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Gene information
General information
TC004374 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_007425.3: 6950748..6954441
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
    TC004374
    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
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    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_03735

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

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
    abdomen posterior partiallyremaining - Penetrance (percentage of animals/eggs on slide): less than 30%

    head not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    procephalic head not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    head not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    thorax not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): 50% - 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: 0.0% (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004374 RA
      MPDSVELSV ERVLGGLAL EGEESEICD FSLEEQNAA 
      CESQGVQPT VSPNFKPVI GETVTYVVA VVLINDHNE 
      VLMMQEAKE SCAGKWYLP AGRIEKGET ISEAGQREV 
      LEETGLHVQ CTTLIMVEC ARGSWIRYV LTGVATGGK 
      LKTPAEADK ESLQAKWVA NLGELTLRA TDIMDLINR 
      ARAFKEARK ARDQTWHKD QLPCLRPHS RLLLRLVVV 
      IKKKATNRV HVLISEKTS WHLPTCEIH PSKNLHSTL 
      KRFMVDLFG ADVGPHRPH GLLSVEYDP RDRKDGACL 
      TLLVAFRPP LEEVPIIGK CVWHEASKE LGERLLAKV 
      ASKNSTIPI HVIC
    CDS sequence
    • >TC004374 RA
      atgcccgac tctgtggaa ctgagcgtg gagcgcgtc 
      ctcggcggc ttggccctc gagggcgaa gagtcggaa 
      atctgcgac ttctcgctc gaggagcag aacgcggct 
      tgcgagagc cagggggtg cagcccaca gtgagcccc 
      aatttcaag ccggtgatt ggcgagacg gtcacttac 
      gtggtggcc gtggtgctc atcaacgac cacaacgag 
      gtgctgatg atgcaggag gccaaggag tcgtgcgcg 
      ggcaaatgg tacttgccg gcgggccgc atcgaaaag 
      ggggagacc atcagcgag gcgggccag agagaggtg 
      ctggaggag acggggctg catgtgcaa tgcaccact 
      ctgataatg gtggagtgt gcaaggggc tcctggata 
      cggtacgtg ctcacgggg gtggccacc gggggcaag 
      ctaaagaca ccggctgag gcagacaag gagtcactg 
      caagccaaa tgggtcgct aatttgggg gaattaacg 
      ctaagggcc accgatatc atggatttg attaacaga 
      gccagggcg ttcaaagag gcaagaaaa gcccgcgac 
      caaacctgg cacaaagac caacttccg tgtcttcgc 
      ccccattcc agactcctc ctgcgacta gtcgtcgta 
      ataaagaaa aaagccacg aatcgcgtc cacgtttta 
      ataagcgag aagacttcg tggcattta cccacttgt 
      gaaatccac ccgtcgaaa aatctgcat tcgactttg 
      aagcgcttt atggtggat ttgttcggg gctgacgtg 
      gggccccac aggccacat gggttgctt tcggtggag 
      tatgacccg cgcgaccgt aaagacggg gcttgtttg 
      acgctgcta gtggcgttt aggccccct ttggaggag 
      gtccccatc atcggcaag tgtgtctgg catgaggcc 
      tccaaggag ctgggggag aggctcctg gccaaggtg 
      gcctccaag aactccacc attccgatc catgtcatt 
      tgttaa
    mRNA sequence
    • >TC004374 RA
      ttggcaacg ccgcccatt ttcctgtac aacccagaa 
      atgtcacga acgtcacag tggaatatg agaacgtag 
      tgtttatta gtcatgtca tttcaagca ttccattca 
      aattcagca attagttca tctcgtcca agtgccccc 
      ttgtgttcg cgggccaat taatgcgct cgcacttaa 
      cctcaaaat gcccgactc tgtggaact gagcgtgga 
      gcgcgtcct cggcggctt ggccctcga gggcgaaga 
      gtcggaaat ctgcgactt ctcgctcga ggagcagaa 
      cgcggcttg cgagagcca gggggtgca gcccacagt 
      gagccccaa tttcaagcc ggtgattgg cgagacggt 
      cacttacgt ggtggccgt ggtgctcat caacgacca 
      caacgaggt gctgatgat gcaggaggc caaggagtc 
      gtgcgcggg caaatggta cttgccggc gggccgcat 
      cgaaaaggg ggagaccat cagcgaggc gggccagag 
      agaggtgct ggaggagac ggggctgca tgtgcaatg 
      caccactct gataatggt ggagtgtgc aaggggctc 
      ctggatacg gtacgtgct cacgggggt ggccaccgg 
      gggcaagct aaagacacc ggctgaggc agacaagga 
      gtcactgca agccaaatg ggtcgctaa tttggggga 
      attaacgct aagggccac cgatatcat ggatttgat 
      taacagagc cagggcgtt caaagaggc aagaaaagc 
      ccgcgacca aacctggca caaagacca acttccgtg 
      tcttcgccc ccattccag actcctcct gcgactagt 
      cgtcgtaat aaagaaaaa agccacgaa tcgcgtcca 
      cgttttaat aagcgagaa gacttcgtg gcatttacc 
      cacttgtga aatccaccc gtcgaaaaa tctgcattc 
      gactttgaa gcgctttat ggtggattt gttcggggc 
      tgacgtggg gccccacag gccacatgg gttgctttc 
      ggtggagta tgacccgcg cgaccgtaa agacggggc 
      ttgtttgac gctgctagt ggcgtttag gcccccttt 
      ggaggaggt ccccatcat cggcaagtg tgtctggca 
      tgaggcctc caaggagct gggggagag gctcctggc 
      caaggtggc ctccaagaa ctccaccat tccgatcca 
      tgtcatttg ttaaggtgc tacgagtac taaccgggc 
      agtattgtg gttaaggaa cgagtaaat tattgttgc 
      ggattaact gtttattat agttttgta ttttattat 
      tgtttgtgc atgttattg taataaatt attatttat 
      acgacaaat caaataaaa tctacaaaa taaa
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY