Status
Please wait ...
Gene information
General information
TC006160 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_007423.3: 4130878..4138572
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
    TC006160
    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_01005

    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 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): 30% - 50%
    embryo/egg with embryonic tissue, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): less than 30%

    larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - 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: > 50
    egg without cuticle embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    cuticle remnants without visible segmentation but polarity - Penetrance (percentage of animals/eggs on slide): less than 30%

    cuticle remnants with some identifiable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

    head not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    thorax not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): more than 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: 10.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 10.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality early (L5/6) - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC006160 RA
      METQSFRSL QKKRTTNFR EDETKLLIQ LWGSPQIQN 
      KLYLTHRKE PVMRLLAAN MQQRGFYRT PDEIKTRIR 
      NLKCLYHRI KRTVQSGSG IGTVDPDWP HYKAMDRIL 
      SKQNQKKES LYKDNVFEG PRCEDIKQE IDDIDINDD 
      MESYTTNSM GGSEYEEEQ VQLPPLTPA PSKDGKKPD 
      NKSVPNRNL PKILPNLTI PLQNQQNGA QNKQTSIPS 
      IPFPLLILN GVQPNANPD KKDAKSPGG IKNDSDVNQ 
      VLKELLEVQ KENLDIERQ RLELEKQRL EFERFVGSQ 
      LLAMGPFIG NLFHRFAFP TEDMTENEK NNSRKRQSS 
      CDIDLLKDS KILKTLLSE GLKKYIVSE DENDDSGIH 
      NDDNSNSSS K
    CDS sequence
    • >TC006160 RA
      atggagacg caaagtttt cgttcgctt caaaagaag 
      cgtacaacg aatttccgc gaggacgaa acgaaattg 
      ttaatacaa ttgtggggc agtccccaa atacaaaac 
      aaactctac ttgacccat cgaaaagaa ccagtaatg 
      cgtcttttg gctgccaac atgcaacaa cgtggtttt 
      tacagaacg cccgatgag atcaaaaca aggataaga 
      aatctcaag tgcctctat cacagaatc aagaggaca 
      gtccaatcg ggatctgga attgggact gtcgatcca 
      gattggcca cactacaaa gccatggac aggattctg 
      agcaaacag aaccagaag aaggagagt ttgtacaag 
      gataatgtc ttcgagggg cctcgctgc gaggacatc 
      aagcaggag attgacgat atcgatatt aacgatgat 
      atggagtcc tacaccacc aacagcatg ggagggtcg 
      gaatatgaa gaagaacaa gtacaactg cctccgctg 
      actccagcc ccaagcaaa gacgggaaa aaaccggac 
      aacaaatcg gtaccgaac cgaaacttg cccaaaatt 
      ttaccaaac cttaccatt cctttgcaa aatcaacaa 
      aacggagcc caaaataaa caaacttca atcccatcg 
      attccattc ccactgtta atcctcaat ggtgttcaa 
      ccaaacgca aacccggac aagaaagac gcaaaaagt 
      ccaggtgga ataaaaaat gattcagac gttaatcaa 
      gtcctgaag gagcttctc gaggtccaa aaggagaat 
      ctggacatc gagcgccaa cgcctggaa ctggaaaaa 
      cagaggctc gaatttgag cgctttgtt ggttcccaa 
      ttactggca atgggccca tttattgga aatttgttc 
      catcgattt gcatttccg accgaagat atgacagaa 
      aacgagaaa aataacagc cgaaagagg caaagtagt 
      tgtgatatt gaccttttg aaggatagt aaaattttg 
      aagactctg ctgagtgag gggctgaag aagtacatt 
      gtgagtgag gatgagaac gacgacagt gggattcac 
      aatgatgac aacagcaac agcagcagt aaataa
    mRNA sequence
    • >TC006160 RA
      tgtccccag aaaaccgtt agatccgca tctgccgct 
      gtattttcc gcatgaaaa agaaccgaa tttcaccat 
      ctctctcga tcctttgta gcaaaaacc taatccttg 
      tttttaccc cctttgcct tgtacttaa gtgtcaagc 
      gaattgcgc ttgtgcgaa tccaagtat cgatcctac 
      ttcagtagg gtggttgag ttccctcgc cgcccttac 
      ctactcagt taacacgac gtcactcta tttaagcca 
      tcagcagct taacaaaat caaatcagc gacaaaaag 
      gcacaaatc gaagacggc gctactcat ttagacaac 
      tcgtgctca gtgcgatgc tcagtccga gtgataatt 
      agtggcgtt ttttggcgg gaatcttca ccgaggatt 
      aaacgatgg agacgcaaa gttttcgtt cgcttcaaa 
      agaagcgta caacgaatt tccgcgagg acgaaacga 
      aattgttaa tacaattgt ggggcagtc cccaaatac 
      aaaacaaac tctacttga cccatcgaa aagaaccag 
      taatgcgtc ttttggctg ccaacatgc aacaacgtg 
      gtttttaca gaacgcccg atgagatca aaacaagga 
      taagaaatc tcaagtgcc tctatcaca gaatcaaga 
      ggacagtcc aatcgggat ctggaattg ggactgtcg 
      atccagatt ggccacact acaaagcca tggacagga 
      ttctgagca aacagaacc agaagaagg agagtttgt 
      acaaggata atgtcttcg aggggcctc gctgcgagg 
      acatcaagc aggagattg acgatatcg atattaacg 
      atgatatgg agtcctaca ccaccaaca gcatgggag 
      ggtcggaat atgaagaag aacaagtac aactgcctc 
      cgctgactc cagccccaa gcaaagacg ggaaaaaac 
      cggacaaca aatcggtac cgaaccgaa acttgccca 
      aaattttac caaacctta ccattcctt tgcaaaatc 
      aacaaaacg gagcccaaa ataaacaaa cttcaatcc 
      catcgattc cattcccac tgttaatcc tcaatggtg 
      ttcaaccaa acgcaaacc cggacaaga aagacgcaa 
      aaagtccag gtggaataa aaaatgatt cagacgtta 
      atcaagtcc tgaaggagc ttctcgagg tccaaaagg 
      agaatctgg acatcgagc gccaacgcc tggaactgg 
      aaaaacaga ggctcgaat ttgagcgct ttgttggtt 
      cccaattac tggcaatgg gcccattta ttggaaatt 
      tgttccatc gatttgcat ttccgaccg aagatatga 
      cagaaaacg agaaaaata acagccgaa agaggcaaa 
      gtagttgtg atattgacc ttttgaagg atagtaaaa 
      ttttgaaga ctctgctga gtgaggggc tgaagaagt 
      acattgtga gtgaggatg agaacgacg acagtggga 
      ttcacaatg atgacaaca gcaacagca gcagtaaat 
      aatttgttc gtttcattc caataa
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY