Status
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Gene information
General information
TC000560 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_007417.3: 9772199..9774108
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
    TC000560
    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_06643

    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)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 1 (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): 30% - 50%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
    embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    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
    • >TC000560 RA
      MSEKVSRCV FFALLLTLL IDRSSSTSH STEKAHPSP 
      PPVTNSSNT TANIWLVDA LKDIAYYLR AHKFNEYDR 
      RYEPDAKLA RREYYRGFP RPPLRSLHW EVHKYCEQS 
      LIECVDYLR KRARKAGMR RSDDTTVVI QEQQWGENN 
      TQQIEIVDK ECRKMQQAD DVQANPFEG PLERFQWRV 
      TASYYMCWY TMKSEPALS HLSDKCDNF ADCLNPDFG 
      PNNGDDRAN DAIPYSCAF YSFCPDPCC PIKHLTRPE 
      NCWDTPENP CFEANPPGQ RECVVDRPQ NTDFSDLIL 
      NRWNVSCKC REKGLEWSS FYGICVDID ECATGAHTC 
      NPEKETCFN LPGSFKCVC KWGHIFNKK SKTCEPSKA 
      LTHLMLRKE EEEEEETSE TPWMKFLRL FRAKSATRP 
      VSVQTYLII LSCICNYFN KLLVH
    CDS sequence
    • >TC000560 RA
      atgtcagag aaagtgtcc cgttgcgtt tttttcgcg 
      ctgcttctc accctccta atcgatcgt tcctcatca 
      acaagtcac tcaacggaa aaagcccac ccttcgccg 
      cctccagta acaaactcc agcaataca accgcaaac 
      atatggctg gttgacgct ctcaaagat atcgcttat 
      tacttacga gcgcacaaa ttcaatgaa tatgacagg 
      agatacgaa cccgacgcg aaactagct cgcagagag 
      tattaccgg ggattcccc cgaccccct ttgcgatcg 
      ttgcactgg gaggtgcac aagtactgc gagcagtct 
      ctgatcgaa tgcgtcgac tatttgagg aaaagggcg 
      aggaaagcc gggatgcgg aggagtgac gatacgact 
      gttgtcatc caggagcaa caatgggga gagaacaac 
      acgcaacaa attgaaatt gtcgataaa gagtgcagg 
      aaaatgcag caagcggat gacgtgcaa gccaatccg 
      ttcgaaggt cctctggaa cgctttcag tggcgtgtc 
      actgcaagt tattacatg tgctggtac acaatgaag 
      tcggagccg gcattgagc cacctttcg gacaaatgc 
      gataatttc gccgattgt ctgaaccct gacttcggc 
      ccgaataac ggggacgat cgcgccaat gatgcaatt 
      ccgtactcg tgcgctttc tacagtttc tgtccggat 
      ccctgctgt cccatcaag cacctgact cgaccggaa 
      aactgctgg gacacgcca gaaaacccc tgctttgaa 
      gctaatccc ccgggtcag cgcgaatgt gtcgtggat 
      cgtccccag aataccgac ttcagtgac ctgatttta 
      aacagatgg aacgtgagt tgcaaatgt cgcgagaaa 
      gggctcgag tggagctct ttctatggc atatgtgta 
      gatatcgac gagtgtgcc acaggagca catacttgt 
      aaccctgaa aaggaaact tgctttaac ttgccgggg 
      tccttcaaa tgtgtttgt aagtggggt cacattttt 
      aataaaaag agcaaaact tgcgagcca agtaaagca 
      ctaactcat ttaatgctg cgcaaagaa gaagaagag 
      gaggaagaa acatcagaa acgccctgg atgaaattc 
      ttacgtctt tttcgtgca aaatcggca acacggcca 
      gtttcggtt caaacttat ttgattatc ttgtcttgt 
      atttgcaat tattttaat aaactacta gttcactga
    mRNA sequence
    • >TC000560 RA
      ttgttagtc ggtcggttt gtaaaaagt gcgcaatat 
      caaaattaa taaatttgc aaacagact tatccacaa 
      atcaaatta aacctatag gctttgtga aatcccccg 
      aatcgcgct gtcaaaagt ataaatgtc agagaaagt 
      gtcccgttg cgttttttt cgcgctgct tctcaccct 
      cctaatcga tcgttcctc atcaacaag tcactcaac 
      ggaaaaagc ccacccttc gccgcctcc agtaacaaa 
      ctccagcaa tacaaccgc aaacatatg gctggttga 
      cgctctcaa agatatcgc ttattactt acgagcgca 
      caaattcaa tgaatatga caggagata cgaacccga 
      cgcgaaact agctcgcag agagtatta ccggggatt 
      cccccgacc ccctttgcg atcgttgca ctgggaggt 
      gcacaagta ctgcgagca gtctctgat cgaatgcgt 
      cgactattt gaggaaaag ggcgaggaa agccgggat 
      gcggaggag tgacgatac gactgttgt catccagga 
      gcaacaatg gggagagaa caacacgca acaaattga 
      aattgtcga taaagagtg caggaaaat gcagcaagc 
      ggatgacgt gcaagccaa tccgttcga aggtcctct 
      ggaacgctt tcagtggcg tgtcactgc aagttatta 
      catgtgctg gtacacaat gaagtcgga gccggcatt 
      gagccacct ttcggacaa atgcgataa tttcgccga 
      ttgtctgaa ccctgactt cggcccgaa taacgggga 
      cgatcgcgc caatgatgc aattccgta ctcgtgcgc 
      tttctacag tttctgtcc ggatccctg ctgtcccat 
      caagcacct gactcgacc ggaaaactg ctgggacac 
      gccagaaaa cccctgctt tgaagctaa tcccccggg 
      tcagcgcga atgtgtcgt ggatcgtcc ccagaatac 
      cgacttcag tgacctgat tttaaacag atggaacgt 
      gagttgcaa atgtcgcga gaaagggct cgagtggag 
      ctctttcta tggcatatg tgtagatat cgacgagtg 
      tgccacagg agcacatac ttgtaaccc tgaaaagga 
      aacttgctt taacttgcc ggggtcctt caaatgtgt 
      ttgtaagtg gggtcacat ttttaataa aaagagcaa 
      aacttgcga gccaagtaa agcactaac tcatttaat 
      gctgcgcaa agaagaaga agaggagga agaaacatc 
      agaaacgcc ctggatgaa attcttacg tctttttcg 
      tgcaaaatc ggcaacacg gccagtttc ggttcaaac 
      ttatttgat tatcttgtc ttgtatttg caattattt 
      taataaact actagttca ctgattgta taatcggca 
      taaaacaag catcaaact tgttccaca ttctgttcg 
      acggtttaa cagtatttc ctaattgtt attttcata 
      gcgaacatg tgcacctac tatacatga atgttatta 
      tgtttgcag caagtgcaa gagacactc cgccgtcga 
      gtaataatt actaatacc ggaa
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY