Status
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Gene information
General information
TC005399 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_007423.3: 13785219..13796807
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
    		TC005399
    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_00846

    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)

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

    Fertility
    ovary without detectable defects - Number of animals showing the phenotype: 4
    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: < 50 embryo/egg not developed/not fertilized - Penetrance (percentage of animals/eggs on slide): more than 80%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): more than 80%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 50
     egg without cuticle embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): more than 80%
    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - 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: 40.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 50.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 4 (11 dpi)
    Days post injection

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

    adult lethality - Number of animals showing the phenotype: 1 (22 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (41 dpi)
    Days post injection

    Fertility
    egg production: number no/almost no eggs -
    vitellogenic egg chamber shape rounded - Number of animals showing the phenotype: 4

    previtellogenic egg chamber sometimespattern irregular - Number of animals showing the phenotype: 4

    Comment: Number of somatic cells sometimes INCREASED.
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC005399 RA
      MPCSAVTLS LATITSIIA VALLAIAFA TDNWLYIEV 
KRTNIQNYL SKHSDVQSQ AQLESLTSK YYYYTRTKG 
LFRICYPKE RPPTVKTYL SPVETHCNN INYYLSDDN 
NETRDFTDD AWARLHMGR SMIALFSLA FAAVFAAFC 
TGVTGCWRR SPSNITATA ILMLLACLL SAGGMGLWH 
GVEYYEKEK VVGEEFYQQ WSNILQENS EIMYDWSFV 
LGWLGVFSA LGASFMFFF GSCCLSTEK EKEQLNNVL 
RDNTRVNYD WSYMIAWVG VGWSLVAAI LFSGAAMCL 
RGEREREEA INMQYLMPV YPQKQQYAY AGYPVPAPQ 
AYAGPYYTT GSAYGPYNY
    CDS sequence
    • >TC005399 RA
      atgccgtgc tctgctgtt actttaagt ttagcaaca 
atcacttcg atcattgct gttgccctc ctggccatc 
gctttcgcc accgataac tggctttat atcgaagtt 
aagcgcaca aatattcag aactatttg agtaaacat 
tcggacgtt caaagccaa gctcagttg gaaagcctc 
acttccaaa tactactac tacacgagg acgaaagga 
ctcttcagg atatgctat ccgaaagaa aggccccca 
acagtgaaa acatacttg agcccagtt gagacgcac 
tgtaacaac atcaactat tacctttcg gacgataac 
aacgagact cgggacttc accgacgat gcttgggct 
agattacat atgggtcgg tccatgatc gcccttttc 
agcttggcc ttcgccgcg gtgttcgca gccttctgc 
acaggagtc accggatgc tggaggagg tcccccagc 
aatatcacg gccactgcg attctgatg ctgcttgca 
tgcttgttg agcgctgga ggaatgggt ctgtggcat 
ggagtggaa tattacgag aaggaaaaa gtcgtcgga 
gaggaattc taccaacaa tggagtaac atcctgcaa 
gagaacagc gaaatcatg tacgactgg agcttcgtc 
ctgggctgg ttgggtgtt ttcagtgca ctgggcgcc 
tcattcatg tttttcttt ggttcgtgt tgcctgagc 
acagaaaaa gaaaaggag caattgaac aacgtccta 
cgtgacaat acaagagtc aactatgat tggagttac 
atgatcgca tgggttggg gtgggatgg tcgttggtt 
gctgccatc ctgttttct ggagccgca atgtgtctt 
cgaggcgaa agggaacgg gaagaagcg atcaacatg 
cagtattta atgcctgtg tatccgcaa aagcagcaa 
tatgcctat gccggatat ccggtgcct gcgccccaa 
gcctacgca ggaccgtat tacacgaca gggtcagcc 
tatgggccg tataattac tga
    mRNA sequence
    • >TC005399 RA
      caggtatga aacaggttc ttggcgttt cctcaagca 
ggtagagga ccactttca gagttgtag tcggtcgtg 
gtttgtagt taacatgtt ccggagttt agtttagtt 
tgtggtgtt gtttttgga atttgttgc aaaatgccg 
tgctctgct gttacttta agtttagca acaatcact 
tcgatcatt gctgttgcc ctcctggcc atcgctttc 
gccaccgat aactggctt tatatcgaa gttaagcgc 
acaaatatt cagaactat ttgagtaaa cattcggac 
gttcaaagc caagctcag ttggaaagc ctcacttcc 
aaatactac tactacacg aggacgaaa ggactcttc 
aggatatgc tatccgaaa gaaaggccc ccaacagtg 
aaaacatac ttgagccca gttgagacg cactgtaac 
aacatcaac tattacctt tcggacgat aacaacgag 
actcgggac ttcaccgac gatgcttgg gctagatta 
catatgggt cggtccatg atcgccctt ttcagcttg 
gccttcgcc gcggtgttc gcagccttc tgcacagga 
gtcaccgga tgctggagg aggtccccc agcaatatc 
acggccact gcgattctg atgctgctt gcatgcttg 
ttgagcgct ggaggaatg ggtctgtgg catggagtg 
gaatattac gagaaggaa aaagtcgtc ggagaggaa 
ttctaccaa caatggagt aacatcctg caagagaac 
agcgaaatc atgtacgac tggagcttc gtcctgggc 
tggttgggt gttttcagt gcactgggc gcctcattc 
atgtttttc tttggttcg tgttgcctg agcacagaa 
aaagaaaag gagcaattg aacaacgtc ctacgtgac 
aatacaaga gtcaactat gattggagt tacatgatc 
gcatgggtt ggggtggga tggtcgttg gttgctgcc 
atcctgttt tctggagcc gcaatgtgt cttcgaggc 
gaaagggaa cgggaagaa gcgatcaac atgcagtat 
ttaatgcct gtgtatccg caaaagcag caatatgcc 
tatgccgga tatccggtg cctgcgccc caagcctac 
gcaggaccg tattacacg acagggtca gcctatggg 
ccgtataat tactgaaag gacaacgac gcatgcaat 
agactgtct tccattttc tacaaatag tattaaatt 
ttgacgttt ttttggcca tcatgcaaa agaatgggt 
gcctcattc gttgtaaat aagtcgtta ggtaatcgc 
agcaggcca gggcgaaac aaaattttt attttcacg 
actaataat aaaattcta gtcgggacc aaacatcag 
tatttttaa atcccgccc tcaacatca actaaccat 
ggtcatttt ttgtaaata gttgtgttt aattgatgt 
cgtgactgc cattttgtt gcatttttc ttagtcatc 
acacagagg cgtatttat tttgatttc gggacacgg 
aatcggaaa gatacctgt tatatgact gtataattg 
taatcatac cgggggttt gggtaaaag cgcggtcaa 
gtgtgcgtg gctatcgcg gcacacttg acggcattt 
tgcccggac tcctcctat ttatgtcta gcaatattt 
gtattttta tatgttgtg tacttaccg taattacgt 
attcagtgt atttttgga ggtttttgt tatcaaaaa 
cgttgcaat aaattcgag acaactta

    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