Status
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Gene information
General information
TC009681 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: 4381095..4382662
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
    TC009681
    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
    You may enter your name. The contact information can help us to clarify any questions. If you agree, we may show your name on this page to honor your contribution.
    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_11039

    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: 30.0% (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


    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: < 50 embryo/egg with muscle fluorescence/pattern, but not hatched (pot. late embryonic lethality) - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): less than 30%
    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: % (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
    • >TC009681 RA
      MKMSRGTKQ QEKDWFQIL AIFLACISS FTDGMIFSW 
      PSPAIPKIV ADKTNYDIS LDEASFFTV LPPMGAILS 
      SFLFAKLND TIGRKFTLL LITIPQIVA LSLIASAKS 
      VYVFYLARF IGGLGDACL FGCLPVYVG EISTPRVRG 
      SWGNFMTFL MYVGQVSIN IIGSYSSIA MTAYICLIF 
      PIFFFCTFI FMPETPYFY LMKGRVEDA RVSLQRLRR 
      VENVEDELT KLKIDIDRQ MSESGTWRD VFAIRSNRR 
      ALFAGIFLR ASQQLGGIS SFTVYTQYI FLKSGGDVS 
      ASTSAIIFM GLCAVLNMF AAFTLDRIG RRRSYFLSL 
      LLCGSVLLC EAVYFLLEQ FYSDLVDVR AVNWIPLVG 
      MILYVVFYS FGLGIVPTL MLGELFSAS IKGKGLFLM 
      NIVLGLFVS VATKLFHLL DTSFGLFSP FLFFAVSCF 
      VSTVLSVRF VPETKGKTL EEIQQLLKG TKEEEQQC
    CDS sequence
    • >TC009681 RA
      atgaaaatg tccagaggc acaaaacag caagaaaag 
      gactggttc caaatcctt gctattttc ctggcttgc 
      atttcctcc ttcactgac ggcatgatt ttctcctgg 
      ccttcaccc gccatcccg aaaatcgta gccgacaaa 
      accaactac gacatatcc ctagacgaa gcttcattt 
      ttcacagtt ttgcccccc atgggggct atactgtcc 
      tcgtttctg ttcgcaaaa ttgaatgac actatcggg 
      cgcaaattc acgctactt ttaatcaca attccccaa 
      attgtggcc ttgagtttg atcgcctca gctaaatct 
      gtctatgtg ttttacttg gctcggttc attggaggc 
      ttgggggac gcttgtctt ttcggctgt ttgcccgtc 
      tacgtgggc gagatttcc acccctcgg gtgcgcggc 
      tcgtgggga aatttcatg acattcctc atgtatgtg 
      ggacaagtg tcgattaat ataataggg agctacagt 
      tccattgcc atgacggcc tacatttgc ctgattttt 
      cccattttt ttcttttgc acttttatt ttcatgccg 
      gaaactccc tatttctac ttgatgaaa ggtcgagtt 
      gaggacgcc agagtgtct ttacagcgt cttcggcga 
      gtcgaaaac gtcgaagac gagttgact aaactaaag 
      attgacata gaccgccaa atgtccgaa tctgggacc 
      tggagggac gtttttgcc attagaagc aaccggagg 
      gctttgttc gctggaata ttcctccga gcgtcgcaa 
      caactcggc ggcatttcc tcctttacg gtctacacg 
      cagtacatt ttcctgaaa tcgggcggc gacgtttcg 
      gccagcacc tcggcgatc atcttcatg ggcctgtgc 
      gcggttttg aacatgttt gcggctttc actctcgat 
      agaatcggc cgccgaaga tcttacttc ttatcgctg 
      ttattgtgc ggttcggtg ctgttgtgc gaggctgtt 
      tactttttg ctcgagcag ttttacagt gatttggtg 
      gatgttaga gccgtgaac tggatcccg ctagtcggg 
      atgattctc tatgtcgta ttttattca tttgggctc 
      gggattgtg cctacgcta atgttggga gagcttttc 
      tcggcgagt attaagggg aaaggtctg ttcttaatg 
      aatatcgtg ttggggctt tttgtaagt gtggccacc 
      aagttgttt catttgctt gatacatcg tttgggttg 
      ttttcgccg tttttattt tttgcggtg agttgcttc 
      gtttccacc gtgctgtcg gtgaggttc gtgccggaa 
      accaagggg aaaacgctg gaggagatc cagcagttg 
      ttgaaaggg acgaaagaa gaggaacaa cagtgttaa
    mRNA sequence
    • >TC009681 RA
      ccgacttaa aaaactact cccaaaaat gaaaatgtc 
      cagaggcac aaaacagca agaaaagga ctggttcca 
      aatccttgc tattttcct ggcttgcat ttcctcctt 
      cactgacgg catgatttt ctcctggcc ttcacccgc 
      catcccgaa aatcgtagc cgacaaaac caactacga 
      catatccct agacgaagc ttcattttt cacagtttt 
      gccccccat gggggctat actgtcctc gtttctgtt 
      cgcaaaatt gaatgacac tatcgggcg caaattcac 
      gctactttt aatcacaat tccccaaat tgtggcctt 
      gagtttgat cgcctcagc taaatctgt ctatgtgtt 
      ttacttggc tcggttcat tggaggctt gggggacgc 
      ttgtctttt cggctgttt gcccgtcta cgtgggcga 
      gatttccac ccctcgggt gcgcggctc gtggggaaa 
      tttcatgac attcctcat gtatgtggg acaagtgtc 
      gattaatat aatagggag ctacagttc cattgccat 
      gacggccta catttgcct gatttttcc cattttttt 
      cttttgcac ttttatttt catgccgga aactcccta 
      tttctactt gatgaaagg tcgagttga ggacgccag 
      agtgtcttt acagcgtct tcggcgagt cgaaaacgt 
      cgaagacga gttgactaa actaaagat tgacataga 
      ccgccaaat gtccgaatc tgggacctg gagggacgt 
      ttttgccat tagaagcaa ccggagggc tttgttcgc 
      tggaatatt cctccgagc gtcgcaaca actcggcgg 
      catttcctc ctttacggt ctacacgca gtacatttt 
      cctgaaatc gggcggcga cgtttcggc cagcacctc 
      ggcgatcat cttcatggg cctgtgcgc ggttttgaa 
      catgtttgc ggctttcac tctcgatag aatcggccg 
      ccgaagatc ttacttctt atcgctgtt attgtgcgg 
      ttcggtgct gttgtgcga ggctgttta ctttttgct 
      cgagcagtt ttacagtga tttggtgga tgttagagc 
      cgtgaactg gatcccgct agtcgggat gattctcta 
      tgtcgtatt ttattcatt tgggctcgg gattgtgcc 
      tacgctaat gttgggaga gcttttctc ggcgagtat 
      taaggggaa aggtctgtt cttaatgaa tatcgtgtt 
      ggggctttt tgtaagtgt ggccaccaa gttgtttca 
      tttgcttga tacatcgtt tgggttgtt ttcgccgtt 
      tttattttt tgcggtgag ttgcttcgt ttccaccgt 
      gctgtcggt gaggttcgt gccggaaac caaggggaa 
      aacgctgga ggagatcca gcagttgtt gaaagggac 
      gaaagaaga ggaacaaca gtgttaatg ctaatattt 
      ttctacttt attaaaaaa aaaattatg attcaagtt 
      ttggactat aaactcaat gttatcatt taataaatg 
      ataactaaa tta
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY