Status
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Gene information
General information
TC000087 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: 11408154..11418276
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
    TC000087
    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
    {{ goGene }}
    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_00017

    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: 30.0% (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: 1 (9 dpi)
    Days post injection


    adult lethality - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection


    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
    egg without cuticle embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): less than 30%
    head not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    head partially not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    head not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    thorax partially not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    thorax not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen partially # of remaining segments not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    abdomen not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    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: 30.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 90.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 3 (11 dpi)
    Days post injection


    pupation delayed (still larva) - Number of animals showing the phenotype: 7 (11 dpi)
    Days post injection


    remarks: later than schedule, hours 24 larva lethality late (L7) - Number of animals showing the phenotype: 5 (19 dpi)
    Days post injection


    pupal molt delayed (still larva) - Number of animals showing the phenotype: 2 (19 dpi)
    Days post injection


    larva lethality late (L7) - Number of animals showing the phenotype: 1 (22 dpi)
    Days post injection


    pupal molt delayed (still larva) - Number of animals showing the phenotype: 1 (22 dpi)
    Days post injection


    Pupal morphology
    remarks: later than schedule, hours 24
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC000087 RA
      MMSRPTDII KGHSQAETP QGSPPDIPK LMPGGNYIK 
      IGRDSAKST CLVFAPLAE EVGVLAKCL NIFKQHGVN 
      LLHIESRPS ARIRNNYEF MVECAPTGD LASAIAEIK 
      KNTEYFNII SRDYKDNKD TVPWFPCRI RDLDKFANQ 
      ILSYGAELD ADHPGFTDP VYRARRKYF ADIAYNYKH 
      GEKLPHVDY TEEEIETWG KVFDQLTTL YPTHACKEH 
      NHVFPLLIE NCGYRRDNI PQLEDVSNF LKDCTGFTL 
      RPVAGLLSS RDFLAGLAF RVFHSTQYI RHPSKPFYT 
      PEPDVCHEL LGHAPLFAD PSFAQFSQQ IGLASLGAP 
      DDYIEKLAT CFWFTVEYG LCREGNELK AYGAGLLSS 
      YGELQYALE NKAEVRPFE PEKTAVQEY PITQYQPVY 
      YVAESFEDA KEKMIKYAA TIPRAFGVR YNAYTQSIE 
      VLDSKPQIE SLVTNISTE ISVLVDSLK KL
    CDS sequence
    • >TC000087 RA
      atgatgtcg agaccgacc gatatcatc aagggacac 
      agccaagcg gagacgccg caagggagt cccccggat 
      attccgaaa ttaatgccc ggcggcaac tacatcaaa 
      atcggtcgc gactcggcc aagagcacg tgcctggtg 
      ttcgccccc ctcgccgaa gaggtgggc gttttggcc 
      aaatgcctc aacatcttc aaacaacac ggcgtcaac 
      ctcctccac atcgaatcg cgaccctcc gcccgcatc 
      cgcaacaac tacgaattc atggtggag tgcgccccc 
      accggagac ctcgcctcc gccatcgcc gaaatcaag 
      aagaacacc gagtacttc aacatcatc tcgcgcgac 
      tacaaagac aacaaggac acggtgccg tggttcccg 
      tgccgtatc cgcgacctg gacaagttt gccaaccaa 
      attttgtcg tatggggcc gagctggat gcggatcat 
      cctgggttt acagacccg gtgtacagg gctcggagg 
      aagtatttc gccgatatt gcttacaat tacaagcat 
      ggggagaag ttgccgcat gtggactac accgaagag 
      gagatcgag acctggggg aaggttttc gatcagttg 
      acgacgctg tatcctacc catgcctgc aaggagcat 
      aatcatgtg ttcccgctc ttgatcgag aactgtggg 
      tatcggagg gacaatatt ccgcagttg gaggatgtc 
      tccaacttt ttgaaagac tgtaccggt ttcactctg 
      cgtccagtt gctggcctt ctctcatct cgcgacttt 
      ttggccggt ctggccttc agagtgttc cactcaacc 
      cagtacatc cggcatcca agcaaaccg ttctacacc 
      cctgaaccg gacgtctgc cacgaactt ttgggacac 
      gctccttta ttcgccgac ccttccttt gcccagttc 
      tcccaacag atcggttta gcttctctt ggggctcca 
      gacgactac atcgaaaaa ctcgcaacg tgcttctgg 
      ttcactgtc gagtacgga ttgtgccgc gaaggcaac 
      gagttgaag gcctacggt gctgggttg ctgtcctcc 
      tatggggag ctccaatac gctctggag aataaggcc 
      gaggtgagg cctttcgag ccggagaaa acggccgtt 
      caggagtat cccatcacg caatatcag cccgtttat 
      tacgtggct gagagtttc gaagatgcc aaagagaaa 
      atgataaaa tatgcagcc acgataccc agagcgttc 
      ggtgttcgg tacaatgcc tacacccaa agtatcgaa 
      gtcttggat tctaaaccg caaatcgaa agcttggtc 
      acgaatatt agtaccgaa atttcggta cttgtagac 
      agtttgaag aaattataa
    mRNA sequence
    • >TC000087 RA
      ctattaaaa gagagcctg tttgcattt gttgctcag 
      tctgttgac aactttaaa acgtgatat ttgaagcca 
      gatttttcg aaatgatgt cgagaccga ccgatatca 
      tcaagggac acagccaag cggagacgc cgcaaggga 
      gtcccccgg atattccga aattaatgc ccggcggca 
      actacatca aaatcggtc gcgactcgg ccaagagca 
      cgtgcctgg tgttcgccc ccctcgccg aagaggtgg 
      gcgttttgg ccaaatgcc tcaacatct tcaaacaac 
      acggcgtca acctcctcc acatcgaat cgcgaccct 
      ccgcccgca tccgcaaca actacgaat tcatggtgg 
      agtgcgccc ccaccggag acctcgcct ccgccatcg 
      ccgaaatca agaagaaca ccgagtact tcaacatca 
      tctcgcgcg actacaaag acaacaagg acacggtgc 
      cgtggttcc cgtgccgta tccgcgacc tggacaagt 
      ttgccaacc aaattttgt cgtatgggg ccgagctgg 
      atgcggatc atcctgggt ttacagacc cggtgtaca 
      gggctcgga ggaagtatt tcgccgata ttgcttaca 
      attacaagc atggggaga agttgccgc atgtggact 
      acaccgaag aggagatcg agacctggg ggaaggttt 
      tcgatcagt tgacgacgc tgtatccta cccatgcct 
      gcaaggagc ataatcatg tgttcccgc tcttgatcg 
      agaactgtg ggtatcgga gggacaata ttccgcagt 
      tggaggatg tctccaact ttttgaaag actgtaccg 
      gtttcactc tgcgtccag ttgctggcc ttctctcat 
      ctcgcgact ttttggccg gtctggcct tcagagtgt 
      tccactcaa cccagtaca tccggcatc caagcaaac 
      cgttctaca cccctgaac cggacgtct gccacgaac 
      ttttgggac acgctcctt tattcgccg acccttcct 
      ttgcccagt tctcccaac agatcggtt tagcttctc 
      ttggggctc cagacgact acatcgaaa aactcgcaa 
      cgtgcttct ggttcactg tcgagtacg gattgtgcc 
      gcgaaggca acgagttga aggcctacg gtgctgggt 
      tgctgtcct cctatgggg agctccaat acgctctgg 
      agaataagg ccgaggtga ggcctttcg agccggaga 
      aaacggccg ttcaggagt atcccatca cgcaatatc 
      agcccgttt attacgtgg ctgagagtt tcgaagatg 
      ccaaagaga aaatgataa aatatgcag ccacgatac 
      ccagagcgt tcggtgttc ggtacaatg cctacaccc 
      aaagtatcg aagtcttgg attctaaac cgcaaatcg 
      aaagcttgg tcacgaata ttagtaccg aaatttcgg 
      tacttgtag acagtttga agaaattat aagtttcgt 
      cgtctgctc caatatttt tataagtat tatgtaaga 
      cataatgat tttgtacga ctcttatgt ttaattgtg 
      tctaaatta ttttttata ataaaaacg ttattccac 
      tttaagtct acttactga ttttggggc gtgttatct 
      atcgttggg ttttgtttt tttataacc acacttttt 
      tgtgtttcc cgcgctcaa attctggca agttgaaaa 
      cagttgcaa ttaaaactc cctaccatt ttggttata 
      ttttgagtt tgaaaagta ggctttgaa tttttttct 
      cttcttgtg gaagtcgcc atattggct tgtgttttt 
      tgtgttgag acttgttgg cgtcgtgtt cgttatttt 
      cttcaaaat agttcaaaa ataaatcac tttttgcga 
      tttaatgaa gtgagacct taatcaaat tgaagagct 
      gaatgcatt tggtcgtca gttaatgga ttggtgaga 
      ttttgttag taacgaatt tactgtctc aagagtgcc 
      tcatttctc acttcaaga ccgttaaat atctaagtg 
      agtagaaat acggtcttt gaacacatt ttgaattgg 
      attttaggt gctgggtct ttttccttt tcctttttt 
      ccactcctt cctgttctt cgtttgagt tttgtttgc 
      gtcgaatta tggggttgc ttttgcgag gacaaggcg 
      gtcgaactg gttatccgt taccgccaa gttctcaca 
      cattccccg ggtctttga agacgatga cgagtttct 
      tcgaacatc gttacaacc tggaccatc tgaaatttt 
      ttccgcaac aagtgttag cacgatacc aaatcaaag 
      ctttacccg taggatcat caacggcat caacaactt 
      cacacttgg gaacaggca acaggagtg taagaagtc 
      tgtggtacg gattgggtt ctatacgtt tgttgctga 
      gtgacaagt taaaatttg tatggaagg taagactga 
      aataatgca aagtaaaac at
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY