Status
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Gene information
General information
TC009289 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: 1860145..1861428
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
    TC009289
    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
    You may enter your name. The contact information can help us to clarify any questions. If you agree, we may show your name on this page to honor your contribution.
    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_01522

    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


    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 20
    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
    • >TC009289 RA
      MKAKTIILS KKFQGYPQE TNFKIVEES LPQLKDGEF 
      LAQAEFLSV DPYIRVFMK AVGAPIIGE QVAKIIESK 
      NSKYPLGEY VVGEFGWRT HTVASEKPG DFFNLPPRL 
      VSFGDLPKS LALGALGMT GVTALYGLQ LCEPAAGKT 
      LVVSGAAGA VGTHVGQLA KLQGCKVVG ITGSDAKGH 
      RLVKELDFD AFVNYKSED FEKKLAEAT PQNIDCYFD 
      NVGGDVSSA VLHRMNKFG HVVICGAIS TYNDENTKA 
      REVQTPVKV NHLVMEGFS VTRWRNKWN KAIDDNLKL 
      IQEGRLKYF ETVTEGFEN TPDAFMKML GGQNFGKAI 
      VKV
    CDS sequence
    • >TC009289 RA
      atgaaggcg aaaaccata atcctgagc aaaaaattt 
      caaggatac ccccaagaa accaacttc aaaatagtc 
      gaagaatcg cttccccag ctaaaagac ggcgaattc 
      ttggcacaa gccgaattc ttgagcgtc gacccttac 
      atccgcgtg tttatgaag gcagttggg gcccccata 
      attggggaa caagtcgca aaaataata gaaagcaag 
      aattcgaaa tatccgctt ggggagtac gtcgtgggg 
      gagtttggt tggaggaca catactgta gcctcagaa 
      aaaccggga gattttttc aatctcccg ccgagactc 
      gtctccttc ggggattta cccaaatcg ctggcgtta 
      ggggctttg ggaatgacg ggggtcaca gccctgtac 
      gggctccag ctgtgcgag cccgcggcg ggcaaaacc 
      ctcgtagtc tcaggagcg gccggggct gtgggcacc 
      cacgtgggc caactggcc aaactacaa gggtgcaaa 
      gtggttggt atcactgga tcggacgct aaaggccac 
      cgattggtc aaagaattg gactttgat gctttcgtt 
      aactataag agtgaagat tttgagaaa aaattggcc 
      gaagctacg ccacaaaac atagactgc tacttcgac 
      aacgtgggg ggcgatgtc agcagcgcc gtcttgcac 
      cgcatgaac aaattcggt catgtggtc atctgtggg 
      gctatttcc acctacaat gacgaaaac accaaagcc 
      cgagaggtg caaacacct gtgaaagtc aaccacctt 
      gtgatggaa gggttcagc gtgactcgg tggcgaaac 
      aaatggaac aaagccatt gacgataac cttaaattg 
      atccaagag gggcgtttg aaatatttc gaaaccgtc 
      actgaaggg ttcgaaaat acgccggac gcgttcatg 
      aagatgcta ggtgggcag aactttggg aaagctatt 
      gttaaagtg tga
    mRNA sequence
    • >TC009289 RA
      tcacaaaca caatgaagg cgaaaacca taatcctga 
      gcaaaaaat ttcaaggat acccccaag aaaccaact 
      tcaaaatag tcgaagaat cgcttcccc agctaaaag 
      acggcgaat tcttggcac aagccgaat tcttgagcg 
      tcgaccctt acatccgcg tgtttatga aggcagttg 
      gggccccca taattgggg aacaagtcg caaaaataa 
      tagaaagca agaattcga aatatccgc ttggggagt 
      acgtcgtgg gggagtttg gttggagga cacatactg 
      tagcctcag aaaaaccgg gagattttt tcaatctcc 
      cgccgagac tcgtctcct tcggggatt tacccaaat 
      cgctggcgt taggggctt tgggaatga cgggggtca 
      cagccctgt acgggctcc agctgtgcg agcccgcgg 
      cgggcaaaa ccctcgtag tctcaggag cggccgggg 
      ctgtgggca cccacgtgg gccaactgg ccaaactac 
      aagggtgca aagtggttg gtatcactg gatcggacg 
      ctaaaggcc accgattgg tcaaagaat tggactttg 
      atgctttcg ttaactata agagtgaag attttgaga 
      aaaaattgg ccgaagcta cgccacaaa acatagact 
      gctacttcg acaacgtgg ggggcgatg tcagcagcg 
      ccgtcttgc accgcatga acaaattcg gtcatgtgg 
      tcatctgtg gggctattt ccacctaca atgacgaaa 
      acaccaaag cccgagagg tgcaaacac ctgtgaaag 
      tcaaccacc ttgtgatgg aagggttca gcgtgactc 
      ggtggcgaa acaaatgga acaaagcca ttgacgata 
      accttaaat tgatccaag aggggcgtt tgaaatatt 
      tcgaaaccg tcactgaag ggttcgaaa atacgccgg 
      acgcgttca tgaagatgc taggtgggc agaactttg 
      ggaaagcta ttgttaaag tgtgaataa attgttaaa 
      actgaagct gtagcattt gaggttaag gttgacgca 
      tgacagtac ttaccgaca agtcctgat aactctcga 
      aataatcac tcgaatcca tcctttcca ctatttaaa 
      gtcagtcgg gggtgtctt gagggggta ttaaggcac 
      aaagttatg ttttttgag aaaataaat tacactgat 
      tgac
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY