Status
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Gene information
General information
TC005548 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: 11434035..11435287
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
    TC005548
    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_03976

    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)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 2 (3 dpi)
    Days post injection


    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 50
    larva shape broader - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    head appendages shape irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    legs podomer shortened - 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: 70.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 70.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 7 (11 dpi)
    Days post injection


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC005548 RA
      MDCKPCGKA TTSPRQPRS PTTCPPCPC CIPVLAEAI 
      PKVQVTPCP PPPAQPPAD CCHVCVPVV TPAPPCEPC 
      RPKRKCKYI QPARPKSYA PERKYLPPA APMDDGTIY 
      RKSYLPAEA ERPPQIRPE NNLCVGEGK MSDNTVHNM 
      SYLPHKVLP PCPIYPCEH RLLGEGPMQ DITTQKHDY 
      VPKPFSRPE KIVPPVNLF SSDCPLSDK TVNRLSYMP 
      VDKPSKVEP FYPVNAIEK PSGKISDKT IHNMSYQPW 
      EPTEPIETP WADKPKYQP PKLRMEDNT VHKMSYMPP 
      GQYVECDDD DPDCVECPE PPCDPHCNP NYRCAMPCC 
      CPKAAC
    CDS sequence
    • >TC005548 RA
      atggactgc aagccatgc ggcaaggcc acgacgtcc 
      ccccggcag ccccgctcg cccaccacg tgcccccct 
      tgcccgtgc tgcatcccg gtgttggcc gaagccatc 
      cccaaagtg caggtgacg ccctgtcca ccgcccccc 
      gcccagccg ccggccgac tgctgccac gtgtgcgtc 
      ccggtggtg acccccgcg cccccatgc gagccctgc 
      cgcccgaaa cgcaaatgc aagtacatc cagccggcg 
      cggcccaag tcctacgcc cccgagcgc aagtacctg 
      cccccggcc gcccccatg gacgacggc accatctac 
      aggaagtcg tacctccct gccgaggcg gaacgtccc 
      ccgcagatc cgccccgag aacaacctc tgcgtgggg 
      gaggggaag atgtcggat aatacggtg cacaacatg 
      tcgtacctc ccccataag gtgctgccc ccatgcccg 
      atctacccc tgcgagcat aggctgctg ggggagggg 
      cccatgcag gatatcacc acgcagaag cacgactat 
      gtgcctaaa ccgttctca aggccggag aagatcgta 
      ccgccggtt aatctcttt tctagtgat tgtcccctg 
      agtgataag actgtgaat aggttgtct tatatgccg 
      gttgataag cctagcaag gttgagccg ttttatccg 
      gtcaatgcg attgagaaa ccgtcgggg aaaatcagt 
      gataagacc atacataac atgtcgtac caaccgtgg 
      gagcccacg gaacccatc gagacacca tgggctgat 
      aagcccaag taccagcca cccaagctg aggatggag 
      gataacaca gtgcacaaa atgagttat atgcctccg 
      gggcaatac gtggagtgt gatgacgat gatccggac 
      tgtgtcgaa tgtccggaa ccgccctgt gatccgcat 
      tgtaatccg aattacagg tgtgcgatg ccgtgctgt 
      tgtcccaag gcggcctgt tag
    mRNA sequence
    • >TC005548 RA
      ttgactttg aaaaattct gacatttct ctcccgtct 
      cccttttct tccctcctc ttcccgaaa atggactgc 
      aagccatgc ggcaaggcc acgacgtcc ccccggcag 
      ccccgctcg cccaccacg tgcccccct tgcccgtgc 
      tgcatcccg gtgttggcc gaagccatc cccaaagtg 
      caggtgacg ccctgtcca ccgcccccc gcccagccg 
      ccggccgac tgctgccac gtgtgcgtc ccggtggtg 
      acccccgcg cccccatgc gagccctgc cgcccgaaa 
      cgcaaatgc aagtacatc cagccggcg cggcccaag 
      tcctacgcc cccgagcgc aagtacctg cccccggcc 
      gcccccatg gacgacggc accatctac aggaagtcg 
      tacctccct gccgaggcg gaacgtccc ccgcagatc 
      cgccccgag aacaacctc tgcgtgggg gaggggaag 
      atgtcggat aatacggtg cacaacatg tcgtacctc 
      ccccataag gtgctgccc ccatgcccg atctacccc 
      tgcgagcat aggctgctg ggggagggg cccatgcag 
      gatatcacc acgcagaag cacgactat gtgcctaaa 
      ccgttctca aggccggag aagatcgta ccgccggtt 
      aatctcttt tctagtgat tgtcccctg agtgataag 
      actgtgaat aggttgtct tatatgccg gttgataag 
      cctagcaag gttgagccg ttttatccg gtcaatgcg 
      attgagaaa ccgtcgggg aaaatcagt gataagacc 
      atacataac atgtcgtac caaccgtgg gagcccacg 
      gaacccatc gagacacca tgggctgat aagcccaag 
      taccagcca cccaagctg aggatggag gataacaca 
      gtgcacaaa atgagttat atgcctccg gggcaatac 
      gtggagtgt gatgacgat gatccggac tgtgtcgaa 
      tgtccggaa ccgccctgt gatccgcat tgtaatccg 
      aattacagg tgtgcgatg ccgtgctgt tgtcccaag 
      gcggcctgt tagagtccc aaactgtcc caaattccc 
      gtgattggt cccttgata gtcccctat ttttatttt 
      tacactata cacttgtat acagtattt ttaagtcca 
      gtgtttgaa cgagcactt tgaaaatta aagtagacg 
      attttcaaa catcgtttt atttgattc ggatttgat 
      aagcgaaaa aataaaaaa acttccaaa aa
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY