Status
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Gene information
General information
TC002948 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: 5890012..5892582
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
    TC002948
    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
    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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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_00475

    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)

    adult lethality - Number of animals showing the phenotype: 2 (9 dpi)
    Days post injection


    adult nutritional state bad (cachectic) - Number of animals showing the phenotype: 3 (11 dpi)
    Days post injection


    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: 60.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 100.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality early (L5/6) - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection


    pupal molt not fulfilled (died as pupa) - Number of animals showing the phenotype: 4 (11 dpi)
    Days post injection


    adult lethality immediately after eclosion - Number of animals showing the phenotype: 4 (19 dpi)
    Days post injection


    Pupal morphology
    wings necrotic - Number of animals showing the phenotype: 4

    legs necrotic - Number of animals showing the phenotype: 4
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC002948 RA
      MLPSCARTF GKKALTQNK ALGLISAKS NYATEAPFE 
      TKAFRLHNL EQGPATNTT LSRDDALLY YRQMHTVRR 
      METSAGNLY KEKIIRGFC HLYSGQEAV AVGIKAALR 
      PHDDVITAY RAHGWSHLM GVNPLGVLA ELTGRQSGC 
      ARGKGGSMH MYTNHFYGG NGIVGAQVP LGVGLALAA 
      KYKGTDGVC VALYGDGAA NQGQVFEVF NMAKLWDIP 
      CIFVCENNG YGMGTSAAR AAANTAYYT RGDVIPGIW 
      IDGMDVLAV REAAKFAVD HCTSGKGPI LLEAATYRY 
      SGHSMSDPG TSYRTREEI QEVRQTRDP ITSFKEKII 
      TANLVSPEE LKAIDTEIR STVDEATKK AKAEKEIPL 
      EELTADIYS LDLEKQIRN IDPFNPLPH KRIGEAVNF 
      K
    CDS sequence
    • >TC002948 RA
      atgttaccc agctgtgct agaactttt ggcaagaaa 
      gccctaacc cagaataaa gccttgggt ttgatctcg 
      gccaagagc aattacgcg actgaggcc ccctttgag 
      acaaaagcc tttcgttta cacaaccta gagcagggc 
      ccagcaaca aacacgacc ctaagccgc gatgacgcc 
      cttttgtac tacagacaa atgcacacc gtccgccgg 
      atggaaacc agtgccggc aacttgtac aaagaaaaa 
      ataatcagg ggcttttgc cacttatat tccggtcag 
      gaagcggtc gctgttggc attaaagcg gcgctgcgc 
      ccccacgac gacgtcata acggcgtac cgggcccac 
      ggctggagc cacttgatg ggggtgaac cccctgggg 
      gtcctcgcc gagctcacg ggccggcag tcggggtgt 
      gcccgcggc aaggggggc tccatgcac atgtacacc 
      aaccatttc tacggaggc aacggcatt gtgggggcg 
      caggtgccg ctaggcgtg gggctagcc ctagctgcg 
      aagtacaag ggcacggat ggggtctgt gtggcgttg 
      tacggggac ggggctgcc aaccagggc caggtgttc 
      gaggtcttc aacatggct aagttatgg gacattccg 
      tgcattttc gtctgcgaa aataatggg tatgggatg 
      gggactagt gcggcccgg gcggctgca aatacagcg 
      tattatacc cgaggggac gttattccg ggaatatgg 
      attgatggg atggatgtt ctggcggtg agggaggcg 
      gcgaagttt gcagtggac cattgcacg tcagggaaa 
      gggcctata cttctggaa gccgccacc tacaggtac 
      tcgggtcat tcaatgtca gatccaggg acgagttac 
      cggacacgt gaagaaatc caagaagtg cgtcaaaca 
      cgtgatccg attacctca ttcaaagag aaaattatc 
      acggctaat ctcgtgtcc cctgaagaa ttaaaggca 
      attgatacg gaaattagg agcactgtt gatgaagca 
      acgaaaaaa gccaaagcg gaaaaggaa attccctta 
      gaagaactg actgctgat atttattcc ctagattta 
      gaaaaacaa atcagaaac attgatcct tttaatcca 
      ctgccacac aagcgcatt ggggaagcg gttaatttc 
      aagtaa
    mRNA sequence
    • >TC002948 RA
      aaagagaca caaacatga taacgagac atgtgaaca 
      gctgatcaa ccaacgacc tttcaggga cctttccct 
      aaccaaaaa ttttaaagg acatccaac ttatcattt 
      agactaaca cagagcccc cacaacgca agatgttac 
      ccagctgtg ctagaactt ttggcaaga aagccctaa 
      cccagaata aagccttgg gtttgatct cggccaaga 
      gcaattacg cgactgagg ccccctttg agacaaaag 
      cctttcgtt tacacaacc tagagcagg gcccagcaa 
      caaacacga ccctaagcc gcgatgacg cccttttgt 
      actacagac aaatgcaca ccgtccgcc ggatggaaa 
      ccagtgccg gcaacttgt acaaagaaa aaataatca 
      ggggctttt gccacttat attccggtc aggaagcgg 
      tcgctgttg gcattaaag cggcgctgc gcccccacg 
      acgacgtca taacggcgt accgggccc acggctgga 
      gccacttga tgggggtga accccctgg gggtcctcg 
      ccgagctca cgggccggc agtcggggt gtgcccgcg 
      gcaaggggg gctccatgc acatgtaca ccaaccatt 
      tctacggag gcaacggca ttgtggggg cgcaggtgc 
      cgctaggcg tggggctag ccctagctg cgaagtaca 
      agggcacgg atggggtct gtgtggcgt tgtacgggg 
      acggggctg ccaaccagg gccaggtgt tcgaggtct 
      tcaacatgg ctaagttat gggacattc cgtgcattt 
      tcgtctgcg aaaataatg ggtatggga tggggacta 
      gtgcggccc gggcggctg caaatacag cgtattata 
      cccgagggg acgttattc cgggaatat ggattgatg 
      ggatggatg ttctggcgg tgagggagg cggcgaagt 
      ttgcagtgg accattgca cgtcaggga aagggccta 
      tacttctgg aagccgcca cctacaggt actcgggtc 
      attcaatgt cagatccag ggacgagtt accggacac 
      gtgaagaaa tccaagaag tgcgtcaaa cacgtgatc 
      cgattacct cattcaaag agaaaatta tcacggcta 
      atctcgtgt cccctgaag aattaaagg caattgata 
      cggaaatta ggagcactg ttgatgaag caacgaaaa 
      aagccaaag cggaaaagg aaattccct tagaagaac 
      tgactgctg atatttatt ccctagatt tagaaaaac 
      aaatcagaa acattgatc cttttaatc cactgccac 
      acaagcgca ttggggaag cggttaatt tcaagtaag 
      atggggagt ttgctcgtg tgtgcaact ttataattt 
      attaatttt acgaaaccg ccgattgta tatacattt 
      agtaccgat tttacttta agtttatcc aaacgtatg 
      gtgccattg tgatcacaa ccataggtc attaaaatt 
      atgtaaata tgatgtgtt tttactttt ttataactc 
      tcccttcat tttttttct ttagtttta ataaagatt 
      gggaattta a
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY