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Gene information
General information
TC006354 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: 7792417..7794136
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
    TC006354
    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_01037

    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: 20.0% (includes death as pupa, adult)

    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 embryo/egg not developed/not fertilized - Penetrance (percentage of animals/eggs on slide): more than 80%
    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 80%
    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): more than 80%
    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)

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


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC006354 RA
      MGVRTLCHG LAAVHFWFG CYYDWNYVQ 
      IPTEVHRMG DSFGKSGKL KFLTYWDAL 
      LQALFFTIC VINDLVGTN EEAPKKAPL 
      IRRVKDLIL PCLAFPLSM FVGLTFWGI 
      YFVDRELIF PRALDQFFP AWLNHVMHT 
      NIMIFILIE LFTSYRKYP ARKVGLTIL 
      SLFMLVYLV WIHIIHAYS GMWVYPILE 
      VLNLPLRIV FFIGLLGLS VSLYIVGEK 
      LNGIVWSQK KHSLKKRSN
    CDS sequence
    • >TC006354 RA
      atgggtgtg agaactttg tgtcatggt ctcgcagcg 
      gttcatttc tggttcggt tgctattac gactggaat 
      tatgttcaa atcccgaca gaggtccac cgcatgggg 
      gactcgttc ggtaaaagc ggaaaattg aagttttta 
      acctactgg gacgcgctc ctccaagcc ctcttcttc 
      accatctgt gtcatcaat gaccttgtg gggaccaac 
      gaggaggcc cccaagaaa gcgccactc atccggaga 
      gtcaaagac ttgattttg ccctgtttg gcgtttccg 
      ttgtcaatg tttgtaggc ctgactttc tgggggatt 
      tacttcgtc gaccgcgag ctgattttc ccgcgggcg 
      ctggaccag ttcttcccc gcgtggctc aaccacgtc 
      atgcacacc aacataatg attttcatc ctaatcgaa 
      ctgttcaca tcttatagg aagtaccca gctaggaaa 
      gttgggctc acgattttg agtctgttc atgttggtt 
      tacttggtg tggattcac atcattcat gcctattcg 
      gggatgtgg gtgtacccc attctggag gtcctgaac 
      ctgccgctg aggatcgtg tttttcata ggcttgttg 
      ggcttgtct gtgagcctg tatattgtg ggtgaaaag 
      ttgaacggg attgtgtgg agccagaag aagcacagt 
      ttgaagaag cgttcaaat tag
    mRNA sequence
    • >TC006354 RA
      ttcgtgttt ccaatttcg ttttattgc caacaatcg 
      tacaaataa taattattt ctcccgact cccccttca 
      aatcctctc aaaccggcc aattacata attcccaat 
      ctgagagga ccaaacgtg cggaaataa acttaacaa 
      tgtctaatt cagttcaac aagtgcttg tgtgtgctt 
      ctatgcgat aactcttat ctactatcg tcattaacg 
      tgaaagtgc ctcatcatg tccctcgtt tttcccttc 
      cattgcctc accctgggg gtgtacatc ctcgccttc 
      tggtacgac ctcacctac gtggatatc ccccaaatg 
      cagcacaag aacgacatg aaattcttc aaaggtcgg 
      ctgaaattt ctcaccatt tggaacatg atcgcgtcc 
      taccctaat cccaaccac actcaatca cgcactcaa 
      tcaacaatc aaacagctt caagcaccg tttaatcaa 
      tttgtaaaa cagggaggg gtgcaagtg cttgtctcg 
      cgtcgggtg aatttaatt gtgtgggtc aaatccgcg 
      atcgcgtcc tgtccatag tcgctaacc tttgccccc 
      atagaaagt ctttaaggc ttttccgag cgagtggca 
      tgtcatttg aagctaggt aatggtaaa atgggtgtg 
      agaactttg tgtcatggt ctcgcagcg gttcatttc 
      tggttcggt tgctattac gactggaat tatgttcaa 
      atcccgaca gaggtccac cgcatgggg gactcgttc 
      ggtaaaagc ggaaaattg aagttttta acctactgg 
      gacgcgctc ctccaagcc ctcttcttc accatctgt 
      gtcatcaat gaccttgtg gggaccaac gaggaggcc 
      cccaagaaa gcgccactc atccggaga gtcaaagac 
      ttgattttg ccctgtttg gcgtttccg ttgtcaatg 
      tttgtaggc ctgactttc tgggggatt tacttcgtc 
      gaccgcgag ctgattttc ccgcgggcg ctggaccag 
      ttcttcccc gcgtggctc aaccacgtc atgcacacc 
      aacataatg attttcatc ctaatcgaa ctgttcaca 
      tcttatagg aagtaccca gctaggaaa gttgggctc 
      acgattttg agtctgttc atgttggtt tacttggtg 
      tggattcac atcattcat gcctattcg gggatgtgg 
      gtgtacccc attctggag gtcctgaac ctgccgctg 
      aggatcgtg tttttcata ggcttgttg ggcttgtct 
      gtgagcctg tatattgtg ggtgaaaag ttgaacggg 
      attgtgtgg agccagaag aagcacagt ttgaagaag 
      cgttcaaat taggcgata atttagcgt agttgaagt 
      gcatttata taaattgtg atagtctgc actgttggg 
      tttttatgt gattttgta aatcgtggc ttaatttat 
      atcgtgagt ggtcataca ctttaaaaa attcaattg 
      tgttagatt gtgcctgag gaaatttgg caataaatt 
      cctttctaa tattttaat aaattccat taaatgtag 
      taaactagg aaacaataa agctagtaa tagtaa
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY