Status
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Gene information
General information
TC005488 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: 12169177..12173329
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
    TC005488
    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_03963

    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: 10.0% (includes death as pupa, adult)

    adult lethality - Number of animals showing the phenotype: 1 (9 dpi)
    Days post injection


    Adult morphology
    abdominal odoriferous glands content darker - Number of animals showing the phenotype: 6 (13 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, but muscle fluorescence - Penetrance (percentage of animals/eggs on slide): less than 30%

    embryo/egg with embryonic tissue potentially present, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 50
    embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    cuticle remnants with unidentifyable segments - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    cuticle remnants with some identifiable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae - 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: % (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
    • >TC005488 RA
      MSGLQQNSS GATSRSSDL EAKCCVALQ RWVFCLLAF 
      LAVFISATM YSLPSLVEE TKTIRVKNI NSSDYCASK 
      INYTRTVVV INDTTLYAI HWGYLVSSL PAAVVSDQF 
      GGKYVVTLS LLFSSFWCL INPAMAALS KRRPGWMAG 
      TRFFRGFFK GFAFPAIMS LLARWAPDT ERTTMTALV 
      YGSYLLAYL LTREIRKMI TNEGCYLVF GSLGVIYSL 
      LWHLFLYPS PDEHPSIMG SELKYLDEN TEDKPIEGR 
      KKIPWLQML TSRPVLALW FFEIGQSWT WVSFIHAYD 
      VYLPQVLKL TDSDNNVLM TPLYLSFGL AVIFGFISD 
      WFIKGKHLS VTTMRKIAA SLGNTGAAC SYMFAIFRR 
      CSTNAVMIH FALGMCFEA FISSSSRVN HLDLASNFV 
      GTLLGISQT LAQILLYVG LSQLPVLLK PESSLTQWA 
      ALFWFTLGL NVVSTTIYL VFGSGVRQE WNFVQ
    CDS sequence
    • >TC005488 RA
      atgtcaggt ttacagcaa aacagttcc ggagcaaca 
      tctcgcagt tccgacctc gaagcaaaa tgctgcgtc 
      gccctgcag cgctgggtg ttttgcctc ctcgccttt 
      ttggccgtc ttcatctcc gcaaccatg tactccctg 
      ccttctctg gtcgaagag acgaaaacc atacgagtg 
      aagaacata aacagttcc gattattgc gcctcaaaa 
      atcaactac actcggacc gttgtcgta ataaacgac 
      accacgctc tacgccata cactggggc tatttggtg 
      tcaagtctg ccagcagcg gtcgtctct gaccaattc 
      ggcggcaaa tacgtggtg actttaagc ctgcttttt 
      tcctcgttc tggtgcttg atcaacccg gccatggca 
      gctttgagc aaaagaagg ccgggctgg atggccggc 
      actaggttt ttccggggg tttttcaaa gggtttgct 
      ttcccggca attatgtcc ctcctggcc cgatgggcg 
      cctgatacg gagagaaca accatgacg gccctagtt 
      tacggtagt tatctgctg gcctatctc ctgacaaga 
      gaaatccgg aaaatgata acaaatgaa ggatgctac 
      ttggtgttt ggttctttg ggggttatt tatagccta 
      ctttggcac ctgtttttg tacccaagt ccggacgaa 
      cacccatcc attatgggc agtgagctc aaatatctg 
      gacgaaaat accgaagat aagcccatc gaagggcgt 
      aaaaaaatc ccatggcta caaatgttg acatcacgg 
      cctgtgtta gctctttgg ttctttgaa attggacag 
      tcctggact tgggtcagc ttcatacac gcgtacgat 
      gtctatttg ccgcaagtt ttgaaactc acagacagc 
      gataataat gtactgatg actccgttg tatttatcg 
      tttggttta gcggtcatt ttcggtttt atttccgac 
      tggtttatc aaagggaag catctcagt gtgaccacg 
      atgcggaaa atcgcagcg tctcttgga aataccgga 
      gctgcttgc agttacatg tttgcgatt ttccgccgc 
      tgcagcaca aatgctgta atgatccat tttgcactt 
      ggcatgtgt tttgaagca tttatctct tcgtcgagt 
      cgtgtcaat catttggac ttggcgtcc aatttcgtg 
      ggaactttg ctgggaatt tcgcaaact cttgctcag 
      attttgtta tatgtgggt ctttcacag cttccagtt 
      ttactaaaa cctgaaagc agtttgaca caatgggcg 
      gctctgttc tggttcact ctggggctc aatgttgtt 
      tcaacgacg atttacctg gtctttgga agcggcgtc 
      agacaagaa tggaatttc gttcaataa
    mRNA sequence
    • >TC005488 RA
      atgaaaaaa aaaattgat ttgtgcttg accttttgg 
      tgtcaaaca gtcaaattt tgacactcc aatgtcagg 
      tttacagca aaacagttc cggagcaac atctcgcag 
      ttccgacct cgaagcaaa atgctgcgt cgccctgca 
      gcgctgggt gttttgcct cctcgcctt tttggccgt 
      cttcatctc cgcaaccat gtactccct gccttctct 
      ggtcgaaga gacgaaaac catacgagt gaagaacat 
      aaacagttc cgattattg cgcctcaaa aatcaacta 
      cactcggac cgttgtcgt aataaacga caccacgct 
      ctacgccat acactgggg ctatttggt gtcaagtct 
      gccagcagc ggtcgtctc tgaccaatt cggcggcaa 
      atacgtggt gactttaag cctgctttt ttcctcgtt 
      ctggtgctt gatcaaccc ggccatggc agctttgag 
      caaaagaag gccgggctg gatggccgg cactaggtt 
      tttccgggg gtttttcaa agggtttgc tttcccggc 
      aattatgtc cctcctggc ccgatgggc gcctgatac 
      ggagagaac aaccatgac ggccctagt ttacggtag 
      ttatctgct ggcctatct cctgacaag agaaatccg 
      gaaaatgat aacaaatga aggatgcta cttggtgtt 
      tggttcttt gggggttat ttatagcct actttggca 
      cctgttttt gtacccaag tccggacga acacccatc 
      cattatggg cagtgagct caaatatct ggacgaaaa 
      taccgaaga taagcccat cgaagggcg taaaaaaat 
      cccatggct acaaatgtt gacatcacg gcctgtgtt 
      agctctttg gttctttga aattggaca gtcctggac 
      ttgggtcag cttcataca cgcgtacga tgtctattt 
      gccgcaagt tttgaaact cacagacag cgataataa 
      tgtactgat gactccgtt gtatttatc gtttggttt 
      agcggtcat tttcggttt tatttccga ctggtttat 
      caaagggaa gcatctcag tgtgaccac gatgcggaa 
      aatcgcagc gtctcttgg aaataccgg agctgcttg 
      cagttacat gtttgcgat tttccgccg ctgcagcac 
      aaatgctgt aatgatcca ttttgcact tggcatgtg 
      ttttgaagc atttatctc ttcgtcgag tcgtgtcaa 
      tcatttgga cttggcgtc caatttcgt gggaacttt 
      gctgggaat ttcgcaaac tcttgctca gattttgtt 
      atatgtggg tctttcaca gcttccagt tttactaaa 
      acctgaaag cagtttgac acaatgggc ggctctgtt 
      ctggttcac tctggggct caatgttgt ttcaacgac 
      gatttacct ggtctttgg aagcggcgt cagacaaga 
      atggaattt cgttcaata aataaaata aattttatc 
      cttattt
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY