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Gene information
General information
TC012887 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: 18699976..18701299
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
    TC012887
    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_09044

    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: 80.0% (includes death as pupa, adult)

    adult lethality - Number of animals showing the phenotype: 8 (11 dpi)
    Days post injection


    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
    • >TC012887 RA
      MNSILLNIF IDLVSRGFC VPHELTDDS EEGVSKPSD 
      GLGLGEGQG EKDVSDKIE SEDQLDDAQ PAGQEKDKE 
      EDADCKEED KGIAMSEDF DSKLQDVEP KDDDEDEED 
      NDSDADEQM GETEKDANR QDKETYGSD NEDENVESE 
      EKEESGEGG EKDGEKELG AKENDKKSE DKPDKDSTN 
      EKEENKKGI NEMEEPEFD DEQTDPYHG NQPELPEPE 
      PMDLPDDLQ LDEGQEPDN NQDEENPFD IDAMKEDNP 
      FEGKEKEEQ GQENEDKPE NEYSSDDEE ITKNEEDLE 
      DQNKKEQDG MKEKLEEPE DEAKTEEYT QVEESGFDQ 
      TQANEDNVE TTDVDKSDA TDKVTANQA ENQSNQPID 
      DWCQENKPD KEGVGQSQM EESSTGHSA QTTNPQEMQ 
      SSKRQKEED LKKHQKPRF RRTEKSR
    CDS sequence
    • >TC012887 RA
      atgaattcg attcttttg aatattttc atcgatttg 
      gtatcgaga ggtttttgt gtcccacat gaactaaca 
      gatgattcg gaagaaggt gtttctaaa ccttcggat 
      ggtcttggt ttgggtgaa ggtcaagga gaaaaagac 
      gtttcagat aaaatcgaa tctgaagat cagttagat 
      gatgcacaa cctgctgga caggaaaaa gacaaagag 
      gaagatgcc gattgtaaa gaagaagat aaaggaatt 
      gcgatgagc gaagatttt gatagtaaa ctacaagat 
      gtcgaaccg aaagatgac gatgaagat gaggaggat 
      aatgattca gatgctgac gaacaaatg ggtgaaaca 
      gagaaagat gcaaatcga caagacaaa gagacttac 
      gggtcagat aatgaagat gaaaatgtt gaaagtgaa 
      gaaaaggaa gagagtggt gaaggaggt gaaaaagat 
      ggtgaaaaa gaattgggg gccaaagag aatgataag 
      aaaagtgaa gataagcct gataaagat tcgacaaat 
      gagaaggaa gaaaacaaa aagggaatt aacgaaatg 
      gaggaaccg gaatttgac gatgaacaa actgatccc 
      taccatggc aaccaaccg gaattgccg gaaccggaa 
      cccatggat ttaccggat gatcttcaa ttggacgaa 
      ggccaagaa ccggataac aatcaagat gaagaaaat 
      ccgtttgat atcgacgcc atgaaggaa gacaatcca 
      ttcgagggt aaggaaaaa gaagagcaa gggcaagaa 
      aatgaagat aaacctgag aatgagtac agtagtgat 
      gatgaagaa attaccaaa aatgaagaa gatttggaa 
      gatcagaat aagaaggaa caagacgga atgaaggag 
      aaacttgag gaaccggaa gacgaagct aaaactgaa 
      gaatatact caagtggaa gaatctggt ttcgaccag 
      actcaggcc aatgaagac aacgttgaa acaacggac 
      gttgataaa tcggacgca actgataaa gtaacagcc 
      aatcaggct gaaaatcaa tccaatcaa ccaatcgac 
      gactggtgc caagaaaac aaaccagat aaagaagga 
      gtcggccaa tcacaaatg gaggaaagt tcaacagga 
      cattcggcc caaacaacc aatccgcaa gaaatgcaa 
      tcttcgaaa aggcaaaaa gaggaagat ttaaaaaaa 
      caccaaaaa ccaagattc cgacgcaca gagaaatct 
      aggtga
    mRNA sequence
    • >TC012887 RA
      ttatcgagt tattaataa aatgaattc gattctttt 
      gaatatttt catcgattt ggtatcgag aggtttttg 
      tgtcccaca tgaactaac agatgattc ggaagaagg 
      tgtttctaa accttcgga tggtcttgg tttgggtga 
      aggtcaagg agaaaaaga cgtttcaga taaaatcga 
      atctgaaga tcagttaga tgatgcaca acctgctgg 
      acaggaaaa agacaaaga ggaagatgc cgattgtaa 
      agaagaaga taaaggaat tgcgatgag cgaagattt 
      tgatagtaa actacaaga tgtcgaacc gaaagatga 
      cgatgaaga tgaggagga taatgattc agatgctga 
      cgaacaaat gggtgaaac agagaaaga tgcaaatcg 
      acaagacaa agagactta cgggtcaga taatgaaga 
      tgaaaatgt tgaaagtga agaaaagga agagagtgg 
      tgaaggagg tgaaaaaga tggtgaaaa agaattggg 
      ggccaaaga gaatgataa gaaaagtga agataagcc 
      tgataaaga ttcgacaaa tgagaagga agaaaacaa 
      aaagggaat taacgaaat ggaggaacc ggaatttga 
      cgatgaaca aactgatcc ctaccatgg caaccaacc 
      ggaattgcc ggaaccgga acccatgga tttaccgga 
      tgatcttca attggacga aggccaaga accggataa 
      caatcaaga tgaagaaaa tccgtttga tatcgacgc 
      catgaagga agacaatcc attcgaggg taaggaaaa 
      agaagagca agggcaaga aaatgaaga taaacctga 
      gaatgagta cagtagtga tgatgaaga aattaccaa 
      aaatgaaga agatttgga agatcagaa taagaagga 
      acaagacgg aatgaagga gaaacttga ggaaccgga 
      agacgaagc taaaactga agaatatac tcaagtgga 
      agaatctgg tttcgacca gactcaggc caatgaaga 
      caacgttga aacaacgga cgttgataa atcggacgc 
      aactgataa agtaacagc caatcaggc tgaaaatca 
      atccaatca accaatcga cgactggtg ccaagaaaa 
      caaaccaga taaagaagg agtcggcca atcacaaat 
      ggaggaaag ttcaacagg acattcggc ccaaacaac 
      caatccgca agaaatgca atcttcgaa aaggcaaaa 
      agaggaaga tttaaaaaa acaccaaaa accaagatt 
      ccgacgcac agagaaatc taggtgatg tgaatgaac 
      tcgtgaaga agaaattga agacgattg a
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY