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Gene information
General information
TC009090 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: 6591252..6595220
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
    TC009090
    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_01469

    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)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 2 (3 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: 20.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 20.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection


    pupal molt delayed (still prepupa) - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC009090 RA
      MALDHVLFK FCVCVLIVT TKAQWVVEE EGCRTPDGG 
      TGTCISIYS CKNVMDVLD KVPQPIPQR ITNLLKSYH 
      CGFDGRNPK VCCPSKPIV LDLVTEKKP DVEGPPNVS 
      RHKNIDLLP KNCGYFDTD NKIVNGNKT GLFEFPWMA 
      LLSYRTGRG PQFKCGATI INERYILTA AHCITNNKF 
      PLIGVRVGE HNIETQKDC ELTTEGDLV CAPPYQDLA 
      IEEIIPHPS YDTSLHTND VGLLRVSPM NLSLENTRP 
      VCLPLERAR NYNFTNRNC VVTGWGVTE TGRSSPDLL 
      KVQIPVVPY EECARLYKD IKITHQQLC AGGKTKGDS 
      CGGDSGGPL HVMSQLFND ARLVQQGIV SFGPRNCGA 
      GILPGVYTR VAYYMDWIL DNMRP
    CDS sequence
    • >TC009090 RA
      atggctctc gatcacgtt ttattcaag ttttgtgtt 
      tgtgtgcta attgtgact accaaagcg caatgggtg 
      gtagaagag gagggttgt cgtacaccc gatggggga 
      acaggaact tgcatttcc atatactcc tgcaaaaac 
      gtcatggat gtcctagat aaagtaccc caacccata 
      ccccagcga atcacgaat ttactcaaa tcataccac 
      tgcggtttt gatggcaga aatcctaaa gtgtgctgt 
      ccttcgaaa cccatagta cttgatctc gtcacggaa 
      aagaaacct gacgtagaa ggacccccc aatgtttct 
      agacataaa aacatagac cttttaccc aaaaactgc 
      ggctatttc gatacagat aacaagatt gttaatgga 
      aacaaaact ggactcttt gaatttccc tggatggcc 
      ctcttgtca tacaggaca ggccgaggt ccccaattt 
      aaatgtgga gctacaatc atcaacgaa agatacatc 
      cttactgct gcacactgc ataacaaac aacaaattt 
      ccactcatt ggagttcga gtcggggaa cacaacatt 
      gagacccaa aaagactgc gaattaaca actgagggc 
      gacctggtg tgcgccccg ccatatcaa gacttggcc 
      atcgaagaa atcattcct cacccttct tacgacacc 
      agtctccat actaacgat gtggggctc cttcgagtt 
      tcaccaatg aatttatca ttagaaaac acacggcca 
      gtgtgttta ccacttgag agggcccgg aattacaat 
      ttcaccaac cggaattgc gtggtgaca gggtggggt 
      gttacagaa actggccgc agcagtccc gacttgctg 
      aaagtgcaa attccggta gtaccttat gaggagtgt 
      gctaggctg tataaagat ataaaaatt acgcaccaa 
      cagttgtgt gcgggtggc aagaccaag ggtgactct 
      tgtgggggg gacagtggg ggacctttg catgtgatg 
      tcccagttg tttaatgat gcgcggttg gtgcaacaa 
      gggattgtc tcgtttggt ccccggaat tgcggtgcg 
      ggaatatta ccgggggtt tacacgaga gttgcgtat 
      tacatggac tggattttg gacaatatg aggccgtag
    mRNA sequence
    • >TC009090 RA
      ttattcagt gacgttaag agactgcat catttaaaa 
      gatctacaa ggacgcgag agatcagtt ggtttggaa 
      gtggtcggt gaaaagcat ggctctcga tcacgtttt 
      attcaagtt ttgtgtttg tgtgctaat tgtgactac 
      caaagcgca atgggtggt agaagagga gggttgtcg 
      tacacccga tgggggaac aggaacttg catttccat 
      atactcctg caaaaacgt catggatgt cctagataa 
      agtacccca acccatacc ccagcgaat cacgaattt 
      actcaaatc ataccactg cggttttga tggcagaaa 
      tcctaaagt gtgctgtcc ttcgaaacc catagtact 
      tgatctcgt cacggaaaa gaaacctga cgtagaagg 
      accccccaa tgtttctag acataaaaa catagacct 
      tttacccaa aaactgcgg ctatttcga tacagataa 
      caagattgt taatggaaa caaaactgg actctttga 
      atttccctg gatggccct cttgtcata caggacagg 
      ccgaggtcc ccaatttaa atgtggagc tacaatcat 
      caacgaaag atacatcct tactgctgc acactgcat 
      aacaaacaa caaatttcc actcattgg agttcgagt 
      cggggaaca caacattga gacccaaaa agactgcga 
      attaacaac tgagggcga cctggtgtg cgccccgcc 
      atatcaaga cttggccat cgaagaaat cattcctca 
      cccttctta cgacaccag tctccatac taacgatgt 
      ggggctcct tcgagtttc accaatgaa tttatcatt 
      agaaaacac acggccagt gtgtttacc acttgagag 
      ggcccggaa ttacaattt caccaaccg gaattgcgt 
      ggtgacagg gtggggtgt tacagaaac tggccgcag 
      cagtcccga cttgctgaa agtgcaaat tccggtagt 
      accttatga ggagtgtgc taggctgta taaagatat 
      aaaaattac gcaccaaca gttgtgtgc gggtggcaa 
      gaccaaggg tgactcttg tggggggga cagtggggg 
      acctttgca tgtgatgtc ccagttgtt taatgatgc 
      gcggttggt gcaacaagg gattgtctc gtttggtcc 
      ccggaattg cggtgcggg aatattacc gggggttta 
      cacgagagt tgcgtatta catggactg gattttgga 
      caatatgag gccgtagag gaatggact tgaagactg 
      tactgtgtt aaatagact gcgattttt atacaatgg 
      actccttca gtttgatat tgtgtaatg cttatttat 
      gtcatgcaa aatatactt tttcaattt tt
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY