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Gene information
General information
TC000962 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_007417.3: 8973980..8976044
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
    TC000962
    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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    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_09634

    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: 50.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 3 (3 dpi)
    Days post injection


    adult lethality - Number of animals showing the phenotype: 2 (9 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: % (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
    • >TC000962 RA
      MSRFLYILS CLSVIFNSF CNCGAIKSI QDDDLMNLI 
      RSETYVVAL FSAKNCELC DNFENILTN LEEEFSKSF 
      EGETVKVVN SQLTRLYSP TKEPVLVFF RHGIPLLYN 
      DIPSEELIL HTFVNNKEP VVKELNDET FEHLTQAAS 
      GATTGDWFV MFYTPDCVD CHRLQARWE TVGAQLKTR 
      MNVARVNKA TDGAATATR FGVSQAPTF ILFRQGKMY 
      KYQIQKYDV ASFTSFAQE WYKNVTPIK VPSPKTPFD 
      NIVENIVLN LKESAMAWK IGLAATVVG FLLIILMKC 
      RKTEKPQKP TSKKDK
    CDS sequence
    • >TC000962 RA
      atgagtagg tttttgtat attttgtcg tgtctgtcc 
      gttattttc aatagtttt tgtaactgt ggtgcaata 
      aaatcaatc caggatgat gatctcatg aacttaatc 
      agaagtgag acttatgtg gttgcgctg ttttctgcg 
      aaaaattgc gaactttgt gataacttc gaaaacatt 
      ttaacaaat ttggaggaa gagttctct aaatcattt 
      gaaggagag actgttaaa gtcgttaac agccagtta 
      acaagactg tatagcccc acgaaggag ccggttttg 
      gtgtttttc agacatgga attcctcta ctttataat 
      gatattcct tcagaagag ctaattctt cacacattt 
      gttaacaat aaagaaccg gtggtgaag gaattaaac 
      gatgagact tttgaacac ttaacccag gccgccagt 
      ggggctacc acaggcgac tggtttgtg atgttttat 
      accccagac tgtgtcgat tgccaccgc cttcaagcc 
      cggtgggag acagtcggg gcacaatta aaaacacga 
      atgaacgtc gcacgagtc aataaggcg acagatggg 
      gccgctacc gccacacga tttggagtc tcccaagcc 
      ccaactttt attctcttc agacaaggc aaaatgtat 
      aaatatcaa atccaaaag tacgacgtt gcgtctttc 
      acttctttt gcccaagaa tggtacaaa aacgtgact 
      cccattaaa gtaccatcg cctaaaacg ccatttgat 
      aatattgtc gaaaatatc gtacttaat ttgaaggaa 
      agcgcaatg gcgtggaaa attggttta gcggcgact 
      gttgttggt ttcttgttg ataatttta atgaaatgt 
      cgtaagact gaaaagccg caaaaaccg acaagcaag 
      aaagacaaa taa
    mRNA sequence
    • >TC000962 RA
      tgctaatta tggttgcaa ttggacaaa cctggattc 
      agttgatca tcacacaag gaaaagtcc acaaaaaca 
      caccgtttt tgcaaataa acccttgca cttcacatt 
      tgtgcacaa atcataaat cgataataa aaaccggca 
      tcactcgtc aacaaaatg gctgatggt tgacaattc 
      tgggggatt ttcgtgttg ttgaatgtt ttgggttat 
      gtgaggtta ttgagctaa aatgagtag gtttttgta 
      tattttgtc gtgtctgtc cgttatttt caatagttt 
      ttgtaactg tggtgcaat aaaatcaat ccaggatga 
      tgatctcat gaacttaat cagaagtga gacttatgt 
      ggttgcgct gttttctgc gaaaaattg cgaactttg 
      tgataactt cgaaaacat tttaacaaa tttggagga 
      agagttctc taaatcatt tgaaggaga gactgttaa 
      agtcgttaa cagccagtt aacaagact gtatagccc 
      cacgaagga gccggtttt ggtgttttt cagacatgg 
      aattcctct actttataa tgatattcc ttcagaaga 
      gctaattct tcacacatt tgttaacaa taaagaacc 
      ggtggtgaa ggaattaaa cgatgagac ttttgaaca 
      cttaaccca ggccgccag tggggctac cacaggcga 
      ctggtttgt gatgtttta taccccaga ctgtgtcga 
      ttgccaccg ccttcaagc ccggtggga gacagtcgg 
      ggcacaatt aaaaacacg aatgaacgt cgcacgagt 
      caataaggc gacagatgg ggccgctac cgccacacg 
      atttggagt ctcccaagc cccaacttt tattctctt 
      cagacaagg caaaatgta taaatatca aatccaaaa 
      gtacgacgt tgcgtcttt cacttcttt tgcccaaga 
      atggtacaa aaacgtgac tcccattaa agtaccatc 
      gcctaaaac gccatttga taatattgt cgaaaatat 
      cgtacttaa tttgaagga aagcgcaat ggcgtggaa 
      aattggttt agcggcgac tgttgttgg tttcttgtt 
      gataatttt aatgaaatg tcgtaagac tgaaaagcc 
      gcaaaaacc gacaagcaa gaaagacaa ataaatttt 
      taacacttt tttattaaa ataaattgg tggctgact 
      tcataactc gttatttac acaatagaa ggttaatga 
      ggcgctggt gtgtggcca tcaacgtaa aagttcctc 
      gttgcttgt ggcaattct aactcaagc ccttctaat 
      tctttggtt aaaataatc tgacaacct aacctagag 
      ttttcttta agaaacggc gccatgtct aacaaatcc 
      tcttctttt tcctcagct ggcgtaagt tcgtgatca 
      cttttcaca taaacgtga caagtggta catgctagg 
      gaggcctca caggcccct tccatggga attttgtat 
      ctgtgagcc aagtatagg acattatca cctactttg 
      ccctttaca gggaccttt tcaccgtct tttgtaaca 
      aaagttatg ttaacactg aaaaaaatg tgtatttta 
      cgtaatata accgcgcga actgttaca cttcatcgg 
      gggatttgg gatcctgcc attcgtatt caccgtgat 
      ttaactcta attaaagac aattggtta cttattaat 
      tgtaatttc tgatggtac tcactcgct gtcgtataa 
      atcttacga aataaagtt tttattgaa aaactgggc 
      tttgtataa cctaaaatt cgcacaaaa gctgtcatt 
      ttgacagta actttcaaa agttact
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY