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Gene information
General information
TC004865 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_007417.3: 3311490..3316364
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
    TC004865
    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
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    Name
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    Email
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    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_10666

    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 muscle fluorescence/pattern, but not hatched (pot. late embryonic lethality) - Penetrance (percentage of animals/eggs on slide): more than 80%

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

    affected eggs/embryos/larvae - 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
    embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    cuticle remnants with some identifiable segments - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    cuticle remnants with unidentifyable segments - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    antenna antennal flagellum not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    vertex vertex triplet posterior potentially not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%

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

    head shape irregular - Penetrance (percentage of animals/eggs on slide): less than 30%
    legs shape irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    thorax not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    thorax shape irregular - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen segment number decreased - Penetrance (percentage of animals/eggs on slide): less than 30%

    abdomen not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen shape irregular - Penetrance (percentage of animals/eggs on slide): less than 30%
    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 50% - 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
    • >TC004865 RA
      MARGGIRGR GGMNRGIGR PPYKVKMFL PRHPFDLAL 
      CESSFPRVK PAPDETAFT QALLKRNVD LSPTPAEQT 
      AILNLVTKI QTVLDNLVV APGAFDACQ LEEVRQVGS 
      FKKGTMVTG HNVADIVVI LKTLPTREA VEALGNKVK 
      EDLKNLMKS EVVTKGEQL NHTTNERGI EISNSFACV 
      RVMVTTLHH NIRKLDPEI HLDQKIMLS HLAAIRHSR 
      WFEENAHHS SIKVLIRLL RDIRSRFEG FEPLTPWML 
      DLLAHFAIM HNPSRQALP INVAFRRVF QLLSAGLFL 
      PGSAGITDP CEGVSLRIH TAMTLEQQD ICCLTAQTL 
      LRVLSHGGY KHILGLEGN ATIAKEMSV WDGVVVSPL 
      DKAYENPPE KKEGEEEDE DMEAEGDES METIDN
    CDS sequence
    • >TC004865 RA
      atggcaaga ggcgggatt agaggcaga ggaggaatg 
      aatcgtgga attggaaga cccccatac aaagtcaag 
      atgtttctg ccaagacat cccttcgat ttggccctt 
      tgtgagtca tcttttcca cgtgttaaa cccgcccct 
      gatgaaaca gcattcaca caagcttta ttaaagcga 
      aatgtcgat ttgtcaccc acgccggcc gaacaaacc 
      gccattctt aacctggtt acgaaaata caaacggtt 
      ttggacaac ctggtcgtg gcccccggc gccttcgac 
      gcttgccaa ttggaagag gtgcgacag gtgggttcg 
      ttcaaaaaa gggacgatg gtaactggc cacaacgtg 
      gccgacatt gtcgtaatc ttgaagact ttgcccacg 
      cgggaagcc gtcgaagcc cttggcaac aaagtgaag 
      gaagatttg aagaattta atgaagagc gaagttgtg 
      accaaaggc gaacaactc aaccacacg accaacgag 
      cgcgggatt gaaatcagc aatagtttt gcttgtgtc 
      cgtgtcatg gtaacaacc ttacaccat aacattcgt 
      aaattggac cctgagatc catttggac caaaaaatc 
      atgttgagc cacttggcc gcgatcaga cacagccgt 
      tggtttgag gaaaacgcc catcactca tcgattaaa 
      gtgttaatt cgtttgttg agagacatt cgttcgaga 
      tttgaaggt ttcgagccg ttgactcca tggatgttg 
      gatttgttg gcacatttt gctatcatg cataatcca 
      agtcgacag gcgttgcca attaatgtc gcctttagg 
      agggttttc cagctgttg tccgccggg ttgtttctg 
      ccggggtca gcggggatt actgatcct tgtgaaggg 
      gttagtttg cggattcat acggcgatg acgttggaa 
      cagcaagat atttgctgt ttgaccgcg cagactttg 
      ttaagggtg ctgtcgcac ggggggtat aagcatatt 
      ttagggttg gaaggtaat gcgaccatt gcgaaggaa 
      atgtcggtt tgggacggg gtggtggtc tcacccctt 
      gataaagcg tatgagaat ccaccggag aagaaggaa 
      ggggaggaa gaggatgag gatatggaa gctgaaggg 
      gatgaaagt atggaaact attgataat tag
    mRNA sequence
    • >TC004865 RA
      ctttcgaaa tcgataacc cgattgttt gtgagtgcg 
      tctaatgcc ggtgttttt gtgtgatta gaatcatta 
      tataatggc aagaggcgg gattagagg cagaggagg 
      aatgaatcg tggaattgg aagaccccc atacaaagt 
      caagatgtt tctgccaag acatccctt cgatttggc 
      cctttgtga gtcatcttt tccacgtgt taaacccgc 
      ccctgatga aacagcatt cacacaagc tttattaaa 
      gcgaaatgt cgatttgtc acccacgcc ggccgaaca 
      aaccgccat tcttaacct ggttacgaa aatacaaac 
      ggttttgga caacctggt cgtggcccc cggcgcctt 
      cgacgcttg ccaattgga agaggtgcg acaggtggg 
      ttcgttcaa aaaagggac gatggtaac tggccacaa 
      cgtggccga cattgtcgt aatcttgaa gactttgcc 
      cacgcggga agccgtcga agcccttgg caacaaagt 
      gaaggaaga tttgaagaa tttaatgaa gagcgaagt 
      tgtgaccaa aggcgaaca actcaacca cacgaccaa 
      cgagcgcgg gattgaaat cagcaatag ttttgcttg 
      tgtccgtgt catggtaac aaccttaca ccataacat 
      tcgtaaatt ggaccctga gatccattt ggaccaaaa 
      aatcatgtt gagccactt ggccgcgat cagacacag 
      ccgttggtt tgaggaaaa cgcccatca ctcatcgat 
      taaagtgtt aattcgttt gttgagaga cattcgttc 
      gagatttga aggtttcga gccgttgac tccatggat 
      gttggattt gttggcaca ttttgctat catgcataa 
      tccaagtcg acaggcgtt gccaattaa tgtcgcctt 
      taggagggt tttccagct gttgtccgc cgggttgtt 
      tctgccggg gtcagcggg gattactga tccttgtga 
      aggggttag tttgcggat tcatacggc gatgacgtt 
      ggaacagca agatatttg ctgtttgac cgcgcagac 
      tttgttaag ggtgctgtc gcacggggg gtataagca 
      tattttagg gttggaagg taatgcgac cattgcgaa 
      ggaaatgtc ggtttggga cggggtggt ggtctcacc 
      ccttgataa agcgtatga gaatccacc ggagaagaa 
      ggaagggga ggaagagga tgaggatat ggaagctga 
      aggggatga aagtatgga aactattga taattaggt 
      attgtcgca cttatttgt atatttcgt gaaaatata 
      atcttgatt tcttattca ttttattat aaatcaaaa 
      actcttgat ctagacatt tatttgaaa gtaaataaa 
      atacagtct attattgtc tattatcaa caatgttgc 
      cagaaataa agttgtaaa cgccttaaa aaaaccttt 
      cttaaaatc cagtttttc tcagaatgc atttttaag 
      gaacaaagt tcgattttt tagtagtta ttaaatagc 
      agatcagac caagagata tttttcagt gatttatta 
      acacttttt tggaaacgc aagtatttt acacattct 
      ggtggaaaa ttttgttgt tttggttaa tttttatca 
      ttttcttta gcagccata actgtttag tgaaatttt 
      ataaaggat aataggtag tatttatag aatgt
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY