Status
Please wait ...
Gene information
General information
TC009484 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: 421339..433103
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
    TC009484
    Gene ontology

    GO terms for Tribolium

    • {{ goTerm.term }}
      ({{ goTerm.evidence }}){{ goTerm.evidenceTooltip }}
      {{goTerm.showAll ? '[-]' : '[+]'}}
      Status: {{ goTerm.status }}
      Evidence: {{ goTerm.evidence }} ({{ goTerm.evidenceTooltip }})
      Reference: {{ goTerm.referenceText }}
      Quotation: {{ goTerm.quotation }}
      Submitter: {{ goTerm.name }}

    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
    {{ goGene }}
    The Tribolium gene the GO term is assigned to.
    GO ID *
    {{ blurIdResult }}
    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
    {{ blurEvidenceResult }}
    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 *
    {{ blurReferenceResult }}
    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
    We will use your email address only for possible questions regarding this annotation. We will never show your address or give it away.
    Publish name
    If you have entered your name and agree by marking the checkbox. we might show your name on this page to honor your contribution.
      {{ unavailableText }}

    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_04642

    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: 2 (3 dpi)
    Days post injection


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


    adult lethality - Number of animals showing the phenotype: 3 (11 dpi)
    Days post injection


    Fertility
    mature egg deposition blocked number 1st lateral oviduct: 3 number 2nd lateral oviduct: 2 - Number of animals showing the phenotype: 2
    ovary without detectable defects - Number of animals showing the phenotype: 1
    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: < 50 embryo/egg not developed/not fertilized - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 80%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 20
    embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    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: 100.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 100.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 10 (11 dpi)
    Days post injection


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC009484 RA
      MRANRPIHV GLTPSHLQL VCVLLVFSH FTVNAANIP 
      VTTNAPEVA SDVRVECNS DEIVVNINT KSGRFNGMI 
      YPRGLSKNS SCMGEWVQR PSPIKYNLP LRGCNTMST 
      ELDDGGIEY FNTIVVQPH LKLVTNQGR GFHIRCRYN 
      TRNNTITND SLKVDLMAA DPITALAPM PGCSMKIFS 
      GDPSYKEVA ENVKIGDPL TLVITLDEQ DTYGIRVTD 
      CLVRDGLGW GEQKLINDE GCPLDAEIM GKFQYSEDK 
      TKASVQFQA HKFPYTASV YYQCNVKLC LKADGGCDI 
      SPPSCGGNR LRRQAADPT EGTPATIEV YSGLYVNEA 
      NDLAKAGLE EDSVFSEKT PEDSICISQ RSFAIGICI 
      AGLILMLCV IAAILCLLA RRRSKKTSS NPGSSIYSG 
      PYTNTAYSH SS
    CDS sequence
    • >TC009484 RA
      atgagagcg aaccgtccg atacatgtt ggcctaaca 
      ccgtctcac cttcaactc gtctgtgtc cttctggtc 
      ttctcgcat ttcactgtc aatgctgcc aatataccc 
      gtcacaacg aacgcaccg gaagtggca tcggatgta 
      cgtgtggaa tgcaacagc gacgaaatc gtagtcaat 
      atcaacaca aaatcgggc cgattcaac ggcatgatc 
      tatcctaga ggtttgtcg aagaacagt tcttgcatg 
      ggagagtgg gtccagcgg ccctccccc atcaagtac 
      aacctgcct ttgagaggg tgcaacacc atgagcacg 
      gaattggat gatggtggt attgaatat tttaatacc 
      atcgttgtg caaccccat ctcaagctg gtcaccaac 
      caagggaga ggtttccat atccggtgt cgctacaac 
      accaggaat aacaccatc acgaatgat tccctcaag 
      gttgatttg atggctgca gatccaatc acagcactg 
      gcccccatg ccgggctgc agcatgaaa atcttttca 
      ggagaccct tcgtacaag gaagttgcc gagaacgtg 
      aaaatcggt gacccttta acacttgtc attactttg 
      gacgagcaa gacacgtac ggaatacgt gttacggat 
      tgtttggtc agagatggg ctaggctgg ggcgaacag 
      aaactgatt aatgacgaa ggctgtcct ttggatgct 
      gaaattatg ggcaagttt cagtattcg gaggacaag 
      acgaaagct tcggtgcag tttcaggcg cacaagttc 
      ccatatacc gcctcggtt tactaccaa tgcaacgtc 
      aagttgtgt ctgaaggct gatggaggg tgcgatatt 
      tccccacca agttgcgga gggaacagg ttgcgcaga 
      caagcagcg gaccccacc gaagggact cctgccact 
      atcgaagta tacagcggc ctttatgtc aatgaggct 
      aacgacctc gccaaagcc ggcttggag gaggattcc 
      gtctttagc gagaagaca cctgaggac agcatctgc 
      atctcgcaa cgcagcttc gctatcgga atttgtata 
      gcgggtctg attttgatg ctttgcgtc atcgctgca 
      atcctctgc cttttggcg agaagacgc tcgaagaag 
      acttcctca aaccctggc agttcgatc tacagcggt 
      ccttacacc aacactgcc tatagtcat agtagttaa
    mRNA sequence
    • >TC009484 RA
      ttcaacgaa cctgaagaa tggtgattt tgacttgag 
      tcagtcctc agccagcaa gttcgaaag taaagtcgg 
      ggcaagtct ccgacaacc tctaggggg cgtattcaa 
      gacatgcac cacaataac tatgtaaaa aacaagtcg 
      cgttttccc cgccggtct tagaagtga tattgttcg 
      attttccga gtgaagtga atcatgaac aggtgaaaa 
      taaataata agtgttgtg gagactgat cttaggtta 
      tttatttaa cgccactct ctgtgatat tttgccgac 
      tctccgtcc gtttattcg acgatgaat aagaaaaca 
      atgagagcg aaccgtccg atacatgtt ggcctaaca 
      ccgtctcac cttcaactc gtctgtgtc cttctggtc 
      ttctcgcat ttcactgtc aatgctgcc aatataccc 
      gtcacaacg aacgcaccg gaagtggca tcggatgta 
      cgtgtggaa tgcaacagc gacgaaatc gtagtcaat 
      atcaacaca aaatcgggc cgattcaac ggcatgatc 
      tatcctaga ggtttgtcg aagaacagt tcttgcatg 
      ggagagtgg gtccagcgg ccctccccc atcaagtac 
      aacctgcct ttgagaggg tgcaacacc atgagcacg 
      gaattggat gatggtggt attgaatat tttaatacc 
      atcgttgtg caaccccat ctcaagctg gtcaccaac 
      caagggaga ggtttccat atccggtgt cgctacaac 
      accaggaat aacaccatc acgaatgat tccctcaag 
      gttgatttg atggctgca gatccaatc acagcactg 
      gcccccatg ccgggctgc agcatgaaa atcttttca 
      ggagaccct tcgtacaag gaagttgcc gagaacgtg 
      aaaatcggt gacccttta acacttgtc attactttg 
      gacgagcaa gacacgtac ggaatacgt gttacggat 
      tgtttggtc agagatggg ctaggctgg ggcgaacag 
      aaactgatt aatgacgaa ggctgtcct ttggatgct 
      gaaattatg ggcaagttt cagtattcg gaggacaag 
      acgaaagct tcggtgcag tttcaggcg cacaagttc 
      ccatatacc gcctcggtt tactaccaa tgcaacgtc 
      aagttgtgt ctgaaggct gatggaggg tgcgatatt 
      tccccacca agttgcgga gggaacagg ttgcgcaga 
      caagcagcg gaccccacc gaagggact cctgccact 
      atcgaagta tacagcggc ctttatgtc aatgaggct 
      aacgacctc gccaaagcc ggcttggag gaggattcc 
      gtctttagc gagaagaca cctgaggac agcatctgc 
      atctcgcaa cgcagcttc gctatcgga atttgtata 
      gcgggtctg attttgatg ctttgcgtc atcgctgca 
      atcctctgc cttttggcg agaagacgc tcgaagaag 
      acttcctca aaccctggc agttcgatc tacagcggt 
      ccttacacc aacactgcc tatagtcat agtagttaa 
      agtcagcga taactaact gccatcact ctatcgaac 
      gaaaattag cttaggtgt gccattcaa aggctcagt 
      gctcatata gttttaaac gtccgtctt ttttcgaat 
      ggtgttcaa gatgaaatc ttc
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY