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Gene information
General information
TC002878 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: 7576438..7593287
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
    TC002878
    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
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    Name
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    Email
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    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_03460

    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: 20.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 2 (3 dpi)
    Days post injection


    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg with embryonic tissue, no cuticle, no fluorescence - 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%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
    egg without cuticle embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): more than 80%

    cuticle remnants with unidentifyable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

    Comment: remnants inside-outed
    cuticle remnants with unidentifyable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

    larva cuticle dorsal irregular - Penetrance (percentage of animals/eggs on slide): less than 30%
    head number decreased - Penetrance (percentage of animals/eggs on slide): less than 30%

    thorax number decreased - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen number decreased - 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%
    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: 0.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 0.0% (includes death as larva, prepupa, pupa, adult)

    adult lethality - Number of animals showing the phenotype: 1 (41 dpi)
    Days post injection


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC002878 RA
      MSPNYKLIY FNARGRAEH IRFIFAYAG 
      VEYEDERIP REKWPEIKK RTPFGMLPV 
      LEIDGKAVA QSNAVARYL ARQYGLAGR 
      NEWEALQCD VLVDTLGDL KQVLAQFRM 
      EQDPIKKEE KKARLMKET IPFYLSKFE 
      KILSENNGF SVGSEITWC DFVFAVSLE 
      NFEHIFGKA ALDQYPALK ALKIKVYSI 
      PSINAWVSK RPATES
    CDS sequence
    • >TC002878 RA
      atgtctcct aactataag ctgatttac ttcaatgct 
      agagggcga gccgagcat atccgtttt atattcgct 
      tatgccggc gtggaatac gaggacgag aggatccct 
      cgagaaaaa tggccagaa atcaaaaaa agaacgccg 
      tttggaatg ctcccagtc cttgaaata gatggaaaa 
      gcggtggct cagagcaac gctgtggca agatatctg 
      gcgagacaa tatggctta gcaggacga aatgaatgg 
      gaagctttg caatgtgac gtcttggtt gacactcta 
      ggagatctc aaacaggtt cttgcacaa tttcgaatg 
      gaacaggat ccgatcaag aaggaagaa aagaaggcc 
      cgcttgatg aaggaaaca atacctttt tatttatcc 
      aaattcgag aaaattctc tcggaaaat aacggattt 
      tcagtggga tctgagata acctggtgc gattttgtg 
      ttcgctgtg tctctcgaa aacttcgag cacatcttt 
      ggcaaagcc gctctggat cagtatccg gccctgaaa 
      gctctaaaa ataaaagtc tatagcatt cctagtata 
      aacgcatgg gtgtcgaag cgacccgcc actgaatcg 
      taa
    mRNA sequence
    • >TC002878 RA
      cgcctgacg tccgatcgg cagtctcaa gttttcagc 
      ggcgcggcg cgcaactgt cgggaaagt cggttctca 
      tcagtgaca ttttccgca agctttcca acctcctga 
      gcccgaatt agattttag aggcatgtc tcctaacta 
      taagctgat ttacttcaa tgctagagg gcgagccga 
      gcatatccg ttttatatt cgcttatgc cggcgtgga 
      atacgagga cgagaggat ccctcgaga aaaatggcc 
      agaaatcaa aaaaagaac gccgtttgg aatgctccc 
      agtccttga aatagatgg aaaagcggt ggctcagag 
      caacgctgt ggcaagata tctggcgag acaatatgg 
      cttagcagg acgaaatga atgggaagc tttgcaatg 
      tgacgtctt ggttgacac tctaggaga tctcaaaca 
      ggttcttgc acaatttcg aatggaaca ggatccgat 
      caagaagga agaaaagaa ggcccgctt gatgaagga 
      aacaatacc tttttattt atccaaatt cgagaaaat 
      tctctcgga aaataacgg attttcagt gggatctga 
      gataacctg gtgcgattt tgtgttcgc tgtgtctct 
      cgaaaactt cgagcacat ctttggcaa agccgctct 
      ggatcagta tccggccct gaaagctct aaaaataaa 
      agtctatag cattcctag tataaacgc atgggtgtc 
      gaagcgacc cgccactga atcgtaaac tgttcgcac 
      atttgtaca tatttcagt tggggactt tgtaattgg 
      acgagcaat tacactccg gccttaatc ggttttatt 
      caactcttg gtttcgacg ataaacata tcaccagat 
      atcccaaat gagtttcta gaagagcga acgagttcg 
      cgaaatgta cctagctgt aagttaagt atgtgttca 
      aaatcaaaa atttataaa cgagttgtt tatcagtgt 
      gtacaatgt aaacatggt atactgcta taaaataca 
      ataacaaaa attgtacat agaatcaaa aattctaga 
      ggattattt tttaggaga ttttagaaa agcacgcta 
      cttgtaata tttttatat tatatctat atttgtaaa 
      aaaaagtcg gttaaattt ccaggttaa gcatttctt 
      tcttcagtt ccagtagag tcaccaaat caatgtaca 
      tgtaatggc tcatgtaaa aagcgcttt acattgctg 
      ttcgataga cttagtaat tgttggatt atttaatag 
      gtgttgtta atacaatga gtttaattt agtttttta 
      ttacatgta atgtttgta ttatttgtt attccatag 
      aaatgtcta gttgtttaa taaaaacct caaaatcaa
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY