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Gene information
General information
TC001339 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: 14775315..14776737
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
    TC001339
    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_00241

    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: 50.0% (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


    adult lethality - Number of animals showing the phenotype: 2 (9 dpi)
    Days post injection


    adult lethality - Number of animals showing the phenotype: 1 (11 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: 30.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 30.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality early (L5/6) - Number of animals showing the phenotype: 3 (11 dpi)
    Days post injection


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC001339 RA
      MKLVLFLLA IFAVALPAK IPDFAPTSS DTLVLLHVL 
      FRHGNRTPD KFSQFPTDP HINDTFEPF GYSQLTTKG 
      KKTEFGIGQ YIRQTYGDF IPEQYGPGV AYAISTDFK 
      RTKMSLELV LAGLFPPLE SDVFSPGLN WQPVPYEID 
      DGIDLIRVP AMYCTTYLQ QYYRYILSK EAQEVLKNY 
      QGLYQQVSN FTGKDIALP EEIFDIYET LESEKDFGL 
      ELPAWTLDI FPEVLEKAS SVYIEFATA TTGLKRLST 
      GRLLKKIID DSLAKRDGT LSEDRKIFL YSAHDYSVG 
      VMLRALEVF YSHVPPYGA TIFFEIHNI DGTYGLKLF 
      YQDYSQETP RLLTIPGCS SFCDLDKVV ELMSENFPT 
      EADVCNYSG ELL
    CDS sequence
    • >TC001339 RA
      atgaagttg gtattgttt ctacttgcg atttttgcg 
      gtcgcctta cctgcaaaa attccagac tttgctcct 
      acaagttca gacactttg gttctccta catgtgcta 
      ttcagacat gggaaccga acgcctgat aaattcagc 
      cagtttcca actgatccc cacattaac gacactttt 
      gaaccattt ggttacagt caattgacc accaaagga 
      aagaaaacc gagtttgga atcgggcaa tacattcga 
      caaacatac ggtgatttt atccccgaa cagtatgga 
      ccgggcgtt gcttacgca atttccacc gactttaaa 
      aggactaaa atgtcgctt gaattagtc ctggcggga 
      ctgtttccg ccacttgag tcggacgtc ttctcccct 
      ggtttaaac tggcagcca gtgccttac gaaattgac 
      gacggaatt gacctaata cgagttccc gccatgtac 
      tgtacgacc tacctccag cagtattac agatacatt 
      ttgtcaaaa gaagcccaa gaagtgttg aaaaattat 
      caaggtctt taccagcaa gtatcaaat ttcacggga 
      aaagatatt gccttacct gaagaaatt ttcgatatt 
      tacgaaaca ctcgaaagt gaaaaagat tttggactc 
      gagctgcct gcatggact ttggatatt tttccagaa 
      gttttggaa aaggcgtct tcagtttat atcgaattt 
      gccaccgcg acaactggc ttaaaacga ttgtccaca 
      gggcgttta cttaaaaaa ataattgac gacagtttg 
      gccaaacga gatgggact ttatcagaa gatcgcaag 
      attttcttg tactcggca catgattac agtgttgga 
      gtaatgtta agagccttg gaggtgttc tactcacac 
      gtaccaccc tatggagct acgattttc ttcgaaatt 
      cacaacatt gatgggact tatggctta aagctattc 
      taccaggat tatagccag gaaacaccc agactgctt 
      actatacct ggctgttca agtttttgc gatcttgac 
      aaagtggta gagctgatg tctgagaat tttccgact 
      gaagccgac gtctgcaat tactcggga gagcttctg 
      taa
    mRNA sequence
    • >TC001339 RA
      ttagtcagc caaaaccat gaagttggt attgtttct 
      acttgcgat ttttgcggt cgccttacc tgcaaaaat 
      tccagactt tgctcctac aagttcaga cactttggt 
      tctcctaca tgtgctatt cagacatgg gaaccgaac 
      gcctgataa attcagcca gtttccaac tgatcccca 
      cattaacga cacttttga accatttgg ttacagtca 
      attgaccac caaaggaaa gaaaaccga gtttggaat 
      cgggcaata cattcgaca aacatacgg tgattttat 
      ccccgaaca gtatggacc gggcgttgc ttacgcaat 
      ttccaccga ctttaaaag gactaaaat gtcgcttga 
      attagtcct ggcgggact gtttccgcc acttgagtc 
      ggacgtctt ctcccctgg tttaaactg gcagccagt 
      gccttacga aattgacga cggaattga cctaatacg 
      agttcccgc catgtactg tacgaccta cctccagca 
      gtattacag atacatttt gtcaaaaga agcccaaga 
      agtgttgaa aaattatca aggtcttta ccagcaagt 
      atcaaattt cacgggaaa agatattgc cttacctga 
      agaaatttt cgatattta cgaaacact cgaaagtga 
      aaaagattt tggactcga gctgcctgc atggacttt 
      ggatatttt tccagaagt tttggaaaa ggcgtcttc 
      agtttatat cgaatttgc caccgcgac aactggctt 
      aaaacgatt gtccacagg gcgtttact taaaaaaat 
      aattgacga cagtttggc caaacgaga tgggacttt 
      atcagaaga tcgcaagat tttcttgta ctcggcaca 
      tgattacag tgttggagt aatgttaag agccttgga 
      ggtgttcta ctcacacgt accacccta tggagctac 
      gattttctt cgaaattca caacattga tgggactta 
      tggcttaaa gctattcta ccaggatta tagccagga 
      aacacccag actgcttac tatacctgg ctgttcaag 
      tttttgcga tcttgacaa agtggtaga gctgatgtc 
      tgagaattt tccgactga agccgacgt ctgcaatta 
      ctcgggaga gcttctgta aataaaaac cgcaatggg 
      ctcacactt aatacaata aaaatattt aaaaaaa
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY