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Gene information
General information
TC013538 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_007420.3: 8270444..8274823
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
    TC013538
    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
    {{ goGene }}
    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_10034

    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: 40.0% (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: 1 (9 dpi)
    Days post injection


    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
    • >TC013538 RA
      MSAFRHDNI LSLLGMVVR EGVVSPMMV FEYMPHGDL 
      AELLRAQKK TAYENEVPQ LKPKDLLSI ALQIASGMK 
      YLAAQRFVH RDLACRNCL VAEGPTVKI ADFGMSRDV 
      YTCDYYKIG GSRLLPVRW MSPESVLYG RFTLESDIW 
      SYGVVLWEI YSFGKQPYY GHTNEEAVK LILDGIMLI 
      APEDCPSLI CELMKNCWK TEPRDRIKF PNICDKLEL 
      AYESFDEDK VSIQYENET QKVNVKNVR SLPRPPPLR 
      MISQEDLLD AQGYLLANE VKEPVQYLE TLPD
    CDS sequence
    • >TC013538 RA
      atgagcgct ttcagacac gataacatt ctttctttg 
      ctgggaatg gtggttcga gaaggtgtg gtaagtccg 
      atgatggtc ttcgaatac atgccccac ggggacttg 
      gcggagctt ctccgagcg caaaagaaa accgcctac 
      gagaacgaa gttccccaa ctaaagccc aaggatctg 
      ctctccatc gctctgcaa atcgccagc ggtatgaaa 
      tacctggcg gcccaacgt ttcgtccat cgcgacctc 
      gcctgcagg aactgcctg gtggccgaa ggacccact 
      gtgaaaatt gcagacttc ggcatgagc agagacgtc 
      tatacgtgc gattattac aagatcggc ggcagccgc 
      ctcctgccc gtgcgctgg atgtcgccc gagagcgtc 
      ctctacggc cgtttcacc ctggagtcg gacatctgg 
      tcgtacgga gtggttctg tgggaaatc tacagtttc 
      ggcaagcaa ccctactac gggcacacc aacgaagag 
      gccgtcaag ctaatccta gacggcata atgttgatc 
      gcgcccgaa gactgtccg tccctcatc tgtgagctg 
      atgaaaaac tgctggaaa acggaaccc cgagaccgc 
      ataaagttc cccaacatt tgcgacaag ctcgagctg 
      gcctacgaa agcttcgac gaagacaaa gtgagcatc 
      cagtacgag aacgaaacc caaaaagtc aacgtgaaa 
      aacgtgcgg agtttaccc agaccgcct ccgctgagg 
      atgatctcc caggaagat ttactggac gcgcaagga 
      tatctgtta gcgaacgag gtcaaggaa cctgtacag 
      tatttagag actttaccg gattga
    mRNA sequence
    • >TC013538 RA
      tttcattta aagtctcgt caccggctt agacccgtg 
      tctgtgttt gaaaatagg aaaaataaa cttgaaaaa 
      atgttgatg aacaaagtg aaggcgtaa atgctgtac 
      cagtaatga aaagccgtc aattattga ccagacaat 
      gctgaaagc tttgttggt cttttcaga ctttgttgt 
      tgactaacg gtgttaaat gatttgttt acaggtgaa 
      cttctaacg gaaggtagt gaccaagtg gaaatagtc 
      gccataaaa gtattaaaa gaaaacgca acgcgagaa 
      gccgaagag gattttata agggaagtt gaaatcatg 
      agcgctttc agacacgat aacattctt tctttgctg 
      ggaatggtg gttcgagaa ggtgtggta agtccgatg 
      atggtcttc gaatacatg ccccacggg gacttggcg 
      gagcttctc cgagcgcaa aagaaaacc gcctacgag 
      aacgaagtt ccccaacta aagcccaag gatctgctc 
      tccatcgct ctgcaaatc gccagcggt atgaaatac 
      ctggcggcc caacgtttc gtccatcgc gacctcgcc 
      tgcaggaac tgcctggtg gccgaagga cccactgtg 
      aaaattgca gacttcggc atgagcaga gacgtctat 
      acgtgcgat tattacaag atcggcggc agccgcctc 
      ctgcccgtg cgctggatg tcgcccgag agcgtcctc 
      tacggccgt ttcaccctg gagtcggac atctggtcg 
      tacggagtg gttctgtgg gaaatctac agtttcggc 
      aagcaaccc tactacggg cacaccaac gaagaggcc 
      gtcaagcta atcctagac ggcataatg ttgatcgcg 
      cccgaagac tgtccgtcc ctcatctgt gagctgatg 
      aaaaactgc tggaaaacg gaaccccga gaccgcata 
      aagttcccc aacatttgc gacaagctc gagctggcc 
      tacgaaagc ttcgacgaa gacaaagtg agcatccag 
      tacgagaac gaaacccaa aaagtcaac gtgaaaaac 
      gtgcggagt ttacccaga ccgcctccg ctgaggatg 
      atctcccag gaagattta ctggacgcg caaggatat 
      ctgttagcg aacgaggtc aaggaacct gtacagtat 
      ttagagact ttaccggat tgacaagga cataagaag 
      aagaagaat acggttgtg tgggcaaat tcgattaaa 
      atgctgggc gcgaatgtg tgaaatttg tgtggattc 
      acttgctgt atatatgga tatgtagta gtttaatta 
      aattatatt tttttaaaa aacagttaa ggtggggca 
      aaaaacaac attagcaat gagtagagt tgggacagg 
      tctttgaaa ttcagttct tcacacgca aaattgctc 
      tcaacgaaa ttaaatacc ctgctcatt atttgacaa 
      tacttgact gaactactt aacttaaaa cgtaaaata 
      ctgacaggg taggtaact gtttaatcg agtgcctta 
      tttatatta ctgagtccg ttcattttg tgagaaata 
      ggaaagcac taaaatgta cctaaaaaa atcgttctc 
      aacttttta acaaatcaa gaaatacga atcaaatgt 
      ctgaggtgt tctaatggt ttaaatatt ttccccaaa 
      acaatgact tctagaatc ttcacgtgt gaacgcgta 
      ctaaattgt aaccgatcg ataatcctc agtgttgtt 
      aaagtaaca aaggtgtta atttgtcct ttgtaacgg 
      gtgttttcg aatatgtgc caaataatt gcaaataaa 
      tcggtgtct tttattccc ctcccccaa tacaaacca 
      aagactcga gactatctc cgatagtac gactgatgt 
      taaacctta cgaaataat taattcaat gttattgcg 
      actgtatcg aattttatt gtaaataaa atattaaac 
      caagc
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY