Status
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Gene information
General information
TC013905 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_007420.3: 488124..499872
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
    TC013905
    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_02224

    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)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 1 (3 dpi)
    Days post injection


    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg not developed/not fertilized - Penetrance (percentage of animals/eggs on slide): less than 30%
    embryo/egg with embryonic tissue, no cuticle, no fluorescence - 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): 30% - 50%
    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): 50% - 80%
    cuticle remnants with some identifiable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

    larva complete circumference irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 50% - 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: 20.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 20.0% (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC013905 RA
      MFAYQDDDM DSDPFINIT GGRAPGGAF 
      RSQSFNFQG SPQRGKDKQ DPAIEHDLY 
      VSLEDIAKG CTKKMKISR KVLQADGST 
      RSEDKVLTI NVKPGWKAG TKITFPREG 
      DQGPNKIPA DIVFIIRDK SHPLFKREG 
      SDIKYVAKI TLKQALCGC SIEVPTLTG 
      QKIPIHFTN EVVKPTTVR RLQGYGLPL 
      PKEPSRRGD LIVNVDIKF PERLSQSAK 
      DILYDTLPN
    CDS sequence
    • >TC013905 RA
      atgtttgcg taccaagac gacgacatg gactccgat 
      ccgtttatt aacatcacg ggtgggagg gctcctggg 
      ggcgccttc cgcagccag tccttcaac ttccagggc 
      agcccccag cgcgggaaa gacaagcag gaccccgct 
      atcgagcac gacctctac gtctcgctg gaggacatc 
      gccaaaggc tgcacgaag aagatgaag attagcagg 
      aaggtgttg caagcggac ggctctacg aggagcgaa 
      gacaaggtt ttgactatt aatgtgaag ccggggtgg 
      aaagcggga actaagatc accttcccc agggaaggg 
      gaccaaggg ccaaataaa atcccggcg gatattgtg 
      tttatcatc agggataag tcgcatcct ttgttcaaa 
      cgtgaggga agtgatatt aaatatgtg gctaagatt 
      acgctcaag caggctttg tgcgggtgt tcgattgaa 
      gtgccaacc ctaaccggc cagaaaatc cctatccat 
      ttcaccaac gaggttgtt aaacccaca acagtgagg 
      aggttgcaa ggttacggc ttgccccta cccaaggaa 
      ccttccaga agaggagat ctcattgtc aatgttgac 
      atcaagttt ccagagagg ctttcacaa tctgctaag 
      gacattttg tacgataca ttgcctaac taa
    mRNA sequence
    • >TC013905 RA
      ttaagagtg tattctcat tttctgcag cccaagtcg 
      atgaatttt tcttcgctc aatttttat tttaaattc 
      tttcagaaa acgtcttta tccattttc cgtcttgcc 
      agaggttct ttataatag tttgcactg tattaatgt 
      ataatacca agagtcccg attagatta tgcttttct 
      tttgatttc tttggttca gcagtaaag ctcttaaac 
      ggtctttac agaattttc cactgcttg ttcgaatgt 
      gtcgtttca ccttgtacg attgtagaa aatgttccg 
      ttaatttta agttgagaa tgttccgtt atcggaaac 
      tgttgtttc tcaatcaac cttctacat tatttacgg 
      ccatttcga gaaaaggtg aatgtaaga aacattggt 
      tttcgtatt tattgtata tcggatttt tcataaggt 
      tctcatggt ctcatttct tgcttggct ttttcttaa 
      catcgtcaa agtacccta tacaatttg tctggtatt 
      tgtgctcgc aatttggtt gttataata tatcaccct 
      acattaatt ttttttcct aagttacct cgttttttc 
      tgtcaaaat acagtttag gaaaaaatt ctaccctat 
      ttctccatt tgcctctcg tcaacttga tttttctca 
      acatattgt ctctttttg tagttaaac ccgataaga 
      aattgctca attttccaa cctgttaag gatttgtgc 
      ccccataaa taatgttga aacttcttc actctatag 
      tatacattg tttccctcc aatccgtcg agtaatttt 
      tctctgttg ctgtcttgt atatgattt aaaactgtt 
      gacattctg tcttttgta gaatcattt tgtcattaa 
      gatggatag ttttatgag gttaaaatg ggctaaaca 
      gaaatgtga agtcaacag tttttttat tttcttaaa 
      tatttcgtc acattagct attcttaat tatttttgc 
      atgtttttt cagtaagtg agtgatggg tttgagtaa 
      taaagccga tgagtgtta gctcaattt cagtttagt 
      ttagtgtta gttgcagtt cagtttcaa ttcaatttt 
      aattaagtt cagctaaca acactgtgg tgacgtgaa 
      caacaggaa ataagtgtt tactgatag aaatagtgt 
      ctctagaaa gtgctttgg gcctcgaaa aagtgtgtg 
      cacattacg aaattgctc agcttggat gccagctag 
      atagtacgt caactgtcg tcgcacatt tggactaca 
      gactcacca tacagaaat tcaccaagc aatgcttca 
      ggaaagaga tgttcgtta taatgaaga ggaggctga 
      tcaacgttg cctcttggt ttttctatg attttattt 
      gcggaaaaa tgctgcttc agcttttcc tgaaatttc 
      cagccgcgt cctccagcg gggtgcgac aattccaga 
      atcttctag aaattccta acctatata aagcatcga 
      cgcgagcgc tcgcgcact caatacgaa acgaacaat 
      cactacgtg tacactaat ttattctcg aagaagctt 
      gtgatttta agtttgtgt ggacttttc gtgacatta 
      gtgcagtga aaatgggaa aagactatt accgaatcc 
      tcggcatat caaaaggag ccagtgacg acgagatca 
      agaaagcct accgcaaac tcgccctca aataccacc 
      cggacaaga acaagtcca aagaggctg aagagcgct 
      tcaaggaag tggccgagg cttacgaag ttctttccg 
      acaagaaaa aacgcgaca tctacgacg cctacggcg 
      aggagggcc tcaaggggg ggcatcccc ggcgactct 
      ggcacctca gcccccggg ggcttcacc tacacctac 
      cacggagac ccgcgcgcc accttcgcc cagttcttc 
      ggcaatgcg agccccttc gaagccttc ttcagaggc 
      aatcagacc atgtttgcg taccaagac gacgacatg 
      gactccgat ccgtttatt aacatcacg ggtgggagg 
      gctcctggg ggcgccttc cgcagccag tccttcaac 
      ttccagggc agcccccag cgcgggaaa gacaagcag 
      gaccccgct atcgagcac gacctctac gtctcgctg 
      gaggacatc gccaaaggc tgcacgaag aagatgaag 
      attagcagg aaggtgttg caagcggac ggctctacg 
      aggagcgaa gacaaggtt ttgactatt aatgtgaag 
      ccggggtgg aaagcggga actaagatc accttcccc 
      agggaaggg gaccaaggg ccaaataaa atcccggcg 
      gatattgtg tttatcatc agggataag tcgcatcct 
      ttgttcaaa cgtgaggga agtgatatt aaatatgtg 
      gctaagatt acgctcaag caggctttg tgcgggtgt 
      tcgattgaa gtgccaacc ctaaccggc cagaaaatc 
      cctatccat ttcaccaac gaggttgtt aaacccaca 
      acagtgagg aggttgcaa ggttacggc ttgccccta 
      cccaaggaa ccttccaga agaggagat ctcattgtc 
      aatgttgac atcaagttt ccagagagg ctttcacaa 
      tctgctaag gacattttg tacgataca ttgcctaac 
      taaacagtt tgtttatgt aattgaata agtcaggct 
      gtacgtttt agtacaaat tagttaaat ttaagcttt 
      gttaattta atcgacttg tatgatgtt tattgtatt 
      ataaagtag cgtcgtgtg tgatatttt atctgttat 
      gaattagta ataaactct tttattatt t
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