Status
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Gene information
General information
TC003400 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_007418.3: 4277942..4297739
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
    TC003400
    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_00564

    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)

    Fertility
    mature egg deposition blocked number 1st lateral oviduct: 3 number 2nd lateral oviduct: 4 - Number of animals showing the phenotype: 1
    ovary without detectable defects - Number of animals showing the phenotype: 3
    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 larval musculature partially not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    abdomen musculature dorsal shortened - Penetrance (percentage of animals/eggs on slide): less than 30%
    thorax musculature partially thinner - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    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: 10.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 10.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality early (L5/6) - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection


    remarks: later than schedule, adult lethality - Number of animals showing the phenotype: 1 (41 dpi)
    Days post injection


    Pupal morphology
    remarks: later than schedule,
    Adult morphology
    remarks: later than schedule,
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC003400 RA
      MKGRHQFRR RFSLQPSFL KEEPDEDKR LHNSRVLRS 
      QKSEDVESL EKDDSVGPV NSVRHKIVV MGAAKVGKS 
      SIITQFLYG TFCSKYKRT VEEMHHGEF NVSGVHLTL 
      DILDTAGSY EFPAMRALS ISSADAFIL VYDVTDSST 
      FEEARALRD QIHETKATT NVPIVVVGN KIDLAGNRQ 
      VDTATTESV VTVDWENGF VEASAKENT NITKVFKEL 
      LTQAKVKYN LSPALRRRR RQSLPSQSG PPPSTPSHA 
      AMIPSAVQL QHLQQIRDR HGKRNSCII S
    CDS sequence
    • >TC003400 RA
      atgaagggt cggcaccag tttcgcagg cggtttagc 
      ttgcaacct tcgttcttg aaagaggag cctgacgaa 
      gacaaacgt ctacacaat tctagggtt ctcaggtcg 
      caaaagagc gaagatgtg gagtcgctg gaaaaggac 
      gacagcgtg ggtcctgtc aacagcgtt cgccataag 
      atagtagta atgggtgcg gctaaagtc ggcaagtct 
      tccatcata acccagttc ttgtacgga accttttgc 
      tccaagtat aagcgaacg gttgaagag atgcatcat 
      ggggaattc aacgtgtct ggagttcat ttaacgtta 
      gacatatta gatactgct ggttcttac gaatttcct 
      gctatgaga gcgttatca atttcttcg gcggatgca 
      ttcatctta gtgtatgac gtgactgac agttccacc 
      ttcgaggaa gcgagagcc ttaagagat caaatacat 
      gaaaccaag gccacgact aatgtgcct atcgttgtt 
      gtggggaac aaaatcgac ctggccgga aacagacag 
      gttgatacc gcaacaacc gagtccgtg gtgacggtc 
      gattgggag aacggcttc gtggaagct tcggcgaaa 
      gagaacacg aacataacc aaggttttc aaagagctt 
      ttaacgcag gctaaggtc aaatacaac ctcagtccg 
      gctttgagg cgtcggagg aggcagtct ctgccctcg 
      caatcgggg ccgccgccc tcgacgccc tctcacgct 
      gcgatgatt ccttcagcc gtccaactc cagcacttg 
      caacaaatt agggaccgt cacggaaaa agaaactcc 
      tgtatcata tcttaa
    mRNA sequence
    • >TC003400 RA
      attcgctgc caacctgtt ggttccagt agtgtagct 
      tagaacagt taatgactt ggctttcat atctcgcca 
      ctgaccact tctccggtg agcaactta cggcttaaa 
      gactggcgt cgaactcga agaatttga tgaagggtc 
      ggcaccagt ttcgcaggc ggtttagct tgcaacctt 
      cgttcttga aagaggagc ctgacgaag acaaacgtc 
      tacacaatt ctagggttc tcaggtcgc aaaagagcg 
      aagatgtgg agtcgctgg aaaaggacg acagcgtgg 
      gtcctgtca acagcgttc gccataaga tagtagtaa 
      tgggtgcgg ctaaagtcg gcaagtctt ccatcataa 
      cccagttct tgtacggaa ccttttgct ccaagtata 
      agcgaacgg ttgaagaga tgcatcatg gggaattca 
      acgtgtctg gagttcatt taacgttag acatattag 
      atactgctg gttcttacg aatttcctg ctatgagag 
      cgttatcaa tttcttcgg cggatgcat tcatcttag 
      tgtatgacg tgactgaca gttccacct tcgaggaag 
      cgagagcct taagagatc aaatacatg aaaccaagg 
      ccacgacta atgtgccta tcgttgttg tggggaaca 
      aaatcgacc tggccggaa acagacagg ttgataccg 
      caacaaccg agtccgtgg tgacggtcg attgggaga 
      acggcttcg tggaagctt cggcgaaag agaacacga 
      acataacca aggttttca aagagcttt taacgcagg 
      ctaaggtca aatacaacc tcagtccgg ctttgaggc 
      gtcggagga ggcagtctc tgccctcgc aatcggggc 
      cgccgccct cgacgccct ctcacgctg cgatgattc 
      cttcagccg tccaactcc agcacttgc aacaaatta 
      gggaccgtc acggaaaaa gaaactcct gtatcatat 
      cttaaacat gtgcatcgt agcaattac ttctttatg 
      tgcagaaaa taatgatcg atgcccaga attgattta 
      acaagtcct gtgtgcagg cacagtttt gcgttcact 
      actttgcat atcaactgc acactgctc tttcttttc 
      ccactactt tcgacaatt ttgaacacc aagggcatg 
      gtttcattg tttttggga acatagacc acaactaat 
      tcttccata tttaataac ttgatgtct atcgattat 
      ctaataagt ggtgtaaat atgctgaat taacaaccg 
      acatgtaac tgcaggttg gatcacttg tcaatatac 
      agagttagt gacttcgat ctacttttt tatgttgat 
      aaaatgtgc aattttata aaggtgtag caataccgg 
      tttattttt caatggttg aaggctgtc ttaaagtag 
      aagcagcgt tacaatttt ttgttgatt ttaattgaa 
      acgttaagt gcatgtttt gcagatctc aaccagtat 
      gtgtactaa gctttttta aataggaat gagtacgta 
      gttctagct tttgtattt ctgttagtt ttagtttct 
      gtattacgt atatgtgac ttcaatctt gacaatcca 
      gaatcaatg tattattaa atataggaa cgatga
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY