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Gene information
General information
TC004989 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_007417.3: 685558..691116
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
    TC004989
    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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    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_00793

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

    cuticle remnants strongly fragmented (cuticle crumbs) - Penetrance (percentage of animals/eggs on slide): less than 30%
    cuticle remnants with some identifiable segments - Penetrance (percentage of animals/eggs on slide): less than 30%
    legs partially remaining - Penetrance (percentage of animals/eggs on slide): less than 30%
    head capsule not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    head appendages position irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    head appendages partially not present - 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): 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: 0.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 0.0% (includes death as larva, prepupa, pupa, adult)

    Fertility
    egg production: number <50% of expected -
    ovary without detectable defects - Number of animals showing the phenotype: 4
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004989 RA
      MLRSSVIFF IVCVLVANA FVRVPLYKV KSARRSLQE 
      VGTHVQQVR MRYGGPTPE PLSNYLDAQ YYGPISIGN 
      PPQNFKVVF DTGSSNLWV PSKKCHYTN IACLLHNKY 
      DSSQSKTYK KNGTDFAIQ YGSGSLSGF LSTDIVTVG 
      GLKVQQQTF AEAMSEPGL AFVAAKFDG ILGMAYNRI 
      SVDGVTPVF YNMIQQNLV AQPVFSFYL NRDPSAAQG 
      GEIILGGSD PAHYKGDFT YLSVDRQAY WQFKMDSIS 
      VGGKNTFCA NGCEAIADT GTSLIAGPV SEVQGINKA 
      IGATPIVGG EYMVDCNLI PNLPLIDFT LGGKNFTLE 
      GKDYVLRVA QMGKTICLS GFMGIDIPP PNGPLWILG 
      DVFIGKFYT EFDLGNNRV GFAVAA
    CDS sequence
    • >TC004989 RA
      atgctgagg tcaagtgtg atatttttc atagtttgt 
      gttcttgtg gcgaatgct tttgtccga gtgccttta 
      tataaggta aagtcggct agacgcagt ctacaagaa 
      gtgggcaca catgtgcaa caagtccgc atgaggtat 
      gggggccct actcctgaa cctctctcc aattatctg 
      gatgcgcaa tattacggg ccgatttca attgggaac 
      cccccgcaa aatttcaag gttgttttt gatacagga 
      tcatccaat ttatgggtg ccttccaag aaatgtcat 
      tatacaaac atagcctgc ttgcttcac aataagtat 
      gattcgtca cagtcaaag acctacaag aaaaacggc 
      accgatttt gctattcaa tatggatcg gggagtttg 
      agtggattc ttatcaact gatattgtt acagttggc 
      ggtttaaag gtacaacaa caaacattt gctgaagcc 
      atgagcgaa ccaggtcta gcatttgtt gccgcaaaa 
      ttcgacgga attttagga atggcctac aaccgcatc 
      tcagttgat ggtgtcact ccagtcttc tataacatg 
      attcaacaa aatttagtc gcccaaccc gtcttctca 
      ttctatctt aatagagat ccaagtgct gcacaaggc 
      ggagaaata attttggga ggatcagat ccagctcac 
      tataaagga gactttacc tatttgtct gttgataga 
      caagcgtat tggcagttc aaaatggat agcataagt 
      gttggtggt aaaaacacg ttctgtgcc aatggttgt 
      gaagctatt gctgacact ggcactagt ttgatcgca 
      ggaccggtt agtgaagtg caaggaatc aacaaagca 
      ataggtgct actcccatt gttggaggg gaatatatg 
      gtggactgt aacttgatt ccaaattta ccattgatc 
      gacttcact ctaggaggc aagaatttc acattggag 
      ggaaaagac tatgttcta agggtggca caaatgggc 
      aaaactatt tgcttgtct ggtttcatg ggcattgat 
      atcccacca ccaaatggg cccttgtgg attttggga 
      gatgtgttt atcgggaaa ttttataca gagtttgat 
      ttaggaaac aaccgagtt gggtttgcc gttgctgct 
      taa
    mRNA sequence
    • >TC004989 RA
      tgtaaacgc caacgtcgc attttacca aataatttt 
      tgtaaataa ggaatttta atgttgtca cattggtac 
      ttgtcattc taacccaac aatttgctc gaacaaaca 
      tatcttatt aatcttttt gttatcgcg cgagttctt 
      ataaataca aatagccgg cagagttaa agttcagtc 
      ggtttattg caatctctc aacacaatg ctgaggtca 
      agtgtgata tttttcata gtttgtgtt cttgtggcg 
      aatgctttt gtccgagtg cctttatat aaggtaaag 
      tcggctaga cgcagtcta caagaagtg ggcacacat 
      gtgcaacaa gtccgcatg aggtatggg ggccctact 
      cctgaacct ctctccaat tatctggat gcgcaatat 
      tacgggccg atttcaatt gggaacccc ccgcaaaat 
      ttcaaggtt gtttttgat acaggatca tccaattta 
      tgggtgcct tccaagaaa tgtcattat acaaacata 
      gcctgcttg cttcacaat aagtatgat tcgtcacag 
      tcaaagacc tacaagaaa aacggcacc gattttgct 
      attcaatat ggatcgggg agtttgagt ggattctta 
      tcaactgat attgttaca gttggcggt ttaaaggta 
      caacaacaa acatttgct gaagccatg agcgaacca 
      ggtctagca tttgttgcc gcaaaattc gacggaatt 
      ttaggaatg gcctacaac cgcatctca gttgatggt 
      gtcactcca gtcttctat aacatgatt caacaaaat 
      ttagtcgcc caacccgtc ttctcattc tatcttaat 
      agagatcca agtgctgca caaggcgga gaaataatt 
      ttgggagga tcagatcca gctcactat aaaggagac 
      tttacctat ttgtctgtt gatagacaa gcgtattgg 
      cagttcaaa atggatagc ataagtgtt ggtggtaaa 
      aacacgttc tgtgccaat ggttgtgaa gctattgct 
      gacactggc actagtttg atcgcagga ccggttagt 
      gaagtgcaa ggaatcaac aaagcaata ggtgctact 
      cccattgtt ggaggggaa tatatggtg gactgtaac 
      ttgattcca aatttacca ttgatcgac ttcactcta 
      ggaggcaag aatttcaca ttggaggga aaagactat 
      gttctaagg gtggcacaa atgggcaaa actatttgc 
      ttgtctggt ttcatgggc attgatatc ccaccacca 
      aatgggccc ttgtggatt ttgggagat gtgtttatc 
      gggaaattt tatacagag tttgattta ggaaacaac 
      cgagttggg tttgccgtt gctgcttaa atagttttc 
      tgtgtttat cgttccaaa gattttttt taagttgta 
      aagcttgta gataccttc aatacaata aagcgtcgt 
      tgcagtttt ccttaatat acagatgta tatttg
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY