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Gene information
General information
TC005904 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: 5785509..5789305
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
    TC005904
    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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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_04033

    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: 0.0% (includes death as pupa, adult)

    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 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: 10.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 10.0% (includes death as larva, prepupa, pupa, adult)

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


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC005904 RA
      MKGPTITTC LYLIYLIVG QASEKISYT GDQLWKITN 
      GNNSTLNLL KTLEQDNYV SIWGHNSTY IDALVHSSA 
      LNKVRDKLQ EHGQEFKVS IEDVQKAID EENPKPANL 
      DGRKGFRLT WNYYHSLAD IYDYLYYLQ QTFPKLCSV 
      HNIGQSVER RPIKLFLIS NGKKANKAI FIEGGINAQ 
      EWISPAVIT YVINQFVSN YQNETLSVQ NIDWYIVPV 
      LNPDGYEYS YNVDRLWKK NRSKNKKCV GVDLSRNWG 
      YNWGKNGSS SDPCSNSYR GRRPFSEPE TAIVANLFI 
      THPEIDWIG YISVRAYGQ YIVYPWGCP NGVLEDHEE 
      LFRVAKEAA VKMVSAGGE SYTVGPAGI ITDSSSGIS 
      IGWAKDAQA IKYAYIMKL RDTGRYGYF LPARFIKPT 
      SEEAVTFLR TIAGIIKS
    CDS sequence
    • >TC005904 RA
      atgaagggt ccaactatc acgacttgt ctttacctt 
      atttatttg atcgttgga caagcgtct gaaaaaatc 
      agttatacc ggcgaccaa ctatggaaa ataaccaac 
      ggtaacaac tcgactcta aatttacta aaaacttta 
      gaacaagat aactatgtc tcaatatgg gggcacaat 
      tctacgtat attgacgca ttggttcac tcatcggct 
      ttaaataaa gtgagagac aagcttcag gagcacgga 
      caagagttt aaggtttca attgaagac gtacagaaa 
      gccatagat gaggaaaac cccaaacct gcaaacctt 
      gacggtcgc aagggattt cgtttgact tggaattac 
      tatcatagt ttggccgac atctacgat tacctctac 
      tatttgcaa caaactttt ccgaaactg tgctcagtt 
      cacaatatc ggacagtca gtcgagcgc cgaccgatc 
      aaacttttc ctaatttct aacggaaag aaagcaaat 
      aaagcgatt ttcatcgag ggaggaatt aacgcccag 
      gaatggata tcaccagcc gtaatcaca tacgtaatc 
      aatcaattc gtttcgaat tatcaaaat gaaacactt 
      tcggtgcaa aacatagac tggtatatc gtaccagtg 
      ttgaaccct gatggttat gaatattcg tacaatgtg 
      gacagattg tggaagaaa aatcgatca aaaaacaag 
      aaatgtgtc ggagttgat cttagtcga aattggggt 
      tataactgg ggtaaaaac gggtcatcg agtgacccg 
      tgtagtaat tcatacaga ggaagaaga ccgttttct 
      gaacccgaa acggcaatt gttgctaat ttgtttatt 
      actcatccg gaaattgac tggattggg tatatttca 
      gttcgtgct tatggacag tacattgtt tatccttgg 
      gggtgcccg aatggggta ctcgaagac cacgaggag 
      ttgtttaga gtggcaaaa gaagcggct gtgaaaatg 
      gtaagcgct ggtggcgaa agctacaca gtaggtcct 
      gcaggaatt atcaccgat agctcatcc ggaatatcc 
      ataggctgg gctaaagat gctcaagcc ataaaatac 
      gcatacatc atgaaactg agagacacc ggacgttac 
      ggctatttc ctaccagca agatttatc aaaccaaca 
      agcgaagaa gctgttacc ttcctcaga actatcgca 
      ggaataatc aaatcttaa
    mRNA sequence
    • >TC005904 RA
      aatctaaac gttttaaaa caagaaata tcttgttta 
      caaaatttt gcttacatt tccttccac ttcccgcag 
      atttataat cttgattga gaccaacgg taccttccc 
      ataaccagg tcaacagtt tctataaaa tcaagaaac 
      atataaact aaagacatt aaaatgaag ggtccaact 
      atcacgact tgtctttac cttatttat ttgatcgtt 
      ggacaagcg tctgaaaaa atcagttat accggcgac 
      caactatgg aaaataacc aacggtaac aactcgact 
      ctaaattta ctaaaaact ttagaacaa gataactat 
      gtctcaata tgggggcac aattctacg tatattgac 
      gcattggtt cactcatcg gctttaaat aaagtgaga 
      gacaagctt caggagcac ggacaagag tttaaggtt 
      tcaattgaa gacgtacag aaagccata gatgaggaa 
      aaccccaaa cctgcaaac cttgacggt cgcaaggga 
      tttcgtttg acttggaat tactatcat agtttggcc 
      gacatctac gattacctc tactatttg caacaaact 
      tttccgaaa ctgtgctca gttcacaat atcggacag 
      tcagtcgag cgccgaccg atcaaactt ttcctaatt 
      tctaacgga aagaaagca aataaagcg attttcatc 
      gagggagga attaacgcc caggaatgg atatcacca 
      gccgtaatc acatacgta atcaatcaa ttcgtttcg 
      aattatcaa aatgaaaca ctttcggtg caaaacata 
      gactggtat atcgtacca gtgttgaac cctgatggt 
      tatgaatat tcgtacaat gtggacaga ttgtggaag 
      aaaaatcga tcaaaaaac aagaaatgt gtcggagtt 
      gatcttagt cgaaattgg ggttataac tggggtaaa 
      aacgggtca tcgagtgac ccgtgtagt aattcatac 
      agaggaaga agaccgttt tctgaaccc gaaacggca 
      attgttgct aatttgttt attactcat ccggaaatt 
      gactggatt gggtatatt tcagttcgt gcttatgga 
      cagtacatt gtttatcct tgggggtgc ccgaatggg 
      gtactcgaa gaccacgag gagttgttt agagtggca 
      aaagaagcg gctgtgaaa atggtaagc gctggtggc 
      gaaagctac acagtaggt cctgcagga attatcacc 
      gatagctca tccggaata tccataggc tgggctaaa 
      gatgctcaa gccataaaa tacgcatac atcatgaaa 
      ctgagagac accggacgt tacggctat ttcctacca 
      gcaagattt atcaaacca acaagcgaa gaagctgtt 
      accttcctc agaactatc gcaggaata atcaaatct 
      taaaattgt ttgtaattt aataataaa gtagtattc 
      aggaa
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY