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General Information
Symbol
Dmel\run
Species
D. melanogaster
Name
runt
Annotation Symbol
CG1849
Feature Type
FlyBase ID
FBgn0003300
Gene Model Status
Stock Availability
Gene Snapshot
runt (run) encodes an alpha-subunit of the transcription factor complex core binding factor, which is involved in transcription regulation. It contributes to axon guidance, dendrite morphogenesis and germ-band extension. [Date last reviewed: 2019-03-14]
Also Known As
leg, AA33
Key Links
Genomic Location
Cytogenetic map
Sequence location
X:20,690,670..20,697,321 [+]
Recombination map
1-65
Sequence
Other Genome Views
The following external sites may use different assemblies or annotations than FlyBase.
Function
GO Summary Ribbons
Protein Family (UniProt)
-
Molecular Function (GO)
[Detailed GO annotations]
Summaries
Gene Group (FlyBase)
RUNT DOMAIN TRANSCRIPTION FACTORS -
Runt-domain (RD) transcription factors are sequence-specific DNA binding proteins that regulate transcription. These proteins are characterized by a Runt domain of 128 amino acids that mediates DNA binding and heterodimerization with a non-DNA binding β-subunit to form the Core Binding Factor transcription factor complex. (Adapted from FBrf0206845 and FBrf0138356).
Protein Function (UniProtKB)
Plays a pivotal role in regulating the expression of other pair-rule genes such as eve, ftz, and h.
(UniProt, P22814)
Phenotypic Description (Red Book; Lindsley and Zimm 1992)
run: runt
A pair-rule embryonic lethal; causes deletions of the dentical belts of the mesothoracic and the first, third, fifth, and seventh abdominal segments, extending through the more anterior naked cuticle and into the denticle belts of the next most anterior segments. Deleted regions appear to be replaced by mirror image duplications of the remaining more anterior pattern elements. Deleted regions exceed duplications in size, resulting in shorter embryos. The amount of material deleted varies among segments, alleles, and among animals with the same alleles. Hypomorphic alleles do not remove as much tissue as amorphs, and weak hypomorphic alleles produce occasional survivors missing methathoracic legs or halteres or both and are frequently missing one or more abdominal tergites. run31, among the weakest alleles, survives to adulthood. Deficiencies for run have discernable dominant effects on embryonic development; extra doses of run+ produce anti-runt phenotype, i.e., 30% of males with two doses of run+ display deletions of portions of the dentical belts of A6 and less frequently of A2 and A8; males with three run+ alleles more severely affected with 70% penetrance. run+ postulated to repress eve function and positively regulate ftz; run mutants show expansion of stripes of eve expression and premature disappearance of stripes of ftz expression in the embryo (Frasch and Levine, 1987, Genes Dev. 1: 981-95). ftz+ expression in cellular blastoderm reduced in four anterior stripes; A5-A7 expression abnormal, possibly reflecting pattern duplication; nuclear shape abnormal [Carroll and Scott, 1986, Cell 45: 113-26 (fig.)]. For expression pattern later in development see Kania, Bonner, Duffy, and Gergen (1990, Genes Dev. 4: 1701-13). run is autonomous in gynandropmorphs both for missing and for mirror-image duplicated phenotypes, suggesting that the duplication does not result from proliferation following cell death (Gergen and Wieschaus, 1985, Dev. Biol. 109: 321-35). Also, the earliest embryonic phenotypes are dosage compensated (Gergen, 1987). run embryos produced by homozygous ovarian clones not different from those produced by heterozygous mothers (Wieschaus and Noell, 1986, Roux's Arch. Dev. Biol. 195: 63-73).
Summary (Interactive Fly)
transcription factor - novel - pair rule gene - contributes to neuroblast cell identity - identities of medulla neurons of the optic lobe are pre-determined in the larval medulla primordium, which is subdivided into concentric zones characterized by the expression of four transcription factors: Drifter, Runt, Homothorax and Brain-specific homeobox
Gene Model and Products
Number of Transcripts
3
Number of Unique Polypeptides
2

Please see the GBrowse view of Dmel\run or the JBrowse view of Dmel\run 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 5.53
Gene model reviewed during 5.56
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Name
FlyBase ID
RefSeq ID
Length (nt)
Assoc. CDS (aa)
FBtr0077279
2474
510
FBtr0304593
2171
507
FBtr0345922
3145
510
Additional Transcript Data and Comments
Reported size (kB)
2.6 (northern blot)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name
FlyBase ID
Predicted MW (kDa)
Length (aa)
Theoretical pI
RefSeq ID
GenBank
FBpp0076971
53.2
510
8.24
FBpp0293135
52.9
507
8.01
FBpp0311837
53.2
510
8.24
Polypeptides with Identical Sequences

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

510 aa isoforms: run-PA, run-PC
Additional Polypeptide Data and Comments
Reported size (kDa)
509 (aa); 68 (kD observed); 53 (kD predicted)
Comments
External Data
Linkouts
Sequences Consistent with the Gene Model
Nucleotide / Polypeptide Records
 
Mapped Features

Click to get a list of regulatory features (enhancers, TFBS, etc.) and gene disruptions (point mutations, indels, etc.) within or overlapping Dmel\run 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 (14 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
inferred from electronic annotation with InterPro:IPR000040
(assigned by InterPro )
Biological Process (10 terms)
Terms Based on Experimental Evidence (6 terms)
CV Term
Evidence
References
Terms Based on Predictions or Assertions (5 terms)
CV Term
Evidence
References
traceable author statement
non-traceable author statement
traceable author statement
Cellular Component (1 term)
Terms Based on Experimental Evidence (1 term)
CV Term
Evidence
References
inferred from direct assay
Terms Based on Predictions or Assertions (0 terms)
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
in situ
Stage
Tissue/Position (including subcellular localization)
Reference
dorsal ectoderm anlage

Comment: anlage in statu nascendi

mesoderm anlage

Comment: anlage in statu nascendi

ventral ectoderm anlage

Comment: anlage in statu nascendi

antennal anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

dorsal head epidermis anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

visual anlage in statu nascendi

Comment: reported as procephalic ectoderm anlage in statu nascendi

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

ventral nerve cord primordium

Comment: reported as ventral nerve cord anlage

antennal primordium

Comment: reported as procephalic ectoderm primordium

central brain primordium

Comment: reported as procephalic ectoderm primordium

visual primordium

Comment: reported as procephalic ectoderm primordium

dorsal head epidermis primordium

Comment: reported as procephalic ectoderm primordium

lateral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

ventral head epidermis primordium

Comment: reported as procephalic ectoderm primordium

northern blot
Stage
Tissue/Position (including subcellular localization)
Reference
radioisotope in situ
Stage
Tissue/Position (including subcellular localization)
Reference
Additional Descriptive Data
Expression was examined at four phases of embryonic stage 5. The striped pattern becomes visible in phase 1 (0-5'), all stripes except stripe 7 are expressed during phase 2 (5-17'), and their spacing and expression levels become largely uniform by phase 3 (17-30'). The stripes initially appear less clearly separated and more graded.
run is expressed in anterior midline glia but not in posterior midline glia in stage 12 embryos. After its early pair rule and segment polarity expression patterns in early embryos, run expression becomes more expansive. At stage 10, run expression along with en expression divides the midline into four regions, anterior (runt[+], en[-]), middle (runt[-], en[-]), posterior (runt[-], en[+]), and extreme posterior (runt[-], en[-]). At stage 10, run is expressed in 4-5 midline cells. At stage 11, expression is initiated in 2-3 additional cells flanking the runt[+] en[-] region, thus generating about six run[+] anterior midline glia in the anterior of each segment. By the end of stage 11, run is expressed in all anterior midline glia.
run transcription is repressed by ectopic eve protein in evehs.PS embryos. Timing suggests that eve is a direct regulator of run. run is activated by ectopic eve if the heat shock (and resulting pulse of eve protein) occurs earlier.
run transcripts are most abundant between 2 and 4 hours of embryonic development on northern blots. They are detected in younger and older embryos at much lower levels. Low levels of transcript are also detected in larvae and adult females. run transcripts are detected by in situ hybridization at embryonic cycle 13 in a broad domain extending from 10% to 70% egg length. Early in stage 14, a pair rule pattern of seven stripes becomes apparent with the stripes of expression appearing to be wider than the intervening gaps of expression. Just prior to the completion of cellularization, the pattern changes to a pattern of expression in every segment. This pattern persists throughout germ band extension. At this time, expression is also observed in the head region from 75-85% egg length and in the proctodeal primordium. The boundaries of the run expression stripes were compared to those of other segmentation genes. The run stripes are as wide or wider than the ftz stripes. The run stripes partially overlap the eve stripes and partilly overlap the ftz stripes but appear to be in direct opposition to the h stripes. A difference was observed in the localization of run and Kr transcripts within the cortical cytoplasm.
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
No Assay Recorded
Stage
Tissue/Position (including subcellular localization)
Reference
immunolocalization
Stage
Tissue/Position (including subcellular localization)
Reference
photoreceptor cell R8
nucleus

Comment: initiates within 1 column posterior to the morphogenetic furrow

photoreceptor cell R7
nucleus

Comment: initiates about 7 columns posterior to the morphogenetic furrow

neuron | subset of medulla

Comment: expression at 24h APF

Additional Descriptive Data
run protein is expressed in the differentiated neurons of the middle domain of the medulla anlage from third instar larvae and in pupa until 12h APF. Its domain is located in between the concentric domains of vvl distally and hth proximally. Thereafter and in adults, run protein is found in layers 8 to 10 of the medulla.
Expression assayed at stages 9, 11, 13, and 17. Expression may be continuous between assayed stages in some tissues.
Expression in procephalic neuroblasts stage 9-11: deuterocerebrum - d1-3, d5, v2, v5-7; protocerebrum - ad3, ad11, cd8-12, cd15-20, pd3, pd9, pd12, pd13, pd17, pd18, pv1
run protein is localized to row 2/3 in wild type embryos but expands posteriorly into row 4 in wg- embryos.
run is expressed extensively in the developing nervous system. Neural expression is first observed in delaminating neuroblasts at 4.5 hours of development (about 5 per hemisegment). Expression is also observed in daughter ganglion mother cells and becomes increasingly complex as development proceeds. Double staining with antibodies against eve protein show that one site of run protein expression is in all of the neurons and GMCs of the EL neuron lineage. Another site of run protein expression is in some of the U neurons (CQ neurons).
run protein is expressed in a pair rule pattern of 7 stripes in the blastoderm embryo. The position of run protein stripes was compared to that of other segmentation genes. The h protein stripes are anterior to and complementary to the run protein stripes. The eve protein stripes lie anterior to the run protein stripes but overlap them partially. Two rows of eve expression are anterior to a two-row region of overlap with run followed by two rows of run expression and then two rows of non-expression before the next eve stripe. Similarly, run and ftz double staining shows that the run stripes are anterior to the ftz stripes but are partially overlapping. In early germ band extension the run pattern changes from a pair rule pattern to a segmental pattern and in addition, expression is observed in the head. Two groups of cells are stained in the head, a dorso-lateral group of 10 cells and a ventral group of 7 less intensely staining cells. The pattern becomes more complex at full germ band extension. At this stage in the segmented part of the embryo, the staining is strongest just off the midline and fades laterally. The stained cells along the midline probably correspond to neuroblasts. During germ band retraction, staining becomes evident in both the CNS and the PNS. Roughly 50 cells per hemi-segment are stained in the CNS at the completion of germ band retraction. PNS staining is also evident.
Marker for
Subcellular Localization
CV Term
Evidence
References
inferred from direct assay
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dmel\run 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) 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 ( 65 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 26 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of run
Transgenic constructs containing regulatory region of run
Deletions and Duplications ( 157 )
Disrupted in
Not disrupted in
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
Orthologs
Human Orthologs (via DIOPT v7.1)
Homo sapiens (Human) (3)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
8 of 15
Yes
Yes
 
7 of 15
No
No
6 of 15
Yes
No
Model Organism Orthologs (via DIOPT v7.1)
Mus musculus (laboratory mouse) (3)
Species\Gene Symbol
Score
Best Score
Best Reverse Score
Alignment
Complementation?
Transgene?
8 of 15
Yes
Yes
7 of 15
Yes
No
6 of 15
No
No
Rattus norvegicus (Norway rat) (3)
7 of 13
Yes
No
5 of 13
No
No
4 of 13
No
No
Xenopus tropicalis (Western clawed frog) (3)
4 of 12
Yes
No
4 of 12
Yes
No
4 of 12
Yes
No
Danio rerio (Zebrafish) (4)
8 of 15
Yes
Yes
6 of 15
No
No
4 of 15
No
No
4 of 15
No
No
Caenorhabditis elegans (Nematode, roundworm) (1)
9 of 15
Yes
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.
Orthologs in Drosophila Species (via OrthoDB v9.1) ( EOG09190C65 )
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) ( EOG091506XY )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Musca domestica
House fly
Glossina morsitans
Tsetse fly
Lucilia cuprina
Australian sheep blowfly
Mayetiola destructor
Hessian fly
Mayetiola destructor
Hessian fly
Aedes aegypti
Yellow fever mosquito
Anopheles gambiae
Malaria mosquito
Culex quinquefasciatus
Southern house mosquito
Orthologs in non-Dipteran Insects (via OrthoDB v9.1) ( EOG090W06AW )
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
Heliconius melpomene
Postman 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 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 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
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
Nasonia vitripennis
Parasitic wasp
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
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
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
Zootermopsis nevadensis
Nevada dampwood termite
Orthologs in non-Insect Arthropods (via OrthoDB v9.1) ( EOG090X095H )
Organism
Common Name
Gene
Multiple Dmel Genes in this Orthologous Group
Ixodes scapularis
Black-legged tick
Tetranychus urticae
Two-spotted spider mite
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) ( EOG091G0CXB )
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
Ciona intestinalis
Vase tunicate
Gallus gallus
Domestic chicken
Gallus gallus
Domestic chicken
Paralogs
Paralogs (via DIOPT v7.1)
Drosophila melanogaster (Fruit fly) (3)
6 of 10
5 of 10
4 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 ( 2 )
    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.
    Interactions
    Summary of Physical Interactions
    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
    Reactome - An open-source, open access, manually curated and peer-reviewed pathway database.
    SignaLink - A signaling pathway resource with multi-layered regulatory networks.
    Genomic Location and Detailed Mapping Data
    Chromosome (arm)
    X
    Recombination map
    1-65
    Cytogenetic map
    Sequence location
    X:20,690,670..20,697,321 [+]
    FlyBase Computed Cytological Location
    Cytogenetic map
    Evidence for location
    19E2-19E2
    Limits computationally determined from genome sequence between P{EP}CG1702EP1525 and P{EP}EP1465&P{EP}CG1486EP1192
    Experimentally Determined Cytological Location
    Cytogenetic map
    Notes
    References
    19E1-19E2
    (determined by in situ hybridisation)
    Experimentally Determined Recombination Data
    Right of (cM)
    Notes
    Stocks and Reagents
    Stocks (14)
    Genomic Clones (26)
    cDNA Clones (11)
     

    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: run CG1849
    Source for database merge of
    Additional comments
    Other Comments
    Haploinsufficient locus (not associated with strong haplolethality or haplosterility).
    DNA-protein interactions: genome-wide binding profile assayed for run protein in 0-12 hr embryos; see mE1_TFBS_run collection report.
    dsRNA has been made from templates generated with primers directed against this gene. RNAi of run results in dorsal overextension of primary dendrites, defects in dendrite morphogenesis and a reduction in lateral branching.
    run directly activates Sxl transcription.
    Many but not all regulatory properties of the '7-stripe' regulatory region are conserved between D.melanogaster and D.virilis. The similarity between the homologous sequences is surprisingly low suggesting pair rule target sequences are less constrained during evolution than gap gene input elements and that functional elements mediating pair rule interactions can be dispersed over many kilobases.
    run is sufficient to activate eve expression in the progeny of specific neuroblasts and acts autonomously.
    run protein interacts with gro protein to repress transcription. This protein-protein interaction is independent of the Runt domain and can be mapped to a 5-amino acid sequence, VWRPY, present at the C-terminus of the run protein.
    A deficiency screen for modifiers of a run mutant phenotype revealed 12 putative loci that act as dosage sensitive maternal modifiers of run.
    In vitro studies reveal Bro or Bgb can stimulate the DNA binding activity of the run domain. run can act as an active repressor in the presence of either partner protein.
    run directly represses eve.
    Ecol\lacZ reporter gene constructs have been used to demonstrate the elaborate pattern of run is generated as the sum of a series of stage-specific and position-specific subcomponents. Results identify several separable cis-regulatory elements that are responsible for mediating the responses to the different regulatory cues.
    run gene functions as a dose-dependent positive regulator of Sxl-Pe.
    The run domain has DNA binding properties and regions outside the domain are important for in vivo function.
    run and h act on ftz with opposing effect via a common 32 bp element, the fDE1. run acts via transcriptional activation and h acts via transcriptional repression.
    Expression of stripes in the blastoderm embryo can be generated by a two-step mode which involves regulatory interactions among the primary pair-rule genes h and run. Expression of h stripes 3 and 4 is directed by a common cis-acting element that results in an initial broad band of gene expression covering three stripe equivalents. Subsequently this expression domain is split by repression in the forthcoming interstripe region, a process mediated by a separate cis-acting element that responds to run activity.
    Comparisons of early development to that in other insects have revealed conservation of some aspects of development, as well as differences that may explain variations in early patterning events.
    Transient over-expression of run affects the expression of the upstream gap genes as well as that of the pair rule genes. Genetic experiments indicate that run plays a normal role in preventing bcd-dependent gene expression in the central region of the embryo.
    Ectopic ttk expression causes complete or near complete repression of ftz and significant repression of eve, odd, h and runt.
    Expression of run has been used as a marker for a subset of neuroblasts in study of requirement for wg gene product for neuroblast specification and formation in the CNS.
    Muscle phenotype of mutants studied using polarised light microscopy and antibody staining to detect Mhc-lacZ reporter gene expression in muscles.
    sc, sisA and run are not required to activate Sxl in the female germline.
    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.
    The run domain identifies an evolutionarily conserved structural motif important for both DNA-binding and protein-protein interaction.
    The regulation of run mRNA expression by maternal, gap, pair-rule and segment polarity genes during early embryogenesis has been investigated.
    The run gene is required to generate asymmetries within parasegmental domains. run is required to limit the domains of en-expression in odd-numbered parasegments, while odd is required to limit the domains of en-expression in even-numbered parasegments. Activation of en at the anterior margins of the parasegments requires repression of run and odd by eve.
    Ecol\lacZ reporter gene constructs demonstrate that cis-regulatory regions that control run expression during neurogenesis are located more than 8.5kb upstream of the run transcription unit and post-blastoderm expression of run is vital to flies.
    Post cellularization run expression is repressed by ectopic eve expression, precellularization ectopic eve expression stimulates run expression.
    run gene product is required for the initial step of Sxl activation by the X:A signal but does not have a major role as an X-counting element. There is a weak female-specific dominant synergism between run and da mutations.
    The sis-b function of sc and the segmentation gene run have a vital interaction in a transheterozygous state: run acts as a numerator element in the signalling of the X:A ratio. run cooperates with sc to activate Sxl in the central region of the embryo. Increases in the dose of run cause segmentation defects that may be lethal.
    The expression of run and its role in neurogenesis has been studied.
    Mutations in zygotic pair rule gene run interact with RpII140wimp.
    run has been cloned and characterised.
    Injection of protein synthesis inhibitors into early embryos induces expression of run mRNA in virtually all regions of the embryo.
    The development of the eve and ftz stripes in h-, run-, eve- and en- embryos demonstrates that individual cells are allocated to parasegments with respect to the anterior margins of the eve and ftz stripes.
    run is expressed and required at the cellular blastoderm stage in cells that will serve as precursors to both the epidermis and CNS.
    Genetic analysis demonstrates that run is dispensable for efficient homeotic gene expression in the visceral mesoderm.
    A screen for X-linked genes that affect embryo morphology revealed run.
    The localised requirements for run have been investigated using mosaic animals.
    run mutants display pair-rule segment defects.
    A pair-rule embryonic lethal; causes deletions of the dentical belts of the mesothoracic and the first, third, fifth and seventh abdominal segments, extending through the more anterior naked cuticle and into the denticle belts of the next most anterior segments. Deleted regions appear to be replaced by mirror image duplications of the remaining more anterior pattern elements. Deleted regions exceed duplications in size, resulting in shorter embryos. The amount of material deleted varies among segments, alleles and among animals with the same alleles. Hypomorphic alleles do not remove as much tissue as amorphs and weak hypomorphic alleles produce occasional survivors missing methathoracic legs or halteres or both and are frequently missing one or more abdominal tergites. run31, among the weakest alleles, survives to adulthood. Deficiencies for run have discernible dominant effects on embryonic development; extra doses of run+ produce anti-runt phenotype, i.e., 30% of males with two doses of run+ display deletions of portions of the dentical belts of A6 and less frequently of A2 and A8; males with three run+ alleles more severely affected with 70% penetrance. run+ postulated to repress eve function and positively regulate ftz; run mutants show expansion of stripes of eve expression and premature disappearance of stripes of ftz expression in the embryo (Frasch and Levine, 1987). ftz+ expression in cellular blastoderm reduced in four anterior stripes; A5-A7 expression abnormal, possibly reflecting pattern duplication; nuclear shape abnormal (Carroll and Scott, 1986). For expression pattern later in development see Kania et al. (1990). run is autonomous in gynandromorphs both for missing and for mirror-image duplicated phenotypes, suggesting that the duplication does not result from proliferation following cell death (Gergen and Wieschaus, 1985). Also, the earliest embryonic phenotypes are dosage compensated (Gergen, 1987). run embryos produced by homozygous ovarian clones not different from those produced by heterozygous mothers (Wieschaus and Noell, 1986).
    Origin and Etymology
    Discoverer
    Etymology
    Identification
    External Crossreferences and Linkouts ( 422 )
    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
    UniProt/TrEMBL - Automatically annotated and unreviewed 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
    KEGG Genes - Molecular building blocks of life in the genomic space.
    modMine - A data warehouse for the modENCODE project
    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
    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 (23)
    Reported As
    Symbol Synonym
    l(1)19Ea
    l(1)B2/13.1
    l(1)LB9
    run
    (Shokri et al., 2019, Bischof et al., 2018, Hu et al., 2017.6.13, Transgenic RNAi Project members, 2017-, Kwon et al., 2016, Louie et al., 2016, Duque and Sinha, 2015, Kok et al., 2015, Ciglar et al., 2014, Eroglu et al., 2014, Jiang and Singh, 2014, Samee and Sinha, 2014, Smith and Shilatifard, 2014, Vernes, 2014, Chen et al., 2013, Combs and Eisen, 2013, Jennings, 2013, Kim et al., 2013, Saunders et al., 2013, Webber et al., 2013, Andrioli et al., 2012, Aswani et al., 2012, Chen et al., 2012, Cook et al., 2012, Nikulova et al., 2012, Kaplan et al., 2011, Kappes et al., 2011, Kuzin et al., 2011, Li et al., 2011, Lott et al., 2011, Nègre et al., 2011, Nien et al., 2011, Pruteanu-Malinici et al., 2011, Schroeder et al., 2011, Toku et al., 2011, Tsurumi et al., 2011, Braid et al., 2010, Frise et al., 2010, Popodi et al., 2010-, Prazak et al., 2010, Ribeiro et al., 2010, The modENCODE Consortium, 2010, The modENCODE Consortium, 2010, Venken et al., 2010, Leung and Eisen, 2009, Liu et al., 2009, Pisarev et al., 2009, Tchuraev and Galimzyanov, 2009, Venken et al., 2009, Venken et al., 2009, Wheeler et al., 2009, Andrioli et al., 2008, Christensen et al., 2008.9.29, Duncan et al., 2008, González et al., 2008, Kwong et al., 2008, Liang et al., 2008, Schroeder and Gaul, 2008, Segal et al., 2008, Surkova et al., 2008, Surkova et al., 2008, Lecuyer et al., 2007, Sandmann et al., 2007, Zeitlinger et al., 2007, Akashi et al., 2006, Jennings et al., 2006, Ko et al., 2006, Wehn and Campbell, 2006, Delanoue and Davis, 2005, Peel et al., 2005, Grad et al., 2004, Gurunathan et al., 2004, Kreiman, 2004, Kaminker et al., 2002, Wilkie et al., 2001)
    Name Synonyms
    legless
    runt
    (Hang and Gergen, 2017, Wieschaus and Nüsslein-Volhard, 2016, Chen et al., 2015, Fiedler et al., 2015, Paré et al., 2014, Samee and Sinha, 2014, Smith and Shilatifard, 2014, Little et al., 2013, Andrioli et al., 2012, Mavromatakis and Tomlinson, 2012, Wheeler et al., 2012, Kappes et al., 2011, Lott et al., 2011, Regnard et al., 2011, Schroeder et al., 2011, Walrad et al., 2011, Watson et al., 2011, Braid et al., 2010, Gladstein et al., 2010, Prazak et al., 2010, Ribeiro et al., 2010, Simões et al., 2010, Tran et al., 2010, Benoit et al., 2009, Dienstbier et al., 2009, Edwards and Meinertzhagen, 2009, Guerin and Kramer, 2009, Iovino et al., 2009, Miller et al., 2009, Pisarev et al., 2009, Sellin et al., 2009, Siddall et al., 2009, Zamparo and Perkins, 2009, Bao and Friedrich, 2008, Dougherty et al., 2008, Duncan et al., 2008, González et al., 2008, Ishihara and Shibata, 2008, Kind et al., 2008, Surkova et al., 2008, Vincent et al., 2008, De Renzis et al., 2007, Kind and Akhtar, 2007, Prazak et al., 2007, Takada et al., 2007, Vanderzwan-Butler et al., 2007, Wang et al., 2007, Bartolome and Charlesworth, 2006, Jennings et al., 2006, Mendjan et al., 2006, Wheeler et al., 2006, Gregor et al., 2005, Shav-Tal and Singer, 2005, Baudry et al., 2004, Rossetti et al., 2004, Rennert et al., 2003, Vander Zwan et al., 2003, Kaminker et al., 2002, Begun, 2001, Wilkie et al., 2001, Begun and Whitley, 2000, Kramer et al., 1999, Tsai et al., 1998, Aronson et al., 1997, Aronson et al., 1997, Li et al., 1997, Golling et al., 1996, Tsai and Gergen, 1995, Yu and Pick, 1995, Daga et al., 1992, Balakrishnan and Rodrigues, 1991, Duffy et al., 1991, Martin-Bermudo et al., 1991, Kania et al., 1990, Coulter and Wieschaus, 1988, Ingham and Gergen, 1988, DiNardo and O'Farrell, 1987, Gergen and Wieschaus, 1985)
    Secondary FlyBase IDs
    • FBgn0019659
    • FBgn0019997
    • FBtr0077279
    • FBpp0076971
    Datasets (2)
    Study focus (2)
    Experimental Role
    Project
    Project Type
    Title
    • 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 (573)