Status
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Gene information
General information
TC001393 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.

NW_015452119.1: 1229..3233
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
    TC001393
    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_00248

    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)

    Fertility
    mature egg deposition blocked number 1st lateral oviduct: 4 number 2nd lateral oviduct: 2 - Number of animals showing the phenotype: 2
    ovary without detectable defects - Number of animals showing the phenotype: 3
    tropharium degenerated - Number of animals showing the phenotype: 3
    vitellogenic egg chamber complete not present - Number of animals showing the phenotype: 3
    previtellogenic egg chamber partially not present - Number of animals showing the phenotype: 3

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: < 50 embryo/egg with embryonic tissue, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 20
    egg without cuticle 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: 0.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 10.0% (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC001393 RA
      MDAFLKRKA ENTGGPSKK PKHEACPHG PKCYRRNPH 
      HFREYEHPH LIKLLEMAK PEIPLDFPL DKSVYLEQV 
      DILRPLLNI KPDVKPSTS SSSVTNTTK PGTMLEKLQ 
      NAAPYNLFF TTIPESAET LKHPTSITF TDLLCPSLG 
      ELKCSLQIN FMIDIMWLM ERYRERNLG KKPLTILYG 
      DEFPKMKEF IEKFLPNVS HHYVKMKDP FGCHHSKIG 
      IYFYEDNSL RVVISTANL YYEDWNHYN QGLWLSPPC 
      PQLPETATE KSGESPTGF KSSLLNYLK HYNLPVLKP 
      WIDYVKRAD FSAVRVFLV TSVPGKHYP GTQGSHVHH 
      VGDLLSRHC SLPAKTGPD SEGPLSWGI IAQASSIGS 
      MGKSPAEWL RSTLLRSLS GHKQTQLVS NSNATLSII 
      FPSVDNVMN GYFGAESGG CLPYSKQTN EKQRWLQSY 
      LHQWKADKL GRSRAMPHI KTYCRVSPC LSKLAWFFI 
      TSANLSKSA WGGNLQKDK GAYVRSYEA GVMFLPKFF 
      DEEYFEIET TLSGKNKKL FPFMYDLPL TEYKSSDYP 
      WCN
    CDS sequence
    • >TC001393 RA
      atggacgca tttttgaag cgtaaggcg gaaaatacc 
      ggcggccct agcaaaaaa cccaagcat gaggcgtgc 
      ccccatggc cccaagtgc taccggcgg aacccgcac 
      catttccgc gaatatgaa cacccccat ttaataaaa 
      ttactcgaa atggctaaa cctgaaata ccgctagac 
      tttcctttg gacaagtct gtttatttg gaacaagtg 
      gacattttg cgcccctta ttgaacatc aaaccggac 
      gttaagcct agcactagc tcgtccagt gttaccaat 
      accacaaaa ccggggact atgctcgaa aaattgcaa 
      aacgcagcc ccttataac ctgtttttt acgacaatt 
      cctgagtcg gcagaaacg ctcaaacac ccgacttcg 
      atcaccttt accgatctg ttgtgcccc agtttgggt 
      gaattaaaa tgttcgtta cagattaat ttcatgatt 
      gatattatg tggttgatg gagcggtac agggagcgt 
      aatttgggg aaaaaaccg ctaacgatt ttatacggg 
      gacgagttc ccgaaaatg aaagaattc atcgagaaa 
      tttctacca aacgtgagc caccattac gtcaaaatg 
      aaagacccg ttcgggtgc caccattcc aaaatcggg 
      atttatttt tacgaagat aattccctt cgtgttgtt 
      atctcaact gcaaattta tactacgag gactggaat 
      cattacaat caagggctc tggttaagt cccccctgt 
      ccgcaactg cccgaaacc gcgacggaa aaatccggt 
      gaatccccg accgggttc aagtcgagt ctcctaaac 
      tacctgaaa cattacaat ttgccggtg ttaaagcca 
      tggattgac tatgtcaaa agggcggat tttagcgcc 
      gttcgggtg tttctcgtg acttccgtc ccggggaaa 
      cactacccg gggacgcaa gggagtcac gtccaccac 
      gtcggtgat ttactgtcg cggcattgt agcctccct 
      gccaagaca gggcccgac agtgagggc cccctctcc 
      tgggggatt atcgcccaa gcgtcgagc atcggctcg 
      atggggaaa tccccggcc gagtggctc cggagcaca 
      cttttgcgc agtctttcc ggccacaaa caaacccaa 
      ctagtttcg aattcgaac gcaacgctt agtattatt 
      ttcccgagt gttgataac gtgatgaat gggtatttc 
      ggggccgaa agtgggggt tgtctgccg tactcgaaa 
      caaacaaat gagaagcag cgctggctg cagagttat 
      ttacaccaa tggaaggcg gataagttg gggcgaagt 
      cgcgcaatg ccacacatt aaaacctac tgtcgcgtc 
      tcgccatgt ttgtccaag ttggcgtgg tttttcatc 
      acgagtgcc aatttatca aagtcggcg tggggtgga 
      aatttacag aaggacaag ggggcgtat gtgaggagt 
      tacgaggcg ggggtcatg tttttgccg aagtttttc 
      gatgaggaa tattttgaa atcgaaact actctcagt 
      ggaaaaaat aaaaaattg ttcccgttt atgtatgat 
      ctgccgctc accgagtac aaatcgagc gactacccg 
      tggtgtaat taa
    mRNA sequence
    • >TC001393 RA
      attcccaaa cgttcaaaa ttccaaccc cactttttt 
      aaacccgaa atggacgca tttttgaag cgtaaggcg 
      gaaaatacc ggcggccct agcaaaaaa cccaagcat 
      gaggcgtgc ccccatggc cccaagtgc taccggcgg 
      aacccgcac catttccgc gaatatgaa cacccccat 
      ttaataaaa ttactcgaa atggctaaa cctgaaata 
      ccgctagac tttcctttg gacaagtct gtttatttg 
      gaacaagtg gacattttg cgcccctta ttgaacatc 
      aaaccggac gttaagcct agcactagc tcgtccagt 
      gttaccaat accacaaaa ccggggact atgctcgaa 
      aaattgcaa aacgcagcc ccttataac ctgtttttt 
      acgacaatt cctgagtcg gcagaaacg ctcaaacac 
      ccgacttcg atcaccttt accgatctg ttgtgcccc 
      agtttgggt gaattaaaa tgttcgtta cagattaat 
      ttcatgatt gatattatg tggttgatg gagcggtac 
      agggagcgt aatttgggg aaaaaaccg ctaacgatt 
      ttatacggg gacgagttc ccgaaaatg aaagaattc 
      atcgagaaa tttctacca aacgtgagc caccattac 
      gtcaaaatg aaagacccg ttcgggtgc caccattcc 
      aaaatcggg atttatttt tacgaagat aattccctt 
      cgtgttgtt atctcaact gcaaattta tactacgag 
      gactggaat cattacaat caagggctc tggttaagt 
      cccccctgt ccgcaactg cccgaaacc gcgacggaa 
      aaatccggt gaatccccg accgggttc aagtcgagt 
      ctcctaaac tacctgaaa cattacaat ttgccggtg 
      ttaaagcca tggattgac tatgtcaaa agggcggat 
      tttagcgcc gttcgggtg tttctcgtg acttccgtc 
      ccggggaaa cactacccg gggacgcaa gggagtcac 
      gtccaccac gtcggtgat ttactgtcg cggcattgt 
      agcctccct gccaagaca gggcccgac agtgagggc 
      cccctctcc tgggggatt atcgcccaa gcgtcgagc 
      atcggctcg atggggaaa tccccggcc gagtggctc 
      cggagcaca cttttgcgc agtctttcc ggccacaaa 
      caaacccaa ctagtttcg aattcgaac gcaacgctt 
      agtattatt ttcccgagt gttgataac gtgatgaat 
      gggtatttc ggggccgaa agtgggggt tgtctgccg 
      tactcgaaa caaacaaat gagaagcag cgctggctg 
      cagagttat ttacaccaa tggaaggcg gataagttg 
      gggcgaagt cgcgcaatg ccacacatt aaaacctac 
      tgtcgcgtc tcgccatgt ttgtccaag ttggcgtgg 
      tttttcatc acgagtgcc aatttatca aagtcggcg 
      tggggtgga aatttacag aaggacaag ggggcgtat 
      gtgaggagt tacgaggcg ggggtcatg tttttgccg 
      aagtttttc gatgaggaa tattttgaa atcgaaact 
      actctcagt ggaaaaaat aaaaaattg ttcccgttt 
      atgtatgat ctgccgctc accgagtac aaatcgagc 
      gactacccg tggtgtaat taatttttt atatcgtat 
      acagtttgt tcaataaaa tttttcaaa aatc
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