Status
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Gene information
General information
TC003117 Gene

The sequence from the iB fragment is matched against the genes from the official gene set. The matche(s) is/are visualizied in a genome browser.

NC_007418.3: 1427487..1429176
Sequence information
Transcripts / Proteins (1) Get mRNA sequence
Get CDS sequence
Get protein sequence
Ortholog information (from OrthoDB)

The information about the homolog genes in Drosophila is provided by OrthoDB http://www.orthodb.org/. The homologs are sorted according to their similarity score. For an orthology statement additional analysis are required.
The data basis for the orthologs is OrthoDB v9 containing OGS3 for Tribolium castaneum and 2015_04 (r6.07) for Drosophila melanogaster.

Closest fly homologs
    TC003117
    Gene ontology

    GO terms for Tribolium

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    There are no GO terms for Tribolium at the moment. You can help the community by providing some GO terms for this gene.


    GO terms for the homologous Drosophila genes


    Assign a GO term to this Tribolium gene by filling in the fields. Repeat to add several GO terms. Search AmiGO for the correct GO ID. Use only the most specific term - use "graph views" to browse related terms ("child terms" are more specific; the more general "parent" terms will be automatically linked). Only information based on Tribolium data should be entered - do not define terms just based on Drosophila knowledge. We will review this information and submit the annotation to the Gene Ontology consortium.


    Gene
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    The Tribolium gene the GO term is assigned to.
    GO ID *
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    The ID of the GO term you assign to the gene. Please enter only the ID of the GO term with proceeding 'GO:'. This information is mandatory.
    Evidence
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    The evidence code describes with which method the function or location, expressed by the GO term, was show for this gene. Please refer to this page for a definition of the evidence code and a decision tree.
    Reference *
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    The reference where the function or location is described for the gene. Please enter a PubMed ID. This information is mandatory.
    Quotation
    If you paste here the relevant section of the reference it is for us a great help to review your annotation. The quotation may be also be displayed to the users of iBeetle-Base.
    Name
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    Email
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    Publish name
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_09735

    Attention! iBeetle is a first pass screen. Hence, the documented phenotypes need to be confirmed by independent experiments using non-overlapping dsRNA fragments! Phenotypes with a penetrance > 50% are frequently reproduced. See Schmitt-Engel et al. 2015 for details on reproducibility.

    iB sequence
    Phenotype after pupal injection
    Usually 10 injected animals

    Pupal injection procedure

    Day 0: 10 female pupae of the pBA19 strain (muscle enhancer trap line) were injected with dsRNA.

    3 days post injection (dpi): Hatch control: Pupal and adult lethality as well as metamorphosis defects (molting, eclosion) were documented. For mating, 4 males of the black strain were added.

    9 dpi: First egg-lay was collected and incubated for cuticle analysis. Adult lethality and egg production (reduced/ no egg-lay) was documented.

    11 dpi: Second egg-lay was collected and incubated for embryonic muscle analysis. Adult lethality and egg production (reduced/ no egg-lay) were documented.

    Note: The adult morphology was not analyzed systematically at 3/9/11 dpi. Only obvious phenotypes, visible without magnification, have been annotated.

    13 dpi: Egg productivity and Ovary analysis
    The percentage of hatched larvae was documented and not hatched larvae/ eggs were embedded for cuticle analysis (15 dpi). In case of a reduction of egg production, 4 injected females were dissected to analyze the gross morphology of the ovaries.

    14 dpi: Analysis of embryonic musculature and early embryonic development
    Offspring of the injected females (hatched and not hatched larvae/ eggs) were analysed for embryonic lethality and muscle defects.

    15 dpi: Analysis of larval instar 1 cuticle
    Offspring of injected females were analysed and cuticle phenotypes were annotated.

    22 dpi: Stink gland analysis
    Documentation of defects in abdominal and thoracic stink glands (colour, size, content) of the injected femals.

    Terms used in the pupal injection procedure

    larval pantagmatic defects
    At least two tagmata (head, thorax, abdomen or terminus) show similar/ comparable defects.
    empty eggs
    Just empty shells are visible, no cuticle has been developed.
    strong defects
    L1 cuticle larvae which show severe defects. These strong defects are subdivided into three categories
    strongly fragmented (cuticle crumbs)
    No segments or appendages are identifiable, only residues of cuticle and bristles can be identified.
    cuticle remnants (with unidentifiable segments)
    Segments or parts of appendages are recognizable, but identity is not clear.
    cuticle remnants (with some identifiable segments)
    At least one segment or appendage is clearly regonizable.
    number of eggs on slide
    affected embryos usually (not always) do not hatch. Only the not hatched were used for cuticle analysis.
    For the embryonic muscle analysis the hatched as well as the not hatched were analysed.
    total number of affected eggs/embryos/larvae
    Summary of all different phenotypes/ phenotypic series which were annotated.
    inside-out
    The L1 larva shows a partial or complete inversion., e.g. bristles, appendages or parts of the abdominal segments are inverted into the interior of the cuticle.
    starved
    Dissected females show a strong resorption of fatbody predominately in the abdomen and the oogenesis is blocked. These are considered as eventually lethal phenotypes and the blocked oogenesis probably a secondary defect due to starvation.
    eclosion not fulfilled
    The emergence of the adult from the pupa stage is interrupted. This phenotype shows pupal as well as adult features.
    Please see the help page for more information
    Metamorphosis and survival

    Lethality 11 days after pupal injection: 10.0% (includes death as pupa, adult)

    adult lethality - Number of animals showing the phenotype: 1 (9 dpi)
    Days post injection


    Fertility
    mature egg deposition blocked number 1st lateral oviduct: number 2nd lateral oviduct: - Number of animals showing the phenotype: 4
    Phenotype after larval injection
    Usually 10 injected animals

    Larval injection procedure

    Day 0: 10 female L5-6 larvae of the D17Xhom strain (females express RFP in the eyes and in the CNS; pupae express GFP in the thorax) were injected with dsRNA.

    11 days post injection (dpi): Pupal morphology Documentation of larval/ pupal death and defects of metamorphosis (eclosion, delayed development). Screening for alterations of pupal head and appendages, pupal thorax, pupal thoracic musculature, pupal legs, pupal wings, pupal abdomen and pupal genital lobes.

    16 dpi: Adult morphology Documentation of larval/ pupal and adult death and defects of metamorphosis (eclosion, delayed development). Screening for alterations of adult head and appendages, adult thorax, adult elytra and hindwings, adult legs and cuticle properties. For mating 4 males of the black strain were added.

    19 dpi: Sieving and egg-lay Documentation of adult lethality and enduring metamorphosis defects.

    22 dpi: Ovary analysis (Fertility) In case of a reduction of egg production 4 females were dissected and the gross morphology of the ovaries were analysed.

    41 dpi: Fertility and stink gland analysis Documentation of defects in abdominal and thoracic stink glands development (colour, size, content) of the injected females. Check for fertility of injected larvae (no or decreased offspring).

    Terms used in the larval injection procedure

    pupal/ adult pantagmatic defects
    At least two tagmata (head, thorax, abdomen or terminus) show similar/ comparable defects.
    pupal molt not fulfilled
    The hatching from the larva to the pupa is interrupted. Either it dies as prepupa or the phenotype shows larval as well as pupal features.
    eclosion not fulfilled
    The emergence of the adult from the pupa stage is interrupted. This phenotype shows pupal as well as adult features.
    starved
    Dissected females show a strong resorption of fatbody predominately in the abdomen and the oogenesis is blocked. These are considered as eventually lethal phenotypes and the blocked oogenesis probably a secondary defect due to starvation.
    Metamorphosis and survival

    Lethalities 11 days after larval injection: % (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: % (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC003117 RA
      MSGFAGPIT RLAGKIAIV TASTDGIGF AIAQRLARE 
      GAKVIVSSR KQNNVDEAV SRLKSEGLD VTGLMCHVS 
      KADHRKKLF DTAKKLGGL DILVSNAAV NPSVAPVLD 
      CDESSWDKI FEVNVKAAF LLAQEALPL LRERPFGRI 
      IFVASIAGF HPFELLGAY SVSKTALFG LTKAAASQL 
      ARENITVNC IAPGIIQTK FSSALTETE AAREEALSR 
      IPMNRLGVP HDISGAAAY LASEDASYM TGETLIVAG 
      GMPSRL
    CDS sequence
    • >TC003117 RA
      atgagtgga ttcgctggg cctataacc cgtctagct 
      gggaaaatc gcaattgtg acagcttca accgatggt 
      attggcttt gccattgcc cagcgtttg gcccgagag 
      ggggccaaa gtgatcgtc agcagccgc aagcaaaac 
      aacgttgac gaagctgtc tcacggctc aagtcggag 
      ggcttggac gtcactggc ttaatgtgt catgtctcg 
      aaagccgac caccgtaag aagctgttc gatactgcg 
      aaaaaactt ggagggctt gatattctc gtgtccaat 
      gctgcggtt aatccatcg gtggcccca gttttggat 
      tgcgatgaa tcgtcctgg gataaaata tttgaggtc 
      aatgtgaaa gcggcgttt ttgttggcc caagaggcc 
      ttgcctttg ttgcgtgaa agaccgttt gggaggatt 
      atttttgtt gcgtccatt gctgggttc catccgttt 
      gaattacta ggggcttat tcggtcagc aagaccgct 
      ctgtttggg ctcactaaa gcggcagct tcgcaatta 
      gcaagggag aatattaca gttaattgt attgctccc 
      ggaataatc caaaccaaa ttttcaagc gctttgact 
      gaaaccgaa gccgcacga gaagaagcc ttgtctagg 
      atcccaatg aacaggttg ggggtcccc cacgacatc 
      agtggagcc gctgcttac ctggcatca gaagacgct 
      agttacatg actggagaa acgctaatt gtagctgga 
      ggaatgcct tcaagactg taa
    mRNA sequence
    • >TC003117 RA
      ttgatgacc gcaataaac cacttttgc gattagtgg 
      cgaccttta cacgatgat gaggcacta aataatctt 
      aaaaacaac ccaagagct gaaaaaatt gtcatttaa 
      taaccgtac acaagcctt tttgtttgc taacatgag 
      tggattcgc tgggcctat aacccgtct agctgggaa 
      aatcgcaat tgtgacagc ttcaaccga tggtattgg 
      ctttgccat tgcccagcg tttggcccg agagggggc 
      caaagtgat cgtcagcag ccgcaagca aaacaacgt 
      tgacgaagc tgtctcacg gctcaagtc ggagggctt 
      ggacgtcac tggcttaat gtgtcatgt ctcgaaagc 
      cgaccaccg taagaagct gttcgatac tgcgaaaaa 
      acttggagg gcttgatat tctcgtgtc caatgctgc 
      ggttaatcc atcggtggc cccagtttt ggattgcga 
      tgaatcgtc ctgggataa aatatttga ggtcaatgt 
      gaaagcggc gtttttgtt ggcccaaga ggccttgcc 
      tttgttgcg tgaaagacc gtttgggag gattatttt 
      tgttgcgtc cattgctgg gttccatcc gtttgaatt 
      actaggggc ttattcggt cagcaagac cgctctgtt 
      tgggctcac taaagcggc agcttcgca attagcaag 
      ggagaatat tacagttaa ttgtattgc tcccggaat 
      aatccaaac caaattttc aagcgcttt gactgaaac 
      cgaagccgc acgagaaga agccttgtc taggatccc 
      aatgaacag gttgggggt cccccacga catcagtgg 
      agccgctgc ttacctggc atcagaaga cgctagtta 
      catgactgg agaaacgct aattgtagc tggaggaat 
      gccttcaag actgtaatt tgttatttt gcaaataaa 
      ttttgaacc ttcaa
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY