Status
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Gene information
General information
TC008549 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.

NW_015451492.1: 159019..166378
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
    TC008549
    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_08961

    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: 60.0% (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: 3 (9 dpi)
    Days post injection


    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: < 50 larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    remarks: muscle pattern potentially obscured by segmentation defect,
    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): 50% - 80%
    head capsule size decreased - Penetrance (percentage of animals/eggs on slide): less than 30%

    head appendages shape irregular - Penetrance (percentage of animals/eggs on slide): less than 30%
    legs podomer potentially fused - Penetrance (percentage of animals/eggs on slide): less than 30%

    legs shortened - Penetrance (percentage of animals/eggs on slide): less than 30%

    abdomen shape irregular - Penetrance (percentage of animals/eggs on slide): less than 30%
    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 50% - 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
    • >TC008549 RA
      MSQDRCFAN PFDDYSSEA ACCVIENGT IKCDCKLSC 
      DLEKKWHDT LAQFKYLDY NDYSVYTGT SGIALLKLK 
      KDPESRQNL QEALQLLSL HRLKGRRHT FLCGDAGPL 
      ALGAIINYK LEDKAYLDC IEKLKALSE DVFDPSSDL 
      PNEYLYGRA GFLFAVLYV NKHVSPVPF EESFIRKII 
      ETIILCGKN EAKAGKFKC PLMYQWHES YYLGAAHGV 
      SGILYLLLQ AKEYLTENE LQTIIKPTV DYLATLRFP 
      SCNFPSSLG RDNDKYVQW CHGAPGFLY LFTTAYKVF 
      GDCKYLQLA LDCGDVIWS RGILRKGYS ICHGVSGNA 
      YCFLELYQT TEDEKHLYR AVRFAEWCF AYNKNHVEH 
      PPDRPLSLF EGLSGPMYL FLDIQKPAE AKFPGYTL
    CDS sequence
    • >TC008549 RA
      atgtcgcaa gatcgatgt ttcgccaat ccatttgat 
      gattattcg tcagaagca gcatgttgt gtaatcgaa 
      aatggaacg attaaatgc gattgtaaa ttatcgtgc 
      gatttggag aaaaagtgg cacgatacg ttggcacag 
      tttaaatat cttgattat aatgattat tctgtgtat 
      acaggaact tccggtatt gctttactg aaactcaaa 
      aaggatcct gaaagtaga caaaacttg caggaggca 
      ttacaactg ttgtcatta catagacta aaaggaaga 
      agacatact tttttgtgt ggagatgcc ggacccctt 
      gctctgggt gctattatc aattataaa ttggaagat 
      aaggcttac ttggactgc atagaaaag cttaaagca 
      ctatcagag gacgttttt gacccaagc tcagattta 
      ccaaacgag tacctttat ggtcgagct ggttttctt 
      tttgcagtt ttatacgtc aataaacat gtttcacct 
      gtaccattt gaagaaagt tttatcaga aaaataatt 
      gaaacaata atactttgt ggaaaaaat gaagcaaag 
      gctggaaaa tttaaatgt ccattgatg tatcagtgg 
      catgagagt tactatctg ggggcagct catggtgtg 
      tctggaatt ctctatttg ctccttcaa gccaaggag 
      tatttaacc gaaaatgaa ctacaaaca ataattaaa 
      ccgactgtt gattacttg gccactttg agatttccg 
      agttgtaat tttccctca tctctggga cgagataac 
      gacaaatat gtccagtgg tgtcatggg gcgcccggc 
      tttttgtat ctcttcact acagcttac aaggttttc 
      ggtgactgc aaatatcta caactggct ttggattgt 
      ggcgacgta atttggtct cgaggcata ttgagaaaa 
      gggtacagt atctgccat ggtgtctca ggcaatgct 
      tattgtttc ttggagttg taccaaacc actgaagat 
      gaaaaacat ttataccgg gctgttcga ttcgcagaa 
      tggtgcttc gcttacaat aaaaaccac gtggagcac 
      cctcctgat cgccccctt tccttattt gaggggcta 
      tcaggacct atgtacttg tttttggat attcaaaaa 
      ccggccgaa gccaaattt cctggatac actttgtaa
    mRNA sequence
    • >TC008549 RA
      cttaaatta ttagttaaa tagttacaa ttgtttgcc 
      tcctggaat taaaacaaa agtccctaa cttgccgca 
      cctgtcaca tttgtaaac aaacatcaa aataataac 
      aaatcaagc aaaattaat tttctcaag tgtttttca 
      gtgaaaatg tcgcaagat cgatgtttc gccaatcca 
      tttgatgat tattcgtca gaagcagca tgttgtgta 
      atcgaaaat ggaacgatt aaatgcgat tgtaaatta 
      tcgtgcgat ttggagaaa aagtggcac gatacgttg 
      gcacagttt aaatatctt gattataat gattattct 
      gtgtataca ggaacttcc ggtattgct ttactgaaa 
      ctcaaaaag gatcctgaa agtagacaa aacttgcag 
      gaggcatta caactgttg tcattacat agactaaaa 
      ggaagaaga catactttt ttgtgtgga gatgccgga 
      ccccttgct ctgggtgct attatcaat tataaattg 
      gaagataag gcttacttg gactgcata gaaaagctt 
      aaagcacta tcagaggac gtttttgac ccaagctca 
      gatttacca aacgagtac ctttatggt cgagctggt 
      tttcttttt gcagtttta tacgtcaat aaacatgtt 
      tcacctgta ccatttgaa gaaagtttt atcagaaaa 
      ataattgaa acaataata ctttgtgga aaaaatgaa 
      gcaaaggct ggaaaattt aaatgtcca ttgatgtat 
      cagtggcat gagagttac tatctgggg gcagctcat 
      ggtgtgtct ggaattctc tatttgctc cttcaagcc 
      aaggagtat ttaaccgaa aatgaacta caaacaata 
      attaaaccg actgttgat tacttggcc actttgaga 
      tttccgagt tgtaatttt ccctcatct ctgggacga 
      gataacgac aaatatgtc cagtggtgt catggggcg 
      cccggcttt ttgtatctc ttcactaca gcttacaag 
      gttttcggt gactgcaaa tatctacaa ctggctttg 
      gattgtggc gacgtaatt tggtctcga ggcatattg 
      agaaaaggg tacagtatc tgccatggt gtctcaggc 
      aatgcttat tgtttcttg gagttgtac caaaccact 
      gaagatgaa aaacattta taccgggct gttcgattc 
      gcagaatgg tgcttcgct tacaataaa aaccacgtg 
      gagcaccct cctgatcgc cccctttcc ttatttgag 
      gggctatca ggacctatg tacttgttt ttggatatt 
      caaaaaccg gccgaagcc aaatttcct ggatacact 
      ttgtaagtg tgcaatcaa aatacgaat aaataaaat 
      atccacttt att
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY