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Gene information
General information
TC004884 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_007417.3: 3698019..3701023
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
    TC004884
    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
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    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_03867

    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: 30.0% (includes death as pupa, adult)

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


    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
    egg without cuticle embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): less than 30%
    larva complete everted (inside-out) - Penetrance (percentage of animals/eggs on slide): less than 30%
    larva circumference decreased - Penetrance (percentage of animals/eggs on slide): less than 30%
    larva cuticle dorsal not closed - Penetrance (percentage of animals/eggs on slide): less than 30%
    head not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    legs segment sometimes broader - Penetrance (percentage of animals/eggs on slide): less than 30%
    thorax not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): 50% - 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: 20.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 30.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection


    adult lethality immediately after eclosion - Number of animals showing the phenotype: 1 (16 dpi)
    Days post injection


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004884 RA
      MIEAGMNIA RLTLSHGTQ EMHTELIQN VRTAVENYS 
      KRLGVMYPL SLALDIKGP EVRTGYMEG GIAAEVELK 
      KGEQIKLTT DKAYLEKGS SSVIYVDYD NIQKVVQPG 
      NRIFLDDGL ISLICTSVQ GSVLTCSVE NGGMLGSCK 
      NVNLPGIDI DLPVVSEKD KEDLLFGVE HGIDTVHAS 
      FIRNAVDVS EVRDVLGRA GNKILIISK IENHQGVHN 
      IDEIIKASD GIMIGRGDL AVEIGPEKL FLAQKSIIA 
      KCNKAGKPV ICANQLLYS MIKRPRPTR AECTDVANA 
      VLDGVDCVM LTGETFLGQ HPIECIRAA SKICKEAEG 
      AIWYKHHFR ELIGHARPP LETSHTICI AAVEAANQC 
      LAAAIIVTS VSGRSAHSL AKYRPNCPI ILVTRDPTV 
      AKQANLFRG IIPLFYEVE RKDDWRRDI EARISFGIS 
      FGKWRGFGV GVH
    CDS sequence
    • >TC004884 RA
      atgatcgaa gctggaatg aacattgcc cgcctaaca 
      ctctcccac ggcacccag gaaatgcac accgaactg 
      atccaaaac gtgagaacc gccgtcgaa aattacagc 
      aaaagactg ggagtcatg tacccctta tccctcgcc 
      ctcgatatc aaaggaccc gaagtccgg accggttac 
      atggaaggc ggcatcgcc gccgaagtc gagctgaaa 
      aagggcgaa caaatcaaa ctgacaaca gacaaagcg 
      tatctggag aagggcagc tcgagcgtg atctacgtc 
      gactacgac aacatccag aaggtggtc caacccggg 
      aaccgtatt ttcctggac gatggtctc atctccctg 
      atttgcaca agcgtccaa ggctcggtc ctgacatgt 
      agtgtggaa aacggggga atgcttggc agttgcaaa 
      aacgtgaac ctccccgga atcgatatc gacttaccc 
      gtggtgtcc gaaaaagac aaggaggat ttgcttttc 
      ggcgtcgaa cacggcatt gacaccgtt cacgcctca 
      ttcatccgc aatgctgtc gatgtgtcg gaggttcga 
      gacgtgcta gggcgggcc ggtaacaag atcttgatc 
      atttcgaaa atcgaaaac caccaaggt gtgcacaac 
      atcgacgaa ataatcaaa gcttccgac ggcattatg 
      atcgggcga ggcgaccta gcggtggaa atcggccct 
      gagaagctt ttcctcgcc cagaagagc atcatagct 
      aagtgtaac aaagcgggg aaaccggtc atttgcgcc 
      aatcagctg ctctactcg atgataaaa cgtccaaga 
      cccactcgg gccgaatgc accgatgtt gcaaacgcg 
      gtgcttgac ggtgttgac tgcgtgatg ttgacgggg 
      gaaactttt cttggccag cacccgatc gagtgcatt 
      cgggccgcg tccaaaatt tgcaaagag gccgaaggg 
      gccatttgg tacaaacac cactttcgg gaattgatc 
      gggcatgcg agacctccg ctagagacg tcgcataca 
      atttgcata gctgcagtc gaagctgca aatcagtgt 
      ctagcagct gcgattatt gtcacgtca gtttcggga 
      cgttcggcc cattcactg gcaaagtat cggcccaac 
      tgccctatt attttagtg acacgtgat ccgactgtc 
      gccaaacaa gcgaactta ttccgggga atcatcccc 
      cttttttac gaagtcgag aggaaagac gattggagg 
      cgagatatt gaagctagg atcagtttc gggatcagt 
      tttggaaag tggaggggg tttggggtc ggggtacac 
      tga
    mRNA sequence
    • >TC004884 RA
      agagtgcac attattgat cactccctt tgaagttct 
      gttgcttaa catcgtgta agtttaata acttttgtt 
      ccatttatt gcaccacaa attagatag acataacat 
      cgaacattg agtaccact tatagccac cctacatat 
      cgagtgtta tatagatct ctctaagaa taatgtcta 
      acatgcaat taagactac atctaaacc aggtgccac 
      gttgcggcc ctattgttt agcaaaaat acttaacgg 
      catcacgcg ctgtgcatg atagccctt gttgttcgg 
      acccttacc agctttaaa caaaaatgt ttttatttg 
      gtcacaggt atattggga ctgattaca atgctgatt 
      attgtctct tcacaataa tcttctttg gagctcgga 
      cctcctgaa ggtaaaata tctgcggag acgacagac 
      agataaaaa cacaacgac cgagtcaca ggttatact 
      gtttggtta tacataatt aacgataaa taagcatca 
      acattaagg tccccttac tgcatcctc gggggctga 
      cccccgcac accaggctt tcccaaaat gatgtgttt 
      tgattggct cagcaattc tcttatatg catatttca 
      gccgaatag ttgctacac aaattataa ataagatta 
      gacactgat gaatattat gctgtatgg caatcatta 
      gccgggctt gagatggga gcgccagta tttcacaaa 
      ttcaagcca ataggtttc ggaatttgg ggacttctg 
      attgcctcg tctcccgca ggactggat tatgtgcag 
      ccattcaca ataatccaa aaacgaggg cccccacac 
      aaacaattt tgacggttg caactccca tcaaagagt 
      cgatttcgg gtacagaag cacgatctt tcttaaaac 
      ttaataaca acacaaata aactctgaa agactgttc 
      atacgctcc cagagcgcg ttaacaata cctcatcca 
      aattttctt tggaacatt aactatctt taacgcatt 
      gccaattta ttcctcttc gtcttcgtt ctggtacgt 
      gacataacg caccgaagt cttctcctc catcagcag 
      catctgaaa tcaacgcat tgtcattat catgacaat 
      tttttgaca tttttttta atcaaaatg gtttggtac 
      acgcgcgaa aatgacgat agcgagcaa attaaaccg 
      ttgcattgt tcacccccg aaacaactc acagcagga 
      gccgcttac acacaactc gaccacaac tcgctgctt 
      gacattcaa tcacatcca ccacaagtg cgtctcact 
      ggaataatc tgcactttg ggaccttca acgacagat 
      gtcgaaacg ttggaaaga atgatcgaa gctggaatg 
      aacattgcc cgcctaaca ctctcccac ggcacccag 
      gaaatgcac accgaactg atccaaaac gtgagaacc 
      gccgtcgaa aattacagc aaaagactg ggagtcatg 
      tacccctta tccctcgcc ctcgatatc aaaggaccc 
      gaagtccgg accggttac atggaaggc ggcatcgcc 
      gccgaagtc gagctgaaa aagggcgaa caaatcaaa 
      ctgacaaca gacaaagcg tatctggag aagggcagc 
      tcgagcgtg atctacgtc gactacgac aacatccag 
      aaggtggtc caacccggg aaccgtatt ttcctggac 
      gatggtctc atctccctg atttgcaca agcgtccaa 
      ggctcggtc ctgacatgt agtgtggaa aacggggga 
      atgcttggc agttgcaaa aacgtgaac ctccccgga 
      atcgatatc gacttaccc gtggtgtcc gaaaaagac 
      aaggaggat ttgcttttc ggcgtcgaa cacggcatt 
      gacaccgtt cacgcctca ttcatccgc aatgctgtc 
      gatgtgtcg gaggttcga gacgtgcta gggcgggcc 
      ggtaacaag atcttgatc atttcgaaa atcgaaaac 
      caccaaggt gtgcacaac atcgacgaa ataatcaaa 
      gcttccgac ggcattatg atcgggcga ggcgaccta 
      gcggtggaa atcggccct gagaagctt ttcctcgcc 
      cagaagagc atcatagct aagtgtaac aaagcgggg 
      aaaccggtc atttgcgcc aatcagctg ctctactcg 
      atgataaaa cgtccaaga cccactcgg gccgaatgc 
      accgatgtt gcaaacgcg gtgcttgac ggtgttgac 
      tgcgtgatg ttgacgggg gaaactttt cttggccag 
      cacccgatc gagtgcatt cgggccgcg tccaaaatt 
      tgcaaagag gccgaaggg gccatttgg tacaaacac 
      cactttcgg gaattgatc gggcatgcg agacctccg 
      ctagagacg tcgcataca atttgcata gctgcagtc 
      gaagctgca aatcagtgt ctagcagct gcgattatt 
      gtcacgtca gtttcggga cgttcggcc cattcactg 
      gcaaagtat cggcccaac tgccctatt attttagtg 
      acacgtgat ccgactgtc gccaaacaa gcgaactta 
      ttccgggga atcatcccc cttttttac gaagtcgag 
      aggaaagac gattggagg cgagatatt gaagctagg 
      atcagtttc gggatcagt tttggaaag tggaggggg 
      tttggggtc ggggtacac tgatacgat ccgagtcct 
      gtacgttat gaggcccat agtggaagg ggactgcac 
      gtgtgataa gaaaacggg tg
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY