Status
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Gene information
General information
TC001559 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_007418.3: 3479628..3495401
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
    TC001559
    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_00260

    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: 40.0% (includes death as pupa, adult)

    pupa eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 1 (3 dpi)
    Days post injection


    adult lethality - Number of animals showing the phenotype: 3 (9 dpi)
    Days post injection


    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 20
    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: 20.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 30.0% (includes death as larva, prepupa, pupa, adult)

    Pupal morphology
    oblique dorsal thoracic muscles anterior shortened - Number of animals showing the phenotype: 3

    Fertility
    egg production: number <50% of expected -
    mature egg deposition blocked number 1st lateral oviduct: 4 number 2nd lateral oviduct: 3 - Number of animals showing the phenotype: 1

    ovary without detectable defects - Number of animals showing the phenotype: 2
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC001559 RA
      MTESFEDGN YLVRVRAQV MSRDDSSGG WVPLGGGGL 
      SNVSVRKRP RPSPSTAPG PDPASKPKH DYLIYGKRI 
      SDQSIVLSC TIKKDFEYN KVMPTFHHW KTGDKKFGL 
      TFQTAADAR AFDKGVRTA VEELLDGFA ETSPSSLLQ 
      KYSKDVDDD VFMTLNLPH EPKDSRSSS DSSSKGTEH 
      LQRVNYIGR DKPLEPRQP TYDPIKGGD KGENYSYVQ 
      LTAVHEYIY PVVEEQHKV SIGRRESGS SLKKCSPEL 
      SAQQPPLPL KSKPKKPPK TQIRCRHCH ELYFEDKNP 
      KGSCEYAPD CIKSSINTI TCIGCAQCI CYHCAADAE 
      GDFAQHPCE CTNEENCSK RWVCLTVLS ILVPCLWLY 
      PPLKICHWC GIRCGMCGG RHSM
    CDS sequence
    • >TC001559 RA
      atgaccgag tcatttgag gatggcaat tacttggtg 
      cgcgtgcgt gcacaggtg atgtcaagg gatgatagc 
      tcagggggc tgggttccg ctgggaggt gggggtctc 
      agtaacgta tcggtacga aaaaggccc cggccctcc 
      ccatctacc gcccctggg cccgatcct gccagcaaa 
      cccaaacat gattacctg atttatgga aaaaggata 
      agtgatcaa tcgattgta ttaagttgc accatcaaa 
      aaagacttt gaatacaac aaagttatg ccaactttt 
      catcactgg aaaacaggg gacaaaaaa tttggactc 
      acatttcag acggctgcc gatgctcga gctttcgac 
      aaaggagtt cggaccgct gttgaggaa ctgctggac 
      ggttttgcc gaaacctct ccttcatca ctgctacaa 
      aaatattcg aaagatgtg gacgacgac gtgtttatg 
      actctgaat cttccacat gaacccaaa gattcccgc 
      agttccagt gattcaagc tcgaaaggt accgaacat 
      ctacaaagg gttaactac ataggacgc gacaaacct 
      ctcgaacct cggcaaccc acttatgat ccgatcaaa 
      ggtggtgac aaaggggag aactattca tacgtgcaa 
      ctgaccgcc gtgcacgag tacatctac cctgtggtg 
      gaggagcag cacaaggtg tcgatcggg cgtcgcgag 
      tccggttcg agtttgaaa aaatgcagt ccggaactg 
      tcggcccag cagccccct ctccccctg aaatccaaa 
      ccgaaaaaa ccgccaaag actcaaatc cgctgtaga 
      cattgccac gagttgtac tttgaagac aaaaacccg 
      aaagggtcc tgtgaatac gccccggac tgtataaaa 
      tcatcgata aacacgatc acttgcatc ggttgtgcg 
      cagtgcatt tgttatcat tgtgcggcg gacgctgag 
      ggcgacttc gcccaacac ccctgcgag tgcaccaac 
      gaagagaac tgctccaag cgctgggtt tgtctcacg 
      gtcttatcc attctcgtg ccgtgtctg tggctctac 
      cctccgctg aagatctgc cactggtgc ggcatcaga 
      tgcggcatg tgcgggggc agacacagc atgtga
    mRNA sequence
    • >TC001559 RA
      actaactga caaacgtta atttagttc aatggattg 
      tccccgtgt tgtttagtt ggatttgat gttgtgcaa 
      aaatgtggt tgtcaaaca aaacatgga ctttcaacg 
      ttaggatat ttcacacga caaatcatg accgagtca 
      tttgaggat ggcaattac ttggtgcgc gtgcgtgca 
      caggtgatg tcaagggat gatagctca gggggctgg 
      gttccgctg ggaggtggg ggtctcagt aacgtatcg 
      gtacgaaaa aggccccgg ccctcccca tctaccgcc 
      cctgggccc gatcctgcc agcaaaccc aaacatgat 
      tacctgatt tatggaaaa aggataagt gatcaatcg 
      attgtatta agttgcacc atcaaaaaa gactttgaa 
      tacaacaaa gttatgcca acttttcat cactggaaa 
      acaggggac aaaaaattt ggactcaca tttcagacg 
      gctgccgat gctcgagct ttcgacaaa ggagttcgg 
      accgctgtt gaggaactg ctggacggt tttgccgaa 
      acctctcct tcatcactg ctacaaaaa tattcgaaa 
      gatgtggac gacgacgtg tttatgact ctgaatctt 
      ccacatgaa cccaaagat tcccgcagt tccagtgat 
      tcaagctcg aaaggtacc gaacatcta caaagggtt 
      aactacata ggacgcgac aaacctctc gaacctcgg 
      caacccact tatgatccg atcaaaggt ggtgacaaa 
      ggggagaac tattcatac gtgcaactg accgccgtg 
      cacgagtac atctaccct gtggtggag gagcagcac 
      aaggtgtcg atcgggcgt cgcgagtcc ggttcgagt 
      ttgaaaaaa tgcagtccg gaactgtcg gcccagcag 
      ccccctctc cccctgaaa tccaaaccg aaaaaaccg 
      ccaaagact caaatccgc tgtagacat tgccacgag 
      ttgtacttt gaagacaaa aacccgaaa gggtcctgt 
      gaatacgcc ccggactgt ataaaatca tcgataaac 
      acgatcact tgcatcggt tgtgcgcag tgcatttgt 
      tatcattgt gcggcggac gctgagggc gacttcgcc 
      caacacccc tgcgagtgc accaacgaa gagaactgc 
      tccaagcgc tgggtttgt ctcacggtc ttatccatt 
      ctcgtgccg tgtctgtgg ctctaccct ccgctgaag 
      atctgccac tggtgcggc atcagatgc ggcatgtgc 
      gggggcaga cacagcatg tgatccaaa acacattat 
      attttacga tattagttt tacttgctc tttaagcac 
      acaaattta ttttttata tggaatttt tttatttat 
      ttaatctcc agatttcat attatatag attaaaaac 
      gtctgtgat ttaatataa gcatttcat agtattaga 
      cgatcaagg ttctgttcg cttggagga gtatatctt 
      gttttacca atagcttta aaattgata tcgtaaagt 
      aacgagtga tgtttaaaa acagtagtg ctcaacaag 
      aagggttgt gaacactga aatgaacaa agtgtctcc 
      acacttaat gtaatgtta caagactgt tcatttata 
      catttttta actgtcctc attactctc tgttgaacg 
      ttttaacct gatattctt tacacagca cgagtctct 
      taaaagcat attccaact tcaaaaaaa atacaatga 
      agtccggct ataacgtac tattgttca agcaccaaa 
      aatttgtct ttctttaag ttcaccaaa attgttttt 
      ggaaagaaa atcaaaata acaccactg atttaataa 
      ttatgtaaa taaattaca atcacaaac acatgatat 
      ctaaattta tcagatcgg taaagaaag gagcttaaa 
      aata
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY