Status
Please wait ...
Gene information
General information
TC006413 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: 8520510..8527212
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
    TC006413
    Gene ontology

    GO terms for Tribolium

    • {{ goTerm.term }}
      ({{ goTerm.evidence }}){{ goTerm.evidenceTooltip }}
      {{goTerm.showAll ? '[-]' : '[+]'}}
      Status: {{ goTerm.status }}
      Evidence: {{ goTerm.evidence }} ({{ goTerm.evidenceTooltip }})
      Reference: {{ goTerm.referenceText }}
      Quotation: {{ goTerm.quotation }}
      Submitter: {{ goTerm.name }}

    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 *
    {{ blurIdResult }}
    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
    {{ blurEvidenceResult }}
    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 *
    {{ blurReferenceResult }}
    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
    You may enter your name. The contact information can help us to clarify any questions. If you agree, we may show your name on this page to honor your contribution.
    Email
    We will use your email address only for possible questions regarding this annotation. We will never show your address or give it away.
    Publish name
    If you have entered your name and agree by marking the checkbox. we might show your name on this page to honor your contribution.
      {{ unavailableText }}

    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_08915

    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)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 4 (3 dpi)
    Days post injection


    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg with embryonic tissue potentially present, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): less than 30%

    larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    cuticle remnants strongly fragmented (cuticle crumbs) - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    cuticle remnants with some identifiable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

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

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

    maxilla potentially everted (inside-out) - Penetrance (percentage of animals/eggs on slide): less than 30%

    labium potentially transformed - Penetrance (percentage of animals/eggs on slide): less than 30%
    Comment: into leg like structure. Just one embryo on slide
    head appendages potentially partiallyfused - Penetrance (percentage of animals/eggs on slide): less than 30%

    legs sometimeseverted (inside-out) - Penetrance (percentage of animals/eggs on slide): less than 30%
    legs pretarsus number increased - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 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
    • >TC006413 RA
      MASAKTRKW ADWLTCTQV LNIMVILGF MFNYMLRVN 
      MTIAVVDMV KKNDTNTTS TSTRFDWSE AQKNDILGS 
      FFWGYVLTE LPGGRLAEI VGARRVFGG GMLLASLIT 
      VLTPAACHL NYYVVLVLR AFLGFFLGA TWPAILPMA 
      AKWIPPMER SKFIANMMA SSLGAALTM PVCGFLISS 
      IGWPSVFYV TGAVGIVWS VAWFLLVFD SPAQHPRIT 
      IEEKLEIES KIAEGSGGK SVKPSKVPW VKIFTSGPV 
      WAIIITHGC SVFCYFTVV NQLPSYMDH VLHFNIKKN 
      GILSSLPYL GKYAMAVIA SYLADRLLK SGRLSRTTT 
      RKAFTTFAV LTPGFLMII QAFLGMDPV ITVVVFTAS 
      LFFNGAVTA GYLSNGLDI APNFSGTIF GMANTLSSF 
      GGWLSTKIV AILTKDEQT FEQWRYVFW ILVGTYATG 
      ALVYLLLGT GELQKWNSA DEEVRVEKE MQPLRRNEK 
      EVLA
    CDS sequence
    • >TC006413 RA
      atggcttcg gcgaagacg cgcaaatgg gcagactgg 
      ctgacctgc acccaagtc ctcaacatc atggtgatc 
      ctcggcttc atgttcaac tacatgctg cgagtcaac 
      atgaccatc gccgtggtg gacatggtg aagaaaaac 
      gacaccaac accacctcc accagcacg cgcttcgac 
      tggtcggag gcgcagaaa aacgacatt ttgggcagc 
      ttcttctgg ggctacgtc ctgacggag cttcccggt 
      ggccgtctc gccgagatc gtgggggcg cggcgggtc 
      ttcgggggc ggcatgctc ctcgccagc ctcataaca 
      gtactcacc ccggccgcg tgccacttg aactactat 
      gtagtgtta gttttacgg gcttttctg ggcttcttc 
      ctgggggcc acgtggccg gcgatcctg cccatggcc 
      gccaagtgg atcccgccc atggagcgg tccaagttc 
      atcgccaac atgatggcc agctcgctg ggggcggcg 
      ttgacgatg cccgtgtgc gggttcttg atttcgtcc 
      attgggtgg ccgagtgtg ttttacgtg acgggggcg 
      gtggggatc gtgtggtcg gtggcgtgg tttttgctt 
      gtgtttgat tctccggca caacacccc agaatcacg 
      attgaggag aagttggag attgagtcg aaaatcgcg 
      gagggaagt ggcgggaaa agtgtgaag ccgtccaag 
      gtgccatgg gtgaagatt tttacttct gggcccgtc 
      tgggcgatt attatcacg catgggtgt tcggttttt 
      tgctacttt accgttgtc aatcaactg ccgtcctat 
      atggaccat gtcttgcat tttaatata aagaagaat 
      gggatattg tccagtttg ccctatctc ggcaaatac 
      gcaatggcc gtcatcgcc agctacctc gcggaccga 
      ctgctcaaa tcgggccgc ctctcgcgc accaccacc 
      cgcaaagcc ttcaccacg ttcgccgtc ctgaccccc 
      ggcttcctc atgataatc caggccttc ctgggcatg 
      gaccccgtc ataacagta gtagtattc accgcgtcc 
      ctgtttttc aacggcgcc gtcaccgcc ggctacctc 
      tccaacggc ctggacatc gcccccaac ttctcgggg 
      acgatcttc ggcatggcc aacaccctc tcgtccttc 
      ggcggctgg ctgtcgacc aaaatcgtg gccatcctc 
      accaaagac gagcagact ttcgagcag tggcggtac 
      gttttctgg attctagtc gggacgtac gccactggg 
      gccctcgtt tatctgcta ctggggacc ggggagtta 
      cagaagtgg aactctgcg gacgaggag gtgcgagtg 
      gagaaggag atgcagccg ttgaggagg aacgagaag 
      gaggtgcta gcgtga
    mRNA sequence
    • >TC006413 RA
      cgttggagg tatagcaaa ggcggtaaa aattgtaag 
      cgccgtttg gttaaacac gagtatgcg gacactact 
      tcgagagat tagacgtgc acctaaata ataaatgac 
      gggtgtttg agatttttt ttaattaat ttatcaaaa 
      ttatttatt aaggtgtga aagtgtccc gtttcagga 
      tggcttcgg cgaagacgc gcaaatggg cagactggc 
      tgacctgca cccaagtcc tcaacatca tggtgatcc 
      tcggcttca tgttcaact acatgctgc gagtcaaca 
      tgaccatcg ccgtggtgg acatggtga agaaaaacg 
      acaccaaca ccacctcca ccagcacgc gcttcgact 
      ggtcggagg cgcagaaaa acgacattt tgggcagct 
      tcttctggg gctacgtcc tgacggagc ttcccggtg 
      gccgtctcg ccgagatcg tgggggcgc ggcgggtct 
      tcgggggcg gcatgctcc tcgccagcc tcataacag 
      tactcaccc cggccgcgt gccacttga actactatg 
      tagtgttag ttttacggg cttttctgg gcttcttcc 
      tgggggcca cgtggccgg cgatcctgc ccatggccg 
      ccaagtgga tcccgccca tggagcggt ccaagttca 
      tcgccaaca tgatggcca gctcgctgg gggcggcgt 
      tgacgatgc ccgtgtgcg ggttcttga tttcgtcca 
      ttgggtggc cgagtgtgt tttacgtga cgggggcgg 
      tggggatcg tgtggtcgg tggcgtggt ttttgcttg 
      tgtttgatt ctccggcac aacacccca gaatcacga 
      ttgaggaga agttggaga ttgagtcga aaatcgcgg 
      agggaagtg gcgggaaaa gtgtgaagc cgtccaagg 
      tgccatggg tgaagattt ttacttctg ggcccgtct 
      gggcgatta ttatcacgc atgggtgtt cggtttttt 
      gctacttta ccgttgtca atcaactgc cgtcctata 
      tggaccatg tcttgcatt ttaatataa agaagaatg 
      ggatattgt ccagtttgc cctatctcg gcaaatacg 
      caatggccg tcatcgcca gctacctcg cggaccgac 
      tgctcaaat cgggccgcc tctcgcgca ccaccaccc 
      gcaaagcct tcaccacgt tcgccgtcc tgacccccg 
      gcttcctca tgataatcc aggccttcc tgggcatgg 
      accccgtca taacagtag tagtattca ccgcgtccc 
      tgtttttca acggcgccg tcaccgccg gctacctct 
      ccaacggcc tggacatcg cccccaact tctcgggga 
      cgatcttcg gcatggcca acaccctct cgtccttcg 
      gcggctggc tgtcgacca aaatcgtgg ccatcctca 
      ccaaagacg agcagactt tcgagcagt ggcggtacg 
      ttttctgga ttctagtcg ggacgtacg ccactgggg 
      ccctcgttt atctgctac tggggaccg gggagttac 
      agaagtgga actctgcgg acgaggagg tgcgagtgg 
      agaaggaga tgcagccgt tgaggagga acgagaagg 
      aggtgctag cgtgatttt tactgtttt tatacttgt 
      acatattgt gattttttt aaataaatt tttgacgat 
      ccg
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY