Status
Please wait ...
Gene information
General information
TC005959 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_007423.3: 4808681..4812747
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
    TC005959
    Gene ontology

    GO terms for Tribolium

    • {{ goTerm.term }}
      ({{ goTerm.evidence }}){{ goTerm.evidenceTooltip }}
      {{goTerm.showAll ? '[-]' : '[+]'}}
      Status: {{ goTerm.status }}
      Evidence: {{ goTerm.evidence }} ({{ goTerm.evidenceTooltip }})
      Reference: {{ goTerm.referenceText }}
      Quotation: {{ goTerm.quotation }}
      Submitter: {{ goTerm.name }}

    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 *
    {{ blurIdResult }}
    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
    {{ blurEvidenceResult }}
    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 *
    {{ blurReferenceResult }}
    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
    If you have entered your name and agree by marking the checkbox. we might show your name on this page to honor your contribution.
      {{ unavailableText }}

    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_04046

    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: 0.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 20.0% (includes death as larva, prepupa, pupa, adult)

    adult lethality - Number of animals showing the phenotype: 2 (22 dpi)
    Days post injection


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


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC005959 RA
      MGDNSVVYW YSSLEKHLC GYCKNPKGN VSHGMWAKI 
      LSVEDYQNL IDRGWRRSG SYCYKPLMN EICCPMYTI 
      KCDALNFQL SKSQKKVIK KFNKFLKDG VLNKNTNPQ 
      ECQDNISEF VHREVPTHV LDKEVVINS DLNCEKDEQ 
      DSSQVAAPS VSQVQEAVP STSSMPKSG LGADPTKPP 
      CKKAKILRL ERKKEKLQK KGIVFEKKP ATNEQKTLE 
      EFLNDTAPD SKHKIKLVL INTSRRSAE WENLKKLEF 
      ELYKKYQTC VHNDPPGKC TMEGFQRFL INSPLQITL 
      EQIHEKHKY FHLTASLFA KYQMAVHNE PPGDCDEDQ 
      YLNFLIDTP LQNVRFSRD SELGFGSFH QLYWLDDKL 
      IAVGVIDIL PKCISAVYF FYDPDYRDL TLGTYGSLR 
      EVEFARTLH RIIPSIDSY YMGFYIHSC PKMRYKGKL 
      SPSYLLCPE TYRWISIEK SVAKLEASK YSRLDNNEA 
      VDENSCTSR DVDEIKILC NRKLVQFKQ YKRKFGGHD 
      MFDTIGRLI GKKCAKSII FIADN
    CDS sequence
    • >TC005959 RA
      atgggtgac aacagtgtt gtttactgg tactccagc 
      cttgagaaa cacttgtgt ggttattgc aaaaatccg 
      aaaggaaat gtgtctcac ggaatgtgg gcaaaaatc 
      ctctcagtt gaagactac caaaatttg atcgatcgg 
      gggtggaga cggtcggga agttactgc tacaagcct 
      ctaatgaac gagatatgt tgccccatg tacaccatt 
      aaatgcgat gctttgaat ttccaatta tccaaatcc 
      cagaagaaa gtgattaaa aagttcaat aaattcctc 
      aaggacgga gttttgaac aaaaatacg aacccgcaa 
      gagtgtcag gacaatatt tctgaattt gtgcataga 
      gaggtcccc actcatgta ttagataaa gaagttgtg 
      ataaatagt gacttaaat tgtgagaaa gatgaacaa 
      gattctagt caagttgca gcccccagt gtgtctcag 
      gtccaagaa gctgtgccc agtaccagt tctatgcct 
      aaaagtggg ctgggggcg gaccctact aaaccccct 
      tgcaaaaaa gcaaaaata cttcgattg gaaaggaag 
      aaggaaaag ttgcagaaa aagggaatt gtctttgag 
      aagaaacca gccacaaat gagcaaaaa accctcgaa 
      gaattttta aatgacacg gcccctgac agcaaacac 
      aaaatcaag cttgtgttg ataaatacg agccgccgt 
      agcgccgag tgggaaaat ttgaaaaag ctcgaattc 
      gagttgtac aaaaagtac caaacatgc gttcataac 
      gacccccct ggcaagtgc acaatggag ggtttccaa 
      agatttttg ataaattcg cctcttcag ataacactc 
      gagcaaatc cacgaaaag cacaaatat tttcacctg 
      actgccagt ttgtttgca aagtatcaa atggcggtg 
      cataatgag cctcccggc gattgcgac gaggatcag 
      tatctgaat tttttaatt gatacacct ttacagaat 
      gtcaggttt tcgagggac tcagagctg ggctttggg 
      tcgtttcat caactttat tggttggat gataaattg 
      atagcagtg ggggttatt gatatttta ccgaaatgt 
      atcagtgct gtgtatttt ttttacgac ccggattac 
      agggacttg actttgggg acgtatgga tcattacgt 
      gaggttgag tttgcgaga actctgcat cgcataatc 
      ccgtcgatt gactcgtat tatatgggt ttttatatt 
      cactcctgt cccaaaatg agatataaa gggaaactg 
      agtccttcc tatctactt tgtcccgaa acttatcgc 
      tggatatct atcgagaaa agtgtagca aaactcgaa 
      gctagtaaa tattcaagg ttagataat aacgaggct 
      gtggatgaa aattcgtgt acgtcaagg gatgtcgat 
      gaaattaag attttgtgc aacagaaag ctcgtccaa 
      tttaaacaa tacaagagg aagtttgga ggtcacgat 
      atgtttgac acaatcggg cgtctaatt gggaagaaa 
      tgtgcaaag tcgatcatt tttatcgct gataattga
    mRNA sequence
    • >TC005959 RA
      tgaaaaaag cattccaaa atgggtgac aacagtgtt 
      gtttactgg tactccagc cttgagaaa cacttgtgt 
      ggttattgc aaaaatccg aaaggaaat gtgtctcac 
      ggaatgtgg gcaaaaatc ctctcagtt gaagactac 
      caaaatttg atcgatcgg gggtggaga cggtcggga 
      agttactgc tacaagcct ctaatgaac gagatatgt 
      tgccccatg tacaccatt aaatgcgat gctttgaat 
      ttccaatta tccaaatcc cagaagaaa gtgattaaa 
      aagttcaat aaattcctc aaggacgga gttttgaac 
      aaaaatacg aacccgcaa gagtgtcag gacaatatt 
      tctgaattt gtgcataga gaggtcccc actcatgta 
      ttagataaa gaagttgtg ataaatagt gacttaaat 
      tgtgagaaa gatgaacaa gattctagt caagttgca 
      gcccccagt gtgtctcag gtccaagaa gctgtgccc 
      agtaccagt tctatgcct aaaagtggg ctgggggcg 
      gaccctact aaaccccct tgcaaaaaa gcaaaaata 
      cttcgattg gaaaggaag aaggaaaag ttgcagaaa 
      aagggaatt gtctttgag aagaaacca gccacaaat 
      gagcaaaaa accctcgaa gaattttta aatgacacg 
      gcccctgac agcaaacac aaaatcaag cttgtgttg 
      ataaatacg agccgccgt agcgccgag tgggaaaat 
      ttgaaaaag ctcgaattc gagttgtac aaaaagtac 
      caaacatgc gttcataac gacccccct ggcaagtgc 
      acaatggag ggtttccaa agatttttg ataaattcg 
      cctcttcag ataacactc gagcaaatc cacgaaaag 
      cacaaatat tttcacctg actgccagt ttgtttgca 
      aagtatcaa atggcggtg cataatgag cctcccggc 
      gattgcgac gaggatcag tatctgaat tttttaatt 
      gatacacct ttacagaat gtcaggttt tcgagggac 
      tcagagctg ggctttggg tcgtttcat caactttat 
      tggttggat gataaattg atagcagtg ggggttatt 
      gatatttta ccgaaatgt atcagtgct gtgtatttt 
      ttttacgac ccggattac agggacttg actttgggg 
      acgtatgga tcattacgt gaggttgag tttgcgaga 
      actctgcat cgcataatc ccgtcgatt gactcgtat 
      tatatgggt ttttatatt cactcctgt cccaaaatg 
      agatataaa gggaaactg agtccttcc tatctactt 
      tgtcccgaa acttatcgc tggatatct atcgagaaa 
      agtgtagca aaactcgaa gctagtaaa tattcaagg 
      ttagataat aacgaggct gtggatgaa aattcgtgt 
      acgtcaagg gatgtcgat gaaattaag attttgtgc 
      aacagaaag ctcgtccaa tttaaacaa tacaagagg 
      aagtttgga ggtcacgat atgtttgac acaatcggg 
      cgtctaatt gggaagaaa tgtgcaaag tcgatcatt 
      tttatcgct gataattga gcgaaaagt gtttatttt 
      ttaataaat gtgcttaag aaca
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY