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Gene information
General information
TC004959 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: 5263680..5264528
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
    		TC004959
    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_03882

    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: < 50
     head appendages shortened - Penetrance (percentage of animals/eggs on slide): less than 30%

    legs tibiotarsus shortened - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    legs podomer shortened - Penetrance (percentage of animals/eggs on slide): less than 30%
    legs podomer potentially fused - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen segment number decreased - Penetrance (percentage of animals/eggs on slide): less than 30%
    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    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: 20.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 40.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection

    eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 2 (16 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004959 RA
      MDEVFSDLA NIPSEPPEV RSTCPTCER PTSVCWCAA 
LPKPRLCPQ SRIILLQHP AEEKRCLRT APMLHFGLS 
EGKCLVYKG KRFPGRYQD LEELLVGSN TILLYPSPT 
AVDLKSLLQ NNTNTSFNL VIIDGTWPQ AKAIYASNP 
ILHKIKQVK LLTKGVSSY IIRTQPTDG CLSTLETAT 
EALCLLEDD EGYRKLLAP LKTLCDFQL KNGAVSHQS 
KEFLIKNNK YPKLIGKRL NKVLNSVEV LRGE
    CDS sequence
    • >TC004959 RA
      atggatgaa gttttttcc gatttagcc aacatccct 
agcgagccc cccgaagtg cggagcact tgccccaca 
tgcgagcgc cccacgagc gtctgttgg tgtgcggcc 
ctccctaag ccacgtctg tgcccccaa agtcgcata 
atactgctc cagcacccg gctgaagag aagcggtgt 
ttgaggaca gcccccatg ctccatttc gggctaagt 
gaggggaag tgtttggtt tataaagga aagcggttt 
cctggcagg taccaggac ctggaggag cttctagtg 
ggttccaat acgatttta ttgtaccct agtccaaca 
gcggttgat ttgaaatcg ctattgcaa aataacacc 
aatacgagt tttaattta gtgataatt gacgggacg 
tggccgcag gcgaaggcg atatacgcg agtaatccg 
attttacat aaaattaaa caagttaag ttgttgact 
aaaggtgtg agtagttat attataagg acgcagcct 
acggatggg tgtttgagt acgctggag acggcgact 
gaagcgttg tgtttgctt gaggatgat gaggggtac 
aggaagttg ttagccccc ttgaaaaca ttgtgtgac 
tttcagtta aaaaatggt gcagtgtca caccagagt 
aaagaattt ctgattaag aataacaaa tatccgaag 
ttaattggc aaaagatta aataaagtg ttaaattcg 
gtggaagtg ttacgtggc gagtga
    mRNA sequence
    • >TC004959 RA
      ttgctaaat tactttatt taaccaaaa atggatgaa 
gttttttcc gatttagcc aacatccct agcgagccc 
cccgaagtg cggagcact tgccccaca tgcgagcgc 
cccacgagc gtctgttgg tgtgcggcc ctccctaag 
ccacgtctg tgcccccaa agtcgcata atactgctc 
cagcacccg gctgaagag aagcggtgt ttgaggaca 
gcccccatg ctccatttc gggctaagt gaggggaag 
tgtttggtt tataaagga aagcggttt cctggcagg 
taccaggac ctggaggag cttctagtg ggttccaat 
acgatttta ttgtaccct agtccaaca gcggttgat 
ttgaaatcg ctattgcaa aataacacc aatacgagt 
tttaattta gtgataatt gacgggacg tggccgcag 
gcgaaggcg atatacgcg agtaatccg attttacat 
aaaattaaa caagttaag ttgttgact aaaggtgtg 
agtagttat attataagg acgcagcct acggatggg 
tgtttgagt acgctggag acggcgact gaagcgttg 
tgtttgctt gaggatgat gaggggtac aggaagttg 
ttagccccc ttgaaaaca ttgtgtgac tttcagtta 
aaaaatggt gcagtgtca caccagagt aaagaattt 
ctgattaag aataacaaa tatccgaag ttaattggc 
aaaagatta aataaagtg ttaaattcg gtggaagtg 
ttacgtggc gagtgattt tttttaaat aaatacatt 
ttcaaaag

    If you use iBeetle-Base, please cite: Dönitz J et al.: Expanded and updated data and a query pipeline for iBeetle-Base,
    Nucleic Acids Res. 2018 Jan 4;46(D1):D831-D835. doi: 10.1093/nar/gkx984.

    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY