Status
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Gene information
General information
TC003998 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_007418.3: 28917148..28921285
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
    TC003998
    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_03667

    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: 4 (3 dpi)
    Days post injection


    adult lethality - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection


    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg with embryonic tissue, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): more than 80%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - 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 total percentage of affected eggs/embryos/larvae on slide - 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: 30.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 80.0% (includes death as larva, prepupa, pupa, adult)

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


    eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 5 (16 dpi)
    Days post injection


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC003998 RA
      MELDYQMAL ILQHRFEQE AGQTEQSDS ELAKQLQEQ 
      FEQEAAVEQ PPSSLVYHQ PKKGSDSTK SLIDPSWEL 
      VDPTPDIHN LFIAFDQRF FWNKLVAVC VSWSKKMTS 
      CAGICSYSG RGGLCSITL SEPLLKLRP RKDLVETLL 
      HEMIHAYLF VTHNNRDRD GHGPEFHKH MYRINNEAG 
      TSITVYHNF HDEVRLYQQ HWWRCDGPC QHRKPFFGM 
      VRRATNRAP GPNDRWWAE HLRTCGGTF IKVKEPEKK 
      KQEKKNETK SVKSKDIRD FMGGNVKGF KDLKNGVVR 
      GKSNSSSTI VVTKNTKTS ETTFKPTIF NASTSTILK 
      TETNSFRAS TSTKPSDDY VAVRNHWAN KFNNANKRQ 
      SSEESSTVS KIPKLFGSS PTSTQKNPN SGEFCECPV 
      CNQRVLMAD LNQHLDQCL LKSPEERDA ESVDLTDSF 
      HEEEDTKEC PLCTKEIVT SKFDTHVEK CLMEVYNGV 
      EEKLAVPKA QEETVSCLA CGKKIVKSE LNSHLDECM 
      VDIFDDEES KDKEVCDKN NSQFNCPFC LKLVEESEM 
      KEHIDGCLM ADNLAEAFA DDDF
    CDS sequence
    • >TC003998 RA
      atggagctg gactaccaa atggcgctc attttgcag 
      cacaggttt gaacaagaa gctgggcaa accgaacag 
      tctgattct gagttggcc aaacaattg caagaacag 
      ttcgaacag gaggctgca gttgaacag cccccttct 
      agtcttgtc tatcaccag cctaaaaag gggtccgac 
      tcgaccaaa tcactcata gacccctca tgggagctc 
      gtggacccc acccccgac atacacaac ctgttcata 
      gcttttgac caacgtttt ttttggaat aaattggtg 
      gcggtttgt gtctcttgg agcaagaaa atgacttcg 
      tgtgctggc atttgctcg tatagtggc agagggggg 
      ctttgtagt atcaccttg agtgaaccg ttacttaaa 
      ttaaggccc aggaaagac ttagttgag actcttctt 
      catgaaatg attcacgct tatttattt gtaacccat 
      aataataga gacagggat gggcacggg cccgagttt 
      cataaacac atgtaccgg atcaataac gaggcaggg 
      actagtatt accgtttac cataacttc catgatgaa 
      gttcgttta tatcagcaa cactggtgg cgctgtgac 
      ggaccttgt cagcaccgg aagcccttt tttggcatg 
      gtcagaagg gccacaaat agggctccg gggcccaat 
      gataggtgg tgggcagag catttaagg acttgcggt 
      ggaaccttt attaaagtc aaagaaccg gaaaagaag 
      aaacaggag aagaagaat gaaacgaaa agtgtgaag 
      agtaaagat attagagat tttatgggt ggtaatgtt 
      aaaggtttc aaagacttg aaaaatggc gttgttagg 
      ggaaaaagc aactcatca agcactata gtagtcact 
      aaaaacact aaaactagt gaaactact ttcaaaccg 
      acgattttt aatgccagt actagtact attttgaag 
      actgaaaca aatagcttt cgtgctagt actagtact 
      aaaccgagt gatgattat gtagctgtt cgaaatcat 
      tgggccaac aaattcaat aatgccaat aaaagacaa 
      tcatccgaa gaatcatca actgtttcc aaaattccg 
      aaattgttt gggtcttcg cctactagc acccaaaaa 
      aatcccaat tctggtgaa ttttgtgaa tgtcctgtt 
      tgtaatcaa agggtgctg atggctgat ttgaaccaa 
      catctcgat cagtgtttg cttaaatca ccggaagaa 
      agagatgca gaaagtgtt gatcttact gattctttc 
      catgaggag gaagataca aaagaatgt ccactttgt 
      accaaagaa attgtaact tccaaattt gacactcat 
      gttgaaaag tgcctaatg gaggtttat aacggagtt 
      gaggaaaag ttggctgtt ccaaaagcc caagaagaa 
      acggtttcg tgtttggct tgtggtaaa aaaatcgta 
      aaaagtgaa cttaattcg catttggat gagtgtatg 
      gttgatatt ttcgatgat gaggaaagt aaagataag 
      gaagtttgt gataagaat aattcgcag tttaattgt 
      ccattttgt ttgaaactg gtggaagag agcgaaatg 
      aaggaacat attgatggg tgtttgatg gctgataat 
      ctcgccgag gcttttgca gatgatgat ttttga
    mRNA sequence
    • >TC003998 RA
      attttacag ctaaaacgc ctcaagaca acgatcagg 
      ggccgtttt tgaggttag gatggagct ggactacca 
      aatggcgct cattttgca gcacaggtt tgaacaaga 
      agctgggca aaccgaaca gtctgattc tgagttggc 
      caaacaatt gcaagaaca gttcgaaca ggaggctgc 
      agttgaaca gcccccttc tagtcttgt ctatcacca 
      gcctaaaaa ggggtccga ctcgaccaa atcactcat 
      agacccctc atgggagct cgtggaccc cacccccga 
      catacacaa cctgttcat agcttttga ccaacgttt 
      tttttggaa taaattggt ggcggtttg tgtctcttg 
      gagcaagaa aatgacttc gtgtgctgg catttgctc 
      gtatagtgg cagaggggg gctttgtag tatcacctt 
      gagtgaacc gttacttaa attaaggcc caggaaaga 
      cttagttga gactcttct tcatgaaat gattcacgc 
      ttatttatt tgtaaccca taataatag agacaggga 
      tgggcacgg gcccgagtt tcataaaca catgtaccg 
      gatcaataa cgaggcagg gactagtat taccgttta 
      ccataactt ccatgatga agttcgttt atatcagca 
      acactggtg gcgctgtga cggaccttg tcagcaccg 
      gaagccctt ttttggcat ggtcagaag ggccacaaa 
      tagggctcc ggggcccaa tgataggtg gtgggcaga 
      gcatttaag gacttgcgg tggaacctt tattaaagt 
      caaagaacc ggaaaagaa gaaacagga gaagaagaa 
      tgaaacgaa aagtgtgaa gagtaaaga tattagaga 
      ttttatggg tggtaatgt taaaggttt caaagactt 
      gaaaaatgg cgttgttag gggaaaaag caactcatc 
      aagcactat agtagtcac taaaaacac taaaactag 
      tgaaactac tttcaaacc gacgatttt taatgccag 
      tactagtac tattttgaa gactgaaac aaatagctt 
      tcgtgctag tactagtac taaaccgag tgatgatta 
      tgtagctgt tcgaaatca ttgggccaa caaattcaa 
      taatgccaa taaaagaca atcatccga agaatcatc 
      aactgtttc caaaattcc gaaattgtt tgggtcttc 
      gcctactag cacccaaaa aaatcccaa ttctggtga 
      attttgtga atgtcctgt ttgtaatca aagggtgct 
      gatggctga tttgaacca acatctcga tcagtgttt 
      gcttaaatc accggaaga aagagatgc agaaagtgt 
      tgatcttac tgattcttt ccatgagga ggaagatac 
      aaaagaatg tccactttg taccaaaga aattgtaac 
      ttccaaatt tgacactca tgttgaaaa gtgcctaat 
      ggaggttta taacggagt tgaggaaaa gttggctgt 
      tccaaaagc ccaagaaga aacggtttc gtgtttggc 
      ttgtggtaa aaaaatcgt aaaaagtga acttaattc 
      gcatttgga tgagtgtat ggttgatat tttcgatga 
      tgaggaaag taaagataa ggaagtttg tgataagaa 
      taattcgca gtttaattg tccattttg tttgaaact 
      ggtggaaga gagcgaaat gaaggaaca tattgatgg 
      gtgtttgat ggctgataa tctcgccga ggcttttgc 
      agatgatga tttttgatt gttaattat ttttgtttt 
      tttttatgc caaatatac atacttttt ctaa
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY