Open Close

Important message

Updated sequence information for this Drosophila species is no longer provided by FlyBase. Gene model annotations for this species are now updated and maintained at NCBI, using the gnomon automated annotation pipeline. See the NCBI page ‘Eukaryotic genomes annotated at NCBI’.

The FlyBase BLAST tool will continue to support queries against the reference genome of this species, but not queries against annotated transcripts or proteins. For the current release, there is no JBrowse or GBrowse view of the gene model annotations for this species.

The FlyBase archived release FB2017_05 includes the last NCBI annotation update for this species that was imported into FlyBase. That sequence data can be accessed from archived gene reports, via the archived GBrowse tool, and via archived bulk-data downloads.

General Information
Symbol
Dsim\per
Species
D. simulans
Name
period
Annotation Symbol
Feature Type
FlyBase ID
FBgn0012888
Gene Model Status
Stock Availability
Gene Summary
Essential for biological clock functions. Determines the period length of circadian and ultradian rhythms; an increase in PER dosage leads to shortened circadian rhythms and a decrease leads to lengthened circadian rhythms. Essential for the circadian rhythmicity of locomotor activity, eclosion behavior, and for the rhythmic component of the male courtship song that originates in the thoracic nervous system. The biological cycle depends on the rhythmic formation and nuclear localization of the TIM-PER complex. Light induces the degradation of TIM, which promotes elimination of PER. Nuclear activity of the heterodimer coordinatively regulates PER and TIM transcription through a negative feedback loop. Behaves as a negative element in circadian transcriptional loop. Does not appear to bind DNA, suggesting indirect transcriptional inhibition (By similarity). (UniProt, Q03355)
Contribute a Gene Snapshot for this gene.
Also Known As

per

Function
GO Summary Ribbons
Gene Ontology (GO) Annotations (1 term)
Molecular Function (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Biological Process (1 term)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (1 term)
CV Term
Evidence
References
inferred from electronic annotation with InterPro:IPR013767
(assigned by InterPro )
Cellular Component (0 terms)
Terms Based on Experimental Evidence (0 terms)
Terms Based on Predictions or Assertions (0 terms)
Gene Group (FlyBase)
Protein Family (UniProt)
-
Summaries
Protein Function (UniProtKB)
Essential for biological clock functions. Determines the period length of circadian and ultradian rhythms; an increase in PER dosage leads to shortened circadian rhythms and a decrease leads to lengthened circadian rhythms. Essential for the circadian rhythmicity of locomotor activity, eclosion behavior, and for the rhythmic component of the male courtship song that originates in the thoracic nervous system. The biological cycle depends on the rhythmic formation and nuclear localization of the TIM-PER complex. Light induces the degradation of TIM, which promotes elimination of PER. Nuclear activity of the heterodimer coordinatively regulates PER and TIM transcription through a negative feedback loop. Behaves as a negative element in circadian transcriptional loop. Does not appear to bind DNA, suggesting indirect transcriptional inhibition (By similarity).
(UniProt, Q03355)
Gene Model and Products
Number of Transcripts
0
Number of Unique Polypeptides
0
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
Sequence Ontology: Class of Gene
Transcript Data
Annotated Transcripts
Additional Transcript Data and Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Polypeptides with Identical Sequences

 

Additional Polypeptide Data and Comments
Reported size (kDa)
Comments
External Data
Subunit Structure (UniProtKB)

Forms a heterodimer with timeless (TIM); the complex then translocates into the nucleus.

(UniProt, Q03355)
Post Translational Modification

Phosphorylated with a circadian rhythmicity, probably by the double-time protein (dbt). Phosphorylation could be implicated in the stability of per monomer and in the formation of heterodimer per-tim (By similarity).

(UniProt, Q03355)
Domain

Contains a remarkable run of alternating Gly-Thr residues which is polymorphic in length. At least four types of Gly-Thr length exist in the natural population, (Gly-Thr)23 (shown here), (Gly-Thr)24, (Gly-Thr)25, and one minor variant (Gly-Thr)21. This Gly-Thr stretch is implicated in the maintenance of circadian period at different temperatures. Deletion of the repeat leads to a shortening of the courtship song cycle period, and thus could be important for determining features of species-specific mating behavior (By similarity).

(UniProt, Q03355)
Crossreferences
InterPro - A database of protein families, domains and functional sites
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 Dsim\per using the Feature Mapper tool.

External Data
Crossreferences
Linkouts
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
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
 
Subcellular Localization
CV Term
Evidence
References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools

GBrowse - Visual display of RNA-Seq signals

View Dsim\per 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
Alleles, Insertions, Transgenic Constructs, and Aberrations
Classical and Insertion Alleles ( 3 )
For All Classical and Insertion Alleles Show
 
Other relevant insertions
Transgenic Constructs ( 1 )
For All Alleles Carried on Transgenic Constructs Show
Transgenic constructs containing/affecting coding region of Dsim\per
Transgenic constructs containing regulatory region of Dsim\per
Aberrations (Deficiencies and Duplications) ( 0 )
Inferred from experimentation ( 0 )
Inferred from location ( 0 )
    Phenotypes
    For more details about a specific phenotype click on the relevant allele symbol.
    Phenotype manifest in
    Allele
    Orthologs
    Human Orthologs (via DIOPT v8.0)
    Homo sapiens (Human) (0)
    No records found.
    Model Organism Orthologs (via DIOPT v8.0)
    Drosophila melanogaster (Fruit fly) (0)
    No records found.
    Ortholog(s) in Drosophila melanogaster (via OrthoDB v9.1) ( None identified )
    No D. melanogaster orthologies identified
    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 ( 0 )
      Human Ortholog
      Disease
      Evidence
      References
      Modifiers Based on Experimental Evidence ( 0 )
      Allele
      Disease
      Interaction
      References
      Disease Associations of Human Orthologs (via DIOPT v8.0 and OMIM)
      Note that ortholog calls supported by only 1 or 2 algorithms (DIOPT score < 3) are not shown.
      Homo sapiens (Human)
      Gene name
      Score
      OMIM
      OMIM Phenotype
      DO term
      Complementation?
      Transgene?
      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
      esyN Network Diagram
      Interactions Browser
      Summary of Genetic Interactions
      esyN Network Diagram
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      Starting gene(s)
      Interaction type
      Interacting gene(s)
      Reference
      External Data
      Subunit Structure (UniProtKB)
      Forms a heterodimer with timeless (TIM); the complex then translocates into the nucleus.
      (UniProt, Q03355 )
      Linkouts
      Pathways
      Signaling Pathways (FlyBase)
      Metabolic Pathways
      External Data
      Linkouts
      Genomic Location and Detailed Mapping Data
      Chromosome (arm)
      Recombination map
      Cytogenetic map
      Sequence location
      FlyBase Computed Cytological Location
      Cytogenetic map
      Evidence for location
      Experimentally Determined Cytological Location
      Cytogenetic map
      Notes
      References
      Experimentally Determined Recombination Data
      Location
      Left of (cM)
      Right of (cM)
      Notes
      Stocks and Reagents
      Stocks (0)
      Genomic Clones (0)
       
        cDNA Clones (0)
         

        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 sequenced
        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
                Other clones
                  RNAi and Array Information
                  Linkouts
                  Antibody Information
                  Laboratory Generated Antibodies
                   
                  Commercially Available Antibodies
                   
                  Other Information
                  Relationship to Other Genes
                  Source for database identify of
                  Source for database merge of
                  Additional comments
                  Other Comments

                  The frequency distribution of "silent" DNA polymorphisms has been studied in a number of D.simulans and D.pseudoobscura.pseudoobscura genes.

                  D.melanogaster females do not discriminate between males carrying D.melanogaster or D.simulans per genes, indicating that the per locus may only make a small contribution to total premating isolation between the two species.

                  A 1.9 kb region of per has been compared in D.melanogaster, D.simulans, D.sechellia and D.mauritiana, and reveals a complex history. D.simulans appears to be a parent species to D.sechellia and D.mauritiana, but the order of appearance of the two species remains unclear. Whereas D.simulans and D.mauritiana share a large number of polymorphisms, D.sechellia shows very little variation.

                  Courtship song rhythms and locomotor activity rhythms were assayed in D.melanogaster carrying the Dsim\per gene or D.melanogaster/D.simulans per gene fusions. In all cases the circadian periodicities were slightly longer than for wild type, suggesting that the 13.2kb per fragment used to make the transgenic constructs is slightly inadequate at performing wild type per function.

                  Chimeric per gene constructs from D.melanogaster and D.simulans have been used to map the genetic control of their courtship song rhythm difference to a small segment of the amino acid encoding information within per.

                  By analysing the singing of D.simulans and D.melanogaster reciprocally hybrid males the genetic etiology of the song rhythm difference is due to 1-4 amino acid replacements that have occurred over evolutionary time.

                  Dsim\per gene has been cloned and sequenced: comparison of the coding regions reveals a pattern of highly diverged areas interwoven with large conserved regions. Transformation experiments involving the Thr-Gly encoding region of per (Yu, Nature 326:765 ) suggest that the Thr-Gly repeat may play a role in determining song cycles, Dyak\per has 24 Thr-Gly pairs and has a short 35 to 40 second song rhythm.

                  Origin and Etymology
                  Discoverer
                  Etymology
                  Identification
                  External Crossreferences and Linkouts ( 466 )
                  Sequence Crossreferences
                  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.
                  UniProt/Swiss-Prot - Manually annotated and reviewed records of protein sequence and functional information
                  Other crossreferences
                  InterPro - A database of protein families, domains and functional sites
                  Synonyms and Secondary IDs (4)
                  Datasets (0)
                  Study focus (0)
                  Experimental Role
                  Project
                  Project Type
                  Title
                  References (72)