Status
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Gene information
General information
TC004559 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: 2483457..2494052
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
    TC004559
    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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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_03785

    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 larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 20
    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)

    larva lethality - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004559 RA
      MSKVENGDE HDNFYHCEE NETKETCNK CEVAKFRYP 
      DGTVRLRNP HIELMDQDI LYHLALGSG SHDLVEMFG 
      DVKFVCMGG TPKRMEAFA YYIMKEIGH KLPTGTTLQ 
      DISQYSYRY SMFKVGPVL SVSHGMGIP SIGILLHEI 
      IKLMYHSKA RDPIFFRIG TCGGIGLEG GTVVISDDA 
      VDEMGNHYY QVPMLGKPV RRPAKLDKR LVRELKGLA 
      DPEDPYDTI IGTTMCAND FYEGQGRTD GAFCDYTES 
      EKMEYLTGL QSNGVKNIE MEVIPFAAL THHAGIRAA 
      VVCVALLDR LKGDQVCAP KEVLDEWQI RPQKLVARY 
      IRRYLQTKG RISFDGHGS MAVKSPRRF KLVQQESET 
      FD
    CDS sequence
    • >TC004559 RA
      atgagcaaa gtagagaat ggagacgaa cacgataat 
      ttctaccac tgcgaagag aacgaaacg aaagaaacg 
      tgtaacaag tgtgaagta gccaagttt agatatcct 
      gatggcacc gttcggctc aggaatccc cacattgaa 
      ctcatggac caggacatt ctctaccac ctggctcta 
      ggaagcggc tcacacgat ctagtcgaa atgttcggc 
      gacgtaaaa ttcgtctgc atgggaggg actccgaaa 
      cgcatggag gccttcgcc tactacata atgaaagaa 
      atcggccac aagctcccg acaggaacc accttgcaa 
      gacatcagc caatattca taccgttac agtatgttc 
      aaagtcggt cctgtcttg tccgttagc catggtatg 
      ggtatccca tccattgga atcctactc cacgaaata 
      atcaaactg atgtaccat tcgaaagcc cgtgatccg 
      atttttttc cgaatcggc acttgcgga ggaatcggt 
      ctcgaaggt ggtactgtg gtaatttcc gacgacgct 
      gtagatgaa atgggaaac cattattat caagtgcca 
      atgttagga aaaccagtt cgaagacca gcaaagtta 
      gacaaacgt ttagttcgg gaattgaag ggtttagcc 
      gatcctgag gacccgtac gatactatt attggaacc 
      acgatgtgt gccaacgat ttctacgaa gggcaggga 
      cgcactgat ggggctttt tgcgactac actgagtcc 
      gaaaaaatg gaatacttg acggggttg caaagcaac 
      ggggtgaaa aatatcgag atggaggtt atacccttt 
      gctgcgttg acccatcat gctgggata agggcagcc 
      gtggtgtgt gttgctttg ctggatcgg ttgaagggg 
      gaccaggtt tgtgcccct aaagaagtg ctggatgag 
      tggcagatc agacctcag aagctagtt gcgcggtat 
      attcgccgg tacttgcaa accaaaggg aggatttcg 
      ttcgatggc catggttcc atggctgtt aaaagtccg 
      cgacgtttc aaactagtc cagcaagag tctgagact 
      tttgattaa
    mRNA sequence
    • >TC004559 RA
      tcgatcttg taactgcaa agtgacgca ccctttctc 
      ttaatttct tagtgtttt agtgatgtt tcagttatt 
      ttaacgaaa caatttttt atcgaaacc tatccttgt 
      acatagttt agtgtcaaa acacaaaaa atgtcggac 
      gaggagagg gacgattag tagtgctgt agcttgagc 
      agtgagaac accatgagc aaagtagag aatggagac 
      gaacacgat aatttctac cactgcgaa gagaacgaa 
      acgaaagaa acgtgtaac aagtgtgaa gtagccaag 
      tttagatat cctgatggc accgttcgg ctcaggaat 
      ccccacatt gaactcatg gaccaggac attctctac 
      cacctggct ctaggaagc ggctcacac gatctagtc 
      gaaatgttc ggcgacgta aaattcgtc tgcatggga 
      gggactccg aaacgcatg gaggccttc gcctactac 
      ataatgaaa gaaatcggc cacaagctc ccgacagga 
      accaccttg caagacatc agccaatat tcataccgt 
      tacagtatg ttcaaagtc ggtcctgtc ttgtccgtt 
      agccatggt atgggtatc ccatccatt ggaatccta 
      ctccacgaa ataatcaaa ctgatgtac cattcgaaa 
      gcccgtgat ccgattttt ttccgaatc ggcacttgc 
      ggaggaatc ggtctcgaa ggtggtact gtggtaatt 
      tccgacgac gctgtagat gaaatggga aaccattat 
      tatcaagtg ccaatgtta ggaaaacca gttcgaaga 
      ccagcaaag ttagacaaa cgtttagtt cgggaattg 
      aagggttta gccgatcct gaggacccg tacgatact 
      attattgga accacgatg tgtgccaac gatttctac 
      gaagggcag ggacgcact gatggggct ttttgcgac 
      tacactgag tccgaaaaa atggaatac ttgacgggg 
      ttgcaaagc aacggggtg aaaaatatc gagatggag 
      gttataccc tttgctgcg ttgacccat catgctggg 
      ataagggca gccgtggtg tgtgttgct ttgctggat 
      cggttgaag ggggaccag gtttgtgcc cctaaagaa 
      gtgctggat gagtggcag atcagacct cagaagcta 
      gttgcgcgg tatattcgc cggtacttg caaaccaaa 
      gggaggatt tcgttcgat ggccatggt tccatggct 
      gttaaaagt ccgcgacgt ttcaaacta gtccagcaa 
      gagtctgag acttttgat taaattaat tgcacaagt 
      tgcttcgtt atagtttca atttaattt attatcgag 
      ttatcggca agtctaagt gtgtgatga tggtgattt 
      tttattaat aagaaaaga aaatagtgt aggggtata 
      ggagttgat gggtggtcg ttgcacaat cctgtactg 
      ttacattat ctagttcta gggaacatt attgttgtt 
      cgtatttgt aaaaaatga gttgtaaaa gcacagact 
      atacttcta ttatcaaaa ctaattctg gattatggt 
      ggtcggaaa ttctattca tcctaaaca tatcagagc 
      ataagactc gtgacattt ttttgcgaa acttccaac 
      acacaattt gaccagaaa ataccatta agcggcttt 
      gcatttaaa tgtttcaac agttggtag tcattaata 
      aagcatggt gttttaatg ttgtgacgt tgtagctat 
      atactggac aatacattt gttacaatt tacacattt 
      tatggtaga caacgacgt agtcatgtg attcaaatc 
      tgcctaatt tgttggtta catcgttat tgttgaatt 
      tgctcacag ttatagggg ttgttcgta ttgaaattt 
      tatataagc attaggaaa tacagcatc ctgtacagg 
      cttcttttc tcaacaccg actcggaaa atctagact 
      ctttctttc tattccatt attgttgat cgatgttca 
      tcctagagt agtctgttt tatgtcgcc tataaacaa 
      taaatattt gccagttac
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY