Status
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Gene information
General information
TC006407 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: 8482279..8483145
Sequence information
Transcripts / Proteins (2) 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
    TC006407
    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
    If you have entered your name and agree by marking the checkbox. we might show your name on this page to honor your contribution.

    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_04135

    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: 0.0% (includes death as pupa, adult)

    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: 20.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 20.0% (includes death as larva, prepupa, pupa, adult)

    pupal molt delayed (still prepupa) - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection


    adult lethality - Number of animals showing the phenotype: 2 (41 dpi)
    Days post injection


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC006407 RA
      MFGTLSQLS HSVFETEIK IEPISFYGC 
      SSSEPDKPS SPPADEPRK KRKPQTCKI 
      CGKVLSSTS SYYVHMKLH SGNKPFQCT 
      QCEACFCRK PYLEVHLRT HTGERPFKC 
      DVCDKRFTQ KSSLNTHKR VHTGLRPYA 
      CDVCEKKFA VRSYLVAHR WSHVSDGLS 
      CPECNAGFS TKSQLVQHV KGHSNRRGF 
      QCEVCQRRF VRDSYLIRH LNKVHKNNA
    • >TC006407 RB
      MFGTLSQLS HSVFETEIK IEPISFYGC 
      SSSEPDKPS SPPADVGSP LAATILTVA 
      LQEPRKKRK PQTCKICGK VLSSTSSYY 
      VHMKLHSGN KPFQCTQCE ACFCRKPYL 
      EVHLRTHTG ERPFKCDVC DKRFTQKSS 
      LNTHKRVHT GLRPYACDV CEKKFAVRS 
      YLVAHRWSH VSDGLSCPE CNAGFSTKS 
      QLVQHVKGH SNRRGFQCE VCQRRFVRD 
      SYLIRHLNK VHKNNA
    CDS sequence
    • >TC006407 RA
      atgttcggc accctgtcg cagttgtcg cacagcgtg 
      ttcgagacg gagataaag atcgagccg atcagcttc 
      tacggctgc tccagctcg gagcccgac aagccgtcg 
      tcgcccccg gccgacgag ccccgcaag aagcgcaag 
      ccccagacg tgcaaaatc tgcggcaaa gtcctctcc 
      tccacgtcc agttactac gtccacatg aagctccat 
      tcgggcaat aagcccttt cagtgtacg caatgcgag 
      gcgtgtttc tgccgcaag ccctatctg gaggtccac 
      ctccgcacg cacacgggc gagaggcct ttcaagtgc 
      gacgtatgc gacaagaga tttacccaa aaatccagt 
      ctaaataca cacaaacgc gtgcatacg gggctgagg 
      ccgtatgcg tgcgatgtg tgcgagaag aaattcgcc 
      gtgaggagt tatctggtg gcgcatcga tggtcgcac 
      gtgtccgat gggctgtcg tgtccggaa tgcaacgcc 
      gggtttagc accaagagc cagttggtg caacatgtc 
      aaagggcat agcaatcgc agggggttc cagtgtgag 
      gtttgtcag aggaggttt gttagggat tcgtatctg 
      attaggcac ttgaataaa gtgcacaag aataatgct 
      tga
    • >TC006407 RB
      atgttcggc accctgtcg cagttgtcg cacagcgtg 
      ttcgagacg gagataaag atcgagccg atcagcttc 
      tacggctgc tccagctcg gagcccgac aagccgtcg 
      tcgcccccg gccgacgta ggtagcccc cttgctgcc 
      acaatcctc actgtcgca ttgcaggag ccccgcaag 
      aagcgcaag ccccagacg tgcaaaatc tgcggcaaa 
      gtcctctcc tccacgtcc agttactac gtccacatg 
      aagctccat tcgggcaat aagcccttt cagtgtacg 
      caatgcgag gcgtgtttc tgccgcaag ccctatctg 
      gaggtccac ctccgcacg cacacgggc gagaggcct 
      ttcaagtgc gacgtatgc gacaagaga tttacccaa 
      aaatccagt ctaaataca cacaaacgc gtgcatacg 
      gggctgagg ccgtatgcg tgcgatgtg tgcgagaag 
      aaattcgcc gtgaggagt tatctggtg gcgcatcga 
      tggtcgcac gtgtccgat gggctgtcg tgtccggaa 
      tgcaacgcc gggtttagc accaagagc cagttggtg 
      caacatgtc aaagggcat agcaatcgc agggggttc 
      cagtgtgag gtttgtcag aggaggttt gttagggat 
      tcgtatctg attaggcac ttgaataaa gtgcacaag 
      aataatgct tga
    mRNA sequence
    • >TC006407 RA
      tccgtaaaa actacacaa agacacaga attggttgt 
      aacgcttta ttcaattca aacaaacaa ttcgtcaaa 
      tgggcacta gtaacaaca aacgcggcc ataacctca 
      ttttcgccg taggcctcc gccatgttc ggcaccctg 
      tcgcagttg tcgcacagc gtgttcgag acggagata 
      aagatcgag ccgatcagc ttctacggc tgctccagc 
      tcggagccc gacaagccg tcgtcgccc ccggccgac 
      gagccccgc aagaagcgc aagccccag acgtgcaaa 
      atctgcggc aaagtcctc tcctccacg tccagttac 
      tacgtccac atgaagctc cattcgggc aataagccc 
      tttcagtgt acgcaatgc gaggcgtgt ttctgccgc 
      aagccctat ctggaggtc cacctccgc acgcacacg 
      ggcgagagg cctttcaag tgcgacgta tgcgacaag 
      agatttacc caaaaatcc agtctaaat acacacaaa 
      cgcgtgcat acggggctg aggccgtat gcgtgcgat 
      gtgtgcgag aagaaattc gccgtgagg agttatctg 
      gtggcgcat cgatggtcg cacgtgtcc gatgggctg 
      tcgtgtccg gaatgcaac gccgggttt agcaccaag 
      agccagttg gtgcaacat gtcaaaggg catagcaat 
      cgcaggggg ttccagtgt gaggtttgt cagaggagg 
      tttgttagg gattcgtat ctgattagg cacttgaat 
      aaagtgcac aagaataat gcttgattg tgataattt 
      cttcttttg taataaagt gtaaaaagt atg
    • >TC006407 RB
      tccgtaaaa actacacaa agacacaga attggttgt 
      aacgcttta ttcaattca aacaaacaa ttcgtcaaa 
      tgggcacta gtaacaaca aacgcggcc ataacctca 
      ttttcgccg taggcctcc gccatgttc ggcaccctg 
      tcgcagttg tcgcacagc gtgttcgag acggagata 
      aagatcgag ccgatcagc ttctacggc tgctccagc 
      tcggagccc gacaagccg tcgtcgccc ccggccgac 
      gtaggtagc ccccttgct gccacaatc ctcactgtc 
      gcattgcag gagccccgc aagaagcgc aagccccag 
      acgtgcaaa atctgcggc aaagtcctc tcctccacg 
      tccagttac tacgtccac atgaagctc cattcgggc 
      aataagccc tttcagtgt acgcaatgc gaggcgtgt 
      ttctgccgc aagccctat ctggaggtc cacctccgc 
      acgcacacg ggcgagagg cctttcaag tgcgacgta 
      tgcgacaag agatttacc caaaaatcc agtctaaat 
      acacacaaa cgcgtgcat acggggctg aggccgtat 
      gcgtgcgat gtgtgcgag aagaaattc gccgtgagg 
      agttatctg gtggcgcat cgatggtcg cacgtgtcc 
      gatgggctg tcgtgtccg gaatgcaac gccgggttt 
      agcaccaag agccagttg gtgcaacat gtcaaaggg 
      catagcaat cgcaggggg ttccagtgt gaggtttgt 
      cagaggagg tttgttagg gattcgtat ctgattagg 
      cacttgaat aaagtgcac aagaataat gcttgattg 
      tgataattt cttcttttg taataaagt gtaaaaagt 
      atg
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY