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Gene information
General information
TC003991 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: 28962771..28968875
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
    TC003991
    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
    {{ goGene }}
    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
    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
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    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.

    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_07283

    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: % (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
    • >TC003991 RA
      MKEFSFVVV FYFITLSLA EFEVPDALV EVFQPQGLR 
      VSIPDQEGI KLFAFHAKV NEEMNGREG GTFSRDITK 
      AKHGRWTFY DPYAKLKIG DTIYYWTYV DYFDGKNKL 
      GYTKDDQEF VVRQLLDKE KSPANPPVK KPEPEIEER 
      LPSGCKASA TISKQKKMC KGEEIFNEN FENLKPELW 
      NREIKYAGK PDFEFVLYT DRKEILSVN NNELTIRPI 
      FTEQLFGKE FVSYEHELD LGEKCTGIH GTTDCVQKA 
      DAFLILPPV ASGRVNTKD KWSFKFGKI EIKAKLPKG 
      DWIYPQLFL NPVSEEYGS DYASGQIRV AFLPGNQAM 
      AQQLYGGCV LGPTTAARN YALKVIRKT DGLWSDDYH 
      KFTAVWKPD QITLSVDDQ VYGYIEPPR GGFVSDFQN 
      LGLDFEIVE RWRNGTSFA PFDKEMYLS IGVGVGGHC 
      FEDRSDGSK PWKNSDPKG QKNFYKASA QWLPTWDNS 
      SVLKVDYVK IWAL
    CDS sequence
    • >TC003991 RA
      atgaaagaa ttctccttt gtagtagtg ttttatttc 
      ataacatta agtttagct gagtttgaa gttccggat 
      gctttggtt gaggttttt caaccacaa ggcttacga 
      gtttcgatt ccagaccaa gaaggcata aaactcttt 
      gcctttcat gccaaagtc aacgaagaa atgaacggc 
      cgcgaaggc ggaacattt tcaagggac atcacaaag 
      gctaaacac ggccgttgg actttttac gatccttac 
      gcaaaacta aaaattgga gacacgatt tattactgg 
      acttatgtt gactatttt gacggaaaa aataaacta 
      ggttacaca aaagacgat caagaattt gtagtcaga 
      caattacta gacaaagaa aagtctcct gcaaaccca 
      ccggtcaaa aaaccagaa cctgaaata gaagaaaga 
      ctgcccagt ggctgtaaa gcaagcgca acaatcagc 
      aaacagaaa aaaatgtgt aaaggagag gaaatcttt 
      aacgaaaat ttcgaaaac ttgaaacca gagttgtgg 
      aaccgcgaa atcaaatat gccggaaaa ccggacttt 
      gaatttgtt ttatacacc gaccggaag gaaatttta 
      tcagtgaac aacaacgag cttacaata cgtccaatt 
      tttaccgaa caactgttc ggaaaagaa ttcgtgagt 
      tacgaacat gaactagat ctcggtgaa aaatgtacc 
      ggaatccac ggcaccacc gactgtgta caaaaagcc 
      gacgctttt ttaatcctt cctccggtg gcttccggt 
      cgcgttaac accaaagac aagtggtct tttaaattt 
      ggaaaaatc gaaatcaag gccaaattg cccaaaggc 
      gattggatt tacccccaa ttgttcctg aatccggtg 
      agtgaggag tacggctcg gattacgcc tccgggcaa 
      atccgggtc gctttcctc cccggaaac caagcaatg 
      gcgcaacaa ttgtacggc gggtgtgtt ctgggaccc 
      accactgct gcaaggaat tacgccttg aaagtaatt 
      cgtaaaact gatggcttg tggagcgat gattatcat 
      aagtttacc gcagtttgg aagccagac caaattact 
      ctcagcgtt gacgaccaa gtttacggc tacattgag 
      cctcctcgt gggggtttt gttagcgac ttccaaaat 
      ttaggatta gactttgaa attgtcgaa agatggcgc 
      aacggcact tccttcgca ccatttgac aaagagatg 
      tatctgtca atcggtgtg ggagtcggg ggtcattgt 
      ttcgaagat cgcagcgat ggcagcaag ccatggaaa 
      aacagcgac cccaaaggc cagaaaaac ttctacaaa 
      gcttccgct caatggttg ccaacttgg gataattcg 
      agcgtgtta aaagtggac tatgtgaaa atatgggcc 
      ctttga
    mRNA sequence
    • >TC003991 RA
      gcttcaata acaacggga aaagcatta ttatttagt 
      cattgtgcg tttgtcgca agagtaaaa atgaaagaa 
      ttctccttt gtagtagtg ttttatttc ataacatta 
      agtttagct gagtttgaa gttccggat gctttggtt 
      gaggttttt caaccacaa ggcttacga gtttcgatt 
      ccagaccaa gaaggcata aaactcttt gcctttcat 
      gccaaagtc aacgaagaa atgaacggc cgcgaaggc 
      ggaacattt tcaagggac atcacaaag gctaaacac 
      ggccgttgg actttttac gatccttac gcaaaacta 
      aaaattgga gacacgatt tattactgg acttatgtt 
      gactatttt gacggaaaa aataaacta ggttacaca 
      aaagacgat caagaattt gtagtcaga caattacta 
      gacaaagaa aagtctcct gcaaaccca ccggtcaaa 
      aaaccagaa cctgaaata gaagaaaga ctgcccagt 
      ggctgtaaa gcaagcgca acaatcagc aaacagaaa 
      aaaatgtgt aaaggagag gaaatcttt aacgaaaat 
      ttcgaaaac ttgaaacca gagttgtgg aaccgcgaa 
      atcaaatat gccggaaaa ccggacttt gaatttgtt 
      ttatacacc gaccggaag gaaatttta tcagtgaac 
      aacaacgag cttacaata cgtccaatt tttaccgaa 
      caactgttc ggaaaagaa ttcgtgagt tacgaacat 
      gaactagat ctcggtgaa aaatgtacc ggaatccac 
      ggcaccacc gactgtgta caaaaagcc gacgctttt 
      ttaatcctt cctccggtg gcttccggt cgcgttaac 
      accaaagac aagtggtct tttaaattt ggaaaaatc 
      gaaatcaag gccaaattg cccaaaggc gattggatt 
      tacccccaa ttgttcctg aatccggtg agtgaggag 
      tacggctcg gattacgcc tccgggcaa atccgggtc 
      gctttcctc cccggaaac caagcaatg gcgcaacaa 
      ttgtacggc gggtgtgtt ctgggaccc accactgct 
      gcaaggaat tacgccttg aaagtaatt cgtaaaact 
      gatggcttg tggagcgat gattatcat aagtttacc 
      gcagtttgg aagccagac caaattact ctcagcgtt 
      gacgaccaa gtttacggc tacattgag cctcctcgt 
      gggggtttt gttagcgac ttccaaaat ttaggatta 
      gactttgaa attgtcgaa agatggcgc aacggcact 
      tccttcgca ccatttgac aaagagatg tatctgtca 
      atcggtgtg ggagtcggg ggtcattgt ttcgaagat 
      cgcagcgat ggcagcaag ccatggaaa aacagcgac 
      cccaaaggc cagaaaaac ttctacaaa gcttccgct 
      caatggttg ccaacttgg gataattcg agcgtgtta 
      aaagtggac tatgtgaaa atatgggcc ctttgattt 
      tttttacac aactttatt aaattattc gaattacac 
      aaaatattg tattgccat ataaaaaca attgcaaaa 
      atattacag caca
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY