Status
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Gene information
General information
TC000380 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: 12244784..12246687
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
    TC000380
    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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    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_09675

    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: 30.0% (includes death as pupa, adult)

    adult lethality - Number of animals showing the phenotype: 3 (9 dpi)
    Days post injection


    adult nutritional state bad (cachectic) - Number of animals showing the phenotype: 4 (11 dpi)
    Days post injection


    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
    • >TC000380 RA
      MDVEVRLVD NSKGKGLFS KKCFKSGAI IFEEEPLVS 
      CQFSWNAAY QYKACDHCL RPLETAEEN ARRLTGKPE 
      LELPFPECC TTDKSKFTS CTLCGTDYC SVECQTTAY 
      NQYHRILCL QTTERNNFH PLEQLNEAW KHVHYPPET 
      NTIMLIVRL LARIIQSPN RDLAIEQTL QFCHRTVNE 
      DAELAHKLL GEKFANQLS LLHSLLLQC VPHEGIEQF 
      LTPAGFQGL LALIGTNGQ GVGTSTISQ WVTRTSDLA 
      ISDDERAVL DKFIDKLYE DMDSHSGNF LNNEGVALF 
      TLQSACNHS CVPNAEPTY LHNNNKLSL VAVRDIQEG 
      EEICISYLD ECNLHRSRH SRRKELMEN YLFACNCPK 
      CEEQADEPD VTSEEEEGE EEMSE
    CDS sequence
    • >TC000380 RA
      atggacgtg gaagttcgc cttgtggac aattccaaa 
      ggtaaaggc ctattttcg aaaaagtgc ttcaaaagc 
      ggtgcaata atattcgaa gaggagccc ttggtgtcg 
      tgccagttc tcctggaat gccgcttac cagtacaaa 
      gcatgcgac cattgtctg aggccttta gagaccgct 
      gaagagaac gcacgccgc ctcaccggc aagcccgag 
      ctcgagtta cccttcccc gaatgttgc accaccgat 
      aaaagtaaa tttacttca tgcaccctt tgcgggact 
      gattattgt tccgtggag tgccaaaca acggcgtac 
      aaccaatac caccgcatt ctctgctta cagacaacc 
      gaacgcaac aatttccac cctctcgag caactcaac 
      gaggcgtgg aaacatgtg cattatccg cctgaaacc 
      aacactata atgctgatt gtgcgtctt ctggcgcga 
      ataatccag tcgccaaac cgcgacttg gccattgag 
      caaaccctc cagttctgc caccggacg gttaacgag 
      gacgcggag ctggcccat aaattactg ggcgaaaaa 
      ttcgcgaat cagttatca cttttacac agtttgctc 
      cttcagtgt gttcctcac gaggggatt gagcagttt 
      ctgactccg gcggggttc caggggctg cttgcgctc 
      atcgggacg aatggtcag ggcgtgggc acgagtacc 
      ataagtcag tgggtcact cgcacctcc gacttggcc 
      atttccgac gacgagaga gcggttctt gataaattt 
      atcgacaag ttgtacgag gatatggac tcacattcg 
      ggcaatttt ttaaataat gagggagtc gccttgttt 
      acgctgcaa agcgcctgc aaccacagt tgtgtcccg 
      aacgccgaa cccacttac cttcacaac aataacaag 
      ttgtctttg gtggctgtt agggacatt caggaaggg 
      gaggaaatt tgtatcagt tatttagac gagtgtaac 
      ttgcataga tcgaggcat tcgagacgg aaagaactg 
      atggagaat tatctcttt gcgtgtaat tgccccaag 
      tgtgaggag caagccgac gaaccggac gtcactagc 
      gaggaggag gaaggagag gaagaaatg agcgaataa
    mRNA sequence
    • >TC000380 RA
      gacgtgggt caggattcg gatactgct taaactgta 
      gaaactttc gctccagga gagtgtctt taagagtac 
      gtggggtac aacattgca aatacccat ctttggcca 
      gttgctggg ccaattcga tttggtggt tgtccatca 
      aatcctcat ttatcacaa ctatcaaag gcttgtgtt 
      gctttaaga cctcaagac acgtccctg cacccgcat 
      gacttataa ttaaatccg aactttcaa tttcttgag 
      caaagttct caaaatagc ggtcgtatt tgatatgaa 
      tttttgggt gttttctct cattagaat cgcctgtcc 
      ccacttgaa actgcacga aagtgtacc ctaacgaat 
      gcagaacct ccagtacct catccttgg acacctcct 
      caatgagct tatcaaatt tcgtggtcc caacggtta 
      caaacactt tttttgcac ccattgcca caattagcc 
      gcaattatt cattatcat tttttacca gaggcaaaa 
      caaatcaat tacataacc ccacatttc acaaacaca 
      catgtttgc cggaaggaa ttaactcgc aatggacgt 
      ggaagttcg ccttgtgga caattccaa aggtaaagg 
      cctattttc gaaaaagtg cttcaaaag cggtgcaat 
      aatattcga agaggagcc cttggtgtc gtgccagtt 
      ctcctggaa tgccgctta ccagtacaa agcatgcga 
      ccattgtct gaggccttt agagaccgc tgaagagaa 
      cgcacgccg cctcaccgg caagcccga gctcgagtt 
      acccttccc cgaatgttg caccaccga taaaagtaa 
      atttacttc atgcaccct ttgcgggac tgattattg 
      ttccgtgga gtgccaaac aacggcgta caaccaata 
      ccaccgcat tctctgctt acagacaac cgaacgcaa 
      caatttcca ccctctcga gcaactcaa cgaggcgtg 
      gaaacatgt gcattatcc gcctgaaac caacactat 
      aatgctgat tgtgcgtct tctggcgcg aataatcca 
      gtcgccaaa ccgcgactt ggccattga gcaaaccct 
      ccagttctg ccaccggac ggttaacga ggacgcgga 
      gctggccca taaattact gggcgaaaa attcgcgaa 
      tcagttatc acttttaca cagtttgct ccttcagtg 
      tgttcctca cgaggggat tgagcagtt tctgactcc 
      ggcggggtt ccaggggct gcttgcgct catcgggac 
      gaatggtca gggcgtggg cacgagtac cataagtca 
      gtgggtcac tcgcacctc cgacttggc catttccga 
      cgacgagag agcggttct tgataaatt tatcgacaa 
      gttgtacga ggatatgga ctcacattc gggcaattt 
      tttaaataa tgagggagt cgccttgtt tacgctgca 
      aagcgcctg caaccacag ttgtgtccc gaacgccga 
      acccactta ccttcacaa caataacaa gttgtcttt 
      ggtggctgt tagggacat tcaggaagg ggaggaaat 
      ttgtatcag ttatttaga cgagtgtaa cttgcatag 
      atcgaggca ttcgagacg gaaagaact gatggagaa 
      ttatctctt tgcgtgtaa ttgccccaa gtgtgagga 
      gcaagccga cgaaccgga cgtcactag cgaggagga 
      ggaaggaga ggaagaaat gagcgaata aagttatgg 
      aaataaatt tattaagac gca
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY