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Gene information
General information
TC004401 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: 7203333..7212964
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 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
    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.

    {{ 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.
    {{ 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 *
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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.
    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.
    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.
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_03745

    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.
    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.
    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: 0.0% (includes death as pupa, adult)

    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.
    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
    Left: Right:
    Protein sequence
    • >TC004401 RA
    CDS sequence
    • >TC004401 RA
      atgacttcg gaagattcg gttccgggg actgccgct 
      ccgccagaa agcggaaat aaaacaacc gaaccgacc 
      gctagtgat tcactcagt tcgcaaaga gtgttcaag 
      aaatcatct cctaataat aagctgaca atgtacttg 
      agttcccgt gatttggtt gtgtccgca ggtagaatc 
      gatcgactc caaggagtc ttactggtc gacccggag 
      tttgtcgag aaccggaaa gtttatgga caggtcaca 
      ctcacgttc agatatgga cgagaagac gaagaagtg 
      atgggttta aaattctgc aacgaagcg atcatgtgt 
      ttggcacaa ttgtatcca cctcatcct gccgctcaa 
      gcgcccgaa ggtaacaca ccattacag gacgcattg 
      ctgaagcgt ttaggtagc aatgcgtat cctttcagc 
      atggaaatt acgcctttg gcaccacct agtgttcaa 
      ttagtgcca gccaaagaa tataacggg gcccccatt 
      gggaccagt tatgatgta agagcttac gtcgctgat 
      cgagccgac gaaaagttt catcgtaaa gcaactgtc 
      cgcatggga atacgagtc gtgcagcga gcgtacgca 
      cccccttca ccccatctg tacaacccc cgtcatttg 
      tcacgatcg caaaacaag aagacgtta ttcggatgt 
      aaaagtgct cccttagac gtcaagttc cccaaagaa 
      caacagaac aaagcaagg tcaatggaa actggcttg 
      gaacagaac aggatcgag gaaacaccg actcatacg 
      ccaccgtca cgaactaat cttcaagtc tcgatagaa 
      tacaaaaac gaaaagaac gaaacacaa agtgacaaa 
      gaaacgcac gtttctttc ggtgaaacg atcacgaac 
      ggaattgaa caagcacaa gatgaaaac gatcgccaa 
      gaatcaccg acgaaatcg catcaacag gacgataac 
      gagcaaaac atcgaagag caatttcgt tctctgtgt 
      ggtggcaaa cgtcccagt ttagcggcg tatctcgct 
      ggcgtcccg gcgccatgt gctcaagtc gaaaaaccg 
      tttcttctg agcgaaggc aaagtgcat ttgcttgca 
      tctctcgac aaagcaatc tattcccat ggcgaggag 
      atacatgtc tttgttcag atcaaaaac aacagcaac 
      aaaacaata cgacggata aaggttttt gtagtgcaa 
      cacgtggac gtttgcatg ttttccaac gggaaattt 
      aagaacgtt gtcgcaatg ataaattca aaggagaat 
      tgccccatt acatcaaac accatctat gagcataca 
      ttttctctg cttcccgtg aaaagttca acgaaaaat 
      tggatcgct ttggaggat tcgtacaca aaacagggc 
      accagtttg gcttcaacg gtcacttgt tcggctaat 
      aaccccgac gaacgcaac gtatttgcc atctatgtc 
      tcctattac gtcaaaatc aaactgctg gtgagcgtg 
      atgggcgga gaagtgtct ttgaaacta cccttcacc 
      ctcatgcac acttgctcc gactttgaa cacactgag 
      acactaatt cgagtctca aaacccgat ttcgaaccg 
      aaacaagtg ctagaatcg gtcaaagat gggacgtga
    mRNA sequence
    • >TC004401 RA
      tattaaaaa aaaatccgt atattccag atcaatgcg 
      aaagaggtt aaagagtgg ggatgaatt ttcagaatc 
      ctaacaggt tacattttc agcgtttca gtctgtaaa 
      ggttgagcg gacgagacg gtttcagtg cccgcgatt 
      cgcttgaaa aatacacgt ttttacatt agaagagga 
      tttttagtt ttagtgatg tttatgtgc tgagataaa 
      ggggatatt ttttgtgga ttcgtcatg ggaaaaact 
      ttgtacata ctcttgaat aaatttgtt tggtcggtg 
      gaattcttg ccatcgttg ctctgaaaa caatttgaa 
      ttatttaca aagcgtttt ttcaaagtt tttcaagtg 
      ctccaaatg acttcggaa gattcggtt ccggggact 
      gccgctccg ccagaaagc ggaaataaa acaaccgaa 
      ccgaccgct agtgattca ctcagttcg caaagagtg 
      ttcaagaaa tcatctcct aataataag ctgacaatg 
      tacttgagt tcccgtgat ttggttgtg tccgcaggt 
      agaatcgat cgactccaa ggagtctta ctggtcgac 
      ccggagttt gtcgagaac cggaaagtt tatggacag 
      gtcacactc acgttcaga tatggacga gaagacgaa 
      gaagtgatg ggtttaaaa ttctgcaac gaagcgatc 
      atgtgtttg gcacaattg tatccacct catcctgcc 
      gctcaagcg cccgaaggt aacacacca ttacaggac 
      gcattgctg aagcgttta ggtagcaat gcgtatcct 
      ttcagcatg gaaattacg cctttggca ccacctagt 
      gttcaatta gtgccagcc aaagaatat aacggggcc 
      cccattggg accagttat gatgtaaga gcttacgtc 
      gctgatcga gccgacgaa aagtttcat cgtaaagca 
      actgtccgc atgggaata cgagtcgtg cagcgagcg 
      tacgcaccc ccttcaccc catctgtac aacccccgt 
      catttgtca cgatcgcaa aacaagaag acgttattc 
      ggatgtaaa agtgctccc ttagacgtc aagttcccc 
      aaagaacaa cagaacaaa gcaaggtca atggaaact 
      ggcttggaa cagaacagg atcgaggaa acaccgact 
      catacgcca ccgtcacga actaatctt caagtctcg 
      atagaatac aaaaacgaa aagaacgaa acacaaagt 
      gacaaagaa acgcacgtt tctttcggt gaaacgatc 
      acgaacgga attgaacaa gcacaagat gaaaacgat 
      cgccaagaa tcaccgacg aaatcgcat caacaggac 
      gataacgag caaaacatc gaagagcaa tttcgttct 
      ctgtgtggt ggcaaacgt cccagttta gcggcgtat 
      ctcgctggc gtcccggcg ccatgtgct caagtcgaa 
      aaaccgttt cttctgagc gaaggcaaa gtgcatttg 
      cttgcatct ctcgacaaa gcaatctat tcccatggc 
      gaggagata catgtcttt gttcagatc aaaaacaac 
      agcaacaaa acaatacga cggataaag gtttttgta 
      gtgcaacac gtggacgtt tgcatgttt tccaacggg 
      aaatttaag aacgttgtc gcaatgata aattcaaag 
      gagaattgc cccattaca tcaaacacc atctatgag 
      catacattt tctctgctt cccgtgaaa agttcaacg 
      aaaaattgg atcgctttg gaggattcg tacacaaaa 
      cagggcacc agtttggct tcaacggtc acttgttcg 
      gctaataac cccgacgaa cgcaacgta tttgccatc 
      tatgtctcc tattacgtc aaaatcaaa ctgctggtg 
      agcgtgatg ggcggagaa gtgtctttg aaactaccc 
      ttcaccctc atgcacact tgctccgac tttgaacac 
      actgagaca ctaattcga gtctcaaaa cccgatttc 
      gaaccgaaa caagtgcta gaatcggtc aaagatggg 
      acgtgagac aaggctgaa gttatcgtc gagattaat 
      aaagctggt gatgaagat aaggtcgtg gtggtgtcc 
      aaaacggat tctgacgaa acagtgcag aaaaaaaca 
      tccattgta cgcaacaat caagtcgat tacgatcaa 
      attgtgcca gtgaaaagt gaaagtgat gtggaggaa 
      atcaaggtg gaaagtgct aaagaaaaa ggattcagt 
      ttgcataga gcgttgtgt tgtttaaga actagaaga 
      acgtcctag tcggattgt atgttattg tatatgggg 
      ccctataat ctagcactg tgtcttaat tcttacaaa 
      catacgtac tataccttt tttcctacc tcatcctta 
      aaaacacaa atttcgatt tttttttac tttaatata 
      cagtcgatg gttacgact acatttttc tgtaaatta 
      ttatttatg tacaaatac tacatataa aataaataa 
      aaaagagca cgataaaat tacacattt ttcaattcc 
      gtttcataa aacaaagaa ttctatttg tgctagtct 
      cttttagca tgagacggc accacaaaa tagtatatt 
      aaaaaaaaa acaagtttc ataagatta gttggactg 
      ggaattttt atcgatatg tcgatacct taaattatt 
      agacttaac tccaaaaat taaacatta attccaaag 
      acaactctt aacaacaat aataaaact aagagctgg 

    If you use iBeetle-Base, please cite: Dönitz J et al.: Expanded and updated data and a query pipeline for iBeetle-Base,
    Nucleic Acids Res. 2018 Jan 4;46(D1):D831-D835. doi: 10.1093/nar/gkx984.

    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY