Status
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Gene information
General information
TC004947 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: 4954589..4957318
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
    TC004947
    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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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_09598

    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: 50.0% (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


    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
    • >TC004947 RA
      MSEFIVIQV GQCGNQIGS FLLPEILQE YGVKTTTDS 
      PAKPKRNKA ELQQFMSSF FNMDPTNTT IETLSDLLK 
      SKAKARFLC IDMEDSVVA RFKSGRLRD LFDSKSLIT 
      HYPGSGNNW AEGYCSHGP KFKQKILKA IQYNVEKCD 
      HLHGFLVLF SMGGGTGSG LGTFIVKLL ADFFPHIDR 
      FVACVYPTG TEDVITGPY NMAFATEQL LESATCVFP 
      VENRALLDI ALRHTGRYS ARNKTYFSP FRPFEDMNK 
      IIVDMILHL TSGSRFGGK MNIDMNEIN TNMVPFPKL 
      NFLASGYSP FRLKNFNSS AHSDQLKNE LFLASCSRN 
      NQLIKVDPF DSRYMAMSV TLLGRGNYS INDMRGYID 
      RLKSKLHFA CWSNKAVKV GLCNVAPKG LDFSMFSLC 
      NTSSTSNLF QEVLNQFTK LYQRKAHVH HYTAISGFD 
      FDQFKECQN SISNIIEFY QEIGKRKTL
    CDS sequence
    • >TC004947 RA
      atgagtgaa tttatcgtg atacaagtc gggcaatgt 
      ggcaaccaa atcggcagt tttctcctc ccggaaatc 
      ctccaagag tatggggtc aagacaacg accgactcc 
      ccagccaaa cccaaacga aacaaagcg gaattgcag 
      caattcatg tcgagtttc ttcaacatg gatccaacg 
      aacacaaca attgagaca ttgagcgac ttgttgaaa 
      agtaaagcc aaagcgaga tttttatgt atcgacatg 
      gaggacagt gtcgttgcc aggttcaag tcggggcgg 
      cttcgcgac ttattcgac agcaaatcc ctgataacg 
      cattatccc ggttctggg aacaactgg gctgagggc 
      tactgcagc catggcccc aaattcaag caaaaaatc 
      ctcaaggcg atccaatac aacgtcgag aaatgtgac 
      catttgcac gggtttttg gttttattt tcaatgggg 
      ggtggcacg ggctcgggg ctggggact ttcattgtg 
      aaactgctt gcagatttc tttccacac atcgaccgg 
      ttcgtagcg tgtgtgtac cccacaggc actgaagac 
      gtgattacg ggcccctat aacatggct ttcgccacg 
      gaacaactg ctggaaagt gccacttgt gtgtttccc 
      gttgaaaat cgggcactt ctggacatt gctttaaga 
      cacacgggg cgatacagt gctagaaat aaaacgtat 
      ttctcccca tttaggccg tttgaagac atgaacaag 
      ataatcgtt gatatgatt ttgcatctc acgagtggc 
      tcgagattt ggggggaaa atgaacatt gatatgaat 
      gagattaat acgaatatg gtgccattc cccaaatta 
      aatttttta gcaagtggc tacagcccg tttagactg 
      aaaaatttt aactcaagc gcacacagt gatcaatta 
      aaaaacgaa ctgttttta gcatcgtgt agtagaaac 
      aatcagcta ataaaagtc gatccgttt gattccagg 
      tacatggcg atgagtgtc actttatta ggcagagga 
      aattattca ataaatgac atgaggggt tacatcgat 
      aggttgaaa agtaagtta cactttgct tgttggtca 
      aacaaagct gttaaagtc ggactgtgc aatgtggcc 
      cccaaggga ctagacttc tcaatgttt tctctatgc 
      aacacctca tcaacgtca aatttattt caagaagtt 
      ttaaaccaa tttacgaag ctataccaa agaaaagcc 
      cacgttcac cattacact gccatatct ggatttgat 
      tttgatcag ttcaaagaa tgccaaaat agcattagt 
      aacatcatt gaattttat caagaaatc ggtaagaga 
      aaaactttg taa
    mRNA sequence
    • >TC004947 RA
      aaatttgaa taaagtgag gttatgtgc cgattgtaa 
      aaaattaat gagtgaatt tatcgtgat acaagtcgg 
      gcaatgtgg caaccaaat cggcagttt tctcctccc 
      ggaaatcct ccaagagta tggggtcaa gacaacgac 
      cgactcccc agccaaacc caaacgaaa caaagcgga 
      attgcagca attcatgtc gagtttctt caacatgga 
      tccaacgaa cacaacaat tgagacatt gagcgactt 
      gttgaaaag taaagccaa agcgagatt tttatgtat 
      cgacatgga ggacagtgt cgttgccag gttcaagtc 
      ggggcggct tcgcgactt attcgacag caaatccct 
      gataacgca ttatcccgg ttctgggaa caactgggc 
      tgagggcta ctgcagcca tggccccaa attcaagca 
      aaaaatcct caaggcgat ccaatacaa cgtcgagaa 
      atgtgacca tttgcacgg gtttttggt tttattttc 
      aatgggggg tggcacggg ctcggggct ggggacttt 
      cattgtgaa actgcttgc agatttctt tccacacat 
      cgaccggtt cgtagcgtg tgtgtaccc cacaggcac 
      tgaagacgt gattacggg cccctataa catggcttt 
      cgccacgga acaactgct ggaaagtgc cacttgtgt 
      gtttcccgt tgaaaatcg ggcacttct ggacattgc 
      tttaagaca cacggggcg atacagtgc tagaaataa 
      aacgtattt ctccccatt taggccgtt tgaagacat 
      gaacaagat aatcgttga tatgatttt gcatctcac 
      gagtggctc gagatttgg ggggaaaat gaacattga 
      tatgaatga gattaatac gaatatggt gccattccc 
      caaattaaa ttttttagc aagtggcta cagcccgtt 
      tagactgaa aaattttaa ctcaagcgc acacagtga 
      tcaattaaa aaacgaact gtttttagc atcgtgtag 
      tagaaacaa tcagctaat aaaagtcga tccgtttga 
      ttccaggta catggcgat gagtgtcac tttattagg 
      cagaggaaa ttattcaat aaatgacat gaggggtta 
      catcgatag gttgaaaag taagttaca ctttgcttg 
      ttggtcaaa caaagctgt taaagtcgg actgtgcaa 
      tgtggcccc caagggact agacttctc aatgttttc 
      tctatgcaa cacctcatc aacgtcaaa tttatttca 
      agaagtttt aaaccaatt tacgaagct ataccaaag 
      aaaagccca cgttcacca ttacactgc catatctgg 
      atttgattt tgatcagtt caaagaatg ccaaaatag 
      cattagtaa catcattga attttatca agaaatcgg 
      taagagaaa aactttgta acttgttaa ctttttaat 
      tagaaaata taaaagcaa aaaattata cacttaaat 
      tgaaataaa tcacataaa aatacattt caactacca 
      ttatgtgca ataataaaa acacgaacc tgta
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY