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Gene information
General information
TC013630 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_007416.3: 2901788..2909655
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
    TC013630
    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
    {{ goGene }}
    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
    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
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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_08367

    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
    vitellogenic egg chamber fused - Number of animals showing the phenotype: 3

    egg chamber pattern irregular - Number of animals showing the phenotype: 2

    mature egg number increased - Number of animals showing the phenotype: 3

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: < 50 larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): less than 30%
    remarks: muscle pattern potentially obscured by segmentation defect,
    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): 30% - 50%
    cuticle remnants with some identifiable segments - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    larva segment random not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    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
    • >TC013630 RA
      MPRPPRETY GDQKPPYSY ISLTAMAIW SSPEKMLPL 
      SEIYRFITD RFPYYRRNT QRWQNSLRH NLSFNDCFI 
      KIPRRPDRP GKGAFWALH PSALDMFEN GSFLRRRKR 
      FKLPKHVHE ELDSLSKLN SSFMGGQTI SPTPSACPP 
      IVCPPELPL PPITPVATT APKSFSIDS IIQSEPKSP 
      QFPTNVPPI QALPSLSWV NMMTPSTSQ SELQSRDDL 
      IMAQKAAFF EYAAAIFSI NASTSAKTG TGVIRPLPI 
      MPNALYPAT CHTVPVPVQ YSFCMPNMR NLEFETEHE 
      CDRTIMDKN ISLNYLIAQ NGQEDNIEI SSSSSEEAT 
      NV
    CDS sequence
    • >TC013630 RA
      atgccaagg ccacctcgt gaaacatac ggggaccag 
      aaaccacca tactcgtac atatctctc acagcgatg 
      gccatctgg agctccccg gagaaaatg ctacccctt 
      tcggagatc taccgattc atcaccgac cgcttcccc 
      tactaccgg cggaacacc cagaggtgg caaaactcc 
      ctgcgacac aacctctcc ttcaacgac tgcttcatc 
      aagatcccg cggcggccc gacaggccc ggcaagggc 
      gccttctgg gccctgcac ccctcggcc ctggacatg 
      ttcgagaac gggagcttc ctcagacgg cggaagcgc 
      ttcaagctg cccaagcac gtccacgag gagctcgac 
      agcctctcg aaactgaac agttccttc atggggggg 
      cagaccatc agcccgacc ccgtccgcc tgccccccg 
      atcgtgtgc ccccccgag ctgccgctc ccgcccatc 
      acccccgtg gccaccacc gcccccaag tccttcagc 
      atcgacagc atcatccaa agcgagccg aagtcgccg 
      cagttcccc acgaacgtg cccccgatc caggccctc 
      cctagcctg tcctgggtc aacatgatg accccctcc 
      acctcccag agcgagctc cagagccga gacgacttg 
      atcatggcc cagaaagcg gcgtttttc gaatacgcc 
      gccgccatt ttttcgata aatgcctcg acgagcgcg 
      aagacgggc actggggtc atacgaccc ctgcccatc 
      atgcccaac gctctctac ccggcgacc tgccatacg 
      gtaccggta ccagtgcaa tactccttc tgcatgccc 
      aatatgcgc aacttggaa tttgagact gagcacgaa 
      tgtgataga accatcatg gacaaaaat atctcactc 
      aactattta atcgcccag aatggccaa gaggacaac 
      atcgaaatc tcctcctcg tcctcggag gaggccacc 
      aacgtgtaa
    mRNA sequence
    • >TC013630 RA
      acacatttt tgatcacac tctcttaga taaaccgat 
      ttgtaaagt taactacaa agctaagcc gacaatccc 
      atcagaaaa taagccgac agtgatttt ctttgtgcg 
      gttgctgaa caccattat gtacactgg tgcggtata 
      gtgtttgtg tacgaagga ctgtacaga tttatttat 
      ttaatttgt catgtggca caaatggat aaaggggac 
      aacttaaaa gtcgtcagc agaaatgcc aaggccacc 
      tcgtgaaac atacgggga ccagaaacc accatactc 
      gtacatatc tctcacagc gatggccat ctggagctc 
      cccggagaa aatgctacc cctttcgga gatctaccg 
      attcatcac cgaccgctt cccctacta ccggcggaa 
      cacccagag gtggcaaaa ctccctgcg acacaacct 
      ctccttcaa cgactgctt catcaagat cccgcggcg 
      gcccgacag gcccggcaa gggcgcctt ctgggccct 
      gcacccctc ggccctgga catgttcga gaacgggag 
      cttcctcag acggcggaa gcgcttcaa gctgcccaa 
      gcacgtcca cgaggagct cgacagcct ctcgaaact 
      gaacagttc cttcatggg ggggcagac catcagccc 
      gaccccgtc cgcctgccc cccgatcgt gtgcccccc 
      cgagctgcc gctcccgcc catcacccc cgtggccac 
      caccgcccc caagtcctt cagcatcga cagcatcat 
      ccaaagcga gccgaagtc gccgcagtt ccccacgaa 
      cgtgccccc gatccaggc cctccctag cctgtcctg 
      ggtcaacat gatgacccc ctccacctc ccagagcga 
      gctccagag ccgagacga cttgatcat ggcccagaa 
      agcggcgtt tttcgaata cgccgccgc cattttttc 
      gataaatgc ctcgacgag cgcgaagac gggcactgg 
      ggtcatacg acccctgcc catcatgcc caacgctct 
      ctacccggc gacctgcca tacggtacc ggtaccagt 
      gcaatactc cttctgcat gcccaatat gcgcaactt 
      ggaatttga gactgagca cgaatgtga tagaaccat 
      catggacaa aaatatctc actcaacta tttaatcgc 
      ccagaatgg ccaagagga caacatcga aatctcctc 
      ctcgtcctc ggaggaggc caccaacgt gtaaatact 
      ccgtgtgca aactgtgtt aatgtattt tagttctta 
      tagttatat ttaaataaa agttgagaa gaaaa
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY