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Gene information
General information
TC009309 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: 213262..217520
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
    TC009309
    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
    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_08620

    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
    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
    • >TC009309 RA
      MEVPSSETV MKPTLSETL TKPVPRPFS 
      IEALMSDSG PKRNNSLAW NFTNQQYQV 
      NNCRDTDSD GSVDMDLAQ DLSRRSQKD 
      GSDLEDDTE ETQNSDGTG TKARRRRTA 
      FTSEQLLEL EREFHAKKY LSLTERSQI 
      ASALRLSEV QVKIWFQNR RAKWKRVKA 
      GLGAGPHQP KSGGQQKSK LVVPIPVHV 
      NRFAVRSQH QQLERALGD LAGRVLASH 
      AALRAGLDL HGYHHPPPP PH
    CDS sequence
    • >TC009309 RA
      atggaagtg ccgtcgagt gaaacggtc atgaaaccg 
      acgttgagt gaaacgttg acgaaaccg gtgccgaga 
      ccgttttct atagaagca ttgatgagt gatagtgga 
      cctaagaga aataatagt cttgcatgg aatttcact 
      aatcaacag tatcaagtg aataattgt agggatacg 
      gattctgat ggcagtgtg gatatggat cttgctcaa 
      gatttgtca aggaggagc caaaaagat ggctcggac 
      ctagaagac gacaccgaa gaaacccaa aactccgac 
      ggcactggc acgaaagcg cgccgccgt cgcaccgcc 
      ttcaccagc gagcaactc ctggagctg gaacgcgaa 
      ttccacgcc aaaaagtat ctgtcgttg acggagcgc 
      agccaaatc gcctccgct ttgcgcctt agcgaagtc 
      caggtgaaa atctggttc cagaacaga cgcgccaaa 
      tggaaacgg gtcaaagcc ggcctcggt gccggtccc 
      caccagccc aaaagtggc ggccagcag aagagcaaa 
      ctcgtcgtc ccgattccc gttcatgtg aaccgattt 
      gctgtcagg agtcagcac cagcagctg gaaagggcc 
      ttgggagac ctggctggg agggttttg gcaagtcat 
      gcagctcta agagcagga cttgacctg catgggtat 
      catcatcca ccgccaccg cctcattga
    mRNA sequence
    • >TC009309 RA
      attcagaga tgccaactt aatttcaac ttaggtata 
      gatttagca gacaacatt gattatcgt gccgcgatt 
      ggtcgaact agaaccaac agactaaca agggaggag 
      tttataaca agaatacgc ccaattcat ctcttcacc 
      ccttacaaa gttaacttg gctttgatc ggatcagtg 
      tcagtgaaa ctttttatg tggaaacgt tgctccgtc 
      tttgaatta gttttcggt ccgatgtga atttgaata 
      aaattaaaa atggaagtg ccgtcgagt gaaacggtc 
      atgaaaccg acgttgagt gaaacgttg acgaaaccg 
      gtgccgaga ccgttttct atagaagca ttgatgagt 
      gatagtgga cctaagaga aataatagt cttgcatgg 
      aatttcact aatcaacag tatcaagtg aataattgt 
      agggatacg gattctgat ggcagtgtg gatatggat 
      cttgctcaa gatttgtca aggaggagc caaaaagat 
      ggctcggac ctagaagac gacaccgaa gaaacccaa 
      aactccgac ggcactggc acgaaagcg cgccgccgt 
      cgcaccgcc ttcaccagc gagcaactc ctggagctg 
      gaacgcgaa ttccacgcc aaaaagtat ctgtcgttg 
      acggagcgc agccaaatc gcctccgct ttgcgcctt 
      agcgaagtc caggtgaaa atctggttc cagaacaga 
      cgcgccaaa tggaaacgg gtcaaagcc ggcctcggt 
      gccggtccc caccagccc aaaagtggc ggccagcag 
      aagagcaaa ctcgtcgtc ccgattccc gttcatgtg 
      aaccgattt gctgtcagg agtcagcac cagcagctg 
      gaaagggcc ttgggagac ctggctggg agggttttg 
      gcaagtcat gcagctcta agagcagga cttgacctg 
      catgggtat catcatcca ccgccaccg cctcattga 
      aacgctgct ggagtttac tgacgattg tggttggtg 
      acaatagtg gcacttatg gacggagta gagacgaga 
      ttttgtatt atggtgcat attttattt aaacactac 
      tgtttaaaa attattata tttgaaagt aataacgtg 
      caataggtt tagatttcc tagattgag aatttttat 
      tattgaaat aaatactta attctttat cagaaatac 
      aaagtattg atcgctaga gacggatca gaacagttt 
      tagcaattt tacaaaaat tataatttt tttaccagc 
      tcgtggctt cttaaacaa ttttaataa aatttttct 
      aaacactaa aatgcgttt tgacttgaa aacctctta 
      aagtactcg aatatgtta tttagttct agtttataa 
      aagttaaag tgtttaaaa aagtaccta tctataaaa 
      tgaaggcat ttttagccc aaatccaag attcttttg 
      taatttttg ataaaattt tgtaacata attgagttt 
      taaagcaaa accttacac acagacgcg ttgtttttc 
      ggtttattt tgccaaaca tttgcgaaa aatcgaatg 
      cgtttcgat aaaacgcaa agcggtaaa aatctgcct 
      ctgttttat aaaaatcgt tttgtagta ggatctgta 
      agtggagag tgactattt gctcaatta ttcgttaac 
      atgtaataa aaatgcagg gtgggacga agataaata 
      ccactatta caataataa cgaatagaa aactaaaag 
      attcaaaaa attcacata cgtttgctg ttttattga 
      aaatttctt ctaaataaa tatacacat aaatttttg 
      taattacaa tgagagtgt aataatggc aactcgttg 
      cactctgta tcataacat aactcattt aatttcatg 
      attgtataa gtttgtttt ggtatgctc cccgttata 
      aaagaactg tcagatctg aatgtatct atacaatgt 
      atttttttg tagtaattt taaaaatta ccaagggtt 
      gtaaatatt tgtgtacaa aattaattt agtacttat 
      aaataaata aagaattat taccatt
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY