Status
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Gene information
General information
TC008646 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_007422.5: 13631783..13634017
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
    TC008646
    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_01379

    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: 3 (3 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): 50% - 80%

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

    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%

    larva cuticle dorsal not closed - Penetrance (percentage of animals/eggs on slide): less than 30%

    legs segment shortened - Penetrance (percentage of animals/eggs on slide): less than 30%

    abdomen complete everted (inside-out) - Penetrance (percentage of animals/eggs on slide): less than 30%

    abdomen segment number decreased - Penetrance (percentage of animals/eggs on slide): less than 30%

    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: 10.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 50.0% (includes death as larva, prepupa, pupa, adult)

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


    adult lethality - Number of animals showing the phenotype: 4 (22 dpi)
    Days post injection


    adult lethality - Number of animals showing the phenotype: 1 (41 dpi)
    Days post injection


    Fertility
    egg production: number no/almost no eggs -
    tropharium shape irregular - Number of animals showing the phenotype: 4

    previtellogenic egg chamber not present - Number of animals showing the phenotype: 4

    vitellogenic egg chamber number decreased - Number of animals showing the phenotype: 4

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC008646 RA
      MGDVTQGAQ GQMKIGHYI LGQTLGVGT FGKVKIGEH 
      QITGHKVAV KILNRQKIK SLDVVGKIR REIQNLKLF 
      RHPHIIKLY QVISTPTDI FMIMEYVSG GELFDYIVK 
      HGKLQEHEA RRFFQQIIS GVDYCHRHM IVHRDLKPE 
      NLLLDHNMH VKIADFGLS NMMMDGEFL RTSCGSPNY 
      AAPEVISGK LYAGPEVDI WSCGVILYA LLCGTLPFD 
      DEHVPTLFR KIKSGIFPI PEYLNKSVV NLLCQMLQI 
      DPMKRASIE EIKKHEWFQ KDCPAYLFP SPVDQDSSV 
      IDTDAVAEV CDKFGVQEK EVHNALLSG DPHDQLAIA 
      YHLIIDNRR IADEAAKAE IKDFYIAGS PPPVSMSPS 
      PSPCDFGSS PLKPHPERI APLRDRMAS NHAASGDRG 
      RVKRAKWHL GIRSQSKPH DIMMEVYRA MKALDYEWK 
      VINPYHVRV RHKNPLHER FVMMSLQLY QVDYKSYLL 
      DFKSLANEE AESNTAAPI MGSLPTPVQ SGESTLNAK 
      PKGHYTMEF FEMCAALII QLAR
    CDS sequence
    • >TC008646 RA
      atgggggat gtgacccag ggggcgcaa ggccagatg 
      aagatcggc cactacatc cttggccag actttgggt 
      gtggggact ttcggcaaa gtcaaaatc ggggaacac 
      caaatcacg gggcacaag gtggcggtc aaaattcta 
      aatcggcag aagatcaag agcctggac gttgtgggg 
      aagatcagg agggagatt cagaacttg aagctgttt 
      cggcacccg catattatc aagctgtat caggtgatc 
      agcacgccg actgatatt tttatgatc atggagtac 
      gtctcgggg ggcgagttg ttcgattac attgtgaag 
      cacgggaag ttgcaagaa catgaggcg aggcggttc 
      ttccagcag atcatttcg ggggttgat tactgccac 
      cggcacatg attgtgcac cgagacctg aagcctgag 
      aacctgctt cttgaccac aacatgcac gtgaaaatc 
      gccgatttt ggtttgtcc aacatgatg atggacggg 
      gagtttttg cgcactagt tgtggttcc cccaattac 
      gcggcaccc gaggtcatt tccggcaaa ctttacgcc 
      gggcctgag gtcgatatc tggtcctgt ggggttatt 
      ctttacgcc cttctttgt gggacttta ccgtttgat 
      gatgagcac gtccccacc ctcttcagg aaaattaaa 
      tcgggcatt tttcctatc cctgaatac ctaaacaaa 
      tcggtggtc aacctactt tgccaaatg ttacaaatc 
      gatcccatg aaacgagca tcaattgaa gaaatcaaa 
      aagcacgaa tggttccaa aaagactgt cctgcttac 
      ttattccca tcacctgtg gaccaagac tcgtcagtg 
      atcgacaca gacgccgtg gctgaagtt tgcgataag 
      tttggggtg caggagaag gaagtccac aatgctctc 
      ctgagtggg gacccccat gatcaactt gcaatcgct 
      taccacctt attatcgat aacaggcgc atagcggat 
      gaagccgca aaggcggaa attaaagat ttttacatc 
      gcggggagt cccccacct gttagtatg agcccgagc 
      ccaagtcct tgcgacttt ggttctagt cctttgaag 
      cctcatccg gagagaatt gcgccgttg cgggacaga 
      atggcttca aatcatgct gcttcaggg gacagggga 
      agagttaag agggctaag tggcattta gggattcgc 
      tcacaaagt aagccccac gatattatg atggaggtt 
      tacagagca atgaaagcg ttggattat gaatggaaa 
      gtcatcaat ccataccat gtaagagtg cgtcataag 
      aatcccttg catgagagg tttgtcatg atgtcgctc 
      caactatat caggtggat tacaagagc tacctcttg 
      gactttaaa agtttggcc aacgaggaa gcggagtcg 
      aacacggcg gcccccatc atggggtca ctgcccacg 
      ccagtgcag tccggcgag agcactttg aacgcgaaa 
      cccaaaggg cattacaca atggaattt tttgaaatg 
      tgtgccgct ttaattata cagttggct cgttaa
    mRNA sequence
    • >TC008646 RA
      ctcctgtca aaggtgttg ttgaaatac gcaattatt 
      tattttgtt aatttacgt ttaaatacg caaaattgt 
      gggcagaag ccaatgagt gctcgccaa tacgtcact 
      tgggtcgat tttagtggc gccggataa taatcatcg 
      ggtaagaat gggggatgt gacccaggg ggcgcaagg 
      ccagatgaa gatcggcca ctacatcct tggccagac 
      tttgggtgt ggggacttt cggcaaagt caaaatcgg 
      ggaacacca aatcacggg gcacaaggt ggcggtcaa 
      aattctaaa tcggcagaa gatcaagag cctggacgt 
      tgtggggaa gatcaggag ggagattca gaacttgaa 
      gctgtttcg gcacccgca tattatcaa gctgtatca 
      ggtgatcag cacgccgac tgatatttt tatgatcat 
      ggagtacgt ctcgggggg cgagttgtt cgattacat 
      tgtgaagca cgggaagtt gcaagaaca tgaggcgag 
      gcggttctt ccagcagat catttcggg ggttgatta 
      ctgccaccg gcacatgat tgtgcaccg agacctgaa 
      gcctgagaa cctgcttct tgaccacaa catgcacgt 
      gaaaatcgc cgattttgg tttgtccaa catgatgat 
      ggacgggga gtttttgcg cactagttg tggttcccc 
      caattacgc ggcacccga ggtcatttc cggcaaact 
      ttacgccgg gcctgaggt cgatatctg gtcctgtgg 
      ggttattct ttacgccct tctttgtgg gactttacc 
      gtttgatga tgagcacgt ccccaccct cttcaggaa 
      aattaaatc gggcatttt tcctatccc tgaatacct 
      aaacaaatc ggtggtcaa cctactttg ccaaatgtt 
      acaaatcga tcccatgaa acgagcatc aattgaaga 
      aatcaaaaa gcacgaatg gttccaaaa agactgtcc 
      tgcttactt attcccatc acctgtgga ccaagactc 
      gtcagtgat cgacacaga cgccgtggc tgaagtttg 
      cgataagtt tggggtgca ggagaagga agtccacaa 
      tgctctcct gagtgggga cccccatga tcaacttgc 
      aatcgctta ccaccttat tatcgataa caggcgcat 
      agcggatga agccgcaaa ggcggaaat taaagattt 
      ttacatcgc ggggagtcc cccacctgt tagtatgag 
      cccgagccc aagtccttg cgactttgg ttctagtcc 
      tttgaagcc tcatccgga gagaattgc gccgttgcg 
      ggacagaat ggcttcaaa tcatgctgc ttcagggga 
      caggggaag agttaagag ggctaagtg gcatttagg 
      gattcgctc acaaagtaa gccccacga tattatgat 
      ggaggttta cagagcaat gaaagcgtt ggattatga 
      atggaaagt catcaatcc ataccatgt aagagtgcg 
      tcataagaa tcccttgca tgagaggtt tgtcatgat 
      gtcgctcca actatatca ggtggatta caagagcta 
      cctcttgga ctttaaaag tttggccaa cgaggaagc 
      ggagtcgaa cacggcggc ccccatcat ggggtcact 
      gcccacgcc agtgcagtc cggcgagag cactttgaa 
      cgcgaaacc caaagggca ttacacaat ggaattttt 
      tgaaatgtg tgccgcttt aattataca gttggctcg 
      ttaatttaa gacaagttt tatcctact aattttacg 
      ttaaaaatg atgttacat gtaattact aagtttttg 
      tttgctctt aattgttta gtgagtttt aagtgattt 
      taccagtga taaactgaa aaaggtatt agtcgcttt 
      ttaaaagcc attagttat gtaaactgg ttagttgtg 
      atgatattt ttgttgcgt aatt
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY