Status
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Gene information
General information
TC009895 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_007422.5: 12626384..12628081
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
    TC009895
    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
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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_01624

    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: < 50
    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
    • >TC009895 RA
      MDFAKKQLE KYGWKDGKG LGKHEDGIS QALKPKLKF 
      DNAGIGHEV GDQFTNNWW ERVFNSAAS NINVAVDQD 
      EVKLHLKEE SVEITTKNY SLKELKKNK HLEYGSFLK 
      SAKLTERGV ETYNVTPIE QFPSCSSLT DDELFAACG 
      GRTAHKGAR HGLKLGGKL SRIEKQEKM LLKKMKNVS 
      LTDDTSNLE KKIKKLKKH KEETVSNTP PQELESPSS 
      RKHKNKRKS VSFNDETVV KYYTPEADT SHESIKDEN 
      SNNPGIADP NSNSCDEGI EQDFEDSNN DSSDHRSFE 
      EAQRTFDDL SKAERKKLK KKRKLEKKK TKTAQFIED 
      VREQMATEE NGKKRKLVA EDVDMETKQ KELCKYSKK 
      FRKEMKREK KMMKSIVKS LDNFCKISD DE
    CDS sequence
    • >TC009895 RA
      atggatttt gcgaaaaaa cagctagaa aaatacggt 
      tggaaagat ggtaaagga ttagggaaa cacgaagac 
      ggaatatca caagcctta aaaccgaaa ttgaagttc 
      gacaatgct ggaattggc cacgaagtt ggagatcaa 
      tttaccaat aactggtgg gaaagagtt tttaacagt 
      gcagccagt aacataaat gttgcagtg gaccaagat 
      gaggtgaag ttgcacttg aaggaagaa tcagttgaa 
      atcacaaca aaaaattat tcacttaaa gagctcaaa 
      aagaacaag catctagag tacggctcg tttttgaaa 
      tctgcaaaa cttaccgaa cgtggagtt gaaacttac 
      aatgtcacg cctattgag cagtttccc tcttgcagt 
      tctctaact gatgacgaa ctatttgca gcctgtggt 
      ggcagaact gctcataag ggtgcgcgc catggctta 
      aaactgggc ggaaagttg tcaaggatt gaaaaacaa 
      gagaaaatg ctgctcaaa aaaatgaaa aacgtttcg 
      ctgaccgac gacaccagc aatttggag aaaaaaatc 
      aagaaactg aagaagcac aaagaagaa accgtaagc 
      aatacacca cctcaggaa cttgagagt ccgagttcc 
      agaaagcac aaaaataag cgcaagagt gtgtccttc 
      aacgatgag actgttgtt aaatactac actcctgag 
      gcggacaca agccatgaa agtattaaa gatgagaat 
      agcaataat ccagggata gctgatccc aattcaaat 
      tcttgcgat gaggggatt gagcaagac tttgaagac 
      tcaaataat gactccagt gaccacagg agttttgaa 
      gaggcacaa aggacgttc gatgatttg tcgaaagcc 
      gaaaggaag aaactgaaa aagaagcgg aagctggaa 
      aagaagaaa acaaaaact gctcaattt attgaagat 
      gtgagggag caaatggcc actgaggag aacggaaaa 
      aagcggaaa ttggtcgct gaggacgtg gatatggaa 
      actaagcaa aaggaactg tgtaaatat tcgaagaaa 
      ttcagaaaa gaaatgaag cgtgagaag aaaatgatg 
      aaatcgata gtaaagtcg ttagataac ttctgtaaa 
      atatctgac gatgaatag
    mRNA sequence
    • >TC009895 RA
      caagtctgt caaaaatca gaattttgt tgttttgat 
      tatttacgt caaatgggc cataagccc acgtgcata 
      aatggattt tgcgaaaaa acagctaga aaaatacgg 
      ttggaaaga tggtaaagg attagggaa acacgaaga 
      cggaatatc acaagcctt aaaaccgaa attgaagtt 
      cgacaatgc tggaattgg ccacgaagt tggagatca 
      atttaccaa taactggtg ggaaagagt ttttaacag 
      tgcagccag taacataaa tgttgcagt ggaccaaga 
      tgaggtgaa gttgcactt gaaggaaga atcagttga 
      aatcacaac aaaaaatta ttcacttaa agagctcaa 
      aaagaacaa gcatctaga gtacggctc gtttttgaa 
      atctgcaaa acttaccga acgtggagt tgaaactta 
      caatgtcac gcctattga gcagtttcc ctcttgcag 
      ttctctaac tgatgacga actatttgc agcctgtgg 
      tggcagaac tgctcataa gggtgcgcg ccatggctt 
      aaaactggg cggaaagtt gtcaaggat tgaaaaaca 
      agagaaaat gctgctcaa aaaaatgaa aaacgtttc 
      gctgaccga cgacaccag caatttgga gaaaaaaat 
      caagaaact gaagaagca caaagaaga aaccgtaag 
      caatacacc acctcagga acttgagag tccgagttc 
      cagaaagca caaaaataa gcgcaagag tgtgtcctt 
      caacgatga gactgttgt taaatacta cactcctga 
      ggcggacac aagccatga aagtattaa agatgagaa 
      tagcaataa tccagggat agctgatcc caattcaaa 
      ttcttgcga tgaggggat tgagcaaga ctttgaaga 
      ctcaaataa tgactccag tgaccacag gagttttga 
      agaggcaca aaggacgtt cgatgattt gtcgaaagc 
      cgaaaggaa gaaactgaa aaagaagcg gaagctgga 
      aaagaagaa aacaaaaac tgctcaatt tattgaaga 
      tgtgaggga gcaaatggc cactgagga gaacggaaa 
      aaagcggaa attggtcgc tgaggacgt ggatatgga 
      aactaagca aaaggaact gtgtaaata ttcgaagaa 
      attcagaaa agaaatgaa gcgtgagaa gaaaatgat 
      gaaatcgat agtaaagtc gttagataa cttctgtaa 
      aatatctga cgatgaata gaaggaaac gaggggata 
      agtacgtat atttcattt aattaacaa ggaaactaa 
      aaaaactta attgtttgg agtacgttc caaaaaaaa 
      agaaaaaca aaaaatatt tttataaaa tgataagta 
      gttggtaat acccaattt tgtgtgagt cgtcctgta 
      tatttagct ttttcgtta atttcgggc caataaaag 
      ttaacaatt taa
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY