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Gene information
General information
TC011059 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: 5431147..5436529
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
    		TC011059
    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
    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
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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_01794

    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: 10.0% (includes death as pupa, adult)

    remarks: later than schedule, adult lethality - Number of animals showing the phenotype: 1 (9 dpi)
    Days post injection

    Pupal morphology
    remarks: later than schedule,
    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 leg musculature femural musculature randomnot present - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    Comment: 50-80 % of the larvae seemed to have no muscles in the femur & tibiotarsus, randomly in 1 up to all 6 legs.
    leg musculature tb1-ptar1 randomnot present - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - 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
     larva appendages shape irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    head capsule size decreased - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    head appendages random shape irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    legs tibiotarsus shape irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    legs pretarsus shape irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    abdomen centraldorsoventral-axis increased - 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%
    remarks: bad quality of preparation,
    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: 50.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 60.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 5 (11 dpi)
    Days post injection

    pupal molt delayed (still prepupa) - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection

    eclosion delayed (still pupa) - Number of animals showing the phenotype: 1 (16 dpi)
    Days post injection

    eclosion delayed (still pupa) - Number of animals showing the phenotype: 1 (19 dpi)
    Days post injection

    eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 1 (22 dpi)
    Days post injection

    Fertility
    fertility after larval injection decreased (no living offspring) -
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC011059 RA
      MIHSLFIIN SSGDVFLEK HWRSVISRS VCDYYLEAQ 
RANPNDIAP VIATPHHYL ISIQRSGVS FVAVCMEEI 
PPLFVIEFL HRVVDTFQD YFSDCTESI IKENYVVIY 
ELLDEMLDN GFPLATESN ILKELIKPP NILRTIANT 
VTGKTNVSE VLPTGQLSN IPWRRTGVK YTNNEAYFD 
VIEEVDAII DKSGSTVFA EIQGYIDCC IKLSGMPDL 
TLSFMNPRL FDDVSFHPC VRFKRWEAE RVLSFIPPD 
GNFRLISYH ISSQSVVAI PIYVRHNLS IKSGEQGRL 
DLTVGPKQT LGRTVEAVK IEVLMPKCI LNCVLTANQ 
GKYNFDPVS KILHWDIGR IDVTKLPNI RGSVSIASG 
ANTAEINPS INVHFTINQ LAVSGLKVN RLDMYGEKY 
KPFKGVKYI TKAGRFQIR M
    CDS sequence
    • >TC011059 RA
      atgattcac agtttgttt attattaat tcgtcaggt 
gacgttttc ctggaaaaa cattggcgc agtgtgatt 
tcacgatcg gtttgtgac tattattta gaggcccaa 
agggcgaac ccgaatgac atagccccc gtgatagcc 
accccccat cactacttg atctcaatc cagcgaagt 
ggtgttagt tttgtcgcc gtgtgtatg gaggagatc 
cccccatta ttcgtgatt gaatttttg cacagagtt 
gttgacacg ttccaagat tatttctcc gactgcacc 
gaatcgata attaaagag aattatgtc gtaatttac 
gaattgcta gacgaaatg ttggataat gggttccct 
ctcgcaact gagagtaat attttgaaa gaattaatc 
aagccgcct aatattcta cgaacaatt gccaacact 
gtcacaggg aaaaccaat gtgagcgaa gtattgcca 
actggacaa ttgtcaaat attccatgg cgacgtact 
ggagtcaaa tacacaaat aacgaggcc tactttgat 
gtgatcgaa gaagtcgac gcgattata gataagtca 
ggctccacg gtttttgcc gaaatccag ggttatatc 
gactgttgc atcaaactg agcggcatg cccgacttg 
actctttcg ttcatgaac ccgcgcctt ttcgacgac 
gtcagtttc cacccttgt gtgcgtttt aagcggtgg 
gaggccgaa cgagtgttg tcatttatt ccaccagat 
ggcaatttc cgcctcatt tcgtaccac ataagcagt 
caaagcgtc gtcgcgatc ccgatttac gtccgacac 
aacctgtcg atcaaatcg ggagagcaa ggacgtctg 
gacttgaca gtgggcccc aaacagacc ctggggcga 
acggtcgag gccgttaaa atcgaggtg ctgatgccg 
aaatgcatc ctcaattgt gtgctcact gcgaatcag 
gggaagtac aactttgac ccggtttcg aaaattttg 
cactgggat attggcagg attgacgtc accaaactg 
ccgaatatt aggggaagt gtgtcaatc gccagtggg 
gccaacact gcggagatt aatccgtcc ataaatgtg 
cattttacg ataaatcag ctcgcagtg agcggattg 
aaagttaat agacttgac atgtatgga gagaagtat 
aagcctttt aagggggtg aaatacata acgaaagcg 
ggacgattc caaatcagg atgtga
    mRNA sequence
    • >TC011059 RA
      caaatgagc gacttttat tagctgacg tgtttttat 
ttacttagg aaaatgcca atggtgata ttccatcac 
agttaatac aattattta cataaaagg gcttaaatt 
aagtttgga gattaataa gtaattttt tgcctttgt 
gcacctcaa gtgtattgt cacttgtca aaagtttgt 
cgcccctaa cctcaaaac ccaaaatga ttcacagtt 
tgtttatta ttaattcgt caggtgacg ttttcctgg 
aaaaacatt ggcgcagtg tgatttcac gatcggttt 
gtgactatt atttagagg cccaaaggg cgaacccga 
atgacatag cccccgtga tagccaccc cccatcact 
acttgatct caatccagc gaagtggtg ttagttttg 
tcgccgtgt gtatggagg agatccccc cattattcg 
tgattgaat ttttgcaca gagttgttg acacgttcc 
aagattatt tctccgact gcaccgaat cgataatta 
aagagaatt atgtcgtaa tttacgaat tgctagacg 
aaatgttgg ataatgggt tccctctcg caactgaga 
gtaatattt tgaaagaat taatcaagc cgcctaata 
ttctacgaa caattgcca acactgtca cagggaaaa 
ccaatgtga gcgaagtat tgccaactg gacaattgt 
caaatattc catggcgac gtactggag tcaaataca 
caaataacg aggcctact ttgatgtga tcgaagaag 
tcgacgcga ttatagata agtcaggct ccacggttt 
ttgccgaaa tccagggtt atatcgact gttgcatca 
aactgagcg gcatgcccg acttgactc tttcgttca 
tgaacccgc gccttttcg acgacgtca gtttccacc 
cttgtgtgc gttttaagc ggtgggagg ccgaacgag 
tgttgtcat ttattccac cagatggca atttccgcc 
tcatttcgt accacataa gcagtcaaa gcgtcgtcg 
cgatcccga tttacgtcc gacacaacc tgtcgatca 
aatcgggag agcaaggac gtctggact tgacagtgg 
gccccaaac agaccctgg ggcgaacgg tcgaggccg 
ttaaaatcg aggtgctga tgccgaaat gcatcctca 
attgtgtgc tcactgcga atcagggga agtacaact 
ttgacccgg tttcgaaaa ttttgcact gggatattg 
gcaggattg acgtcacca aactgccga atattaggg 
gaagtgtgt caatcgcca gtggggcca acactgcgg 
agattaatc cgtccataa atgtgcatt ttacgataa 
atcagctcg cagtgagcg gattgaaag ttaatagac 
ttgacatgt atggagaga agtataagc cttttaagg 
gggtgaaat acataacga aagcgggac gattccaaa 
tcaggatgt gagaaaaat gtgcaagaa ccgattttt 
atttttata taaataagt tgcaaatgt attatctca 
ttgtcaata aatgttgat tatttaa

    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