Status
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Gene information
General information
TC009298 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_007422.5: 1781680..1783841
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
    		TC009298
    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_08625

    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: 30.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 1 (3 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 2 (9 dpi)
    Days post injection

    Adult morphology
    abdominal odoriferous glands size decreased - Number of animals showing the phenotype: 5 (13 dpi)
    Days post injection


    abdominal odoriferous glands content opaque - Number of animals showing the phenotype: 5 (13 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg with embryonic tissue potentially present, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    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): less than 30%
    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): 50% - 80%

    mandible not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    head appendages partially not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    legs podomer partially not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    abdomen segment number decreased - 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
    • >TC009298 RA
      MTNNKPNCA CLFPFLPCW YPLSPDDLI KKRRSNDID 
KQIAKDKEE FNKTLRLLL LGAGESGKS TIIKQMQLI 
HVDKFSDTV RKQRRDDIR DNLADAIVS ILGAMPKIT 
PPVRLDNER HETMAKWVL DNATKQDFD YPSQFYEFT 
KILWKDTGV QATFERSNE YQLVDSAKY FLEKIDEIA 
RDDYMPTDQ DIIRCRVLT TGIYELSFQ VKEINFQII 
DVGGQRDER RKWFLCFND VTAIIFVTA CSSYNLVLR 
EDPSKNRLK ESLELFKIV WNNRWLCRI SVIVFLNKQ 
DLFREKILS GRSKLEDYF PEYKDFKTS HVERDEHPE 
VNRAKHFIK NEFEKISRL SNQSLQHRF YPHFTCAVD 
TDDVKRVFD VCQTVFDDC RKNIQIKHL IEHDLM
    CDS sequence
    • >TC009298 RA
      atgactaac aataaacca aactgcgcg tgtttgttt 
ccattcttg ccctgttgg taccccctg agccccgac 
gatttgatc aagaagcgg cgcagcaat gacatcgac 
aagcagatt gctaaagac aaggaggag tttaataaa 
accctccgc ttgttactg ttgggggcc ggggagtca 
ggcaagtcc accatcatc aaacagatg cagcttatc 
cacgtggat aagttcagt gatacggtt aggaagcaa 
agacgggac gatattaga gacaatctg gctgatgcg 
atagtgagc atacttggg gccatgccc aaaatcact 
ccgccagtc agattagat aatgagagg catgagaca 
atggcaaag tgggtgcta gataacgca actaagcag 
gattttgat tatccgagc cagttttac gagtttacg 
aaaattttg tggaaggat acaggcgtt caggccact 
tttgagagg agtaacgaa tatcagttg gtagacagt 
gctaagtat tttttggaa aagatcgac gaaattgca 
agggatgat tacatgccc actgatcag gatattata 
agatgcagg gtcctaact acgggtatt tacgaactc 
tccttccaa gtcaaggaa attaatttc caaataatc 
gacgttggg gggcagcgg gacgagcgc cgcaagtgg 
ttcttgtgc ttcaatgac gtcacggcg attatcttc 
gtcacagct tgtagttcc tataatttg gttttgcgc 
gaagacccg tccaaaaac cgcctcaaa gagagcctc 
gaattgttc aaaatcgtg tggaacaac cgctggttg 
tgccgcatt tccgtgata gtgttctta aataagcag 
gatctcttc agggaaaaa atcctctca gggcgcagt 
aaactcgag gactacttt cccgaatat aaagacttc 
aagacgtcg cacgtggaa cgcgacgag catcccgag 
gtgaatcgg gccaaacat tttataaaa aacgagttt 
gaaaaaatt agccgattg agcaatcaa tcgttacag 
caccggttt tacccccat ttcacgtgt gcggtagac 
actgacgac gttaagagg gtctttgat gtgtgtcaa 
acggtgttt gacgactgt cgcaaaaac atccaaatc 
aagcatctc atcgaacac gatttaatg taa
    mRNA sequence
    • >TC009298 RA
      gccacccaa cgtcaacca actgtcacg ttgacacgt 
cgcctaacc caacttatt tgtttatga ttttcggct 
tgtttttcg cggtgattc gactagatt taagttcag 
gatgtacta tgactaaca ataaaccaa actgcgcgt 
gtttgtttc cattcttgc cctgttggt accccctga 
gccccgacg atttgatca agaagcggc gcagcaatg 
acatcgaca agcagattg ctaaagaca aggaggagt 
ttaataaaa ccctccgct tgttactgt tgggggccg 
gggagtcag gcaagtcca ccatcatca aacagatgc 
agcttatcc acgtggata agttcagtg atacggtta 
ggaagcaaa gacgggacg atattagag acaatctgg 
ctgatgcga tagtgagca tacttgggg ccatgccca 
aaatcactc cgccagtca gattagata atgagaggc 
atgagacaa tggcaaagt gggtgctag ataacgcaa 
ctaagcagg attttgatt atccgagcc agttttacg 
agtttacga aaattttgt ggaaggata caggcgttc 
aggccactt ttgagagga gtaacgaat atcagttgg 
tagacagtg ctaagtatt ttttggaaa agatcgacg 
aaattgcaa gggatgatt acatgccca ctgatcagg 
atattataa gatgcaggg tcctaacta cgggtattt 
acgaactct ccttccaag tcaaggaaa ttaatttcc 
aaataatcg acgttgggg ggcagcggg acgagcgcc 
gcaagtggt tcttgtgct tcaatgacg tcacggcga 
ttatcttcg tcacagctt gtagttcct ataatttgg 
ttttgcgcg aagacccgt ccaaaaacc gcctcaaag 
agagcctcg aattgttca aaatcgtgt ggaacaacc 
gctggttgt gccgcattt ccgtgatag tgttcttaa 
ataagcagg atctcttca gggaaaaaa tcctctcag 
ggcgcagta aactcgagg actactttc ccgaatata 
aagacttca agacgtcgc acgtggaac gcgacgagc 
atcccgagg tgaatcggg ccaaacatt ttataaaaa 
acgagtttg aaaaaatta gccgattga gcaatcaat 
cgttacagc accggtttt acccccatt tcacgtgtg 
cggtagaca ctgacgacg ttaagaggg tctttgatg 
tgtgtcaaa cggtgtttg acgactgtc gcaaaaaca 
tccaaatca agcatctca tcgaacacg atttaatgt 
aactgtggt acttatgca agcatttat ttttgttat 
ctattgtag tttactttt atgttctca aagaacgaa 
aactagtct agtcggttt ctgattcag tatttgtat 
gtgatatag cgagagtcg aaataaaac gcggtcaag 
agtgctgtg acattatgt aaattaaac aattggtat 
atttgacag attattgat aggtgttga cgttcatgt 
catagcacc cttgaccac gcttacttg ttaaaacga 
atttttatg cttcctcca gtggcgcct cggcagttc 
aaaactagg caaaattgt atcaaaatt gataaaaat 
caatcagtt aactacctg gaaaattac gttattttg 
aggtacaaa cccaagaag gagaaaaga ttcattact 
attcattaa ttttaggtg gagtcactt cacctattt 
gattaagcg agtcgccac tggcttttt tagttttca 
tcctgttat tcgtgcctt tacacgaac taaaatctg 
gacaaaatt atttgtgcc ttaatttat ttttttatt 
gttttctct aataaagat ctgtctgat cttaatctc 
ccagtagtt gagtatctc acactgtaa taaataagt 
caataaatt aactgcggc taa

    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