)
Summaries
Gene Group (FlyBase)
PAIRED HOMEOBOX TRANSCRIPTION FACTORS -
Paired homeobox transcription factors are sequence-specific DNA binding proteins that regulate transcription. They have a characteristic paired domain in association with the homeodomain. (Adapted from FBrf0135231 and PMID:1672661).
Protein Function (UniProtKB)
Pair-rule protein expressed in a segmentally repeating pattern to define the polarity of embryonic segments. Capable of sequence-specific DNA-binding.
(UniProt, P06601)
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
prd: paired
The wild-type allele of prd is required for normal segmentation in embryos and larvae. Mutant alleles and deficiencies show no maternal effects 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 et al., 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 et al., 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).
Summary (Interactive Fly)
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
Gene Model and Products
Number of Transcripts
2
Number of Unique Polypeptides
2

Please see the GBrowse view of Dmel\prd or the JBrowse view of Dmel\prd 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 5.51
Annotated transcripts do not represent all supported alternative splices within 5' UTR.
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0080299
2330
590
FBtr0080298
2459
613
Additional Transcript Data and Comments
Reported size (kB)
3.6, 2.5 (northern blot)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0079883
62.9
590
7.46
FBpp0079882
65.5
613
7.47
Polypeptides with Identical Sequences

None of the polypeptides share 100% sequence identity.

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Crossreferences
PDB - An information portal to biological macromolecular structures
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\prd 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 (8 terms)
Molecular Function (3 terms)
Terms Based on Experimental Evidence (2 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
non-traceable author statement
(assigned by UniProt )
Biological Process (4 terms)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (3 terms)
CV Term
Evidence
References
traceable author statement
non-traceable author statement
(assigned by UniProt )
non-traceable author statement
non-traceable author statement
(assigned by UniProt )
non-traceable author statement
(assigned by UniProt )
Cellular Component (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
non-traceable author statement
(assigned by UniProt )
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
No Assay Recorded
Stage
Tissue/Position (including subcellular localization)
Reference
expression microarray
Stage
Tissue/Position (including subcellular localization)
Reference
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
antennal anlage

Comment: reported as procephalic ectoderm anlage

central brain anlage

Comment: reported as procephalic ectoderm anlage

dorsal head epidermis anlage

Comment: reported as procephalic ectoderm anlage

visual anlage

Comment: reported as procephalic ectoderm anlage

fat body | subset

Comment: expressed in female fat tissue surrounding the spermothecae

Additional Descriptive Data
prd expression is enriched in adult males.
prd transcription is repressed by ectopic eve protein in evehs.PS embryos. Timing suggests that eve is a direct regulator of prd.
prd transcripts rise to a sharp peak in 2-4 hr embryos, rapidly decline and are undetectable after 12 hrs. They are absent in oocytes. prd is initially expressed with double segment periodicity (7 stripes) but switches at cellular blastoderm to a pattern of single segment periodicity (14 stripes).
A 3.6kb prd transcript is observed in addition to the 2.5kb transcript in 0-4hr embryo RNA from prd4 heterozygous mothers.
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
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 level s 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.
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\prd in GBrowse 2
RNA-Seq by Region - Search RNA-Seq expression levels by exon or genomic region
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
FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
Fly-FISH - A database of Drosophila embryo and larvae mRNA localization patterns
Flygut - An atlas of the Drosophila adult midgut
Images
FlyExpress - Embryonic expression images (BDGP data)
  • Stages(s) 1-3
  • Stages(s) 4-6
  • Stages(s) 7-8
  • Stages(s) 9-10
  • Stages(s) 11-12
  • Stages(s) 13-16
Alleles, Insertions, and Transgenic Constructs
Classical and Insertion Alleles ( 16 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 42 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of prd
Transgenic constructs containing regulatory region of prd
Deletions and Duplications ( 17 )
Phenotypes
For more details about a specific phenotype click on the relevant allele symbol.
Lethality
Allele
Sterility
Allele
Other Phenotypes
Allele
Phenotype manifest in
Allele
abdomen & cuticle & adult
embryonic/first instar larval cuticle & abdominal segment 1
embryonic/first instar larval cuticle & abdominal segment 3
embryonic/first instar larval cuticle & abdominal segment 5
embryonic/first instar larval cuticle & abdominal segment 7
embryonic/first instar larval cuticle & mesothoracic segment
larval midgut & embryo & epidermis
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (15)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
10 of 15
Yes
Yes
 
10 of 15
Yes
Yes
 
2 of 15
No
No
 
1 of 15
No
No
1 of 15
No
Yes
 
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
 
1 of 15
No
No
1 of 15
No
No
 
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (16)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
10 of 15
Yes
Yes
 
 
10 of 15
Yes
Yes
2 of 15
No
No
2 of 15
No
No
 
1 of 15
No
No
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
 
1 of 15
No
No
Rattus norvegicus (Norway rat) (10)
10 of 13
Yes
Yes
8 of 13
No
Yes
2 of 13
No
No
1 of 13
No
No
1 of 13
No
Yes
1 of 13
No
Yes
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
1 of 13
No
No
Xenopus tropicalis (Western clawed frog) (10)
8 of 12
Yes
Yes
4 of 12
No
Yes
1 of 12
No
Yes
1 of 12
No
Yes
1 of 12
No
Yes
1 of 12
No
Yes
1 of 12
No
No
1 of 12
No
No
1 of 12
No
No
1 of 12
No
Yes
Danio rerio (Zebrafish) (18)
10 of 15
Yes
Yes
8 of 15
No
Yes
8 of 15
No
No
5 of 15
No
Yes
2 of 15
No
No
2 of 15
No
No
2 of 15
No
No
1 of 15
No
No
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
Yes
Caenorhabditis elegans (Nematode, roundworm) (11)
6 of 15
Yes
Yes
2 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
No
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
Yes
1 of 15
No
No
1 of 15
No
No
Arabidopsis thaliana (thale-cress) (1)
1 of 9
Yes
No
Saccharomyces cerevisiae (Brewer's yeast) (0)
No records found.
Schizosaccharomyces pombe (Fission yeast) (0)
No records found.
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG091906JC )
Organism
Common Name
Gene
AAA Syntenic Ortholog
Multiple Dmel Genes in this Orthologous Group
Drosophila melanogaster
fruit fly
Drosophila suzukii
Spotted wing Drosophila
Drosophila simulans
Drosophila sechellia
Drosophila erecta
Drosophila yakuba
Drosophila ananassae
Drosophila pseudoobscura pseudoobscura
Drosophila persimilis
Drosophila willistoni
Drosophila virilis
Drosophila mojavensis
Drosophila grimshawi
Orthologs in non-Drosophila Dipterans (via OrthoDB v9.1) ( EOG091506LL )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Musca domestica
House fly
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Glossina morsitans
Tsetse fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Lucilia cuprina
Australian sheep blowfly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Mayetiola destructor
Hessian fly
Mayetiola destructor
Hessian fly
Anopheles darlingi
American malaria mosquito
Anopheles darlingi
American malaria mosquito
Anopheles gambiae
Malaria mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W09TG )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Bombyx mori
Silkmoth
Bombyx mori
Silkmoth
Bombyx mori
Silkmoth
Bombyx mori
Silkmoth
Danaus plexippus
Monarch butterfly
Danaus plexippus
Monarch butterfly
Danaus plexippus
Monarch butterfly
Danaus plexippus
Monarch butterfly
Danaus plexippus
Monarch butterfly
Heliconius melpomene
Postman butterfly
Heliconius melpomene
Postman butterfly
Heliconius melpomene
Postman butterfly
Heliconius melpomene
Postman butterfly
Apis florea
Little honeybee
Apis florea
Little honeybee
Apis florea
Little honeybee
Apis florea
Little honeybee
Apis florea
Little honeybee
Apis florea
Little honeybee
Apis mellifera
Western honey bee
Apis mellifera
Western honey bee
Apis mellifera
Western honey bee
Apis mellifera
Western honey bee
Apis mellifera
Western honey bee
Bombus impatiens
Common eastern bumble bee
Bombus impatiens
Common eastern bumble bee
Bombus impatiens
Common eastern bumble bee
Bombus impatiens
Common eastern bumble bee
Bombus impatiens
Common eastern bumble bee
Bombus terrestris
Buff-tailed bumblebee
Bombus terrestris
Buff-tailed bumblebee
Bombus terrestris
Buff-tailed bumblebee
Bombus terrestris
Buff-tailed bumblebee
Linepithema humile
Argentine ant
Linepithema humile
Argentine ant
Linepithema humile
Argentine ant
Linepithema humile
Argentine ant
Linepithema humile
Argentine ant
Linepithema humile
Argentine ant
Linepithema humile
Argentine ant
Linepithema humile
Argentine ant
Linepithema humile
Argentine ant
Megachile rotundata
Alfalfa leafcutting bee
Megachile rotundata
Alfalfa leafcutting bee
Megachile rotundata
Alfalfa leafcutting bee
Megachile rotundata
Alfalfa leafcutting bee
Megachile rotundata
Alfalfa leafcutting bee
Nasonia vitripennis
Parasitic wasp
Nasonia vitripennis
Parasitic wasp
Nasonia vitripennis
Parasitic wasp
Dendroctonus ponderosae
Mountain pine beetle
Dendroctonus ponderosae
Mountain pine beetle
Dendroctonus ponderosae
Mountain pine beetle
Dendroctonus ponderosae
Mountain pine beetle
Dendroctonus ponderosae
Mountain pine beetle
Dendroctonus ponderosae
Mountain pine beetle
Tribolium castaneum
Red flour beetle
Tribolium castaneum
Red flour beetle
Tribolium castaneum
Red flour beetle
Tribolium castaneum
Red flour beetle
Tribolium castaneum
Red flour beetle
Pediculus humanus
Human body louse
Pediculus humanus
Human body louse
Pediculus humanus
Human body louse
Pediculus humanus
Human body louse
Pediculus humanus
Human body louse
Rhodnius prolixus
Kissing bug
Rhodnius prolixus
Kissing bug
Rhodnius prolixus
Kissing bug
Rhodnius prolixus
Kissing bug
Rhodnius prolixus
Kissing bug
Cimex lectularius
Bed bug
Cimex lectularius
Bed bug
Cimex lectularius
Bed bug
Cimex lectularius
Bed bug
Cimex lectularius
Bed bug
Acyrthosiphon pisum
Pea aphid
Acyrthosiphon pisum
Pea aphid
Acyrthosiphon pisum
Pea aphid
Acyrthosiphon pisum
Pea aphid
Acyrthosiphon pisum
Pea aphid
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X0HFF )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strigamia maritima
European centipede
Strigamia maritima
European centipede
Strigamia maritima
European centipede
Strigamia maritima
European centipede
Ixodes scapularis
Black-legged tick
Ixodes scapularis
Black-legged tick
Ixodes scapularis
Black-legged tick
Ixodes scapularis
Black-legged tick
Ixodes scapularis
Black-legged tick
Stegodyphus mimosarum
African social velvet spider
Stegodyphus mimosarum
African social velvet spider
Stegodyphus mimosarum
African social velvet spider
Tetranychus urticae
Two-spotted spider mite
Tetranychus urticae
Two-spotted spider mite
Tetranychus urticae
Two-spotted spider mite
Tetranychus urticae
Two-spotted spider mite
Tetranychus urticae
Two-spotted spider mite
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Daphnia pulex
Water flea
Orthologs in non-Arthropod Metazoa (via OrthoDB v9.1) ( EOG091G0S4E )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Strongylocentrotus purpuratus
Purple sea urchin
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (10)
6 of 10
6 of 10
4 of 10
4 of 10
4 of 10
3 of 10
3 of 10
3 of 10
3 of 10
1 of 10
Human Disease Associations
FlyBase Human Disease Model Reports
Disease Model Summary Ribbon
Disease Ontology (DO) Annotations
Models Based on Experimental Evidence ( 1 )
Allele
Disease
Evidence
References
Potential Models Based on Orthology ( 4 )
Human Ortholog
Disease
Evidence
References
inferred from electronic annotation
inferred from electronic annotation
inferred from electronic annotation
inferred from electronic annotation
Modifiers Based on Experimental Evidence ( 0 )
Allele
Disease
Interaction
References
Comments on Models/Modifiers Based on Experimental Evidence ( 0 )
 
Disease Associations of Human Orthologs (via DIOPT v7.1 and OMIM)
Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
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.
Dmel gene
Ortholog showing functional complementation
Supporting References
Interactions
Summary of Physical Interactions
esyN Network Diagram
Show neighbor-neighbor interactions:
Select Layout:
Legend:
Protein
RNA
Selected Interactor(s)
Interactions Browser

Please see the Physical Interaction reports below for full details
protein-protein
Physical Interaction
Assay
References
Summary of Genetic Interactions
esyN Network Diagram
esyN Network Key:
Suppression
Enhancement

Please look at the allele data for full details of the genetic interactions
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.
MIST (genetic) - An integrated Molecular Interaction Database
MIST (protein-protein) - An integrated Molecular Interaction Database
Pathways
Gene Group - Pathway Membership (FlyBase)
External Data
Linkouts
SignaLink - A signaling pathway resource with multi-layered regulatory networks.
Genomic Location and Detailed Mapping Data
Chromosome (arm)
2L
Recombination map
2-46
Cytogenetic map
Sequence location
2L:12,082,995..12,085,827 [-]
FlyBase Computed Cytological Location
Cytogenetic map
Evidence for location
33C3-33C3
Limits computationally determined from genome sequence between P{EP}JhI-21EP1187 and P{lacW}Aats-thrk04203
Experimentally Determined Cytological Location
Cytogenetic map
Notes
References
33B1-33C1
(determined by in situ hybridisation)
33C1-33C1
(determined by in situ hybridisation)
Experimentally Determined Recombination Data
Left of (cM)
Right of (cM)
Notes
Stocks and Reagents
Stocks (18)
Genomic Clones (15)
 

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

cDNA Clones (6)
 

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
    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 identity of: prd CG6716
    Source for database merge of
    Additional comments
    Other Comments
    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 embryos, prd and bcd gene products bind most strongly to known target elements within a promoter. In addition, they may also bind at significant levels to the majority of genes, as do the selector homeoproteins.
    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.
    ftz protein lacking the homeodomain can directly regulate ftz-dependent segmentation, suggesting that it can control target gene expression through interactions with other proteins. A likely candidate is the pair-rule protein prd.
    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.
    gsb and prd show functional equivalence; gsb is able to substitute for all functions of prd required to support development to adults. Mmus\Pax3 protein cannot substitute for all prd functions.
    The PRD-repeat domains of slou and prd protein are sufficient to mediate protein-protein interaction, suggesting that the PRD-domain functions as a protein-binding interface and thereby may increase the DNA binding specificity of homeodomain transcription factors.
    wg expression is regulated by odd and prd. odd represses wg expression, prd restricts the domain of expression of odd.
    Induction of anti-prd ribozymes specifically reduces prd protein levels. Induction of the ribozymes at late stages does not affect embryonic segmentation but leads to specific defects in head structures.
    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.
    An 18kb genomic fragment consisting of the transcribed region and 10kb of 5' and 5kb of 3' flanking sequences is able to rescue prd mutant embryos to full viability. Regulation of prd by pair-rule and gap gene products is mediated by upstream and downstream cis-regulatory elements.
    Ectopic expression analysis demonstrates that the gsb and gsb-n gene product can substitute the function of the prd gene product during early embryonic development and prd gene product can substitute gsb and gsb-n gene product during late embryonic development in regulating expression of wg and en.
    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.
    The role of prd in the regulation of run mRNA expression in the early embryo has been investigated.
    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 DNA binding activities of the en, eve, prd and zen proteins have been compared.
    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).
    Origin and Etymology
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    External Crossreferences and Linkouts ( 51 )
    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/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
    Other crossreferences
    BDGP expression data - Patterns of gene expression in Drosophila embryogenesis
    Drosophila Genomics Resource Center - Drosophila Genomics Resource Center (DGRC) cDNA clones
    Eukaryotic Promoter Database - A collection of databases of experimentally validated promoters for selected model organisms.
    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)
    KEGG Genes - Molecular building blocks of life in the genomic space.
    modMine - A data warehouse for the modENCODE project
    PDB - An information portal to biological macromolecular structures
    SignaLink - A signaling pathway resource with multi-layered regulatory networks.
    Linkouts
    BioGRID - A database of protein and genetic interactions.
    DroID - A comprehensive database of gene and protein interactions.
    DRSC - Results frm RNAi screens
    FLIGHT - Cell culture data for RNAi and other high-throughput technologies
    FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array
    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
    InterologFinder - Protein-protein interactions (PPI) from both known and predicted PPI data sets.
    MIST (genetic) - An integrated Molecular Interaction Database
    MIST (protein-protein) - An integrated Molecular Interaction Database
    Synonyms and Secondary IDs (7)
    Reported As
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    Secondary FlyBase IDs
      Datasets (3)
      Study focus (3)
      Experimental Role
      Project
      Project Type
      Title
      • overexpressed_factor
      BDGP generated cDNA and EST libraries.
      • bait_protein
      ChIP characterization of transcription factor genome binding, Berkeley Drosophila Transcription Factor Network Project.
      • bait_protein
      Genome-wide localization of transcription factors by ChIP-chip and ChIP-Seq.
      References (377)