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Gene information
General information
TC003527 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_007418.3: 6256442..6261146
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
    TC003527
    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
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    Email
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_09763

    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: 70.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 5 (3 dpi)
    Days post injection


    adult lethality - Number of animals showing the phenotype: 2 (9 dpi)
    Days post injection


    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): more than 80%

    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: > 50
    thorax segment number decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    thorax number decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    abdomen segment number decreased - Penetrance (percentage of animals/eggs on slide): more than 80%

    abdomen not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    abdomen number decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    affected eggs/embryos/larvae - 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: % (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
    • >TC003527 RA
      MSWNSGPYP QGNQGYYGG PPPQQPYPG GYPGAPPSG 
      YPGAPPPGY PGAPGGYPG QPGFNPPPP QPPYGNPYD 
      SAPQQGEAA PFNNHTGMY SGEDPTVKG FDFSDKSIR 
      RGFIRKVYS ILMVQLSIS LAFIAWFLF HTPTRKFVQ 
      SHGELLIIS LVIIFVTMI ALACCGEVR RKAPTNYIF 
      LFIFTLAES FVLAVCSST YESQEVMMA VGITAAVCL 
      GLTLFAFQT KYDFTMCGG ILFVAVLIL FIFGIVTIF 
      VHTKVVKLV YASLGALIF SIYLVYDTQ LMMGGNHKY 
      SISPEEYVF AALNLYIDV INIFMYILS IIGTSRD
    CDS sequence
    • >TC003527 RA
      atgtcttgg aacagtgga ccatatcca caaggaaat 
      caaggatat tatggtggc cctccacca cagcaaccg 
      tacccaggc ggttatccc ggggcgcct ccgtcagga 
      tacccgggt gctccgccg ccaggttat cccggtgct 
      ccaggagga tacccagga caacctggt ttcaatccc 
      ccacctcca caaccaccc tatggaaac ccatatgat 
      tcggcaccg caacaaggt gaagctgca ccctttaat 
      aatcacact gggatgtat agcggcgag gaccccact 
      gtcaaagga tttgacttt tcggacaag agcatccgg 
      cgcggtttc atccgtaag gtctattca attctgatg 
      gttcagcta tcgatatct ctcgcattt atcgcctgg 
      ttcttattc cacacaccg acgaggaag tttgttcag 
      agccacggc gaattatta attatttct ctagtcatc 
      attttcgtt acgatgatc gcactcgct tgctgcggg 
      gaagtacga agaaaagcg cctacgaat tacattttc 
      ctcttcatt ttcacgctt gctgaatct ttcgtgctt 
      gcagtatgt tcgtcaaca tacgagtcg caagaagtc 
      atgatggca gtcggcata actgccgct gtctgtctc 
      gggctcact ttgtttgct ttccaaacg aaatacgat 
      tttacaatg tgtgggggg atacttttt gttgccgtc 
      ctgatcttg ttcattttc ggaattgtt accattttt 
      gttcacacc aaagttgta aagttggtc tatgcatct 
      ttgggggct ttgattttc tcgatttat ttagtttac 
      gacacgcag cttatgatg ggcggaaac cacaagtat 
      tctatctca cctgaagag tacgttttc gccgctttg 
      aatttgtac atcgacgtt atcaacatt ttcatgtac 
      attttatca attattggt acttcaagg gattag
    mRNA sequence
    • >TC003527 RA
      ttccagata attttgttg ccttttcca ttttccaga 
      atagcgata agacagttt tcctgtggc ggaagtgat 
      taattgccg acaacagca ggtatgtgt tttgtgatt 
      tgacccata ttatttaca cctactttc atcactgct 
      tgttgtggt ttacacggg cgtatgtct tgtaaatat 
      tgaaaatca actttattt cgcaatcaa aaaggttaa 
      tcttggtct ggctctagt cgttgaggg aattttact 
      taatgcgtc taacatttt taatattga tttttatac 
      attgatgag tcatgtatt tacgagtgg tagcttttc 
      ggaaatgaa atgaaattc agaacttag ccgattgtt 
      aacgttttc ttcacgttc gccaagttt cattcttgt 
      aaactgttt ttttctatt acagcatgt cttggaaca 
      gtggaccat atccacaag gaaatcaag gatattatg 
      gtggccctc caccacagc aaccgtacc caggcggtt 
      atcccgggg cgcctccgt caggatacc cgggtgctc 
      cgccgccag gttatcccg gtgctccag gaggatacc 
      caggacaac ctggtttca atcccccac ctccacaac 
      caccctatg gaaacccat atgattcgg caccgcaac 
      aaggtgaag ctgcaccct ttaataatc acactggga 
      tgtatagcg gcgaggacc ccactgtca aaggatttg 
      acttttcgg acaagagca tccggcgcg gtttcatcc 
      gtaaggtct attcaattc tgatggttc agctatcga 
      tatctctcg catttatcg cctggttct tattccaca 
      caccgacga ggaagtttg ttcagagcc acggcgaat 
      tattaatta tttctctag tcatcattt tcgttacga 
      tgatcgcac tcgcttgct gcggggaag tacgaagaa 
      aagcgccta cgaattaca ttttcctct tcattttca 
      cgcttgctg aatctttcg tgcttgcag tatgttcgt 
      caacatacg agtcgcaag aagtcatga tggcagtcg 
      gcataactg ccgctgtct gtctcgggc tcactttgt 
      ttgctttcc aaacgaaat acgatttta caatgtgtg 
      gggggatac tttttgttg ccgtcctga tcttgttca 
      ttttcggaa ttgttacca tttttgttc acaccaaag 
      ttgtaaagt tggtctatg catctttgg gggctttga 
      ttttctcga tttatttag tttacgaca cgcagctta 
      tgatgggcg gaaaccaca agtattcta tctcacctg 
      aagagtacg ttttcgccg ctttgaatt tgtacatcg 
      acgttatca acattttca tgtacattt tatcaatta 
      ttggtactt caagggatt agaagtagc ggttttatt 
      ttttcaact gttgtattt gttgtgttg gtaagaatt 
      gagttttgt ttaatacag agtattaat aaattctcc 
      actgttttt tgaataata tcattttcg taaaaattg 
      caatataac tattatttt gctagatat aaatgtaca 
      gattaagaa accaatcct attagtggg aggtaagga 
      gaatggaag tagatttta gatattaaa gccagtggt 
      tatttattg ttaactgta gtaaaacca ctattacga 
      acgcttcta tacttactc aaacgaccc aagtgttat 
      gaatgtgat gaattacta ctattacct tgatcacaa 
      taaaaaatt ccttcgtta cttgtaata tttataaca 
      tgtaagtat aaagattag gaaaataac tatagtttt 
      tgatgttta ctcgtttta ctgtaatgc ttgtaaaaa 
      ataaatgca ctgaaatat t
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY