Status
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Gene information
General information
TC031227 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_007424.3: 4609563..4612987
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
    TC031227
    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
    {{ goGene }}
    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
    You may enter your name. The contact information can help us to clarify any questions. If you agree, we may show your name on this page to honor your contribution.
    Email
    We will use your email address only for possible questions regarding this annotation. We will never show your address or give it away.
    Publish name
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_05192

    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 larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 50
    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: 40.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 40.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 4 (11 dpi)
    Days post injection


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC031227 RA
      MAEYLASIF GTEKDKVNC SFYFKIGAC 
      RHGDRCSRI HNKPTFSQT CLLQNLYVN 
      PQNSAKSAD GSHLVANVS DEEMQEHYD 
      NFFEDVFVE CEDKYGEIE EMNVCDNLG 
      DHLVGNVYI KFRREEDAE RAVNDLNNR 
      WFGGRPVYA ELSPVTDFR EACCRQYEM 
      GECTRSGFC NFMHLKPIS RELRRYLYS 
      RRKSGRRRS RSKSPRRRS RSRERRSRS 
      PRHRSGRSG RY
    CDS sequence
    • >TC031227 RA
      atggccgaa tacttggct tcgattttc ggaactgaa 
      aaagataaa gtcaactgc tctttctac ttcaaaatc 
      ggggcttgc cggcatggc gatcgttgt tccagaata 
      cacaacaaa ccaacgttt tcccaaacg tgtcttttg 
      cagaatttg tacgtgaat ccccaaaac tccgcgaaa 
      tctgccgat gggagtcac ttggttgca aacgtctct 
      gacgaagag atgcaagag cattacgat aactttttc 
      gaggacgtt ttcgtagaa tgtgaagat aagtacggg 
      gaaattgag gaaatgaac gtgtgcgat aatttgggg 
      gaccacctt gtcggaaat gtctacatt aaatttcga 
      cgtgaggaa gacgctgag agggctgtt aacgatttg 
      aataatcgt tggttcggg gggcgacct gtttatgcc 
      gagctgagc cccgtgact gactttagg gaagcttgc 
      tgtcgccag tacgaaatg ggggagtgt acgcgctca 
      ggtttttgc aatttcatg cacctgaag ccgatttct 
      cgcgagttg cgaagatac ttgtattct cggcgaaaa 
      tctggccgc aggcgttct aggtctaaa tcaccaaga 
      agacgttct cggtcgagg gaaagaagg tctcgctcc 
      ccacgccat cgctcgggg cgcagcggc agatattaa
    mRNA sequence
    • >TC031227 RA
      gttcaacta aaccgttct ttaagattg attgaacgc 
      gcagaatag caatatatc ccacatctt tactcatag 
      cagcagaac gggagttgt gaaaagttg catacgagc 
      gacaatcgg gcgagttat gacaatgac atgatgatt 
      aatattata cttaactat aaataaagt catttatta 
      ttcaattca tcacaagtt ttttgcaac tgttcgatt 
      aaaacatcc aacatttcg agattcgcc tcaaaatta 
      accgtgttt ttctttgat ttatcgtca tcgtttttc 
      acacagtgc agatccact tgtaccaat ggttctctc 
      actgccgct aatttcgag tttccgagg acccacttc 
      actttccag tcaatattt tgaaccaag ttatgtcca 
      ctacttact aacttctcc tttacaagt gtttgaaaa 
      atatcatcc ttccgcaac tcgagacac tttcgaatt 
      tcatcttgc acattctct ccaaaatca gtttttaaa 
      tcgaaatcg ttgttgata acactttcg cggcaaatt 
      ttttgaaca cattttttg gctttgttg aagtcgtca 
      accgtccac tcgatgtcg ctattgtag ttgtcaaaa 
      ctcgcctgt tttatgccg gttaaatca tcgatacag 
      tcatgtaaa aactgaaac attgaaaat tagtagttt 
      tttattacc ctcaataaa atcggttta ttacttgtt 
      gtaaaaccg gcgaattgc ttattttca acaaggaat 
      caacaaact ctgccatgt ttacaccac acgaatcag 
      gaaactgca ctaccgacc gagcagttt ttgacaatt 
      tggcgtgtt atggcgtca gtttttcca gcattgtaa 
      attctcaaa aaacttgct gaattatgg ccgaatact 
      tggcttcga ttttcggaa ctgaaaaag ataaagtca 
      actgctctt tctacttca aaatcgggg cttgccggc 
      atggcgatc gttgttcca gaatacaca acaaaccaa 
      cgttttccc aaacgtgtc ttttgcaga atttgtacg 
      tgaatcccc aaaactccg cgaaatctg ccgatggga 
      gtcacttgg ttgcaaacg tctctgacg aagagatgc 
      aagagcatt acgataact ttttcgagg acgttttcg 
      tagaatgtg aagataagt acggggaaa ttgaggaaa 
      tgaacgtgt gcgataatt tgggggacc accttgtcg 
      gaaatgtct acattaaat ttcgacgtg aggaagacg 
      ctgagaggg ctgttaacg atttgaata atcgttggt 
      tcggggggc gacctgttt atgccgagc tgagccccg 
      tgactgact ttagggaag cttgctgtc gccagtacg 
      aaatggggg agtgtacgc gctcaggtt tttgcaatt 
      tcatgcacc tgaagccga tttctcgcg agttgcgaa 
      gatacttgt attctcggc gaaaatctg gccgcaggc 
      gttctaggt ctaaatcac caagaagac gttctcggt 
      cgagggaaa gaaggtctc gctccccac gccatcgct 
      cggggcgca gcggcagat attaagttc ataattatt 
      tttacacag gagttttga gtttggatt tcgtgtagt 
      gtctagttg taagtgatt tcgttccaa ataataaag 
      gatttaaat taat

    If you use iBeetle-Base, please cite: Dönitz J et al.: Expanded and updated data and a query pipeline for iBeetle-Base,
    Nucleic Acids Res. 2018 Jan 4;46(D1):D831-D835. doi: 10.1093/nar/gkx984.

    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY