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Gene information
General information
TC008002 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_007419.2: 3763815..3765190
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
    TC008002
    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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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_04412

    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: 0.0% (includes death as pupa, adult)

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

    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
    > 100 larvae on the slide

    larva complete everted (inside-out) - Penetrance (percentage of animals/eggs on slide): less than 30%

    larva dorsal bent - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    larva cuticle dorsal not closed - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    abdomen partially everted (inside-out) - 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: 10.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 10.0% (includes death as larva, prepupa, pupa, adult)

    Fertility
    egg production: number no/almost no eggs -
    ovary without detectable defects - Number of animals showing the phenotype: 3
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC008002 RA
      MTVQLKPGD RVLLENRSS EVYAGTIEY ISAKSVNLH 
      TITCHSTNI EYEGNMTFY RNEVVKIVP ISDTEPAST 
      PDETPEVSE DSLLRSRKI NMHPDEFAR LRQVTFDFV 
      FIDTFGTQF ENAVEVLNN RESVAVAVL GNYGRNKPM 
      SVLVMADFK QVFIFDMLC LGKLKTLRE VLESGYICK 
      VVHDGGALF DCLYHKYGV EMKNIFDTQ AVDSMLSKE 
      NDDVEIKRN ISECLTYHF NFPAALLSA VLETMNDKT 
      WFIRPLTKS DKIKSAQLV AYLLSLRDQ LMKQILKKY 
      TDVIAKDYG RYKQMSDIE VLKLRKQ
    CDS sequence
    • >TC008002 RA
      atgaccgtg caactgaaa cccggggac cgtgtcctc 
      cttgaaaac cgttcttct gaggtttac gcgggtaca 
      attgaatat atctctgcc aaaagtgtg aatctccat 
      accataacc tgccacagc accaatatc gaatatgag 
      ggcaatatg accttctat cgcaacgaa gttgtgaaa 
      attgtgcct atttctgac accgaacct gcttccacc 
      cccgatgag acgcctgag gtgtcggaa gactctctt 
      ctaaggtcg cgaaaaatt aacatgcac ccggacgaa 
      ttcgctcgt ctgagacaa gttacgttt gattttgtg 
      ttcatcgac acgtttgga acgcaattt gagaatgcg 
      gttgaggtt ttgaacaat cgggaatcc gtggcagtg 
      gctgtgtta gggaattac gggaggaac aaaccgatg 
      agtgtgttg gtgatggct gactttaag caagttttt 
      atcttcgat atgttgtgt ttggggaaa ttgaaaacg 
      ctgagggag gttttagag tcggggtat atatgtaaa 
      gtggtgcac gatgggggc gcactgttc gattgcctc 
      taccacaag tatggagtg gaaatgaaa aatattttt 
      gatacacag gctgttgat tccatgtta tcaaaggaa 
      aatgacgat gttgaaatt aaacggaac attagtgag 
      tgtctcact tatcatttc aattttccg gcggcactg 
      ctatcagca gttttggaa actatgaat gataaaacg 
      tggtttata aggcccttg acaaagagt gacaaaatt 
      aaatcggcc caattagtt gcgtattta ttgagtctc 
      agagaccag cttatgaag caaatatta aaaaaatat 
      acagacgtg atagcgaaa gactatgga agatataaa 
      caaatgagt gatatagaa gtgttgaag ttgcggaaa 
      caatag
    mRNA sequence
    • >TC008002 RA
      tgaacatta aactgtcaa tttttttcc cttgtaacc 
      taacttttt tgtggccta ttgtgcccc aaaatgacc 
      gtgcaactg aaacccggg gaccgtgtc ctccttgaa 
      aaccgttct tctgaggtt tacgcgggt acaattgaa 
      tatatctct gccaaaagt gtgaatctc cataccata 
      acctgccac agcaccaat atcgaatat gagggcaat 
      atgaccttc tatcgcaac gaagttgtg aaaattgtg 
      cctatttct gacaccgaa cctgcttcc acccccgat 
      gagacgcct gaggtgtcg gaagactct cttctaagg 
      tcgcgaaaa attaacatg cacccggac gaattcgct 
      cgtctgaga caagttacg tttgatttt gtgttcatc 
      gacacgttt ggaacgcaa tttgagaat gcggttgag 
      gttttgaac aatcgggaa tccgtggca gtggctgtg 
      ttagggaat tacgggagg aacaaaccg atgagtgtg 
      ttggtgatg gctgacttt aagcaagtt tttatcttc 
      gatatgttg tgtttgggg aaattgaaa acgctgagg 
      gaggtttta gagtcgggg tatatatgt aaagtggtg 
      cacgatggg ggcgcactg ttcgattgc ctctaccac 
      aagtatgga gtggaaatg aaaaatatt tttgataca 
      caggctgtt gattccatg ttatcaaag gaaaatgac 
      gatgttgaa attaaacgg aacattagt gagtgtctc 
      acttatcat ttcaatttt ccggcggca ctgctatca 
      gcagttttg gaaactatg aatgataaa acgtggttt 
      ataaggccc ttgacaaag agtgacaaa attaaatcg 
      gcccaatta gttgcgtat ttattgagt ctcagagac 
      cagcttatg aagcaaata ttaaaaaaa tatacagac 
      gtgatagcg aaagactat ggaagatat aaacaaatg 
      agtgatata gaagtgttg aagttgcgg aaacaatag 
      actgaatac aaattatga tttgctctt ccgagaatt 
      tcttatcca aaaataaat aattaagac cttctggga 
      aattttagg ccagttagc tactggtta gtaagcggc 
      atttatgac ccaaggatt aactcaaat tacaggtaa 
      aaggaacgc ctaatataa agccaagaa ggtttattg 
      cgcacccct ttcatgttt cgggtgcag cgagttgat 
      ttttcgaac ttttacgtt tatactttt ttaaatttt 
      gtaaacaat gccaagttt ttgtgttgt tattattat 
      taataaata aattagtta ctgacat
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY