Status
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Gene information
General information
TC005542 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_007423.3: 11519148..11521338
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
    TC005542
    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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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_08928

    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: 1 (3 dpi)
    Days post injection


    adult lethality - Number of animals showing the phenotype: 2 (9 dpi)
    Days post injection


    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg with embryonic tissue potentially present, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): more than 80%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 80%
    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): more than 80%
    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
    • >TC005542 RA
      MGEIAPRVV TAKDKDFCH NLRKYFREF TEVTGIHGL 
      RYVSEKRSR TEKVIWVII LLISLGGCI YMIYEVLDK 
      YNKSPVVVS FATEDTPLY QIAFPAVTI CPESKYSRE 
      KFNYSGVYS KLVEEESVT IDERRKFDY LSMLCDDSP 
      DNVATTQNF GNEFYEIIH KMKLNQSEL FPLCIFDNK 
      FTECDRIFT PIFIDEGIC YSFNIQGAH EIFRDHVYN 
      FKDYYKVSN NSEKYFDPE FGYRPSAGV HTYPRRALR 
      SGADSAFGI FFNYDTADT DFNCKNFLQ GFRVLIHNS 
      SNVPRVSEH YFRIPFDKV VVAAMEPVL VVTSQNVRG 
      FRPEKRKCF MRNERFLKH FLYYSQPNC MLECLTNYT 
      LAKCGCVQF YMPRDNSTL ICGPNSEQC TENAESEMQ 
      IKDLEYRIS GRSLCDCKP TCTNMKYNV ETSHSDFYF 
      KEYFKVHNE FNLGDGGHW SVLQLYFKD EQFMTMERN 
      ELYGISDLI SNLGGLLGL FTGFSLVTM AEIIYFCSL 
      RVVYNRRLY GLWSGPN
    CDS sequence
    • >TC005542 RA
      atgggtgaa attgcgccg agagttgtc accgcaaaa 
      gacaaagac ttttgccac aatttgcgc aaatatttc 
      cgcgagttc acggaagtg accggaatc cacggtctg 
      cgatatgtg tctgaaaag cggtcacga accgaaaag 
      gttatttgg gtaattatt ttgctgatt agtttgggc 
      ggctgtatc tacatgatt tacgaggtc ttggacaag 
      tacaataaa agcccagtt gttgtgagt tttgctacg 
      gaggatacg ccactttac caaattgcg tttcctgcc 
      gtaacgatc tgtccagaa tcgaagtac tcgcgtgag 
      aaattcaat tacagtggc gtttattcc aagctagtt 
      gaagaggaa agtgtgacc attgatgag cgccgaaaa 
      tttgattat ttgagcatg ttgtgcgac gacagtcct 
      gacaatgtc gcgaccacg caaaatttt ggcaacgaa 
      ttttacgaa atcatccac aaaatgaaa ctgaaccaa 
      agcgagttg ttcccactc tgcatcttt gacaataaa 
      ttcacggag tgtgaccgc attttcacc ccgattttc 
      atcgacgag ggaatttgc tactcgttt aacatccaa 
      ggcgcccat gagattttc cgcgaccac gtttacaac 
      tttaaggat tattacaag gtttccaac aattcggaa 
      aaatacttt gacccagaa tttggctat agaccttca 
      gccggggtc cacacctac ccccggcgg gccctcagg 
      tcaggggcg gactctgcc tttggcatt tttttcaac 
      tacgacacg gcagacacc gatttcaat tgcaaaaat 
      ttcctgcaa ggcttccgg gtcttgatt cacaactcc 
      tccaacgtg ccacgcgtc tcagagcat tatttccgg 
      atcccgttt gataaggtg gtagtggcg gccatggag 
      ccggtcctg gtcgtcacc tcgcaaaat gtgcgcgga 
      tttcggccc gaaaaacgc aaatgtttc atgcggaac 
      gagcgattt ttgaaacat ttcctctac tactcccag 
      cccaattgc atgcttgag tgcttgacg aattatacg 
      ctcgctaaa tgtggttgc gtccagttt tacatgcct 
      cgggacaac agtacgttg atttgtggc ccgaactcc 
      gaacagtgc accgaaaac gccgaaagc gagatgcaa 
      atcaaagac ctggagtat cgaatttca gggcggtct 
      ctgtgtgat tgcaagccc acgtgtact aacatgaag 
      tacaacgtt gagacgtcc cacagcgat ttttatttt 
      aaggaatat ttcaaagtg cacaatgag tttaatctg 
      ggtgatggg gggcattgg tccgtcttg caactgtat 
      ttcaaagac gagcaattt atgacaatg gagcggaac 
      gaattgtat ggaatttcc gacttgatt tcgaacctt 
      gggggcctt ttgggcctt tttaccgga ttttctttg 
      gtcacaatg gctgaaatt atctacttt tgctcgctc 
      agagtcgtg tataatcgg cggttgtac gggctttgg 
      tcaggccct aattga
    mRNA sequence
    • >TC005542 RA
      gaatcgatt ttcgcgttt gaacgaagt aatacgtca 
      ttggcataa atttagatc ggctccaaa ttaacaatg 
      cagtgctct tcatccggg agtgaatcg ttacgtaat 
      tttgtactc ctttttgat gctaaaccg ctgaccttg 
      ctggcctcg tctttgccc acaacccac tcccattat 
      taaagtcgt caatcaaat tcgacccag acatgggtg 
      aaattgcgc cgagagttg tcaccgcaa aagacaaag 
      acttttgcc acaatttgc gcaaatatt tccgcgagt 
      tcacggaag tgaccggaa tccacggtc tgcgatatg 
      tgtctgaaa agcggtcac gaaccgaaa aggttattt 
      gggtaatta ttttgctga ttagtttgg gcggctgta 
      tctacatga tttacgagg tcttggaca agtacaata 
      aaagcccag ttgttgtga gttttgcta cggaggata 
      cgccacttt accaaattg cgtttcctg ccgtaacga 
      tctgtccag aatcgaagt actcgcgtg agaaattca 
      attacagtg gcgtttatt ccaagctag ttgaagagg 
      aaagtgtga ccattgatg agcgccgaa aatttgatt 
      atttgagca tgttgtgcg acgacagtc ctgacaatg 
      tcgcgacca cgcaaaatt ttggcaacg aattttacg 
      aaatcatcc acaaaatga aactgaacc aaagcgagt 
      tgttcccac tctgcatct ttgacaata aattcacgg 
      agtgtgacc gcattttca ccccgattt tcatcgacg 
      agggaattt gctactcgt ttaacatcc aaggcgccc 
      atgagattt tccgcgacc acgtttaca actttaagg 
      attattaca aggtttcca acaattcgg aaaaatact 
      ttgacccag aatttggct atagacctt cagccgggg 
      tccacacct acccccggc gggccctca ggtcagggg 
      cggactctg cctttggca tttttttca actacgaca 
      cggcagaca ccgatttca attgcaaaa atttcctgc 
      aaggcttcc gggtcttga ttcacaact cctccaacg 
      tgccacgcg tctcagagc attatttcc ggatcccgt 
      ttgataagg tggtagtgg cggccatgg agccggtcc 
      tggtcgtca cctcgcaaa atgtgcgcg gatttcggc 
      ccgaaaaac gcaaatgtt tcatgcgga acgagcgat 
      ttttgaaac atttcctct actactccc agcccaatt 
      gcatgcttg agtgcttga cgaattata cgctcgcta 
      aatgtggtt gcgtccagt tttacatgc ctcgggaca 
      acagtacgt tgatttgtg gcccgaact ccgaacagt 
      gcaccgaaa acgccgaaa gcgagatgc aaatcaaag 
      acctggagt atcgaattt cagggcggt ctctgtgtg 
      attgcaagc ccacgtgta ctaacatga agtacaacg 
      ttgagacgt cccacagcg atttttatt ttaaggaat 
      atttcaaag tgcacaatg agtttaatc tgggtgatg 
      gggggcatt ggtccgtct tgcaactgt atttcaaag 
      acgagcaat ttatgacaa tggagcgga acgaattgt 
      atggaattt ccgacttga tttcgaacc ttgggggcc 
      ttttgggcc tttttaccg gattttctt tggtcacaa 
      tggctgaaa ttatctact tttgctcgc tcagagtcg 
      tgtataatc ggcggttgt acgggcttt ggtcaggcc 
      ctaattgaa aacgtttaa gtaattttt aagaaaagt 
      atcaaacag ta
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY