Status
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Gene information
General information
TC001000 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_007417.3: 9577618..9579998
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
    TC001000
    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_00205

    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)

    adult lethality - Number of animals showing the phenotype: 2 (9 dpi)
    Days post injection


    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
    embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    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: % (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
    • >TC001000 RA
      MPVRKYRRE TSEVSSCLK YMIFGFNVL FWLLGLGIL 
      TVGVWAWSE KDIFNNLGK VANVALDPA FILICIGTV 
      TFIIGFTGC VGALRENTC LLATYAIFL SVLLLFEMT 
      AGILGFIFK DWIKSQATI GFQTFIIHY REDPDQQNL 
      IDWIQEDWL QCCGIEGPK DWDRNNYFN CSSRDVGSR 
      EACGVPFSC CKRKPNEII KNKQCGYDV RKPGFNFDV 
      SKIINEKGC LEAIEEWLE RNMISLATF GFIILFLQI 
      LGICFAQNL RADIFAQKA KWH
    CDS sequence
    • >TC001000 RA
      atgcctgtg aggaagtac aggcgagag accagcgaa 
      gtcagcagt tgtttgaag tacatgata ttcgggttt 
      aacgtgttg ttttggctg ttaggatta ggtattttg 
      actgtggga gtgtgggct tggagcgag aaagatatt 
      tttaataat ttagggaaa gtggcaaat gttgctctc 
      gatccagcg tttattttg atatgcatt ggaacggtg 
      actttcatt atcgggttc acaggatgt gtgggggca 
      ctgcgggaa aatacttgt cttttagct acatatgcc 
      atattttta tctgtgtta cttttattc gaaatgacg 
      gctggaatt cttggattt atttttaag gactggatt 
      aagtcacaa gccacgata ggtttccag acgtttatt 
      attcactat agagaggat ccagatcag cagaactta 
      attgactgg atccaggag gactggttg caatgttgc 
      ggcatcgaa gggccgaaa gattgggac cgtaacaat 
      tattttaat tgttcgtcg cgtgatgtt ggcagtagg 
      gaggcttgt ggagtccct ttctcgtgt tgtaaacgc 
      aagccaaat gaaattatc aagaataag cagtgcggt 
      tacgacgtg cgaaaacca ggtttcaat ttcgatgtg 
      tcaaagata attaacgag aaagggtgt ctggaagcg 
      attgaagaa tggctggag cgaaatatg atttcttta 
      gccactttt ggttttatt attttgttt ttgcaaatt 
      ttggggatc tgtttcgcg caaaacctg cgagctgat 
      atttttgca cagaaggcg aaatggcat tga
    mRNA sequence
    • >TC001000 RA
      caacacgca aaaaccaac agtagtttt taccaaaaa 
      gaaagtgtg tgagtgttt tccgaaatt ttttgtctc 
      ccaaatgtg aaatgccgt gtgagccac cgatttcca 
      aattatcgt tcgtttgtg tgggttagc aaagaaatt 
      ttcgtcaag gccagtcaa acaatgata catttcctg 
      attttcctt gtttaatta aaatttcaa acctaatta 
      attggaaat ggccgtgaa tctaccgac aatgcctgt 
      gaggaagta caggcgaga gaccagcga agtcagcag 
      ttgtttgaa gtacatgat attcgggtt taacgtgtt 
      gttttggct gttaggatt aggtatttt gactgtggg 
      agtgtgggc ttggagcga gaaagatat ttttaataa 
      tttagggaa agtggcaaa tgttgctct cgatccagc 
      gtttatttt gatatgcat tggaacggt gactttcat 
      tatcgggtt cacaggatg tgtgggggc actgcggga 
      aaatacttg tcttttagc tacatatgc catattttt 
      atctgtgtt acttttatt cgaaatgac ggctggaat 
      tcttggatt tatttttaa ggactggat taagtcaca 
      agccacgat aggtttcca gacgtttat tattcacta 
      tagagagga tccagatca gcagaactt aattgactg 
      gatccagga ggactggtt gcaatgttg cggcatcga 
      agggccgaa agattggga ccgtaacaa ttattttaa 
      ttgttcgtc gcgtgatgt tggcagtag ggaggcttg 
      tggagtccc tttctcgtg ttgtaaacg caagccaaa 
      tgaaattat caagaataa gcagtgcgg ttacgacgt 
      gcgaaaacc aggtttcaa tttcgatgt gtcaaagat 
      aattaacga gaaagggtg tctggaagc gattgaaga 
      atggctgga gcgaaatat gatttcttt agccacttt 
      tggttttat tattttgtt tttgcaaat tttggggat 
      ctgtttcgc gcaaaacct gcgagctga tatttttgc 
      acagaaggc gaaatggca ttgacaatc gaggactcc 
      cactgcggt gtagtacag tcttgcctg tcgcattgc 
      gtgggagcc tttttcgac ccagtttga ttttgtata 
      aggtgcttt aacactttg tagtgtgca attggtttc 
      attgtaatg gatgcacaa caattacta aaaaacatt 
      gagcaaatt ctagatttt gggctcaag tggggagct 
      gccagtttt tattgtggg gcagtctct tcgattttt 
      atcaataat tactaatat ttaatgtgc ctgttttaa 
      tgtaacaac tgacttaag gcccactaa ttgattgca 
      tgtttcttt gataattgt agtattcgt aattgtgat 
      attattttc tcatcgtta aaatactca gttatgcaa 
      ctgccaatc agcatttcc aagtgtaca ttccattgt 
      tttatttat tttttactc atttattta ttgacatca 
      agacagtct ttgtatatt gtctcgaga agtactaac 
      ttgtattga cataattgt ataaattgt taaactatt 
      gtaatcttt atattgaca agatctgga aataaattg 
      taaaataaa ac
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY