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Gene information
General information
TC003354 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_007418.3: 2040407..2068548
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
    TC003354
    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
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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_07391

    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 embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg with embryonic tissue, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): less than 30%

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

    abdomen musculature random 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%
    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%
    larva dorsal not closed - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    head mostly not present - Penetrance (percentage of animals/eggs on slide): more than 80%

    antenna not present - Penetrance (percentage of animals/eggs on slide): more than 80%
    mandible not present - Penetrance (percentage of animals/eggs on slide): more than 80%
    labrum not present - 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
    • >TC003354 RA
      MWPPEAVHS LERFCTYGN VNYRQRRSQ PLKISCLKT 
      TPPPEEDNR GCAASVGEG SFYLPMNMQ GFVKQQTAP 
      HGPPYAPHP SLSSGLGGG LSGMPMPAL GFGLGHPLE 
      SVPFPQVYS YFAGVNPRK QRRERTTFT RAQLDLLEG 
      LFAKTRYPD IFMREEVAV KINLPESRV QVWFKNRRA 
      KCRQQLQQQ QNKSASRTT TSPTKVKAS KASPAAAPR 
      SVATPTGIP TPSTSASPP TVNIKKESP QMQSYRPTG 
      NITPHGSNT SSLITTPSP SASPLAYQH EYNSFNWTA 
      NGHGHNTSS HNYYAQNYA PTYYGQMQP DYLNSQTTQ 
      NHMQAMNNM AGTYQMTGY SAMGMAAPH HQNFGPRHP 
      PDCSMEFAN MA
    CDS sequence
    • >TC003354 RA
      atgtggcct ccagaggca gtacatagt ttggaaagg 
      ttttgtact tatggaaat gtgaattat agacaacga 
      cgatcgcag ccattaaaa atatcctgc ctcaaaacg 
      acccctcca ccagaagaa gataacaga gggtgtgcg 
      gcaagtgtc ggtgaagga agtttttat ctcccaatg 
      aacatgcaa ggatttgtt aagcaacaa acggcaccg 
      cacggaccg ccgtatgcg ccgcatcct tcgcttagt 
      tccggactg ggtggcggc ctttccggg atgcccatg 
      cctgccctt ggcttcggc ctgggacac ccgctggag 
      tccgtcccc ttcccgcaa gtttattca tattttgca 
      ggcgtcaac cccagaaag cagcggcgc gaaaggacg 
      acattcacc agagcccag cttgacctt cttgaagga 
      ctcttcgcc aaaacacgc tacccggac atcttcatg 
      cgcgaagaa gtcgccgtc aagatcaat ctccccgag 
      tccagagtg caggtctgg ttcaagaac aggcgcgcc 
      aagtgccgg cagcagctc cagcagcag cagaacaag 
      agcgcctcg cggaccacc acctccccc acgaaggtc 
      aaggctagc aaagcgtcg ccagcggcc gcccccagg 
      tccgtggcc acccccacg ggcatcccg acgccgtcc 
      acgtcggcg tcgcccccg acagtcaac atcaaaaag 
      gaatcgccc cagatgcag agctacaga cccacgggc 
      aacatcaca ccccacggc agcaacacc tcgagcttg 
      atcacgacg ccgtcgccg tcggcgtcg cccctggcc 
      taccagcac gagtacaac tcgttcaac tggacggcc 
      aatgggcat gggcacaac acctcctca cacaactac 
      tatgcccag aattacgcg cccacgtat tatgggcaa 
      atgcagccc gattatctc aattcgcag accacccag 
      aaccatatg caagccatg aacaacatg gcagggacg 
      taccagatg actgggtac agtgccatg ggcatggcg 
      gccccgcac caccaaaac ttcggcccc aggcatccg 
      cccgactgc agtatggag tttgcaaat atggcttaa
    mRNA sequence
    • >TC003354 RA
      tgtaagaaa caccgtgat agtgcctag catgtggtg 
      tgtgttctg tttgttgca acttttcca gtgagcttt 
      attcccagt gggttttaa tttatttta atgtaggag 
      aatgtgtgc gactgtcaa cagcattag gaatgcttg 
      aggactcaa aaaagatga aaaaatgtg gcctccaga 
      ggcagtaca tagtttgga aaggttttg tacttatgg 
      aaatgtgaa ttatagaca acgacgatc gcagccatt 
      aaaaatatc ctgcctcaa aacgacccc tccaccaga 
      agaagataa cagagggtg tgcggcaag tgtcggtga 
      aggaagttt ttatctccc aatgaacat gcaaggatt 
      tgttaagca acaaacggc accgcacgg accgccgta 
      tgcgccgca tccttcgct tagttccgg actgggtgg 
      cggcctttc cgggatgcc catgcctgc ccttggctt 
      cggcctggg acacccgct ggagtccgt ccccttccc 
      gcaagttta ttcatattt tgcaggcgt caaccccag 
      aaagcagcg gcgcgaaag gacgacatt caccagagc 
      ccagcttga ccttcttga aggactctt cgccaaaac 
      acgctaccc ggacatctt catgcgcga agaagtcgc 
      cgtcaagat caatctccc cgagtccag agtgcaggt 
      ctggttcaa gaacaggcg cgccaagtg ccggcagca 
      gctccagca gcagcagaa caagagcgc ctcgcggac 
      caccacctc ccccacgaa ggtcaaggc tagcaaagc 
      gtcgccagc ggccgcccc caggtccgt ggccacccc 
      cacgggcat cccgacgcc gtccacgtc ggcgtcgcc 
      cccgacagt caacatcaa aaaggaatc gccccagat 
      gcagagcta cagacccac gggcaacat cacacccca 
      cggcagcaa cacctcgag cttgatcac gacgccgtc 
      gccgtcggc gtcgcccct ggcctacca gcacgagta 
      caactcgtt caactggac ggccaatgg gcatgggca 
      caacacctc ctcacacaa ctactatgc ccagaatta 
      cgcgcccac gtattatgg gcaaatgca gcccgatta 
      tctcaattc gcagaccac ccagaacca tatgcaagc 
      catgaacaa catggcagg gacgtacca gatgactgg 
      gtacagtgc catgggcat ggcggcccc gcaccacca 
      aaacttcgg ccccaggca tccgcccga ctgcagtat 
      ggagtttgc aaatatggc ttaattacc tcaagtaca 
      aatcgagac tttagtgta catatcatc gaaagacgc 
      aataattgt gtgtgtgca tgtgtaagt aaaattgta 
      aattgcgaa agcgaacgg cactatatt gaaaaccgc 
      caaggatta ttaaatttg taaataaca atttatttc 
      gtccatggg ttaagcgga ctgtaaccc agatggttg 
      tattataat tgtaggtag gtagctata tcatttgtt 
      tgatatcag ggtcactga tacgttgta gattaaact 
      agctttata aaaattacc taactttgg gccaaatgg 
      catccgtct ttatcttac cagaagcaa cgaattaca 
      taaaatgat aatggtaac gtaaaaaac taatgcgat 
      ttgctccca tccacactc gtttaaata ttttatttg 
      taagtctgg ctttgtccg cctcattca tttgacaaa 
      gtatacatc atacgttaa gtttcggat caatcttac 
      aattcggta aatttggaa agcgactta ctgataaaa 
      tgttactga aaagccaaa agttcttgg tgattagat 
      tgggttgat tcagtcaga ctattttaa attttataa 
      cgctttata ctatttttt gtaatatta tgtacaact 
      ctgtaagtc tttgtcgtg aaaacaaac taaattttg 
      tgtatgcag tttaaatct tactttgaa actacttga 
      aataaatac gtatttatt tt
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY