Status
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Gene information
General information
TC004647 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_007416.3: 4502820..4506874
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
    TC004647
    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_08575

    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)

    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: 1 (9 dpi)
    Days post injection


    Fertility
    eggs lost during procedure: potentially due to defects in egg-shells egg-morphology or egg-size, (14 dpi)
    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: < 50 embryo/egg with embryonic tissue potentially present, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): more than 80%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 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): more than 80%
    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
    • >TC004647 RA
      MGDFGEDSD DSDGEGGLG NVNRIIMRP PGHSGKAKR 
      GHLCFDASF ESGNLGRVD LVNEYEYDL FIRPDTCSP 
      RIRFWFNFT VDNVKQDQR VIFNIVNIS KNRNLFNDN 
      LTPLVKSSS RQKWQRIPK QHVYYHKSS AHQGHYVLS 
      FSFGFDRED EVFQFALAP PFTYSKLQM FLSILESKG 
      SYLNESFQR ELLGSSVQK RRLDLITIG SLDRSKPNS 
      KRRVIAIMA RVHPGESPA SFVCQGLLE LLISSNAIA 
      STLRDHVIF KIIPMLNPD GVFLGNYRS TVMGIDLNR 
      SWHLTTPWS HPTLKAATE MLLTLDKNK EFQLDFVID 
      IHAHSSLKG CFIYGNTYE DVYRYERHI LFPKLLATT 
      ADDYLTENA MFNADPKKI GTARRYLCQ LLSDRVNCY 
      TFEVSFFGY KLKGSDVTI PYTEDSYMR CGRNLVKTF 
      LEYYHSTGA IPIELAMEV QNKKRRPRT HHSRSTTRN 
      SYRQRPHTT KTQALLHFK DLNINYESD TSIDDTYRK 
      PETSRFFEK FSDYMKKSE RIGSPPPTT IVVIPEPSL 
      SIIDFNLIT RNDIEKASR KNRRVT
    CDS sequence
    • >TC004647 RA
      atgggcgat tttggagaa gatagcgac gacagtgac 
      ggagagggt ggtttaggt aatgtaaat cgaattata 
      atgagaccg ccaggccac agtggtaaa gcaaaacga 
      ggtcatttg tgttttgat gcttctttc gaatcagga 
      aatttgggt agagtcgat ttagtcaac gaatatgag 
      tatgattta ttcattcga cctgatacc tgtagcccc 
      cgaattagg ttctggttt aattttaca gtcgataat 
      gttaaacaa gaccagagg gtcattttt aacattgtc 
      aacattagc aagaatcga aatttattt aacgacaat 
      ctgactccg ttagttaag tcttcgagc cggcaaaaa 
      tggcaaaga atcccaaaa caacatgtt tattatcac 
      aaatcttcg gcacatcaa gggcactat gtgttaagt 
      ttctcgttc ggttttgac cgggaagac gaagtcttc 
      cagtttgct ttagcccca ccttttacc tattccaaa 
      cttcaaatg ttcttatct atattagaa tcgaaaggg 
      tcgtatttg aacgagtcg tttcagagg gaactttta 
      ggcagtagc gtgcaaaaa cgaaggtta gacctgatc 
      acaatcggc tctttagac cggtctaag cctaattca 
      aaacggcga gttattgcg ataatggcg cgagtccat 
      cccggtgaa tcaccggct agttttgta tgtcaaggg 
      cttttggaa ctgttgata agttctaat gcgatagca 
      agcacttta cgggaccac gttattttt aaaataatt 
      ccaatgctg aaccctgat ggggtcttt ttggggaat 
      taccgaagt acggtgatg ggaattgat ttaaacagg 
      tcgtggcat ttgaccaca ccctggagc cacccgacc 
      ctgaaggca gcaacagaa atgttgcta actttggac 
      aaaaataag gaatttcaa ctagacttt gtgatcgat 
      atccatgcc cattcgagc ctgaaaggt tgttttatt 
      tatggtaac acctacgaa gacgtctac aggtatgag 
      cggcatatt ctatttccg aaactacta gcgacaact 
      gccgacgat tatttaacc gaaaatgcg atgttcaac 
      gccgatccg aagaaaatt ggcactgct agaagatac 
      ctatgccaa ctattaagc gaccgcgtc aactgttac 
      acatttgaa gtgtcattt tttggatac aaactcaaa 
      ggatctgac gtcaccatt ccgtatacg gaagacagt 
      tatatgaga tgtggccgc aacttggtc aaaactttc 
      ctcgaatat taccacagc actggagcg atcccgatt 
      gagctggcg atggaggtt cagaataaa aaacgcagg 
      cctcggact catcattcg aggtctacc acacgcaat 
      tcctacagg cagagacct cacacgacc aaaactcaa 
      gcacttctt cacttcaaa gacctaaat atcaactac 
      gagagtgat acttcaatc gatgacacg tatcggaag 
      cccgaaacg agccgattt tttgaaaaa ttttccgat 
      tatatgaag aaatctgag aggattggg tcgccaccc 
      cccaccacg atcgtggta atcccagag cccagcctc 
      tccataatc gacttcaac ttaataaca aggaatgat 
      attgagaag gcttccaga aagaacaga cgggttact 
      taa
    mRNA sequence
    • >TC004647 RA
      tgtcgggca gaataatgg gcgattttg gagaagata 
      gcgacgaca gtgacggag agggtggtt taggtaatg 
      taaatcgaa ttataatga gaccgccag gccacagtg 
      gtaaagcaa aacgaggtc atttgtgtt ttgatgctt 
      ctttcgaat caggaaatt tgggtagag tcgatttag 
      tcaacgaat atgagtatg atttattca ttcgacctg 
      atacctgta gcccccgaa ttaggttct ggtttaatt 
      ttacagtcg ataatgtta aacaagacc agagggtca 
      tttttaaca ttgtcaaca ttagcaaga atcgaaatt 
      tatttaacg acaatctga ctccgttag ttaagtctt 
      cgagccggc aaaaatggc aaagaatcc caaaacaac 
      atgtttatt atcacaaat cttcggcac atcaagggc 
      actatgtgt taagtttct cgttcggtt ttgaccggg 
      aagacgaag tcttccagt ttgctttag ccccacctt 
      ttacctatt ccaaacttc aaatgttct tatctatat 
      tagaatcga aagggtcgt atttgaacg agtcgtttc 
      agagggaac ttttaggca gtagcgtgc aaaaacgaa 
      ggttagacc tgatcacaa tcggctctt tagaccggt 
      ctaagccta attcaaaac ggcgagtta ttgcgataa 
      tggcgcgag tccatcccg gtgaatcac cggctagtt 
      ttgtatgtc aagggcttt tggaactgt tgataagtt 
      ctaatgcga tagcaagca ctttacggg accacgtta 
      tttttaaaa taattccaa tgctgaacc ctgatgggg 
      tctttttgg ggaattacc gaagtacgg tgatgggaa 
      ttgatttaa acaggtcgt ggcatttga ccacaccct 
      ggagccacc cgaccctga aggcagcaa cagaaatgt 
      tgctaactt tggacaaaa ataaggaat ttcaactag 
      actttgtga tcgatatcc atgcccatt cgagcctga 
      aaggttgtt ttatttatg gtaacacct acgaagacg 
      tctacaggt atgagcggc atattctat ttccgaaac 
      tactagcga caactgccg acgattatt taaccgaaa 
      atgcgatgt tcaacgccg atccgaaga aaattggca 
      ctgctagaa gatacctat gccaactat taagcgacc 
      gcgtcaact gttacacat ttgaagtgt cattttttg 
      gatacaaac tcaaaggat ctgacgtca ccattccgt 
      atacggaag acagttata tgagatgtg gccgcaact 
      tggtcaaaa ctttcctcg aatattacc acagcactg 
      gagcgatcc cgattgagc tggcgatgg aggttcaga 
      ataaaaaac gcaggcctc ggactcatc attcgaggt 
      ctaccacac gcaattcct acaggcaga gacctcaca 
      cgaccaaaa ctcaagcac ttcttcact tcaaagacc 
      taaatatca actacgaga gtgatactt caatcgatg 
      acacgtatc ggaagcccg aaacgagcc gattttttg 
      aaaaatttt ccgattata tgaagaaat ctgagagga 
      ttgggtcgc cacccccca ccacgatcg tggtaatcc 
      cagagccca gcctctcca taatcgact tcaacttaa 
      taacaagga atgatattg agaaggctt ccagaaaga 
      acagacggg ttacttaat gattattta ttcaacttg 
      tgaacaaaa cgctataat tgttataaa acaaaa
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