Status
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Gene information
General information
TC013890 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_007420.3: 240424..251749
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
    TC013890
    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_05517

    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: 50.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 100.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality early (L5/6) - Number of animals showing the phenotype: 5 (11 dpi)
    Days post injection


    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 4 (16 dpi)
    Days post injection



    adult lethality - Number of animals showing the phenotype: 1 (19 dpi)
    Days post injection


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC013890 RA
      MGNKNSCCS YSSPQTSHR VIIPIEDTL NEGEVSVSN 
      LQHISEREA DDGDADPSQ DPTAKTIFI ERSKTAIEN 
      GMIRRKSQH QIADLRPLK KSSSCSTIY LDDSTVSQP 
      NLKNTVKCV ALAIYYHIK NRDSQREID IFDEKLHPL 
      TRDGVSDDY DKHNPEHRQ IYKFVRTLF NAAQLTAEC 
      AIITLVYLE RLLTYAELD IQPSNWKRI VLGAILLAS 
      KVWDDQAVW NVDYCQILK DITVEDMNE LERQFLELL 
      QFNINVPSS VYAKYYFDL RTLAEANDL TFPSEPLSK 
      DRAQKLEAM SRVMEDKYT TEAIKNGLK KWSSLDNIT 
      NGGTAARRS VAILS
    CDS sequence
    • >TC013890 RA
      atgggcaac aagaacagc tgctgctcg tactccagc 
      ccgcagacc agccaccgc gtcatcatc cccattgaa 
      gatacgcta aatgagggc gaggtcagt gtcagtaac 
      ctgcagcat atcagcgag cgggaggca gacgacggc 
      gacgccgac ccctcgcaa gaccctacg gcgaaaacc 
      atcttcatt gaacgctcc aagacggcc atcgagaat 
      ggcatgatc cgcaggaag agccagcac cagatcgcc 
      gatttgcgc cccctgaag aagagcagc tcgtgttcg 
      acgatttat ttggacgac agcacagtg tcgcagccc 
      aatttgaag aacacggtc aagtgtgtg gcattggcg 
      atttactac cacatcaaa aacagggat tcgcaaaga 
      gagattgat atctttgat gagaagctg catccactg 
      accagggat ggggttagt gacgattac gacaagcat 
      aatcccgaa caccgacaa atttacaag tttgtgagg 
      actttgttc aatgctgct caactgact gctgagtgt 
      gccattatt actctagtg tatttagaa cggctgttg 
      acatatgca gagttggat atacaacct tccaattgg 
      aaaagaata gtcttaggt gcaatcctc ttagcttcc 
      aaagtgtgg gatgaccaa gctgtgtgg aacgtagat 
      tactgccaa atcctcaaa gacataacc gtggaggac 
      atgaatgaa ttagaacgt cagtttctc gagttgctc 
      caatttaac ataaatgtc ccttcaagc gtatacgca 
      aaatattac ttcgatcta cgtacctta gcagaagca 
      aacgatttg acgtttcct agtgaaccc ttaagcaaa 
      gatagagcg cagaaatta gaagccatg tccagagta 
      atggaagat aaatacaca acggaagcg atcaaaaac 
      ggactaaaa aaatggtcc agtttagat aatattacg 
      aacggtggg actgcggcg agaagaagc gtcgccatt 
      ttgtcgtga
    mRNA sequence
    • >TC013890 RA
      ataaaacta tgaatggtg cgtttttca aaaaatagt 
      aaaataatt ttttgttaa aattataag tggatacta 
      ctgaaggtg gtaataaac aaatcgttt ataatttat 
      aatatccta cggactgtt ctgtttata atattgata 
      acaatttgc acgttgcat gttgcaagt tgcaaccgt 
      ccaaagcat ccttcaaag tttgacagt tcggttcct 
      tgtccgaaa aatgtgttt aattcgccg tttgaaaca 
      acaatccac ataaaacca tgtaatagt aaacaagtt 
      gtgcgcacc gtcgaaatc cacaaactc ctcaccggc 
      tgcattcgc aattgccgg ctgaaacaa ggcgttcac 
      tcgtgggtg ttgatctaa aatcggctt atctgcgtg 
      gacacaatc ggtgataag atgagctgc cgcagatag 
      cgatggcac gctaagggg gccaccatg ggcaacaag 
      aacagctgc tgctcgtac tccagcccg cagaccagc 
      caccgcgtc atcatcccc attgaagat acgctaaat 
      gagggcgag gtcagtgtc agtaacctg cagcatatc 
      agcgagcgg gaggcagac gacggcgac gccgacccc 
      tcgcaagac cctacggcg aaaaccatc ttcattgaa 
      cgctccaag acggccatc gagaatggc atgatccgc 
      aggaagagc cagcaccag atcgccgat ttgcgcccc 
      ctgaagaag agcagctcg tgttcgacg atttatttg 
      gacgacagc acagtgtcg cagcccaat ttgaagaac 
      acggtcaag tgtgtggca ttggcgatt tactaccac 
      atcaaaaac agggattcg caaagagag attgatatc 
      tttgatgag aagctgcat ccactgacc agggatggg 
      gttagtgac gattacgac aagcataat cccgaacac 
      cgacaaatt tacaagttt gtgaggact ttgttcaat 
      gctgctcaa ctgactgct gagtgtgcc attattact 
      ctagtgtat ttagaacgg ctgttgaca tatgcagag 
      ttggatata caaccttcc aattggaaa agaatagtc 
      ttaggtgca atcctctta gcttccaaa gtgtgggat 
      gaccaagct gtgtggaac gtagattac tgccaaatc 
      ctcaaagac ataaccgtg gaggacatg aatgaatta 
      gaacgtcag tttctcgag ttgctccaa tttaacata 
      aatgtccct tcaagcgta tacgcaaaa tattacttc 
      gatctacgt accttagca gaagcaaac gatttgacg 
      tttcctagt gaaccctta agcaaagat agagcgcag 
      aaattagaa gccatgtcc agagtaatg gaagataaa 
      tacacaacg gaagcgatc aaaaacgga ctaaaaaaa 
      tggtccagt ttagataat attacgaac ggtgggact 
      gcggcgaga agaagcgtc gccattttg tcgtgatca 
      aaaggattt ttttatttt ttaagagat ctaccaaag 
      tatttctag tggaagttt ttattttta ttttttctt 
      agatctttt tatttccga ttcatattt attatattg 
      atgcttttg tgtttgact tatttatta ctggcgact 
      cactcaatt atgttacgt aatttaatg gaaaaagcc 
      taattgact gtatttact tattatact tatgttaaa 
      tgttattct tttgtttct gttgcagtg tgtcacatg 
      acagatggc gatttgata gtgatgcac tgccaaatc 
      aaatgccaa catgtatat aaaaattag tgattaaaa 
      ctttccatt ccagaataa aagtatgtc agggagagt 
      gtttatcca taaatgaag atgagatta tatttaaaa 
      ttgcacaac cctgctttt aatacacgt ccactatat 
      gaaataagt gatttttga taattatgt tggaggaca 
      atcctgtaa tatgatgcc tattttcaa tttttatac 
      tataccagg ctttgtcta gaaaaagta aaatatacc 
      tgtaaaaac tat
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY