Status
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Gene information
General information
TC000296 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: 13342702..13377879
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
    TC000296
    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
    We will use your email address only for possible questions regarding this annotation. We will never show your address or give it away.
    Publish name
    If you have entered your name and agree by marking the checkbox. we might show your name on this page to honor your contribution.
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_09696

    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: < 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: % (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
    • >TC000296 RA
      MYPMVQQQQ QQQQPQQPP QQQRQAPDN ESPEETNGI 
      RHHRSRRPL YRRLFSYVR EAWTGVKFA LDSELEDLE 
      TPPRYRPDS LEALCKATR FTQAEIKRI YRGFKAECP 
      TGVVKEETF KMIYSQFFP QGANTSQYA HYVFNTLDQ 
      QHSGLISFE DFVQNLSIL SRGSLDEKL RWAFTLYDI 
      NGDGCITRE EMTDIVSAV YDLMGKVAE PCVDEDTVK 
      EKVDRIFQK MDKNKDGVV TLDEFLECC RKDEDISSS 
      MAVFDSSI
    CDS sequence
    • >TC000296 RA
      atgtacccc atggtgcaa caacaacag cagcagcaa 
      cagccccaa cagccaccc cagcagcaa aggcaagcg 
      ccagacaac gagagtccg gaagagact aacggaatt 
      agacatcat agatctcgc aggccgttg tacagacga 
      cttttcagc tacgttaga gaagcctgg accggagtt 
      aaattcgct ttagactcg gagctcgag gacttggag 
      acaccgccg cgctaccgc ccggacagc ttggaggcc 
      ctttgcaag gcgaccagg ttcacgcaa gcggaaatc 
      aagaggata tatcgcggc ttcaaggcg gagtgtccg 
      actggtgtc gttaaagaa gagacgttt aaaatgatt 
      tattcgcag ttctttcca caaggtgcc aacaccagc 
      caatatgct cattacgtg ttcaatact ctggatcag 
      caacacagc ggactaatt agctttgag gacttcgtg 
      cagaatttg tccatttta tcgcgaggt tcactagac 
      gagaaactg cgctgggct ttcaccttg tacgatatt 
      aatggagat gggtgcata acgcgcgag gaaatgacg 
      gacattgtt agtgcggtt tatgatttg atggggaag 
      gtggcggag ccgtgcgtt gacgaagac accgtcaag 
      gaaaaggtc gacaggata tttcagaaa atggacaag 
      aataaggac ggcgtcgtc actttggac gaatttctc 
      gagtgctgc aggaaagac gaagacatc tcttcttcc 
      atggctgtt ttcgattca tcgatatga
    mRNA sequence
    • >TC000296 RA
      aaagcttca tcgaaagct ctatggaat atacgttgt 
      ttgtataat cggtgaagg atttgccag tgttggagg 
      aacatattg tggacttat ttgttgcga cttttatgt 
      ctggaaaag cgaactaac ccgactaac cgccccgtt 
      tactaacgc taacacaat gctcctcag tcttcactt 
      gatttcagc gttttatcc taggatgta gtaaagggg 
      tggcgctgt cgtggcgcg ggtcggctt taggatgcc 
      gggcgcatg atgtacccc atggtgcaa caacaacag 
      cagcagcaa cagccccaa cagccaccc cagcagcaa 
      aggcaagcg ccagacaac gagagtccg gaagagact 
      aacggaatt agacatcat agatctcgc aggccgttg 
      tacagacga cttttcagc tacgttaga gaagcctgg 
      accggagtt aaattcgct ttagactcg gagctcgag 
      gacttggag acaccgccg cgctaccgc ccggacagc 
      ttggaggcc ctttgcaag gcgaccagg ttcacgcaa 
      gcggaaatc aagaggata tatcgcggc ttcaaggcg 
      gagtgtccg actggtgtc gttaaagaa gagacgttt 
      aaaatgatt tattcgcag ttctttcca caaggtgcc 
      aacaccagc caatatgct cattacgtg ttcaatact 
      ctggatcag caacacagc ggactaatt agctttgag 
      gacttcgtg cagaatttg tccatttta tcgcgaggt 
      tcactagac gagaaactg cgctgggct ttcaccttg 
      tacgatatt aatggagat gggtgcata acgcgcgag 
      gaaatgacg gacattgtt agtgcggtt tatgatttg 
      atggggaag gtggcggag ccgtgcgtt gacgaagac 
      accgtcaag gaaaaggtc gacaggata tttcagaaa 
      atggacaag aataaggac ggcgtcgtc actttggac 
      gaatttctc gagtgctgc aggaaagac gaagacatc 
      tcttcttcc atggctgtt ttcgattca tcgatatga 
      cgttcacca gtcggcgtt cgtccaccg ccctcctgg 
      acatgaacg aatgccgac cgcgataca atgaccaac 
      gtaattaaa ttatttaaa acagtgata aattaataa 
      caaaacgat ttatgaaaa gccaacaag ctgcggtgt 
      gggacgaat taccggaac gataactca tctcggggt 
      tcgctggct ttgcggttc gtttgacac cgtaagttt 
      gtacattta taccaaatt tcttacagt ttttataaa 
      agaggatgt agataaaat aatatattt taaatatat 
      agaaactaa acatcagat aaatatagc atagataaa 
      taacaaata ttatttaag caaatgtac ctatcgcat 
      ttttgcatt aattaccaa aaaaaattg ctgctaatg 
      cggtttatt tattctgct aaaagtcgc ttgatttgt 
      aataagatt actcaaccg tttcaccaa tggtttaga 
      atttttgtt accctaaag tagatattt ttatattgt 
      ccaacaaaa ttgtggaat tgggtataa agcttttaa 
      aagtttccc caaaattcg ggtattatt cgggaaacg 
      tcttagcga tataaataa agcgacgat atcattact 
      agtgagcca tattcgtta gacatatct gtatgtcac 
      tatataaag tctagatta tattattgt tgatatatg 
      taagactgt tcaatgtac taggatcta aatgtgtga 
      tgtatgtta gtcaaaaga ttgacaata ttttggtta 
      gaaaaacct aagatacct aaattatgt agctttttt 
      attacgaca gttatttta taatggagc gtctatggt 
      gctatgtac caagttgat aaggataat gttcttcta 
      tatgttgtt aatgtttat catttctgt atatgttta 
      atgggtaaa aattagagc tgtgccaaa tacgaacgt 
      tacaaaaaa agctgcaag gcgcagatt acgtttatt 
      tgtagtaag gcttactgt taccaaaat atggtcgag 
      ataatccac gcatattcc taatcctca tcctaatca 
      ctgtttata tctgtatag agtagtcta aggcccatt 
      ttaatgtta cccatctaa ataactcat tgttatttg 
      taaataaga caagtcagg agatctatt atgtactca 
      tttttaatg tta
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY