Status
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Gene information
General information
TC004980 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: 5473007..5475010
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
    TC004980
    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
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    Name
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    Email
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    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_08985

    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: 20.0% (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


    adult lethality - Number of animals showing the phenotype: 1 (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: % (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
    • >TC004980 RA
      MSSKLSVLV LFAVFVNVF SHDDDVHTV KYTTENFAQ 
      ELPKKNHFV MFYAPWCGH CQRLGPTWE QLAEMLNED 
      DSNIRIAKV DCTTDSSLC SEHDVTGYP TLKFFKVGA 
      SEGIKFRGT RDLPTLTTF INEQLREGD EEDAEKKPP 
      QPVSGLVEL TEDTFEKFV ATGKHFIKF YAPWCGHCQ 
      KLAPVWEQL AKSLEFDSS ISIAKVDCT QWRLVCNQF 
      EVKGYPTLL WIEDGKKVD KYQGDRTHE DLKNYVSKM 
      MGSSEIPTE TEKPQSEEG AVGILTGDT FKHGIETGI 
      TFVKFFAPW CGHCKRLAP TWDELGKKF VADSNVNIA 
      KVDCTLDLN KDLCNEQEV EGFPTIFLY KNGDKISEY 
      SGSRTLEDL YEFVKQHVG HDEL
    CDS sequence
    • >TC004980 RA
      atgtcttca aaactatca gtgttagtg ttatttgcg 
      gtcttcgta aatgtattc agtcacgat gatgatgtg 
      cacactgtc aaatacacc acagagaat tttgcccaa 
      gaattacca aagaaaaac cattttgtc atgttctac 
      gccccttgg tgtgggcat tgccaaaga cttggcccc 
      acttgggaa caacttgcc gaaatgctc aatgaagac 
      gatagtaac ataagaatc gctaaagtg gactgcaca 
      acggatagc tccttgtgt tcggagcat gacgtaacg 
      ggctaccct accctcaag ttcttcaaa gttggggct 
      tctgaaggt atcaagttt aggggtacg agggattta 
      cccacgctt actacgttc ataaatgag cagttgaga 
      gagggggat gaggaagac gctgaaaag aagccccca 
      cagcctgtg agtggactc gttgaattg actgaagac 
      acttttgaa aaatttgtg gccactggg aagcatttt 
      attaagttt tatgcgccg tggtgtggc cattgtcag 
      aaactggct ccagtgtgg gaacagttg gccaaatct 
      ttagaattc gattcaagt atttctatc gcgaaagtt 
      gattgcacc caatggagg ctagtttgt aaccagttt 
      gaagtcaag ggttaccca actctttta tggatcgaa 
      gatggtaaa aaagttgac aaataccaa ggcgacaga 
      acgcacgaa gatttgaaa aactatgtt agcaaaatg 
      atgggttct tctgaaata ccaactgag acggaaaaa 
      ccgcagtct gaggaaggt gctgtcgga atcctcact 
      ggtgatacg ttcaagcat ggcatagag acaggtatc 
      acttttgtt aaatttttt gcgccatgg tgtggtcat 
      tgtaagcgt ttggcgccc acttgggac gagttaggc 
      aaaaaattt gtagcagac tcgaacgta aatattgcc 
      aaagttgat tgtactctt gatctaaat aaagatttg 
      tgcaatgag caggaggtt gaagggttt ccaacaatc 
      tttctctat aaaaatggc gataaaata tcggaatat 
      agtggaagt cggactttg gaagatttg tacgaattt 
      gttaaacaa catgtgggg catgatgag ctttaa
    mRNA sequence
    • >TC004980 RA
      tggaggtgg atttcgata tcaagacag cgagttcca 
      catctgtca ccaaaattt gggcaactt tattgttta 
      ctgttggct gtgataagt acttttgta cctatttcc 
      atctataaa acccttagt tttatttcg caatgtctt 
      caaaactat cagtgttag tgttatttg cggtcttcg 
      taaatgtat tcagtcacg atgatgatg tgcacactg 
      tcaaataca ccacagaga attttgccc aagaattac 
      caaagaaaa accattttg tcatgttct acgcccctt 
      ggtgtgggc attgccaaa gacttggcc ccacttggg 
      aacaacttg ccgaaatgc tcaatgaag acgatagta 
      acataagaa tcgctaaag tggactgca caacggata 
      gctccttgt gttcggagc atgacgtaa cgggctacc 
      ctaccctca agttcttca aagttgggg cttctgaag 
      gtatcaagt ttaggggta cgagggatt tacccacgc 
      ttactacgt tcataaatg agcagttga gagaggggg 
      atgaggaag acgctgaaa agaagcccc cacagcctg 
      tgagtggac tcgttgaat tgactgaag acacttttg 
      aaaaatttg tggccactg ggaagcatt ttattaagt 
      tttatgcgc cgtggtgtg gccattgtc agaaactgg 
      ctccagtgt gggaacagt tggccaaat ctttagaat 
      tcgattcaa gtatttcta tcgcgaaag ttgattgca 
      cccaatgga ggctagttt gtaaccagt ttgaagtca 
      agggttacc caactcttt tatggatcg aagatggta 
      aaaaagttg acaaatacc aaggcgaca gaacgcacg 
      aagatttga aaaactatg ttagcaaaa tgatgggtt 
      cttctgaaa taccaactg agacggaaa aaccgcagt 
      ctgaggaag gtgctgtcg gaatcctca ctggtgata 
      cgttcaagc atggcatag agacaggta tcacttttg 
      ttaaatttt ttgcgccat ggtgtggtc attgtaagc 
      gtttggcgc ccacttggg acgagttag gcaaaaaat 
      ttgtagcag actcgaacg taaatattg ccaaagttg 
      attgtactc ttgatctaa ataaagatt tgtgcaatg 
      agcaggagg ttgaagggt ttccaacaa tctttctct 
      ataaaaatg gcgataaaa tatcggaat atagtggaa 
      gtcggactt tggaagatt tgtacgaat ttgttaaac 
      aacatgtgg ggcatgatg agctttaaa tttttggtg 
      tttgttgcg tgtgttgca gtttgtaat tccatttct 
      gagtgacta ttgtaattc ctttccaac ccgatgtgt 
      taaataaag ttttttaaa aagg
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY