Status
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Gene information
General information
TC009001 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: 8914248..8916425
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
    		TC009001
    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
    {{ goGene }}
    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
    You may enter your name. The contact information can help us to clarify any questions. If you agree, we may show your name on this page to honor your contribution.
    Email
    We will use your email address only for possible questions regarding this annotation. We will never show your address or give it away.
    Publish name
    If you have entered your name and agree by marking the checkbox. we might show your name on this page to honor your contribution.
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_01454

    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: 40.0% (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

    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 larval musculature irregular - 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): less than 30%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 50
     cuticle remnants strongly fragmented (cuticle crumbs) - 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): less than 30%
    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: 10.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 20.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (16 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 2 (41 dpi)
    Days post injection

    Fertility
    egg production: number <50% of expected -
    mature egg deposition blocked number 1st lateral oviduct: 3 number 2nd lateral oviduct: 2 - Number of animals showing the phenotype: 4
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC009001 RA
      MILEQGISE QFKINNDMI HDARRFLEL KSQGDVGKS 
SIKDFQDFK LPVLVFACN RVSVSRCLD RLLQYRPDP 
DKFPIIVSQ DCNHEETTE TIRRYGSQV SLIQQPDQS 
DIQVPPKEK KFKGYFKIA RHYGWALNQ MFFNFNFST 
VIIVEDDLE VAPDFFEYF LGTYSILTR DPTLWCVSA 
WNDNGKEGL VDENRPDLL YRTDFFPGL GWMLTKSLW 
LELYTKWPR AYWDDWIRD PSQRKGRAC VRPEISRTR 
TFGKFGVSN GMFFEKHLK YIKLNEKFV PFTKMNLSY 
LVKQAYDRD FIRDVYQSV IVSYQELKE GKVAHDGPV 
RIVYRSKEE YKIFTKKLG LMDDFKSGV PRTAYKGIV 
TFHYKGRMV HLAPNVNWK GYDLTWS
    CDS sequence
    • >TC009001 RA
      atgatactg gaacaaggc atatcagaa cagtttaaa 
ataaacaat gacatgatc catgacgct aggaggttt 
ttggaattg aagagccaa ggggacgtt ggcaaaagt 
agtataaag gatttccaa gacttcaaa ttgccagta 
ctagtattt gcgtgcaat agagttagt gtcagtagg 
tgcttagat aggcttttg caatacaga ccagaccct 
gacaaattt ccaataatc gtgagccaa gactgcaat 
catgaggaa accaccgag actataaga cggtacgga 
tctcaagtg tcacttatc cagcaacca gaccaatcc 
gatattcag gtacctccc aaagaaaaa aagttcaag 
ggatatttc aaaattgcg cgtcactac ggctgggcc 
ctcaaccaa atgtttttt aattttaac tttagtact 
gttattata gttgaagac gacttggag gtggctcca 
gacttcttt gagtatttc cttggtact tactccatt 
ttaacgcgc gacccgacc ctctggtgc gtctccgcc 
tggaacgac aacgggaag gagggtctg gtggacgaa 
aatcgccca gatttgttg taccgcacg gacttcttt 
cccggcttg gggtggatg ttgacgaag tccttgtgg 
ctggaactg tacaccaag tggccgagg gcctattgg 
gacgattgg atacgcgac ccgtcgcag agaaagggc 
agggcgtgc gttagaccg gaaatatcg aggacgagg 
acgtttggc aagtttggg gtttcaaat ggtatgttt 
ttcgagaag cacttaaag tacataaaa ctgaacgag 
aagtttgtg ccttttacc aaaatgaac ctgagctac 
ttagtgaag caggcgtat gatagggat tttattaga 
gatgtttac caaagcgtg atagtcagt taccaggag 
ttgaaagag ggcaaagtc gcccacgat gggcccgtg 
aggatcgtt tatcgctca aaggaagag tataaaata 
ttcacgaaa aagttgggg ctcatggac gattttaag 
agtggggtc ccccgaact gcgtacaag ggtattgtc 
actttccac tacaagggc cgaatggtg cacttggcc 
cccaatgtg aactggaag gggtacgac ctgacgtgg 
agctaa
    mRNA sequence
    • >TC009001 RA
      aatatactt gtgacgtta gttggtccc caaatgtta 
aaaactatt aatttgtta aaatgctac gtgtttaat 
gtaaatgat acgttgtgt gataaacaa tagcacttc 
cgcaaaatg gctaaacat ccgacagtg atagaaatc 
aaatcatta tgattttgc aggataggg acactctaa 
gataataaa ataacatgc gactgaaac gcacaaact 
tcgtactag gaatattcg taataactt gggctttag 
tgttgtatt ttgcattcc tgtcccatc taacaacta 
aaagtgaac caaatggaa acgtcgata gccaaatca 
tgatactgg aacaaggca tatcagaac agtttaaaa 
taaacaatg acatgatcc atgacgcta ggaggtttt 
tggaattga agagccaag gggacgttg gcaaaagta 
gtataaagg atttccaag acttcaaat tgccagtac 
tagtatttg cgtgcaata gagttagtg tcagtaggt 
gcttagata ggcttttgc aatacagac cagaccctg 
acaaatttc caataatcg tgagccaag actgcaatc 
atgaggaaa ccaccgaga ctataagac ggtacggat 
ctcaagtgt cacttatcc agcaaccag accaatccg 
atattcagg tacctccca aagaaaaaa agttcaagg 
gatatttca aaattgcgc gtcactacg gctgggccc 
tcaaccaaa tgtttttta attttaact ttagtactg 
ttattatag ttgaagacg acttggagg tggctccag 
acttctttg agtatttcc ttggtactt actccattt 
taacgcgcg acccgaccc tctggtgcg tctccgcct 
ggaacgaca acgggaagg agggtctgg tggacgaaa 
atcgcccag atttgttgt accgcacgg acttctttc 
ccggcttgg ggtggatgt tgacgaagt ccttgtggc 
tggaactgt acaccaagt ggccgaggg cctattggg 
acgattgga tacgcgacc cgtcgcaga gaaagggca 
gggcgtgcg ttagaccgg aaatatcga ggacgagga 
cgtttggca agtttgggg tttcaaatg gtatgtttt 
tcgagaagc acttaaagt acataaaac tgaacgaga 
agtttgtgc cttttacca aaatgaacc tgagctact 
tagtgaagc aggcgtatg atagggatt ttattagag 
atgtttacc aaagcgtga tagtcagtt accaggagt 
tgaaagagg gcaaagtcg cccacgatg ggcccgtga 
ggatcgttt atcgctcaa aggaagagt ataaaatat 
tcacgaaaa agttggggc tcatggacg attttaaga 
gtggggtcc cccgaactg cgtacaagg gtattgtca 
ctttccact acaagggcc gaatggtgc acttggccc 
ccaatgtga actggaagg ggtacgacc tgacgtgga 
gctaaccga aagattcct agttactta cacaattcc 
atgtttgat attaatata tttgttgtt ttatgtttg 
cacattaaa aatgtggac tgttggaat tttaatttt 
gttctaatc aagttgaaa attgtgata aagtttgta 
atggcaact tgcgagttg gctagataa atgcgagca 
tttagtcta gcccgctaa tctgtataa gttcaaata 
tcgactgct cgataaatt gttatgcca attaagaca 
tgtacatag aaagcgagc gagctgcca atatttatg 
ttttatatt ctaaacatt tttgcattt atacaatag 
aatacgcaa gattgtaaa atatgtagt tcaatttag 
caatatctt atgttgtaa gttttgaca gctcattcg 
cagtatatg aatcgcgct tcttaatgt aaataaaag 
tggataatt aataaaatt gtacaaagt tt

    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