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Gene information
General information
TC009054 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_007422.5: 7988663..7989390
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
    TC009054
    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
    If you have entered your name and agree by marking the checkbox. we might show your name on this page to honor your contribution.

    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_01466

    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: 0.0% (includes death as pupa, adult)

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg with embryonic tissue, no cuticle, but muscle fluorescence - Penetrance (percentage of animals/eggs on slide): less than 30%

    embryo/egg with embryonic tissue, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    embryo/egg not developed/not fertilized - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    larval musculature irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): more than 80%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
    antenna shortened - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    head shape irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    legs orientation irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    thorax shape irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    abdomen shape irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    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: 10.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 10.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection


    pupal molt delayed (still prepupa) - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection


    Fertility
    egg production: number no/almost no eggs -
    ovariole mostly not present - Number of animals showing the phenotype: 4

    Comment: just terminal filaments left
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC009054 RA
      MSDSSDTSW SRFAKYYDP IKIGSIDGT 
      DTEPHDKGI VRALNSEYH PNRHVKGRP 
      ECTIFVSRL SLKTTKDTI KDIFSKYGP 
      LRRFRLVKD IVTGMPKGY AFIEYENEL 
      DAEEAYCKA NKMNIDGNI IFVDFECER 
      LLKGWRPRR LGGGFGGKK ESGQLRFGG 
      RDRPFKKPI SLEIKERRE RSRRDRSES 
      RRDRK
    CDS sequence
    • >TC009054 RA
      atgagcgac tcttcggac acttcatgg tcccgtttt 
      gccaaatat tacgacccg ataaaaatt ggttccatc 
      gacggcacc gacacggag ccccacgac aaaggcatc 
      gtccgagcc ctaaattcc gaataccac cccaaccgc 
      cacgttaaa ggccgtccc gagtgcaca attttcgtc 
      agccgtctt agtctcaaa accacaaaa gacacaatt 
      aaggacatt ttttccaaa tatggccct ttgcgccga 
      tttcgttta gttaaagac atagtcaca gggatgccc 
      aaaggctac gctttcatc gaatacgaa aatgagctc 
      gacgctgag gaagcgtat tgtaaagcg aataaaatg 
      aatattgat ggaaacata attttcgta gattttgaa 
      tgtgagagg ttattaaag gggtggcga ccgagacga 
      cttggaggc ggctttggt gggaaaaag gagtccgga 
      cagttgcgg ttcggtggc cgtgatcga cccttcaaa 
      aaacccatc agtttggag ataaaagag aggcgggaa 
      aggagtagg agagacagg agtgaaagt agacgtgat 
      cgtaaataa
    mRNA sequence
    • >TC009054 RA
      acaggtgac agttgttta acctaattt ttttcaaac 
      aagacgatg agcgactct tcggacact tcatggtcc 
      cgttttgcc aaatattac gacccgata aaaattggt 
      tccatcgac ggcaccgac acggagccc cacgacaaa 
      ggcatcgtc cgagcccta aattccgaa taccacccc 
      aaccgccac gttaaaggc cgtcccgag tgcacaatt 
      ttcgtcagc cgtcttagt ctcaaaacc acaaaagac 
      acaattaag gacattttt tccaaatat ggccctttg 
      cgccgattt cgtttagtt aaagacata gtcacaggg 
      atgcccaaa ggctacgct ttcatcgaa tacgaaaat 
      gagctcgac gctgaggaa gcgtattgt aaagcgaat 
      aaaatgaat attgatgga aacataatt ttcgtagat 
      tttgaatgt gagaggtta ttaaagggg tggcgaccg 
      agacgactt ggaggcggc tttggtggg aaaaaggag 
      tccggacag ttgcggttc ggtggccgt gatcgaccc 
      ttcaaaaaa cccatcagt ttggagata aaagagagg 
      cgggaaagg agtaggaga gacaggagt gaaagtaga 
      cgtgatcgt aaataatgt tttatattg aaaagtgtt 
      taaacatac atattttaa caaaaaaaa aataata
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY