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Gene information
General information
TC009280 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: 1967285..1969093
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
    TC009280
    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
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    Name
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    Email
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    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_10575

    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 nutritional state potentially bad (cachectic) - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection


    Fertility
    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 pattern irregular - Penetrance (percentage of animals/eggs on slide): more than 80%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 80%
    remarks: muscle pattern potentially obscured by segmentation defect,
    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): less than 30%
    cuticle remnants with unidentifyable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

    larva constricted - Penetrance (percentage of animals/eggs on slide): less than 30%
    head capsule mostlynot present - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    head capsule size decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    antenna not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    labrum not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    mandible not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    labium -
    thorax posterior constricted - Penetrance (percentage of animals/eggs on slide): less than 30%

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

    legs size decreased - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    legs femur potentially fused - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    legs tibiotarsus potentially fused - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    legs shape irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    abdomen segment number decreased - Penetrance (percentage of animals/eggs on slide): less than 30%

    posterior terminus not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 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
    • >TC009280 RA
      MPKRKSSSS DDENRKKHK FTKSVLTDT TNITKNNNP 
      NEEQITWPQ DAVLQLISN IEENIPSDD NLSFHTRLE 
      KLNWENIAF GDYSPKECQ DKWASLCKQ VRKYRLLGE 
      IATDIRQWV TNPKVRPGA KHPDKPKQP KNSYMFFFE 
      AKRSEVMAQ NPDLHPVEV SRKLGELFK NLTMKEKEK 
      YEQLAKIAR QEYLEKLQV FYEAHPDLV PKKTPRRGK 
      SYEGPEKPK TPFELFVKV ESEKEESEV SRYVVIQKC 
      RERWNEFSD KEKFFWINW AEEEYAKYL EDLKEYIKE 
      HPDYEPGKL KPLLNKNEQ KIKQRASGK PQRPPKGPY 
      QLFLKMMME TDEIRKINS RDCVNYISD KWRACSEEE 
      KAEYRTRVE QMWLEYDSK LEEYIATLP PEKRDQVRE 
      EESRNKKIK SPTVAPKIE DQPKERLEK PTMPPSNEY 
      KFFLSVYKG KEKPETIWK AMTKKEKEV FATKLNELR 
      RKYIADYEL YLKSLSREE LEKLGESLA ASCDSSSES 
      ESDMEAED
    CDS sequence
    • >TC009280 RA
      atgcccaaa cgaaagtct tcaagctca gatgacgaa 
      aaccgcaag aaacataaa tttaccaag agtgtgctt 
      acggacacg actaacata accaagaac aacaaccca 
      aacgaagag caaattaca tggccccag gacgccgtc 
      cttcaacta atctcaaac attgaggaa aacatccca 
      agtgacgat aacctttct ttccatacc cgtttagaa 
      aaactaaac tgggaaaac atcgcgttt ggagactac 
      tccccaaag gagtgccaa gacaagtgg gcctctctg 
      tgcaagcag gtgcgcaaa taccgactt ttgggcgag 
      atcgcgacc gatatccgg caatgggtg acgaacccg 
      aaggtccgt ccgggggcg aagcacccc gacaagccc 
      aaacagccc aaaaattcc tacatgttt ttcttcgaa 
      gccaagcgg tccgaagtc atggcccaa aaccccgac 
      ctccacccg gtcgaagtg tcccgcaag ttgggcgag 
      ttgttcaaa aacttgacc atgaaggag aaggaaaag 
      tacgaacag ttggccaaa atcgcacga caggagtac 
      ctggagaag ttgcaagtg ttctacgag gcgcatcca 
      gacctagtc ccgaaaaaa acgccccga cgtggcaaa 
      tcctacgaa gggcctgag aaacccaag actccgttc 
      gaactcttc gtcaaagtg gagtccgag aaggaggag 
      agcgaagtc tctcgatac gtggtgatc cagaagtgt 
      cgcgagcgc tggaacgag tttagcgac aaggagaag 
      ttcttctgg atcaactgg gccgaggag gagtacgcc 
      aagtatttg gaggacttg aaggagtac attaaggag 
      caccctgac tacgaaccg gggaagctg aagccgctc 
      ctcaacaaa aacgagcaa aagatcaag cagcgcgcc 
      tccgggaag ccccaaagg ccgcccaag gggccctac 
      cagctgttc ctcaaaatg atgatggag acggacgag 
      atccggaaa attaacagc cgcgactgc gttaattac 
      atttcggac aagtggagg gcctgttct gaggaagag 
      aaggctgag tacaggact cgggtcgag cagatgtgg 
      cttgaatac gattcgaaa cttgaagaa tacattgcg 
      actttacct ccagaaaaa cgggaccag gtgcgggag 
      gaggaaagt cgcaataaa aaaattaag agccccact 
      gttgccccg aaaattgaa gaccaaccg aaagagagg 
      ttggagaaa cccacaatg cctccctcc aacgagtat 
      aagtttttc ttgagtgtt tacaaaggc aaggagaag 
      ccggagacg atttggaag gccatgacc aagaaggag 
      aaggaggtt tttgcgacc aagttgaat gaactcagg 
      cggaagtac atcgctgat tatgagctc tacttgaag 
      agtttgagc agggaggag ttggagaag ttaggggag 
      tcgcttgca gcgtcctgt gactcctcc agcgagtcc 
      gagtcggac atggaagcc gaagactga
    mRNA sequence
    • >TC009280 RA
      gggccttaa tttccagtt aaattaata ttttaccgg 
      gattaaaag tggggtttt gttcataag ttggcgacc 
      ctgctgttt aagtttcga aaatcgtgg cgtgctttt 
      gcccatttt gccccaatt ccctttgat tcgtgcgca 
      aaaatgccc aaacgaaag tcttcaagc tcagatgac 
      gaaaaccgc aagaaacat aaatttacc aagagtgtg 
      cttacggac acgactaac ataaccaag aacaacaac 
      ccaaacgaa gagcaaatt acatggccc caggacgcc 
      gtccttcaa ctaatctca aacattgag gaaaacatc 
      ccaagtgac gataacctt tctttccat acccgttta 
      gaaaaacta aactgggaa aacatcgcg tttggagac 
      tactcccca aaggagtgc caagacaag tgggcctct 
      ctgtgcaag caggtgcgc aaataccga cttttgggc 
      gagatcgcg accgatatc cggcaatgg gtgacgaac 
      ccgaaggtc cgtccgggg gcgaagcac cccgacaag 
      cccaaacag cccaaaaat tcctacatg tttttcttc 
      gaagccaag cggtccgaa gtcatggcc caaaacccc 
      gacctccac ccggtcgaa gtgtcccgc aagttgggc 
      gagttgttc aaaaacttg accatgaag gagaaggaa 
      aagtacgaa cagttggcc aaaatcgca cgacaggag 
      tacctggag aagttgcaa gtgttctac gaggcgcat 
      ccagaccta gtcccgaaa aaaacgccc cgacgtggc 
      aaatcctac gaagggcct gagaaaccc aagactccg 
      ttcgaactc ttcgtcaaa gtggagtcc gagaaggag 
      gagagcgaa gtctctcga tacgtggtg atccagaag 
      tgtcgcgag cgctggaac gagtttagc gacaaggag 
      aagttcttc tggatcaac tgggccgag gaggagtac 
      gccaagtat ttggaggac ttgaaggag tacattaag 
      gagcaccct gactacgaa ccggggaag ctgaagccg 
      ctcctcaac aaaaacgag caaaagatc aagcagcgc 
      gcctccggg aagccccaa aggccgccc aaggggccc 
      taccagctg ttcctcaaa atgatgatg gagacggac 
      gagatccgg aaaattaac agccgcgac tgcgttaat 
      tacatttcg gacaagtgg agggcctgt tctgaggaa 
      gagaaggct gagtacagg actcgggtc gagcagatg 
      tggcttgaa tacgattcg aaacttgaa gaatacatt 
      gcgacttta cctccagaa aaacgggac caggtgcgg 
      gaggaggaa agtcgcaat aaaaaaatt aagagcccc 
      actgttgcc ccgaaaatt gaagaccaa ccgaaagag 
      aggttggag aaacccaca atgcctccc tccaacgag 
      tataagttt ttcttgagt gtttacaaa ggcaaggag 
      aagccggag acgatttgg aaggccatg accaagaag 
      gagaaggag gtttttgcg accaagttg aatgaactc 
      aggcggaag tacatcgct gattatgag ctctacttg 
      aagagtttg agcagggag gagttggag aagttaggg 
      gagtcgctt gcagcgtcc tgtgactcc tccagcgag 
      tccgagtcg gacatggaa gccgaagac tgaagtttt 
      ttttgttca cttgattcg ttcgttttg cttctaagc 
      taataaaat taatttatt tttgtttgt gtatccatt 
      gtttttgtt tcttgtgtt gtatttaaa taaagttct 
      atcgtttga
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY