Status
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Gene information
General information
TC005473 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: 12557163..12570259
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
    TC005473
    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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    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_03959

    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)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 1 (3 dpi)
    Days post injection


    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 50
    larva cuticle dorsal not closed - Penetrance (percentage of animals/eggs on slide): less than 30%
    head appendages size decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    head appendages shape rounded - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    head irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    thorax partially not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    legs podomer shortened - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    legs tibiotarsus potentially fused - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    legs femur potentially fused - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    thorax irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    abdomen shortened - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen 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): 30% - 50%
    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: 20.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 20.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC005473 RA
      MTASTTTVE TSSNFSRKF LEPTPALNQ TQKSIKELF 
      YNGTGYYIE DEVDTGLND LQTLFLACF ATLIPLVIS 
      LLTAFGIRV LWTKYKRQK ENSKYDGMA KRDASDDNA 
      KPLHSHLLN SDKKCETHL AITTEEVEV CDDTGVSQI 
      RSNNHSSTN GSIITMTLK NNHLIVETE ERNDIEEDS 
      RETTMKYSP GARDGVFVV EVQQGVRRS PGSGPQSGA 
      DPELSVSVS DQCALVHNP PDRYSDDET LEECDDYYI 
      ETASPARAT PDSLVAQIR TGLAQSDPT LNEEHPSYS 
      YSTQQCYDS GFYGYHIYN GYINDEPLQ RLKAASTKP 
      KITAAVYKN RAEDDVHIF ANDISYTTE PDVGSGEYE 
      NKGFD
    CDS sequence
    • >TC005473 RA
      atgacggcc tccaccacc accgtcgag acctcttcg 
      aacttttcg cgaaaattt ctagaacca actccggcg 
      cttaatcaa acacaaaag tcaattaaa gagctgttc 
      tacaacggg acggggtat tacatagag gatgaagtg 
      gacacaggt ctgaatgat ctccaaacg ttgttccta 
      gcttgtttt gccacatta attccgtta gttatttcg 
      ttgctcaca gcatttgga ataagggta ctttggacc 
      aaatacaaa agacaaaag gaaaattcc aagtatgat 
      ggcatggcc aaaagggac gcctcggac gacaacgcc 
      aagcccttg cactcgcat ttgctgaac agcgacaag 
      aaatgcgag acgcatctg gcgataacc accgaggaa 
      gtcgaggtg tgtgacgac acaggtgtg agccaaata 
      aggagcaac aaccactcc agcaccaat ggcagcatc 
      atcaccatg accctgaag aacaaccac ctaatcgtc 
      gaaacggag gagagaaac gacatcgag gaagacagt 
      cgtgaaaca acaatgaaa tactctcca ggggcgcgg 
      gatggggtt tttgtggtg gaggtgcag cagggagtg 
      aggaggagt cccgggtcg gggccgcag tcgggggct 
      gatcccgaa ttgtcggtt tcagtgagc gatcagtgc 
      gctctggtg cataatcct ccagacagg tacagtgac 
      gacgaaacg ttggaggaa tgcgacgac tactacata 
      gaaacagca tctccggca cgtgccacc cccgactcc 
      ctggtggcg cagatcagg accggcttg gcccaatcg 
      gaccccacc ctgaacgag gagcacccc agctacagc 
      tacagcacc cagcagtgc tacgacagc ggcttctac 
      ggctaccac atctacaac ggctacatc aacgacgag 
      cccctgcag cgtctcaag gccgccagc accaagccc 
      aagatcacg gccgccgtg tacaagaac cgcgctgaa 
      gacgacgtc cacattttc gccaacgac atatcgtac 
      acgacggaa ccggatgtc gggtctgga gagtacgaa 
      aataaaggc ttcgactaa
    mRNA sequence
    • >TC005473 RA
      tacgacgtt aaccccaga accggaaaa accgtgcct 
      aaaatgtga ccacttcgg gctccgggt gttgcaaat 
      cgcgagatt ggcactcgt ggaatttcg tctacatga 
      agaaacaca aaaggttca aacgctgag aaatgacgg 
      cctccacca ccaccgtcg agacctctt cgaactttt 
      cgcgaaaat ttctagaac caactccgg cgcttaatc 
      aaacacaaa agtcaatta aagagctgt tctacaacg 
      ggacggggt attacatag aggatgaag tggacacag 
      gtctgaatg atctccaaa cgttgttcc tagcttgtt 
      ttgccacat taattccgt tagttattt cgttgctca 
      cagcatttg gaataaggg tactttgga ccaaataca 
      aaagacaaa aggaaaatt ccaagtatg atggcatgg 
      ccaaaaggg acgcctcgg acgacaacg ccaagccct 
      tgcactcgc atttgctga acagcgaca agaaatgcg 
      agacgcatc tggcgataa ccaccgagg aagtcgagg 
      tgtgtgacg acacaggtg tgagccaaa taaggagca 
      acaaccact ccagcacca atggcagca tcatcacca 
      tgaccctga agaacaacc acctaatcg tcgaaacgg 
      aggagagaa acgacatcg aggaagaca gtcgtgaaa 
      caacaatga aatactctc caggggcgc gggatgggg 
      tttttgtgg tggaggtgc agcagggag tgaggagga 
      gtcccgggt cggggccgc agtcggggg ctgatcccg 
      aattgtcgg tttcagtga gcgatcagt gcgctctgg 
      tgcataatc ctccagaca ggtacagtg acgacgaaa 
      cgttggagg aatgcgacg actactaca tagaaacag 
      catctccgg cacgtgcca cccccgact ccctggtgg 
      cgcagatca ggaccggct tggcccaat cggacccca 
      ccctgaacg aggagcacc ccagctaca gctacagca 
      cccagcagt gctacgaca gcggcttct acggctacc 
      acatctaca acggctaca tcaacgacg agcccctgc 
      agcgtctca aggccgcca gcaccaagc ccaagatca 
      cggccgccg tgtacaaga accgcgctg aagacgacg 
      tccacattt tcgccaacg acatatcgt acacgacgg 
      aaccggatg tcgggtctg gagagtacg aaaataaag 
      gcttcgact aagattttt gggagcgcg atgacccca 
      aggtcttta aaccttatt tgaacaggt tctcgtctt 
      ccaacaaac ccttagagt gcatggcgg gaattatct 
      gcatttttg ctgcgttga gacgactgg atggaggac 
      caagtgtag atcactttt ctagatgtc tctaatgct 
      ttcgatgta ttatacaag tgcaaaaca catagagtg 
      agaatttta gattcggtc gctgatgcg gccaatcag 
      ccttttatg ttgtacttg tgtatatag tttgtagcg 
      tttttttct aatgcacct cagctggaa tttgcactc 
      tttagacga ataggagtt ttgttgggt tgggatgga 
      aagtgttgt attttttta ttactgtat acattgtac 
      ataggttat gattaccgt ccgatttct ctgaggata 
      actcattgt aaatatgtt attggcatt tttttgcat 
      tacaatcgg ttcggtggc aagagcagg gcgaatttt 
      acagggttg aaggaccaa ctaggtaaa gcacgacca 
      aatttacac agaaacaaa cttagaaaa ctgagaaat 
      ttaaaaagg gaaatttta acacctaga aataatgaa 
      aaaatgtta aaaaaaatt ctgaataaa aactaaaaa 
      cttgt
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY