Status
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Gene information
General information
TC009623 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: 3345946..3350633
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
    TC009623
    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
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    Email
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    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.

    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_01584

    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


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

    larval musculature irregular - 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): more than 80%
    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%

    cuticle remnants - Penetrance (percentage of animals/eggs on slide): less than 30%

    head not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    head not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    thorax not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    thorax not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    abdomen partially everted (inside-out) - Penetrance (percentage of animals/eggs on slide): less than 30%

    abdomen not present - 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): 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: 0.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 10.0% (includes death as larva, prepupa, pupa, adult)

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


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC009623 RA
      MTETLFPER YRERFQSSS STDENESGS EQEDHHQLM 
      QIANLNNLS VEPTRKRRG NLPKHSVKI LKRWLYEHR 
      YNAYPSDAE KMTLSQEAN LTVLQVCNW FINARRRIL 
      PEMIRREGH DPLHYTISR RGKKLTTSG SMGVEQTRA 
      QWDEEIATV GGKRIRLDH DYDDSMNLM YRSEEDSPN 
      EYESSSPSE EEKFNPWQT VIRYGVAKE APYPTKRSD 
      EGQITANQY WTAPHPQLS HLPQLPHPL STPKVQVMP 
      AHQINPLHT ESDPLSTND EEDKDKFKC LYLLVETAV 
      AVRQREKEQ GNVQV
    CDS sequence
    • >TC009623 RA
      atgacggaa acactattt cccgaacga taccgcgaa 
      cgattccaa tcgagcagc agtacggac gaaaatgaa 
      tccggatcc gaacaagag gatcatcat caattgatg 
      caaatcgcc aatctgaat aatctttcg gtagaaccg 
      acgaggaaa cgcagaggg aatttgccc aaacattcg 
      gtcaagata ctcaagagg tggctgtac gagcacaga 
      tacaatgca tacccgagc gacgccgaa aaaatgacc 
      ctgtctcag gaagccaac ttgaccgtt ctccaggtg 
      tgtaattgg tttataaac gcgcgtcgt cgcatcctt 
      cccgaaatg ataagacgt gaaggtcac gacccactc 
      cactataca atttcgcga cgcggcaaa aaattgacc 
      acttcgggt tcgatggga gtggaacaa acgcgcgca 
      caatgggac gaagaaatc gcaacggtt ggaggaaaa 
      cgaattcgt ctcgatcac gattacgac gattcaatg 
      aatctcatg tatcgctcg gaggaggac agtcccaat 
      gaatacgaa agctcgagt ccgagcgaa gaggagaaa 
      ttcaacccg tggcagacg gtcattcgg tatggggtg 
      gccaaggag gccccctat cccaccaaa aggtctgac 
      gagggccag atcacggcg aaccagtat tggacggcg 
      ccgcacccc cagctctcg cacttgccc cagctgccg 
      caccccttg agcaccccg aaggtgcaa gtaatgcca 
      gcccatcaa atcaatccg ctgcacacg gagtcggac 
      cctctcagc acaaacgac gaagaggac aaagacaag 
      ttcaaatgt ttgtatttg ttggtggaa acggccgtc 
      gctgtacga cagagagag aaggagcaa ggaaacgtc 
      caagtatag
    mRNA sequence
    • >TC009623 RA
      ttactagcc gtgattgtg catattttt agctcattg 
      gagactgac cattgatca agcaaacac aagtggcaa 
      tattaacaa aacaaacga tgaattatc gcctattat 
      cacaatttc attaataat ggctacgtt tttttttaa 
      ataaatttc caaaactgg aaactgtta tacgctgtg 
      tgggtgact ttggctcac tttatcgaa atgtggacg 
      acccgccaa ggccgcaaa ggccaagac cttgctcat 
      gaatccaca attggtgaa ttaaaactt gtttatcac 
      ttatcgttt aaatttggc gcgttcatg tcatgttac 
      tgcgcctgt cacacaacc atcagtttg accgccatc 
      gaaactgtc atcgcgaag cacgcgtga cactatttg 
      tgacatttt actcaaaat cgtcaaaaa aaagtgtta 
      aatcacgcg tgggggccg cgtttgagc gtgaaacat 
      gtgcgtttt gttcgtccg agttgtggc aacatctga 
      gtgcacgtg acaccgctg acaggcatt tatttgccg 
      agttttgac tggtttttc gctggtgga aaagtggcg 
      gaaaactgg aaaattgtg aaaatttca actgttacg 
      taaattgat gctttgaca ggattccga agaaaatga 
      aagtccgta attgtcact caaacgtgc tttggtgtt 
      gcttttaaa aatcgtcga ttaaaggca ttgattttg 
      tgaatttct gaaaatttt ctgcgtccg attgtcgat 
      tgaagtctg gtcgtgaaa atgacggaa acactattt 
      cccgaacga taccgcgaa cgattccaa tcgagcagc 
      agtacggac gaaaatgaa tccggatcc gaacaagag 
      gatcatcat caattgatg caaatcgcc aatctgaat 
      aatctttcg gtagaaccg acgaggaaa cgcagaggg 
      aatttgccc aaacattcg gtcaagata ctcaagagg 
      tggctgtac gagcacaga tacaatgca tacccgagc 
      gacgccgaa aaaatgacc ctgtctcag gaagccaac 
      ttgaccgtt ctccaggtg tgtaattgg tttataaac 
      gcgcgtcgt cgcatcctt cccgaaatg ataagacgt 
      gaaggtcac gacccactc cactataca atttcgcga 
      cgcggcaaa aaattgacc acttcgggt tcgatggga 
      gtggaacaa acgcgcgca caatgggac gaagaaatc 
      gcaacggtt ggaggaaaa cgaattcgt ctcgatcac 
      gattacgac gattcaatg aatctcatg tatcgctcg 
      gaggaggac agtcccaat gaatacgaa agctcgagt 
      ccgagcgaa gaggagaaa ttcaacccg tggcagacg 
      gtcattcgg tatggggtg gccaaggag gccccctat 
      cccaccaaa aggtctgac gagggccag atcacggcg 
      aaccagtat tggacggcg ccgcacccc cagctctcg 
      cacttgccc cagctgccg caccccttg agcaccccg 
      aaggtgcaa gtaatgcca gcccatcaa atcaatccg 
      ctgcacacg gagtcggac cctctcagc acaaacgac 
      gaagaggac aaagacaag ttcaaatgt ttgtatttg 
      ttggtggaa acggccgtc gctgtacga cagagagag 
      aaggagcaa ggaaacgtc caagtatag ccgttaaag 
      ggcgtcgtt gtttcactc gtgccttgc ttaaatttc 
      gttgtgagt cagttctat ggcaaaaag ttttacgag 
      cgttgttgt gatataaat tgccaaaat ttgaaagag 
      ggaaaaggg tgaaacttt ttgttttga attatttga 
      aacggttca tgtagttgt ttaattttt ctttctcct 
      agctttagc gaatttgga gtgacttag ttgtaattt 
      gatgagtga tattaatga ttggatgaa agagttgcg 
      ttttttttc ttaattttt cggagtgga ttatctcat 
      taaaatttc actcggatg cattgcttt tctctctgt 
      gataaaact gatacgaac aaggcttac taatctccg 
      gaattcatg acatttgca taactgtgc cataagatg 
      tttgatggg ataatctga ttgtactta gtgtaatga 
      cgtacctgt cgtggcatt ttcggactt ctcttcttc 
      aaaatttca gaacgtttt aaagtgtag ttttctaag 
      gaattttta tataccgaa cggttgtac attttgtaa 
      aagtatcat gtttattgt tgataagat gtagtagca 
      attagctta tcaattttt taagttgtc gtaatcatg 
      aggtactct gaacgattt gtaaatacc cgtcatttc 
      gcacatatt tctcgcgca aattgctca aacgtcaca 
      agtacaaaa tcacgtatt gtaaataag agagaacga
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY