Status
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Gene information
General information
TC005943 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: 5126229..5128606
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
    TC005943
    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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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_09280

    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
    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
    • >TC005943 RA
      MVHIKCRTG LYPFSEIRR LVLTDAQVP WAVPVENYT 
      PPNYDAPVL RNKPWADPP CDDPNFHPK WNNLDGTIN 
      RKSHTGPYK IVDGRPLNP EGRTGLAGR GVLGKWGPN 
      HAADPIVTR WKSPKELHR ETKLPILQF CAIQRRDCG 
      QWAIPGGMV DPGEKISET LKREFLEEA FNSLENTDK 
      MSEELIEGF FSKGEEIFK GYVDDPRNT DNAWMETVA 
      VNFHDDNNE TVGKFKLQA GDDAKNVKW VDIDSKLDL 
      YASHSNFIQ AVAKLRQAH W
    CDS sequence
    • >TC005943 RA
      atggtgcac ataaaatgc aggaccggc ctttacccg 
      tttagcgaa atccgccgt ttggtcctc accgatgcc 
      caagtaccc tgggccgta ccggtcgaa aattatacg 
      ccccccaac tatgacgcc cctgtcttg cgcaacaaa 
      ccatgggcg gacccccct tgtgacgac ccaaatttc 
      cacccaaaa tggaacaac cttgacggt acaatcaac 
      cgtaagagc cacaccggc ccttataaa attgttgat 
      gggcgccca cttaatccc gagggcagg accggcctg 
      gccggacgg ggggttttg ggcaaatgg ggccccaac 
      catgccgct gatcctatt gtcacacgg tggaagtca 
      ccgaaagaa ttgcatcga gagacaaaa ttgcccatt 
      ttgcagttc tgcgctatc cagagacgg gattgcggc 
      caatgggcc attcctgga ggaatggtc gatccaggt 
      gagaaaatc agcgagact ttaaaacgg gaatttctg 
      gaagaagcg ttcaacagt ttggaaaat acagacaag 
      atgagtgag gaattgatt gaggggttt ttctcaaag 
      ggtgaggag atttttaag ggctatgtg gacgaccct 
      agaaacact gataatgca tggatggag accgtagct 
      gtgaatttc cacgatgat aataacgaa actgtcggg 
      aaatttaaa ctacaggcg ggggatgat gctaaaaac 
      gtcaagtgg gttgatatt gactcaaaa ttggatttg 
      tacgcaagt cattctaat ttcatccaa gctgtggca 
      aaactgaga caggcacat tggtaa
    mRNA sequence
    • >TC005943 RA
      attataatt agtttccta acctcaaaa atggtgcac 
      ataaaatgc aggaccggc ctttacccg tttagcgaa 
      atccgccgt ttggtcctc accgatgcc caagtaccc 
      tgggccgta ccggtcgaa aattatacg ccccccaac 
      tatgacgcc cctgtcttg cgcaacaaa ccatgggcg 
      gacccccct tgtgacgac ccaaatttc cacccaaaa 
      tggaacaac cttgacggt acaatcaac cgtaagagc 
      cacaccggc ccttataaa attgttgat gggcgccca 
      cttaatccc gagggcagg accggcctg gccggacgg 
      ggggttttg ggcaaatgg ggccccaac catgccgct 
      gatcctatt gtcacacgg tggaagtca ccgaaagaa 
      ttgcatcga gagacaaaa ttgcccatt ttgcagttc 
      tgcgctatc cagagacgg gattgcggc caatgggcc 
      attcctgga ggaatggtc gatccaggt gagaaaatc 
      agcgagact ttaaaacgg gaatttctg gaagaagcg 
      ttcaacagt ttggaaaat acagacaag atgagtgag 
      gaattgatt gaggggttt ttctcaaag ggtgaggag 
      atttttaag ggctatgtg gacgaccct agaaacact 
      gataatgca tggatggag accgtagct gtgaatttc 
      cacgatgat aataacgaa actgtcggg aaatttaaa 
      ctacaggcg ggggatgat gctaaaaac gtcaagtgg 
      gttgatatt gactcaaaa ttggatttg tacgcaagt 
      cattctaat ttcatccaa gctgtggca aaactgaga 
      caggcacat tggtaaaaa cataagtta ttataaata 
      atctatttt atacagaat ttcataatt atgttacgc 
      cactcctgg agataatta actctctcg agcgctctg 
      ttttgtact atgatatgc acaacacaa aataattct 
      ttttttttt ctttcaata aatatttat gtaattgcg 
      attacctaa ttgtaccta cgctttaca ttattttat 
      gtttacaac aaacttgtt cattagtaa attccctac 
      gaacatttt atgctagag aggaaaatt atgagaaag 
      aaaaaaaca taacgtaat accagtgct tgataaaaa 
      attaaaatg cataaaata tacacaaga gaaaacccg 
      aaattcata ctaatactg acggtgatt tttcttaca 
      ccgttaaaa tcatattta cagcgccga gtcgggtta 
      atcgggccg gtaacgcag acgtcgctc ttaccgaca 
      tcgcaagtc atatacagt gcgatctta aaaactaat 
      tcggtcgtt ttctactca caaaaaaga tttttgggc 
      aatactcgg gtggccaga cgtcctttt ttatgaaca 
      taaatttta actgaattt tatagtaaa acgttctct 
      attcgctga aattttgct attttgaga ctatcgtat 
      aaaaagtta cataagttt agaaatggt atgaaaaaa 
      atcactgta tatggaggc ttcaagttt aagttttaa 
      cggccttaa caatatttt gacaatttt tatgaggtg 
      atcgaattt acatcctaa ggtgaggtc tttattatt 
      tgtagtaga aatacaaat ttcaactta atattgcag 
      ttatgccta aaacaaaac gtaaatttg aagatgaat 
      taaaagctg tgtaaccaa tcacaaaat ttttcaact 
      gtgaaaaaa ggtgctcta ggtttggag caacattta 
      ggcacagga aagcataaa taaaaaaat agtggtgca 
      gaaactttt gtgttacga tttcaaatg gtgaagagt 
      taatagcag aagcagaag gaactttag ttttcgctc 
      aaatgattg tacaatcaa gttattaca aaagtgtta 
      cctatctcg aatttggca aaagaaaat gtgcgcgaa 
      caaaatcac aagctatca ttgtagctg tcttgcttt 
      tcagacttc tagttacat tggtatttc tacagatgc 
      taatagttt aaaaatgtt acaaaggaa ttcctatga 
      taagttaac caacaaaac gacatggaa aaggtacaa 
      ttactaatt tgaaccatt tgaattgaa caatttcaa 
      aaatattat tatttataa tttccactt gacggcaaa 
      atgtccagt aactgccga acatttaaa taagaaact 
      gacgaagtc cttggctgg aaaagcagc acgtcacgt 
      cttagaaga atagaaaaa ttctaattg aaattaaaa 
      tttggtaac atgtgttaa gcgtg
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY