Status
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Gene information
General information
TC000540 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: 10017588..10019938
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
    TC000540
    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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    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_08997

    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: 20.0% (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


    adult lethality - Number of animals showing the phenotype: 1 (9 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): more than 80%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 80%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
    embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): more than 80%
    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 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: % (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: % (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC000540 RA
      MRPNKNQDY DACIEALNN LQTNAQYIK TKALTNNHN 
      GDQLTQVKK YLYRAGLSL ENLDDLSVI HVAGTKGKG 
      TTCAFTERI LREHGYKTG FFSSPHLIE VRERIRING 
      KPISKPDFV KSFWKIYNA LDQKKNDEH DMPLFFRFL 
      TIMAFSVFL ERKVDVAII EVGIGGEYD CTNVLRKVP 
      VVGITSLGI DHVTLLGAT IESIAWNKA GIMKENCRA 
      FTVPQCQAA MTVLQERSI EKKCQLEIV DDLQFKFPP 
      NKSAHPPHI LNLNASLAV ALCNAWFLQ KNNNNLGPV 
      MSKEITEKA LFATTWPGR FHVKHDKNI SYYLDGAHT 
      LESITICSS WFKDITRNS QKKKALMFN VTGDRCAEN 
      LLKQLQTCH FDAVLFVSN SATRCRPDN SNHASSDEL 
      LEKCHQHKK LWLKLEEDS LKKSQMCKA FLTVDEALE 
      FLVNQDQFD LLVTGSIHL VGSVLSLID PNLND
    CDS sequence
    • >TC000540 RA
      atgaggccg aacaaaaac caagactat gacgcctgt 
      attgaggct ctaaataac ttacaaact aacgcgcaa 
      tacatcaaa acgaaagca ctgacgaat aatcacaac 
      ggcgatcaa cttactcaa gtaaaaaaa tatctctac 
      agggctggg ctatctttg gaaaatctc gacgactta 
      tcggtgatt cacgtcgct gggaccaaa ggcaaaggc 
      acgacgtgc gccttcacc gagcgcatt ttacgcgaa 
      catggctat aaaacagga tttttctcc tcaccgcac 
      ctgatcgaa gtcagagaa aggatccga ataaacggc 
      aagccgatc tcaaaaccc gactttgtc aagtcgttt 
      tggaaaatt tacaacgcc ctagatcag aaaaagaat 
      gacgagcat gacatgcca ctcttcttc cggttctta 
      acgataatg gcattcagc gttttcctc gaacgcaaa 
      gtcgatgtt gcgatcatt gaggtcggg attggggga 
      gagtacgat tgcaccaat gttctaagg aaagtcccc 
      gttgtgggt attacatca ctcggtatc gaccacgtg 
      actttacta ggcgccact atagagtca atagcgtgg 
      aataaagcc ggaattatg aaagaaaat tgccgggcc 
      ttcactgtg ccccaatgc caggccgct atgacggtt 
      ttacaggaa cgcagtatt gaaaaaaaa tgccaactc 
      gaaattgtg gatgattta cagttcaaa ttcccccca 
      aacaaatcg gcacatccg ccccacatt ttaaattta 
      aacgctagt cttgccgtg gcactgtgt aacgcctgg 
      tttttacaa aaaaataac aataattta gggcccgtc 
      atgtcgaaa gaaatcacc gaaaaagca ctgtttgcc 
      accacctgg cctggccgg ttccacgtt aaacacgat 
      aagaacata tcatattac ctagatggg gcgcacacg 
      cttgagagc atcacaatc tgctccagt tggttcaaa 
      gacattacc agaaattcg caaaagaag aaggctcta 
      atgtttaac gttactggt gataggtgt gccgaaaac 
      ttactgaaa caattgcaa acctgtcac tttgatgct 
      gttttgttt gttagtaat agtgcgacg aggtgtagg 
      cctgataac agtaatcac gcgtcttca gacgagttg 
      ctggagaag tgtcaccag cataaaaag ttgtggttg 
      aagctggaa gaagacagt ttgaagaaa agccaaatg 
      tgtaaagct ttcttgacg gttgatgag gcactggag 
      tttttggta aatcaggat cagttcgat ttgttggtc 
      acagggtcc atccattta gttggtagt gttttaagt 
      ttgatcgat cccaattta aacgattaa
    mRNA sequence
    • >TC000540 RA
      gcaaaaatg ggtgaatca cacaatctg acttgcaaa 
      ttttcgaaa aaattggtc acatgactc cagttttga 
      ccggtttac gtaacacag tcgacttga tcagttatc 
      aaataggtt gtcaatgtc acattttct aacctcatt 
      tcgaaagaa aatttttat ttatattta cagtgtgga 
      aaagaaaat tttccacct ttcccggca agataatga 
      ggccgaaca aaaaccaag actatgacg cctgtattg 
      aggctctaa ataacttac aaactaacg cgcaataca 
      tcaaaacga aagcactga cgaataatc acaacggcg 
      atcaactta ctcaagtaa aaaaatatc tctacaggg 
      ctgggctat ctttggaaa atctcgacg acttatcgg 
      tgattcacg tcgctggga ccaaaggca aaggcacga 
      cgtgcgcct tcaccgagc gcattttac gcgaacatg 
      gctataaaa caggatttt tctcctcac cgcacctga 
      tcgaagtca gagaaagga tccgaataa acggcaagc 
      cgatctcaa aacccgact ttgtcaagt cgttttgga 
      aaatttaca acgccctag atcagaaaa agaatgacg 
      agcatgaca tgccactct tcttccggt tcttaacga 
      taatggcat tcagcgttt tcctcgaac gcaaagtcg 
      atgttgcga tcattgagg tcgggattg ggggagagt 
      acgattgca ccaatgttc taaggaaag tccccgttg 
      tgggtatta catcactcg gtatcgacc acgtgactt 
      tactaggcg ccactatag agtcaatag cgtggaata 
      aagccggaa ttatgaaag aaaattgcc gggccttca 
      ctgtgcccc aatgccagg ccgctatga cggttttac 
      aggaacgca gtattgaaa aaaaatgcc aactcgaaa 
      ttgtggatg atttacagt tcaaattcc ccccaaaca 
      aatcggcac atccgcccc acattttaa atttaaacg 
      ctagtcttg ccgtggcac tgtgtaacg cctggtttt 
      tacaaaaaa ataacaata atttagggc ccgtcatgt 
      cgaaagaaa tcaccgaaa aagcactgt ttgccacca 
      cctggcctg gccggttcc acgttaaac acgataaga 
      acatatcat attacctag atggggcgc acacgcttg 
      agagcatca caatctgct ccagttggt tcaaagaca 
      ttaccagaa attcgcaaa agaagaagg ctctaatgt 
      ttaacgtta ctggtgata ggtgtgccg aaaacttac 
      tgaaacaat tgcaaacct gtcactttg atgctgttt 
      tgtttgtta gtaatagtg cgacgaggt gtaggcctg 
      ataacagta atcacgcgt cttcagacg agttgctgg 
      agaagtgtc accagcata aaaagttgt ggttgaagc 
      tggaagaag acagtttga agaaaagcc aaatgtgta 
      aagctttct tgacggttg atgaggcac tggagtttt 
      tggtaaatc aggatcagt tcgatttgt tggtcacag 
      ggtccatcc atttagttg gtagtgttt taagtttga 
      tcgatccca atttaaacg attaaggta aacaagtaa 
      ataagaaaa cactgataa gattttttt tctttatta 
      tgtttaaaa aaatatgta tacagagat cacttcaag 
      gattgtaaa tatcgttag tcgagtgaa attgttttt 
      aattacaat aaaaactac acttgtct
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY