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Gene information
General information
TC003990 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_007418.3: 28980452..28981445
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
    TC003990
    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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    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_07096

    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: 50.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 4 (3 dpi)
    Days post injection


    adult lethality - Number of animals showing the phenotype: 1 (9 dpi)
    Days post injection


    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): 50% - 80%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    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): less than 30%

    head capsule size decreased - Penetrance (percentage of animals/eggs on slide): less than 30%

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

    head appendages random not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    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
    • >TC003990 RA
      MKIFLLLIP LWASAQSHD IYVHMMPWF 
      ETKETNGGT WGIHWTMAN RNPDNIIDG 
      KQDIASFYH PEIGAYASA DPNVIDWQM 
      GYMKTAGIK GIFLDWPGT TQAMDYPKN 
      RENCEAIIA GTERAGLQF AVVYEDNNL 
      NLAGVPDKI AQGTADMQY LQDNYFSKS 
      NYVKVNGAP LLLDFGPQA LFDANWDAI 
      FTPLNPKPT FLTLWNQHQ QGGSMVAGE 
      YAWVYSNFL DGLNNWLVH
    CDS sequence
    • >TC003990 RA
      atgaaaata tttctattg ttaatcccc ctctgggct 
      tcggcccaa agccacgac atctacgtc cacatgatg 
      ccctggttc gagaccaag gaaaccaac ggcggcacc 
      tggggcatc cactggacc atggccaac agaaacccc 
      gacaacatc atcgacggc aagcaagac atagcctcc 
      ttctaccac cctgaaatc ggggcttac gcctccgca 
      gaccccaac gtcatcgac tggcaaatg gggtacatg 
      aagaccgcc gggatcaag ggaattttc ctagactgg 
      cccggaacc acccaagcc atggactac ccgaaaaat 
      agggaaaat tgcgaagct ataattgcc ggaactgaa 
      agagcgggc ctccagttc gcagtagtg tacgaagac 
      aacaactta aaccttgcc ggagtcccc gataaaatt 
      gcacaaggt accgccgac atgcagtac ctccaagac 
      aattatttc agcaaaagc aactacgtg aaagtgaat 
      ggggccccc ttgttgctg gattttggg ccccaagcg 
      ttgtttgac gccaactgg gacgctatt ttcacaccc 
      ttgaacccc aaacccacg tttctgacg ctatggaac 
      caacatcag cagggaggg agtatggtg gcgggcgaa 
      tatgcgtgg gtgtattca aattttctt gatgggctc 
      aataattgg ttagtgcac taa
    mRNA sequence
    • >TC003990 RA
      tgatttgca aatatataa acaccacat cgtgaaaaa 
      ttgccagaa aaatgaaaa tatttctat tgttaatcc 
      ccctctggg cttcggccc aaagccacg acatctacg 
      tccacatga tgccctggt tcgagacca aggaaacca 
      acggcggca cctggggca tccactgga ccatggcca 
      acagaaacc ccgacaaca tcatcgacg gcaagcaag 
      acatagcct ccttctacc accctgaaa tcggggctt 
      acgcctccg cagacccca acgtcatcg actggcaaa 
      tggggtaca tgaagaccg ccgggatca agggaattt 
      tcctagact ggcccggaa ccacccaag ccatggact 
      acccgaaaa atagggaaa attgcgaag ctataattg 
      ccggaactg aaagagcgg gcctccagt tcgcagtag 
      tgtacgaag acaacaact taaaccttg ccggagtcc 
      ccgataaaa ttgcacaag gtaccgccg acatgcagt 
      acctccaag acaattatt tcagcaaaa gcaactacg 
      tgaaagtga atggggccc ccttgttgc tggattttg 
      ggccccaag cgttgtttg acgccaact gggacgcta 
      ttttcacac ccttgaacc ccaaaccca cgtttctga 
      cgctatgga accaacatc agcagggag ggagtatgg 
      tggcgggcg aatatgcgt gggtgtatt caaattttc 
      ttgatgggc tcaataatt ggttagtgc actaacgct 
      tttgcttta catacattc tacaacttc gaaaaaatt 
      cgattcaga tgcaactct tagtcattt aatggaaac 
      agaaacact acatagagg aattggaag attcagaaa 
      cattcaatt gaagtcctg gatatacct catattcta 
      tctatttac tctgaatca taaaagaaa taacaagcc 
      gaaaa
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY