Status
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Gene information
General information
TC000588 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_007417.3: 9360869..9368296
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
    TC000588
    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
    You may enter your name. The contact information can help us to clarify any questions. If you agree, we may show your name on this page to honor your contribution.
    Email
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    Publish name
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_03048

    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: < 20
    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
    • >TC000588 RA
      MIRIAILFL TVLSAFPDL LHGITTIHH DKPEESNIP 
      KMASKMTTN PETVERHKR LLPYMNYYI SNNQKFTPF 
      LESNALPGP FIPIKPTQK YLPEPEKTS SPNYALIYD 
      TLSQLKMRQ RYHQNLRYF EQPRIKTVI ETYTPSNID 
      IEADTRKYR PIPSDSHYK IYKPQVDYV LDRPLISYQ 
      PQPKPFFGD KIIYQKPQP QTETPIIYI ETTPKPPQV 
      NTIVDDKYV AQKFVPVQQ YYNVPTENT NILAKILKQ 
      LQNSNALPQ TLTTHNIDN SIKTLVKIL NGLRKQQGL 
      KTKPIVVVD ENSSEEEVE EEEKPTYAP GTITQTFPA 
      NTVNGGTPG RPGIDYPAL STIPQTSFN CKTQRYKGF 
      FGDPHTNCQ VWHYCDLNG GQASFLCPN GTIFSQVAL 
      TCDWWYNVK CSSTTQLYV LNERLYKYI LPLAPKFPE 
      DYSGPLVDR YLALKFQEM EEKMKNEKK KKEDKSEEK 
      DDSDQLQDI NNEKAKSEE S
    CDS sequence
    • >TC000588 RA
      atgatcaga attgctatt ttatttctg acagtgctt 
      tcagcattc cctgattta ctacacggc attacgacc 
      atacaccat gacaaaccc gaagagtca aatattccc 
      aaaatggct tcgaaaatg acaacaaat cccgaaact 
      gttgaacgt cacaaaaga ctcctacct tatatgaac 
      tactacatt agtaacaat caaaaattc acgccgttc 
      cttgaaagt aacgcttta cccggccct ttcatcccc 
      atcaaaccc acgcaaaaa tacctcccc gaacctgag 
      aaaacctca agccctaac tatgcccta atctacgat 
      accttaagc cagcttaaa atgagacaa aggtaccat 
      caaaatctc cgctacttt gagcaacca cgtattaaa 
      acagtcata gaaacgtac actccttca aacatagac 
      atcgaagcg gatacgaga aaatacaga ccgatacca 
      agtgactca cactacaag atttataaa ccacaagta 
      gactacgtg ctcgatcga ccgttaatt agttatcaa 
      ccacaacct aaacctttc ttcggcgat aaaataatc 
      taccaaaag ccacaacca caaactgaa acccctatc 
      atttacatc gaaaccacc ccaaaacca cctcaagtc 
      aatacaatc gtcgacgat aagtacgtc gctcaaaaa 
      ttcgtgcca gtgcaacaa tattacaac gtcccaact 
      gaaaacaca aacatactc gcaaaaatc ctcaaacaa 
      ttacaaaat tccaacgct ctacctcaa accctcaca 
      acgcataat atagacaac agcattaaa actctggtg 
      aagattttg aacggtttg aggaaacaa caaggtttg 
      aaaacgaaa cccattgtt gtcgtggac gagaacagt 
      tcagaggag gaagttgaa gaggaggaa aaacccact 
      tacgctcca ggaacgata acgcaaact tttcccgcc 
      aatactgtg aatggcggg actccggga cgtccgggg 
      attgattat ccggcgctt tcgaccata ccacagaca 
      agttttaat tgcaagacg cagagatat aaggggttc 
      tttggggac ccccacacc aactgccaa gtctggcac 
      tactgcgac ttaaacgga ggtcaagcc tcatttttg 
      tgtcccaac ggaacgatt ttcagtcaa gtcgctctc 
      acttgtgac tggtggtat aacgtaaaa tgttcatca 
      acgacacaa ctttacgtt ttaaacgaa agactttac 
      aaatatatt ttgccacta gcaccgaaa tttccggag 
      gattatagt ggacctctt gtggacagg taccttgca 
      cttaagttc caggaaatg gaagagaag atgaaaaat 
      gagaagaag aaaaaagag gataagagt gaagaaaaa 
      gacgattct gaccagttg caagatatt aacaatgaa 
      aaggccaaa tctgaggaa agctag
    mRNA sequence
    • >TC000588 RA
      attcaccac cacacgggg cgaaccact ttcaagaca 
      taatattcg tctttgaga ccgtcgccg gtgcttgat 
      gcagctatg cacttgtga gagtgacat ggtgccagt 
      gctagtgct acaatttcc caaaaatta ttttctgga 
      tgattgaaa aatgatcag aattgctat tttatttct 
      gacagtgct ttcagcatt ccctgattt actacacgg 
      cattacgac catacacca tgacaaacc cgaagagtc 
      aaatattcc caaaatggc ttcgaaaat gacaacaaa 
      tcccgaaac tgttgaacg tcacaaaag actcctacc 
      ttatatgaa ctactacat tagtaacaa tcaaaaatt 
      cacgccgtt ccttgaaag taacgcttt acccggccc 
      tttcatccc catcaaacc cacgcaaaa atacctccc 
      cgaacctga gaaaacctc aagccctaa ctatgccct 
      aatctacga taccttaag ccagcttaa aatgagaca 
      aaggtacca tcaaaatct ccgctactt tgagcaacc 
      acgtattaa aacagtcat agaaacgta cactccttc 
      aaacataga catcgaagc ggatacgag aaaatacag 
      accgatacc aagtgactc acactacaa gatttataa 
      accacaagt agactacgt gctcgatcg accgttaat 
      tagttatca accacaacc taaaccttt cttcggcga 
      taaaataat ctaccaaaa gccacaacc acaaactga 
      aacccctat catttacat cgaaaccac cccaaaacc 
      acctcaagt caatacaat cgtcgacga taagtacgt 
      cgctcaaaa attcgtgcc agtgcaaca atattacaa 
      cgtcccaac tgaaaacac aaacatact cgcaaaaat 
      cctcaaaca attacaaaa ttccaacgc tctacctca 
      aaccctcac aacgcataa tatagacaa cagcattaa 
      aactctggt gaagatttt gaacggttt gaggaaaca 
      acaaggttt gaaaacgaa acccattgt tgtcgtgga 
      cgagaacag ttcagagga ggaagttga agaggagga 
      aaaacccac ttacgctcc aggaacgat aacgcaaac 
      ttttcccgc caatactgt gaatggcgg gactccggg 
      acgtccggg gattgatta tccggcgct ttcgaccat 
      accacagac aagttttaa ttgcaagac gcagagata 
      taaggggtt ctttgggga cccccacac caactgcca 
      agtctggca ctactgcga cttaaacgg aggtcaagc 
      ctcattttt gtgtcccaa cggaacgat tttcagtca 
      agtcgctct cacttgtga ctggtggta taacgtaaa 
      atgttcatc aacgacaca actttacgt tttaaacga 
      aagacttta caaatatat tttgccact agcaccgaa 
      atttccgga ggattatag tggacctct tgtggacag 
      gtaccttgc acttaagtt ccaggaaat ggaagagaa 
      gatgaaaaa tgagaagaa gaaaaaaga ggataagag 
      tgaagaaaa agacgattc tgaccagtt gcaagatat 
      taacaatga aaaggccaa atctgagga aagctagac 
      tgggataat ttgttttat tttttatat tgccatagt 
      tagattaat ttattgtta agaggttgt tgattgttt 
      t
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