Status
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Gene information
General information
TC006028 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_007423.3: 2832053..2833133
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
    TC006028
    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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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_10644

    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: 1 (3 dpi)
    Days post injection


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


    Fertility
    mature egg not present - Number of animals showing the phenotype: 3

    egg chamber late number decreased - Number of animals showing the phenotype: 3

    vitellarium potentially size decreased - Number of animals showing the phenotype: 3
    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
    • >TC006028 RA
      MDKPRPCGC KGCRTCLIC ESTFGLSAK KFARRREDT 
      YVYCPQCNV AFPGWDPPK HPDHSGAPI TFPGIYIQL 
      DFLTPEEEA KLMQGIDDM SWDSSQSGR RKQNFGPKC 
      NFKKNKLRE GDFTGFPKF TEFVQEKFR NVPILSDFQ 
      TIEQCSLEY DPEKGASID PHVDDCWVW GERVVTVNL 
      LSDSVLTMT YNRKNNYYN LHLVGKYPA VLDEKGDRN 
      FTESCYKVK EFENDRFYP TVRVPMPRR SLLVMFNSA 
      RYDWEHQIL REDIRERRV CLAYREFTP IYLKGGDKE 
      QEGAPILRQ ARNFWEHLR
    CDS sequence
    • >TC006028 RA
      atggataag ccgcgcccc tgtgggtgc aagggctgc 
      cgcacgtgt ctgatttgc gagtcgacg ttcgggctt 
      tcggccaaa aaattcgca cgtcggagg gaagacacc 
      tacgtttat tgcccccag tgtaatgtt gcgtttccc 
      ggctgggac cccccgaaa cacccggac cattccggg 
      gcccccatt acattccca ggaatttac atacaactc 
      gatttctta acaccggaa gaagaggcg aaattaatg 
      caaggtata gatgatatg tcttgggac tcctctcag 
      agcgggcgc cgcaaacag aattttggg cctaagtgt 
      aatttcaag aaaaataag ctacgtgaa ggggacttt 
      accggattt ccgaaattc accgaattc gtgcaagag 
      aagttccga aatgtgccg attttgagt gattttcaa 
      acgatcgaa cagtgttcg ctggaatat gaccctgaa 
      aagggggct tcaattgac ccgcacgtt gatgattgt 
      tgggtttgg ggcgagaga gttgttacg gttaatttg 
      ttatcggat tcggtgctt acgatgacg tacaatagg 
      aaaaataat tattataat ttgcatttg gttgggaaa 
      tatccggca gttttggac gaaaaaggc gacaggaat 
      ttcaccgaa agttgttac aaagtgaag gagtttgaa 
      aatgatagg ttttacccc actgtgagg gttccaatg 
      cctcgaagg tctttactt gtgatgttt aattcggca 
      aggtacgac tgggagcac caaatttta agggaggat 
      attagggag aggagggtg tgtttggcc tatcgagag 
      ttcaccccc atttatctg aaagggggc gacaaggag 
      caagagggt gcgccgatt ttgaggcag gcgaggaat 
      ttttgggag cacttgagg tga
    mRNA sequence
    • >TC006028 RA
      cgaacgttg tgttgtgtt tgttgatct gtcattgaa 
      attttttga ggttaggtt gtttgaaac aattttgtt 
      ttttttttg tgatggata agccgcgcc cctgtgggt 
      gcaagggct gccgcacgt gtctgattt gcgagtcga 
      cgttcgggc tttcggcca aaaaattcg cacgtcgga 
      gggaagaca cctacgttt attgccccc agtgtaatg 
      ttgcgtttc ccggctggg accccccga aacacccgg 
      accattccg gggccccca ttacattcc caggaattt 
      acatacaac tcgatttct taacaccgg aagaagagg 
      cgaaattaa tgcaaggta tagatgata tgtcttggg 
      actcctctc agagcgggc gccgcaaac agaattttg 
      ggcctaagt gtaatttca agaaaaata agctacgtg 
      aaggggact ttaccggat ttccgaaat tcaccgaat 
      tcgtgcaag agaagttcc gaaatgtgc cgattttga 
      gtgattttc aaacgatcg aacagtgtt cgctggaat 
      atgaccctg aaaaggggg cttcaattg acccgcacg 
      ttgatgatt gttgggttt ggggcgaga gagttgtta 
      cggttaatt tgttatcgg attcggtgc ttacgatga 
      cgtacaata ggaaaaata attattata atttgcatt 
      tggttggga aatatccgg cagttttgg acgaaaaag 
      gcgacagga atttcaccg aaagttgtt acaaagtga 
      aggagtttg aaaatgata ggttttacc ccactgtga 
      gggttccaa tgcctcgaa ggtctttac ttgtgatgt 
      ttaattcgg caaggtacg actgggagc accaaattt 
      taagggagg atattaggg agaggaggg tgtgtttgg 
      cctatcgag agttcaccc ccatttatc tgaaagggg 
      gcgacaagg agcaagagg gtgcgccga ttttgaggc 
      aggcgagga atttttggg agcacttga ggtgattgt 
      gtaaataaa cacaaaaaa taaacaagt tatgtggca 
      gattgtatt ttatttcca ataaaaaat tagtaacac 
      a
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