Status
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Gene information
General information
TC004389 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_007425.3: 7098653..7100424
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
    TC004389
    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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    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_09822

    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: 50.0% (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


    adult lethality - Number of animals showing the phenotype: 1 (9 dpi)
    Days post injection


    Fertility
    mature egg not present - Number of animals showing the phenotype: 4
    egg chamber mostly not present - Number of animals showing the phenotype: 4

    tropharium structure irregular - Number of animals showing the phenotype: 4

    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
    • >TC004389 RA
      MTSRQGILF PLTSLYVGD LHPDVTEAL LYEKFSPAG 
      QILSLRVCR DSRTKQSLG YAYVNFSQT IEAERVLDT 
      MNFDLLKGK PIRIMWSQR DPSLRKSGI GNVFIKNLD 
      KSIDNKAMY DTFSAFGNI LSCKVAIDD DGVSKGYGF 
      VHFESIEAA NKAIEKVNG MLLNGKKVY VGKFIPRAE 
      REKEIGEKS KKYTNVYVK NFGRNLTQE QLYDLFKNY 
      GTITSCVVM ANPDGTSKG FGFIAFEEP ESAEKAVTE 
      MNNYELNGT NLYVGRAQK KSERIKELK KCYEQMKLE 
      RYNRIQGAN VYIKNLDDT FDNDRLRKE FSQFGAITS 
      AKVMTEGGR SKGFGFVCF STPEEASKA ITEMDGRMI 
      GSKPIYVAL AQRYEDRRA YLSAQCMQR IRHQTMSPP 
      LTTPQFLIP TLPRFYNHM AQIRPTPRW TAQVPRLNG 
      TYNMPLLPA TPYRSTSRP QVQINRSAR PITGQQVPI 
      ARPNSKYTA SAPPRGVSV GVGNGGDPG ADDKRMLGE 
      RMYRVIEKT YPEIAGKIT GMLLEIDIS ELKALVNNE 
      GSLKAKVEE AVAVLQAHN KGLTVQD
    CDS sequence
    • >TC004389 RA
      atgacttcc cgtcaagga atcctcttc ccgctaacg 
      tctctgtac gttggtgac ttgcatccg gacgtcacc 
      gaagcccta ctttacgag aaattttcc ccggctggt 
      cagatcctg tctttgagg gtttgccgc gactcaaga 
      accaaacaa agtctgggc tatgcctac gtgaacttc 
      agtcaaacc atagaagct gaacgggtc ctggacacc 
      atgaacttt gacctcctg aaggggaaa cccatcagg 
      ataatgtgg agtcaaagg gacccctcg ttacgcaag 
      tcgggcatt ggtaacgta tttatcaag aatctggac 
      aaaagcatc gacaataag gcaatgtac gacactttt 
      tcggccttt ggaaacata ctttcgtgt aaggttgcc 
      attgacgac gatggtgtt tcaaaaggc tatggtttc 
      gtccatttc gagagtatc gaagctgcg aataaagca 
      atcgaaaaa gtcaacggt atgctcttg aacggcaaa 
      aaagtctac gtcgggaaa tttataccg cgcgccgaa 
      cgcgagaaa gaaatcggc gaaaaatcc aagaaatac 
      accaacgtt tacgtgaaa aatttcggc cgcaattta 
      acacaggag cagctgtac gacttgttt aaaaactac 
      ggcaccatc acatcatgc gtggtcatg gccaaccca 
      gacgggacg tcgaaaggt ttcggcttc atcgccttc 
      gaagagccg gaaagtgcc gaaaaagcc gtcaccgaa 
      atgaacaat tacgaacta aacggcaca aacttgtac 
      gtcggacgc gcccaaaaa aaatccgaa cgaatcaaa 
      gaactgaaa aaatgttac gaacaaatg aaactcgaa 
      cggtacaat cgcatacag ggcgcaaat gtttacatt 
      aaaaacctt gacgatact ttcgataat gaccgctta 
      cgcaaggaa ttctcccag tttggggcc atcacatca 
      gcgaaggtc atgactgag ggtgggcgg agcaaaggt 
      ttcggtttc gtttgtttc tccaccccg gaggaggcg 
      tccaaggcg ataacggaa atggacggg cgtatgatt 
      ggctcaaag ccgatttac gtggcgctt gcgcagcgt 
      tacgaggat cgaagggcg tatttaagt gcgcagtgt 
      atgcaaagg atccggcat cagacgatg tcgccgcct 
      ttgaccacg cctcagttt cttattccc acccttccg 
      cggttttac aaccatatg gcacagatc aggccgacg 
      ccgcgttgg actgcacaa gtgccacgt ttgaatggg 
      acctataat atgcccctc ctaccggca acgccctat 
      aggtcgacg tcgcgtccc caagttcag attaatcga 
      agcgcgagg ccaattacg gggcaacaa gtgccaatt 
      gcgaggccg aatagtaag tatacggcc agtgcgccc 
      ccacggggg gtcagtgtg ggggtgggg aatgggggc 
      gatccgggg gcggatgat aagaggatg ttgggcgag 
      aggatgtat cgggtgatt gagaagacg tatcccgag 
      attgcgggg aaaattact gggatgttg ttggagatt 
      gatataagt gagctgaag gctttggtt aataatgaa 
      ggttcgctg aaggcgaaa gtggaggag gcggtcgct 
      gtgttgcaa gcgcataat aaggggttg acggtgcag 
      gattaa
    mRNA sequence
    • >TC004389 RA
      ttaaattag tgttaagct gaaatgact tcccgtcaa 
      ggaatcctc ttcccgcta acgtctctg tacgttggt 
      gacttgcat ccggacgtc accgaagcc ctactttac 
      gagaaattt tccccggct ggtcagatc ctgtctttg 
      agggtttgc cgcgactca agaaccaaa caaagtctg 
      ggctatgcc tacgtgaac ttcagtcaa accatagaa 
      gctgaacgg gtcctggac accatgaac tttgacctc 
      ctgaagggg aaacccatc aggataatg tggagtcaa 
      agggacccc tcgttacgc aagtcgggc attggtaac 
      gtatttatc aagaatctg gacaaaagc atcgacaat 
      aaggcaatg tacgacact ttttcggcc tttggaaac 
      atactttcg tgtaaggtt gccattgac gacgatggt 
      gtttcaaaa ggctatggt ttcgtccat ttcgagagt 
      atcgaagct gcgaataaa gcaatcgaa aaagtcaac 
      ggtatgctc ttgaacggc aaaaaagtc tacgtcggg 
      aaatttata ccgcgcgcc gaacgcgag aaagaaatc 
      ggcgaaaaa tccaagaaa tacaccaac gtttacgtg 
      aaaaatttc ggccgcaat ttaacacag gagcagctg 
      tacgacttg tttaaaaac tacggcacc atcacatca 
      tgcgtggtc atggccaac ccagacggg acgtcgaaa 
      ggtttcggc ttcatcgcc ttcgaagag ccggaaagt 
      gccgaaaaa gccgtcacc gaaatgaac aattacgaa 
      ctaaacggc acaaacttg tacgtcgga cgcgcccaa 
      aaaaaatcc gaacgaatc aaagaactg aaaaaatgt 
      tacgaacaa atgaaactc gaacggtac aatcgcata 
      cagggcgca aatgtttac attaaaaac cttgacgat 
      actttcgat aatgaccgc ttacgcaag gaattctcc 
      cagtttggg gccatcaca tcagcgaag gtcatgact 
      gagggtggg cggagcaaa ggtttcggt ttcgtttgt 
      ttctccacc ccggaggag gcgtccaag gcgataacg 
      gaaatggac gggcgtatg attggctca aagccgatt 
      tacgtggcg cttgcgcag cgttacgag gatcgaagg 
      gcgtattta agtgcgcag tgtatgcaa aggatccgg 
      catcagacg atgtcgccg cctttgacc acgcctcag 
      tttcttatt cccaccctt ccgcggttt tacaaccat 
      atggcacag atcaggccg acgccgcgt tggactgca 
      caagtgcca cgtttgaat gggacctat aatatgccc 
      ctcctaccg gcaacgccc tataggtcg acgtcgcgt 
      ccccaagtt cagattaat cgaagcgcg aggccaatt 
      acggggcaa caagtgcca attgcgagg ccgaatagt 
      aagtatacg gccagtgcg cccccacgg ggggtcagt 
      gtgggggtg gggaatggg ggcgatccg ggggcggat 
      gataagagg atgttgggc gagaggatg tatcgggtg 
      attgagaag acgtatccc gagattgcg gggaaaatt 
      actgggatg ttgttggag attgatata agtgagctg 
      aaggctttg gttaataat gaaggttcg ctgaaggcg 
      aaagtggag gaggcggtc gctgtgttg caagcgcat 
      aataagggg ttgacggtg caggattaa tttttaagt 
      tgttgcaat ttatttaat ttatgtatt aaatgttaa 
      ttttttca
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY