Status
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Gene information
General information
TC005954 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_007423.3: 4881599..4882989
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
    TC005954
    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_04044

    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)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 1 (3 dpi)
    Days post injection


    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 50
    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: 0.0% (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC005954 RA
      MQKLLLLCA LLPLSWTKP NASLINQIN SQQSAWTAG 
      INPFDDIES RLGFLGIHP DPNFKPEIK EPQATQNVI 
      PETFDAREY WPECADIIG NIRNQGKCS SSWAFAAAE 
      VMSDRLCIA TNGKVKIQL SPEDLIDCC HYCGNQCKG 
      GYTYYAWNY FMLTGLVSG GDYNTSTGC QPYSELNYY 
      RITPPCNTT CQNDKYPIP YVSDKHFGD SIYYIPQNE 
      TAIQNEILS GGGPVVAAF DVYGDFKIY RDGVYIYTS 
      GALFGRTAV KIIGWGTEN GWAYWLAAN SWGKDWGAL 
      GGFFKIRRG TNECGFEES IIAGQVREG GSTSPTPVT 
      FTATVTPPT TPGSGVRVA GCGIGLVLS MMLFYLLKF
    CDS sequence
    • >TC005954 RA
      atgcaaaaa ttacttctt ttatgtgct ttattacca 
      ttatcatgg acaaaaccc aacgcttct cttatcaat 
      cagattaat tcccaacaa tcagcatgg acagccggg 
      attaaccct tttgacgac atcgagtcc cgcttggga 
      tttctgggg attcaccca gatccaaat ttcaaacca 
      gaaattaaa gaaccacaa gcgacccaa aacgtaata 
      cctgaaacc ttcgacgct cgggaatac tggcccgaa 
      tgtgcagac ataatcggc aatattcgt aatcaggga 
      aaatgtagc tcgtcttgg gcgtttgct gctgccgaa 
      gtcatgtca gaccgattg tgcatagca acgaacggt 
      aaagtcaaa attcagctg tcgcccgaa gatcttatc 
      gactgttgt cattattgt ggcaatcaa tgtaaaggg 
      ggttacaca tattacgct tggaactat ttcatgtta 
      acaggcctc gtgtctggg ggtgattac aacacatcg 
      acgggatgc caaccttat tcggagttg aattactac 
      agaatcact cctccgtgc aacacaact tgtcaaaac 
      gacaaatac cccatacca tacgtcagt gataaacat 
      ttcggtgac agcatttac tatattccc caaaatgag 
      actgctatc caaaacgaa attttatcc gggggtggt 
      ccagtcgta gccgccttc gatgtctat ggagatttt 
      aagatatac cgagacggt gtttatatt tacacatct 
      ggtgctcta tttggtcgc actgctgtt aaaatcatt 
      gggtggggg acggagaat gggtgggcc tattggttg 
      gcggcgaat tcgtggggg aaagactgg ggcgcgttg 
      gggggattt ttcaaaatc cgaagaggg acgaatgaa 
      tgcgggttt gaagagtcg atcatagcc ggacaagtg 
      agggaaggt ggtagtaca agtcctaca cctgttact 
      tttacagca actgtcaca ccgcctact acgccaggt 
      tcaggggtt agggtggca gggtgcgga atcgggctt 
      gttctgtcc atgatgctg ttttatttg ttaaagttt 
      taa
    mRNA sequence
    • >TC005954 RA
      gaattaaat aaatgtgat tacaccatg caaaaatta 
      cttctttta tgtgcttta ttaccatta tcatggaca 
      aaacccaac gcttctctt atcaatcag attaattcc 
      caacaatca gcatggaca gccgggatt aaccctttt 
      gacgacatc gagtcccgc ttgggattt ctggggatt 
      cacccagat ccaaatttc aaaccagaa attaaagaa 
      ccacaagcg acccaaaac gtaatacct gaaaccttc 
      gacgctcgg gaatactgg cccgaatgt gcagacata 
      atcggcaat attcgtaat cagggaaaa tgtagctcg 
      tcttgggcg tttgctgct gccgaagtc atgtcagac 
      cgattgtgc atagcaacg aacggtaaa gtcaaaatt 
      cagctgtcg cccgaagat cttatcgac tgttgtcat 
      tattgtggc aatcaatgt aaagggggt tacacatat 
      tacgcttgg aactatttc atgttaaca ggcctcgtg 
      tctgggggt gattacaac acatcgacg ggatgccaa 
      ccttattcg gagttgaat tactacaga atcactcct 
      ccgtgcaac acaacttgt caaaacgac aaatacccc 
      ataccatac gtcagtgat aaacatttc ggtgacagc 
      atttactat attccccaa aatgagact gctatccaa 
      aacgaaatt ttatccggg ggtggtcca gtcgtagcc 
      gccttcgat gtctatgga gattttaag atataccga 
      gacggtgtt tatatttac acatctggt gctctattt 
      ggtcgcact gctgttaaa atcattggg tgggggacg 
      gagaatggg tgggcctat tggttggcg gcgaattcg 
      tgggggaaa gactggggc gcgttgggg ggatttttc 
      aaaatccga agagggacg aatgaatgc gggtttgaa 
      gagtcgatc atagccgga caagtgagg gaaggtggt 
      agtacaagt cctacacct gttactttt acagcaact 
      gtcacaccg cctactacg ccaggttca ggggttagg 
      gtggcaggg tgcggaatc gggcttgtt ctgtccatg 
      atgctgttt tatttgtta aagttttaa tgatagtga 
      agtgaccac attcataaa acttctatt atttagtta 
      tgtagataa tcgaatttt ttacggtgc ctaactatt 
      gtgtatttt gtaacaatt ttttatata aataaaata 
      ttatttcta cg
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY