Status
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Gene information
General information
TC005409 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: 13580099..13582246
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
    TC005409
    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_09408

    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: 50.0% (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


    adult lethality - Number of animals showing the phenotype: 3 (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
    • >TC005409 RA
      MAFGKVVAF FVTVFGALA ASTHSEKIK CVENGRFYR 
      DPDRPPQKV WTSSECSKY YLCLEGEVF DFRCSSGLL 
      FDVIKQICD VKINVDNCD ITSETITPR PTTINKCPN 
      NHQKCTNGT CLPQKYFCD GSLDCPDGS DEKFCDPKN 
      DPFGAPECN SSCSLPHCF CSPDGTQIP GNLEPSKVP 
      QMVLLTFDG PVNSHNWVL LDGLLNGAL NPNGCPIKA 
      TFFVSHESN NYHQTQKLW NEGHEIAVH SITYGRWLL 
      NATIEDWFD EMVGQANII HRFSGVRLR ELRGLRAPF 
      LQIGSNRQF LMMKEFGFV YDSSIVAPF THLPLWPYT 
      LDHKLPHEC IKQECPTRP YPGVWEMVL NPFEARDYS 
      CARLDACPG GLTGDDVFK ILANNFKRH YLGNRAPFG 
      LHLDTAWLK NRDYFDALQ DFIGEILQQ PDVWFVTNS 
      QAIEWMQNP TPIDHLNGF KAWDCAKFF KKQELACKV 
      PNVCKLYSS FFQQERYLY TCFECPVNY PWIRNEFGL 
      N
    CDS sequence
    • >TC005409 RA
      atggccttt ggcaaggtg gttgctttt tttgttact 
      gtttttggg gctttagcc gcgagcact cacagtgag 
      aaaataaaa tgcgtggaa aacggtcgt ttttaccgc 
      gaccctgac cgccccccg caaaaagtt tggacgtct 
      agcgaatgc tccaaatat tatctttgt ctcgagggc 
      gaagtcttt gacttccgg tgctcctcg gggcttcta 
      ttcgacgtc atcaaacaa atttgtgac gtaaaaata 
      aacgtagac aactgcgac atcacttca gaaacaatc 
      acccctcgc ccaacaacc atcaacaaa tgccccaac 
      aaccatcag aaatgtacc aatggtacc tgcctcccc 
      cagaaatat ttctgtgac ggctcatta gattgcccc 
      gacggaagc gacgaaaaa ttttgcgac cccaaaaac 
      gacccattt ggggcacca gagtgcaac tcgagttgt 
      tccctaccc cattgtttc tgttcacct gatggtacc 
      caaatccct ggtaatttg gaaccatca aaagtcccc 
      caaatggta cttttgact tttgatggt cccgtcaat 
      tcccacaat tgggtgtta ctggatggg ttgttaaac 
      ggggcccta aaccccaat gggtgtccc atcaaagcc 
      acatttttc gtgagccat gagtccaat aattaccat 
      caaacccag aaattgtgg aacgaaggg cacgaaatc 
      gccgtccat tccattact tatgggcgt tggttactg 
      aacgcaacc attgaggat tggttcgac gaaatggta 
      ggccaggct aatataatt caccgcttt tcgggcgtt 
      cgtttgagg gagttgagg gggctgagg gcccccttc 
      ctccaaatt ggctcaaac cgccagttt ttaatgatg 
      aaggagttt gggtttgtt tacgacagt tccatagtg 
      gcccctttt acccatttg cccttatgg ccctacacg 
      ctagaccat aaactaccc catgagtgt attaaacaa 
      gagtgtccg acgagacca tacccaggt gtgtgggaa 
      atggttttg aacccgttc gaggctagg gactactcc 
      tgtgcgagg ctagacgcc tgcccaggt ggtttaaca 
      ggagacgat gttttcaaa attctggct aataatttc 
      aaacggcat tatttgggc aatagggcg ccgtttggg 
      ctgcatttg gacacagcc tggctcaaa aatagggac 
      tattttgac gcgctccag gattttatc ggtgaaatt 
      ttgcaacaa ccagacgtc tggtttgtg actaattca 
      caagccatt gaatggatg caaaacccg acccctatt 
      gaccattta aacgggttt aaagcctgg gactgtgct 
      aaatttttc aaaaaacag gagctggcc tgcaaggtg 
      cccaacgtt tgcaagctc tattccagt ttttttcaa 
      caggagagg tatctgtac acttgtttt gagtgcccg 
      gtgaattat ccctggatc aggaacgag ttcgggctc 
      aactag
    mRNA sequence
    • >TC005409 RA
      acatgtgtt agagcagtg cagtgatgg cctttggca 
      aggtggttg ctttttttg ttactgttt ttggggctt 
      tagccgcga gcactcaca gtgagaaaa taaaatgcg 
      tggaaaacg gtcgttttt accgcgacc ctgaccgcc 
      ccccgcaaa aagtttgga cgtctagcg aatgctcca 
      aatattatc tttgtctcg agggcgaag tctttgact 
      tccggtgct cctcggggc ttctattcg acgtcatca 
      aacaaattt gtgacgtaa aaataaacg tagacaact 
      gcgacatca cttcagaaa caatcaccc ctcgcccaa 
      caaccatca acaaatgcc ccaacaacc atcagaaat 
      gtaccaatg gtacctgcc tcccccaga aatatttct 
      gtgacggct cattagatt gccccgacg gaagcgacg 
      aaaaatttt gcgacccca aaaacgacc catttgggg 
      caccagagt gcaactcga gttgttccc taccccatt 
      gtttctgtt cacctgatg gtacccaaa tccctggta 
      atttggaac catcaaaag tcccccaaa tggtacttt 
      tgacttttg atggtcccg tcaattccc acaattggg 
      tgttactgg atgggttgt taaacgggg ccctaaacc 
      ccaatgggt gtcccatca aagccacat ttttcgtga 
      gccatgagt ccaataatt accatcaaa cccagaaat 
      tgtggaacg aagggcacg aaatcgccg tccattcca 
      ttacttatg ggcgttggt tactgaacg caaccattg 
      aggattggt tcgacgaaa tggtaggcc aggctaata 
      taattcacc gcttttcgg gcgttcgtt tgagggagt 
      tgagggggc tgagggccc ccttcctcc aaattggct 
      caaaccgcc agtttttaa tgatgaagg agtttgggt 
      ttgtttacg acagttcca tagtggccc cttttaccc 
      atttgccct tatggccct acacgctag accataaac 
      taccccatg agtgtatta aacaagagt gtccgacga 
      gaccatacc caggtgtgt gggaaatgg ttttgaacc 
      cgttcgagg ctagggact actcctgtg cgaggctag 
      acgcctgcc caggtggtt taacaggag acgatgttt 
      tcaaaattc tggctaata atttcaaac ggcattatt 
      tgggcaata gggcgccgt ttgggctgc atttggaca 
      cagcctggc tcaaaaata gggactatt ttgacgcgc 
      tccaggatt ttatcggtg aaattttgc aacaaccag 
      acgtctggt ttgtgacta attcacaag ccattgaat 
      ggatgcaaa acccgaccc ctattgacc atttaaacg 
      ggtttaaag cctgggact gtgctaaat ttttcaaaa 
      aacaggagc tggcctgca aggtgccca acgtttgca 
      agctctatt ccagttttt ttcaacagg agaggtatc 
      tgtacactt gttttgagt gcccggtga attatccct 
      ggatcagga acgagttcg ggctcaact agcccttga 
      aaaaacaga ctgtttgtt attttatgt attt
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY