Status
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Gene information
General information
TC001616 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_007416.3: 1368171..1380308
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
    TC001616
    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
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_00271

    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: 0.0% (includes death as pupa, adult)

    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): less than 30%

    embryo/egg with embryonic tissue, no cuticle, but muscle fluorescence - 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): 30% - 50%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
    thorax segment number decreased - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen segment number decreased - 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: 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: 0.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 20.0% (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC001616 RA
      MVLLRHSES AHTMLGAEG VTDAEIATS PNQDNRLGS 
      AAEKPFNKD LNGSISQKW RRLRNCCAS LRGISTQSS 
      PEASRDTLL NSPSPRILV STPHPHATS SLRLPGAKK 
      NSVQDVLRA KLSRIHVGL RKRRALSVQ EFFHSPTHE 
      PQQPQPTFY VPSPVSPDS GSASLPTID CDHPEEKVQ 
      TRRRARSRQ RTVNSVNLT RDYGYDSES QGYDSLPYE 
      PPPDYDLDE NQATRRWSV VGSILHKNN QDNKTKNLI 
      KLENVNIKI PKTKLKFER ARSHSPNKN KYQTKPIKS 
      EADTRNFNS KVVTSKSHY ELMSAKQRP DVGQNGECE 
      RMSSDHKQD WIEELEEIE EEEESKFCT LPRGGGSTF 
      TIRQVVFQK GPGYKALGF SIVGGRDSP KGSMGIYVK 
      TIFPNGQAA DSGTLKEGD EILAVNSKP LHGASHQEA 
      IAVFKQIRS GQVLLHIGR RVAKKPRER VA
    CDS sequence
    • >TC001616 RA
      atggtactt ctgcgacac tcggagtcc gcacacacc 
      atgctcggg gccgagggt gtgaccgac gccgaaatc 
      gccacttcg cccaaccaa gacaaccgt ctcggcagc 
      gccgccgaa aaaccattc aacaaagac ctgaacggc 
      agcatctcg cagaaatgg aggcggtta cgtaactgc 
      tgcgcctcc ttgcggggc atcagcacc caaagcagc 
      cccgaggcg tctcgggac accctcctc aatagtcct 
      agtccgcga attctagtc agtactccg cacccgcac 
      gccacttcg tcgctgcgc ctccccggg gcgaagaag 
      aacagcgtc caggacgtc ctgcgggcg aagctgagc 
      cgcatccat gtggggctc cgcaagcgc cgggccttg 
      tccgttcag gagttcttc cacagcccg acccacgag 
      ccccagcag ccccagccc acgttctac gtcccttcg 
      cccgtctcg cccgactcg ggctccgcc tcgctcccg 
      accatcgac tgcgatcac ccggaggag aaggtgcag 
      acgcggcga agggcgcgc tcacgccaa agaacagtc 
      aattcggtg aatttaact cgggattac ggctatgat 
      agtgagagt caagggtac gattccctc ccgtatgag 
      ccgccccct gactacgac ctggacgaa aaccaagca 
      acgaggcgc tggtcggtg gttgggagt attcttcat 
      aagaataac caagataac aaaacgaag aatctaatt 
      aagttagaa aatgtaaat attaaaatt cccaaaacg 
      aagcttaag tttgaacgg gcgagatcg cattcgccc 
      aacaagaat aaataccag acgaagcca attaaaagt 
      gaagccgac acgagaaat tttaattcc aaagttgtt 
      acctccaaa agccattat gaacttatg agtgctaaa 
      caaaggccg gatgttgga caaaatggt gaatgtgaa 
      cggatgagt agcgaccat aaacaggac tggattgag 
      gagctcgag gagatcgag gaagaggaa gagagcaag 
      ttctgcacg ctccctcgc ggaggcggc agtacgttt 
      acgataaga caggttgtt ttccaaaag ggccccggt 
      tacaaggct ttaggtttt agcatcgtc ggagggagg 
      gactctccg aaaggcagc atgggaatt tacgtaaaa 
      actatcttt cctaacggt caggcagca gatagcggg 
      actttaaaa gaaggtgat gaaattttg gctgttaac 
      agtaaaccc ctccatgga gcttcgcac caggaagct 
      atcgccgtt ttcaagcaa atccgttca ggtcaagtg 
      ctgcttcac atagggcgg cgcgttgcg aaaaaaccg 
      cgcgagaga gttgcttaa
    mRNA sequence
    • >TC001616 RA
      ccctttttg gggttccac cggcgagca gcgacgtac 
      gtcgcacgt gtgtggacc gaaccgaca gagtcggaa 
      ataaaatgt ttgcgccct cggaattcc catctcccc 
      gtccgtcgc gtatttcgg gagtcttta tccgcatcc 
      ctctccttc ggcagtgcg atgtgcgac gtgcagcat 
      cattcatct gcaattgtg ggagcatgt gcgcattgc 
      ccgtcacat tgccggcga gtaaactca ctgaaagcc 
      acgatgcgg acactgctc gacgtcctc gcagccagt 
      gccccaatt cgcgacacc tgaagtgat cccgcatat 
      aatggtact tctgcgaca ctcggagtc cgcacacac 
      catgctcgg ggccgaggg tgtgaccga cgccgaaat 
      cgccacttc gcccaacca agacaaccg tctcggcag 
      cgccgccga aaaaccatt caacaaaga cctgaacgg 
      cagcatctc gcagaaatg gaggcggtt acgtaactg 
      ctgcgcctc cttgcgggg catcagcac ccaaagcag 
      ccccgaggc gtctcggga caccctcct caatagtcc 
      tagtccgcg aattctagt cagtactcc gcacccgca 
      cgccacttc gtcgctgcg cctccccgg ggcgaagaa 
      gaacagcgt ccaggacgt cctgcgggc gaagctgag 
      ccgcatcca tgtggggct ccgcaagcg ccgggcctt 
      gtccgttca ggagttctt ccacagccc gacccacga 
      gccccagca gccccagcc cacgttcta cgtcccttc 
      gcccgtctc gcccgactc gggctccgc ctcgctccc 
      gaccatcga ctgcgatca cccggagga gaaggtgca 
      gacgcggcg aagggcgcg ctcacgcca aagaacagt 
      caattcggt gaatttaac tcgggatta cggctatga 
      tagtgagag tcaagggta cgattccct cccgtatga 
      gccgccccc tgactacga cctggacga aaaccaagc 
      aacgaggcg ctggtcggt ggttgggag tattcttca 
      taagaataa ccaagataa caaaacgaa gaatctaat 
      taagttaga aaatgtaaa tattaaaat tcccaaaac 
      gaagcttaa gtttgaacg ggcgagatc gcattcgcc 
      caacaagaa taaatacca gacgaagcc aattaaaag 
      tgaagccga cacgagaaa ttttaattc caaagttgt 
      tacctccaa aagccatta tgaacttat gagtgctaa 
      acaaaggcc ggatgttgg acaaaatgg tgaatgtga 
      acggatgag tagcgacca taaacagga ctggattga 
      ggagctcga ggagatcga ggaagagga agagagcaa 
      gttctgcac gctccctcg cggaggcgg cagtacgtt 
      tacgataag acaggttgt tttccaaaa gggccccgg 
      ttacaaggc tttaggttt tagcatcgt cggagggag 
      ggactctcc gaaaggcag catgggaat ttacgtaaa 
      aactatctt tcctaacgg tcaggcagc agatagcgg 
      gactttaaa agaaggtga tgaaatttt ggctgttaa 
      cagtaaacc cctccatgg agcttcgca ccaggaagc 
      tatcgccgt tttcaagca aatccgttc aggtcaagt 
      gctgcttca catagggcg gcgcgttgc gaaaaaacc 
      gcgcgagag agttgctta aggaaacgt cttctcgat 
      tctatgtat tccaaagac tatttagta taagcgttt 
      tatgtagat atcttaccc taatgtttt ttatactgc 
      taataaaca tttaaatcg ctg
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY