Status
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Gene information
General information
TC009896 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_007422.5: 12572530..12604454
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
    TC009896
    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_06279

    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: 10.0% (includes death as pupa, adult)

    adult lethality - Number of animals showing the phenotype: 1 (9 dpi)
    Days post injection


    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 20
    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: 10.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 10.0% (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC009896 RA
      MAALTSNMV PQPHHFSRQ NLESTDGSV SMDSSDHFD 
      RESPNIDHN SCSSDDTVL SVGNENPPP EDTPLSFKN 
      IESHLNAIS QITNSTLDP GRKSPSSPR ISSPSSTKS 
      GSPGFLTYT KADRDVDLF RGSSTPESP EHYYNQKTL 
      QANNNDASN GNLKFSIDN ILKADFGRR ITDPINIRK 
      CKPKKVVPE VGGVEEAKG PVDLSKSEP EKKTESQPM 
      LWPAWVYCT RYSDRPSSG RSPRTRRVK KPGAKQGAP 
      TAEEKRPRT AFSGAQLAR LKHEFAENR YLTERRRQQ 
      LSAELGLNE AQIKIWFQN KRAKIKKAS GQKNPLALQ 
      LMAQGLYNH STIPLTKEE EELQEMQGT KSPA
    CDS sequence
    • >TC009896 RA
      atggcggcg ttgacgagc aacatggtc ccccaaccg 
      caccacttc tcccgacag aacctggag agcaccgat 
      ggctccgtc tccatggac tccagcgac cacttcgac 
      cgggaatcc cccaacatc gaccacaac agctgcagc 
      agcgacgac accgtgctt tccgtcggc aacgagaac 
      ccgccaccg gaagacact ccgctctcc ttcaagaac 
      atcgagagc cacctcaac gccatttcg caaatcacg 
      aacagtacc ttagacccg ggccgcaag agcccctct 
      agtcccagg ataagcagt ccgtcgagt acgaagtcc 
      ggctcgccc ggatttttg acctacacg aaggcggac 
      cgggacgtg gacctgttc cggggatcg tccaccccg 
      gagtcgccg gaacactac tacaaccag aagacgctt 
      caggctaat aataacgac gcgagtaat gggaatctc 
      aagttttcg atagataat attctgaag gcggatttt 
      ggacggagg atcacggat ccgattaac atccggaag 
      tgcaagccg aagaaggtt gtgccggaa gttgggggt 
      gttgaagag gctaaagga cctgtagat ttgagtaag 
      agtgagccg gagaagaag actgagagt cagccgatg 
      ttgtggcca gcctgggtt tactgcacg aggtacagc 
      gaccgaccc agttcagga cgaagtccg cgaaccagg 
      cgagtcaag aaacccggg gccaagcag ggggcgccc 
      accgccgag gaaaagcgg ccccggacg gccttttca 
      ggggcgcag ttagcccgg ctgaagcac gagttcgcc 
      gaaaaccgc tatctgacc gagaggcgg cggcagcag 
      ctcagtgcg gagctgggg ctcaacgag gcccagatc 
      aaaatctgg ttccagaac aaaagggcc aaaatcaaa 
      aaggcctcc ggccagaaa aacccccta gccctccag 
      ctgatggcg caggggctg tacaaccac tccaccatt 
      ccgctgacg aaggaggag gaagagctg caggagatg 
      caaggcact aagagcccc gcgtag
    mRNA sequence
    • >TC009896 RA
      cgtggtgtg tagatcgga ctcgaatcg tccctaatt 
      gtatcagtt gaagcggcc tagctgtgc ctaaaacca 
      agtgggtgc tagtgactg ggaaaatgc cggtttgag 
      ggtgaaatg gcggcgttg acgagcaac atggtcccc 
      caaccgcac cacttctcc cgacagaac ctggagagc 
      accgatggc tccgtctcc atggactcc agcgaccac 
      ttcgaccgg gaatccccc aacatcgac cacaacagc 
      tgcagcagc gacgacacc gtgctttcc gtcggcaac 
      gagaacccg ccaccggaa gacactccg ctctccttc 
      aagaacatc gagagccac ctcaacgcc atttcgcaa 
      atcacgaac agtacctta gacccgggc cgcaagagc 
      ccctctagt cccaggata agcagtccg tcgagtacg 
      aagtccggc tcgcccgga tttttgacc tacacgaag 
      gcggaccgg gacgtggac ctgttccgg ggatcgtcc 
      accccggag tcgccggaa cactactac aaccagaag 
      acgcttcag gctaataat aacgacgcg agtaatggg 
      aatctcaag ttttcgata gataatatt ctgaaggcg 
      gattttgga cggaggatc acggatccg attaacatc 
      cggaagtgc aagccgaag aaggttgtg ccggaagtt 
      gggggtgtt gaagaggct aaaggacct gtagatttg 
      agtaagagt gagccggag aagaagact gagagtcag 
      ccgatgttg tggccagcc tgggtttac tgcacgagg 
      tacagcgac cgacccagt tcaggacga agtccgcga 
      accaggcga gtcaagaaa cccggggcc aagcagggg 
      gcgcccacc gccgaggaa aagcggccc cggacggcc 
      ttttcaggg gcgcagtta gcccggctg aagcacgag 
      ttcgccgaa aaccgctat ctgaccgag aggcggcgg 
      cagcagctc agtgcggag ctggggctc aacgaggcc 
      cagatcaaa atctggttc cagaacaaa agggccaaa 
      atcaaaaag gcctccggc cagaaaaac cccctagcc 
      ctccagctg atggcgcag gggctgtac aaccactcc 
      accattccg ctgacgaag gaggaggaa gagctgcag 
      gagatgcaa ggcactaag agccccgcg tagggccgc 
      tggttttgt tcgtgataa tttgatgct tccagttgt 
      ttattgtga tttgttgtg attcgtccg tggatgagg 
      tgagagtgg attctttgg atttttaca gtgatttgc 
      gagcgtttt tgcctcgtc caaagacga agtcgggta 
      agctgtcaa tggtctact taagagttg ggcaacttt 
      ttgcggtga tctctcgag tatgttagc attgtttct 
      ttaattcta caattctca gagcttcgt gttacaaaa 
      aatgtatta atgtaccat tcatttaaa cacaattgc 
      gagctgtgt ggtactaaa taacagttt ttacaaacg 
      gtgccatta ttgtttaaa tcgcatggg atcatattc 
      ttgtttggt ttttcttgc acgactacc aaagaccgt 
      gcaagacac gggattttt gatccgacc ttgtacata 
      acactctgt aaaaattac aactaggac tagttattt 
      attgtatta gcaaaataa ttcggaatc gaaagcaat 
      atttattag gcaaaactt gaacctaat gtatattta 
      aatgaaact attgtaaat atttatata atactgtct 
      gtgagttga agcttattt ataatgtat tcgacctaa 
      gtaatagtg aaaaatatg tacctacag aaattgttt 
      ataattcaa ctgtaaaat atagattat ataaaataa 
      atactattc aagcga
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY