Status
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Gene information
General information
TC000546 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: 9929129..9930866
Sequence information
Transcripts / Proteins (2) 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
    TC000546
    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
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_03038

    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: 3 (3 dpi)
    Days post injection


    adult lethality - Number of animals showing the phenotype: 2 (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
    • >TC000546 RA
      MAVNHGKIA RVLWISCLL IVPSAKGHI APVKKNRFQ 
      VTNSTRNGK FLFNQLVGL TSFLTGGTD SSEDDDDEG 
      KTRNCTCDF SSECGQSNQ ENRIVGGRP TGINRYPWV 
      ARIVYDGHF HCGASLLTE DYVLTAAHC VRRLKRSKI 
      RVILGDHDQ STTEDTPAK MRAVSAVIR HRNFDQESY 
      NHDIALLKL RKPVEFTKN IRPICLPTG KDPAGKTGT 
      VVGWGRTTE GGMLPNVVQ EVQVPILTL SQCRAMKYR 
      ASRITSYML CAGRGAMDS CQGDSGGPL LVPNGDKFE 
      IVGIVSWGV GCGRPGYPG VYTRVSKYI NWLKYNLDD 
      TCICS
    • >TC000546 RB
      MAVNHGKIA RVLWISCLL IVPSAKGHI APVKKNRFQ 
      VTNSTRNGK FLFNQLVGL TSFLTGGTD SSEDDDDEG 
      KTRNCTCEC GQSNQENRI VGGRPTGIN RYPWVARIV 
      YDGHFHCGA SLLTEDYVL TAAHCVRRL KRSKIRVIL 
      GDHDQSTTE DTPAKMRAV SAVIRHRNF DQESYNHDI 
      ALLKLRKPV EFTKNIRPI CLPTGKDPA GKTGTVVGW 
      GRTTEGGML PNVVQEVQV PILTLSQCR AMKYRASRI 
      TSYMLCAGR GAMDSCQGD SGGPLLVPN GDKFEIVGI 
      VSWGVGCGR PGYPGVYTR VSKYINWLK YNLDDTCIC 
      S
    CDS sequence
    • >TC000546 RA
      atggctgtg aaccacggg aaaatcgcg cgcgtgctt 
      tggatctcc tgcctgctc atcgtgcca tccgcgaaa 
      ggacacata gccccagta aaaaaaaac cgatttcaa 
      gtgaccaac tcgacgcga aacggcaaa ttcctcttt 
      aaccagcta gtcggccta acatcattc ctaaccggc 
      gggaccgac tccagcgag gacgacgac gacgagggc 
      aagacgcgg aactgcact tgcgatttt tcttcagaa 
      tgtggccaa agcaaccaa gagaaccga atcgttggg 
      gggcgcccg accgggata aaccgctac ccctgggtg 
      gccaggatc gtctacgac ggccacttc cactgcggg 
      gcctccctg ctgacagaa gactacgtc ttgaccgct 
      gcacactgc gtccgacgg ctgaagcgg tcgaaaatt 
      cgcgtgatt ttgggcgac catgaccag tccaccacc 
      gaggacact ccggccaaa atgcgcgcg gtttcggcg 
      gtcatcagg cacaggaac ttcgaccag gagtcgtac 
      aaccacgac atcgcgctg ctaaagttg cgaaaaccg 
      gtcgagttt acgaaaaat atccgcccg atttgcttg 
      cccacaggg aaggatccg gcggggaaa accgggact 
      gtggtcggc tggggccgg actacagag ggtgggatg 
      ttaccgaat gtcgtccaa gaagtacaa gtgccaatt 
      ctaacactg tcgcagtgt cgggccatg aaatacagg 
      gcgtccaga atcacgtct tatatgctc tgtgcaggg 
      aggggggcc atggattcc tgccaaggg gacagtgga 
      ggcccgctt ttggtccca aacggggac aagttcgaa 
      attgtaggt attgtgtcg tggggtgtt ggatgcggc 
      cgccccgga taccccgga gtttacaca agagtctca 
      aaatacatc aactggctc aagtacaac ctcgacgat 
      acgtgtata tgttcatag
    • >TC000546 RB
      atggctgtg aaccacggg aaaatcgcg cgcgtgctt 
      tggatctcc tgcctgctc atcgtgcca tccgcgaaa 
      ggacacata gccccagta aaaaaaaac cgatttcaa 
      gtgaccaac tcgacgcga aacggcaaa ttcctcttt 
      aaccagcta gtcggccta acatcattc ctaaccggc 
      gggaccgac tccagcgag gacgacgac gacgagggc 
      aagacgcgg aactgcact tgcgaatgt ggccaaagc 
      aaccaagag aaccgaatc gttgggggg cgcccgacc 
      gggataaac cgctacccc tgggtggcc aggatcgtc 
      tacgacggc cacttccac tgcggggcc tccctgctg 
      acagaagac tacgtcttg accgctgca cactgcgtc 
      cgacggctg aagcggtcg aaaattcgc gtgattttg 
      ggcgaccat gaccagtcc accaccgag gacactccg 
      gccaaaatg cgcgcggtt tcggcggtc atcaggcac 
      aggaacttc gaccaggag tcgtacaac cacgacatc 
      gcgctgcta aagttgcga aaaccggtc gagtttacg 
      aaaaatatc cgcccgatt tgcttgccc acagggaag 
      gatccggcg gggaaaacc gggactgtg gtcggctgg 
      ggccggact acagagggt gggatgtta ccgaatgtc 
      gtccaagaa gtacaagtg ccaattcta acactgtcg 
      cagtgtcgg gccatgaaa tacagggcg tccagaatc 
      acgtcttat atgctctgt gcagggagg ggggccatg 
      gattcctgc caaggggac agtggaggc ccgcttttg 
      gtcccaaac ggggacaag ttcgaaatt gtaggtatt 
      gtgtcgtgg ggtgttgga tgcggccgc cccggatac 
      cccggagtt tacacaaga gtctcaaaa tacatcaac 
      tggctcaag tacaacctc gacgatacg tgtatatgt 
      tcatag
    mRNA sequence
    • >TC000546 RA
      agagctaac agtgtttcg tagacggtg aaagcacca 
      cgtgaatct atactaatt attattttt aaccttact 
      aacccaaaa cgtaaataa aatagcgac gttttgtaa 
      tttattcaa attgggaaa agtgcaagt gattatgat 
      tttgtgcta agtgggaaa atggctgtg aaccacggg 
      aaaatcgcg cgcgtgctt tggatctcc tgcctgctc 
      atcgtgcca tccgcgaaa ggacacata gccccagta 
      aaaaaaaac cgatttcaa gtgaccaac tcgacgcga 
      aacggcaaa ttcctcttt aaccagcta gtcggccta 
      acatcattc ctaaccggc gggaccgac tccagcgag 
      gacgacgac gacgagggc aagacgcgg aactgcact 
      tgcgatttt tcttcagaa tgtggccaa agcaaccaa 
      gagaaccga atcgttggg gggcgcccg accgggata 
      aaccgctac ccctgggtg gccaggatc gtctacgac 
      ggccacttc cactgcggg gcctccctg ctgacagaa 
      gactacgtc ttgaccgct gcacactgc gtccgacgg 
      ctgaagcgg tcgaaaatt cgcgtgatt ttgggcgac 
      catgaccag tccaccacc gaggacact ccggccaaa 
      atgcgcgcg gtttcggcg gtcatcagg cacaggaac 
      ttcgaccag gagtcgtac aaccacgac atcgcgctg 
      ctaaagttg cgaaaaccg gtcgagttt acgaaaaat 
      atccgcccg atttgcttg cccacaggg aaggatccg 
      gcggggaaa accgggact gtggtcggc tggggccgg 
      actacagag ggtgggatg ttaccgaat gtcgtccaa 
      gaagtacaa gtgccaatt ctaacactg tcgcagtgt 
      cgggccatg aaatacagg gcgtccaga atcacgtct 
      tatatgctc tgtgcaggg aggggggcc atggattcc 
      tgccaaggg gacagtgga ggcccgctt ttggtccca 
      aacggggac aagttcgaa attgtaggt attgtgtcg 
      tggggtgtt ggatgcggc cgccccgga taccccgga 
      gtttacaca agagtctca aaatacatc aactggctc 
      aagtacaac ctcgacgat acgtgtata tgttcatag 
      tgcaaataa attattttt tcttct
    • >TC000546 RB
      agagctaac agtgtttcg tagacggtg aaagcacca 
      cgtgaatct atactaatt attattttt aaccttact 
      aacccaaaa cgtaaataa aatagcgac gttttgtaa 
      tttattcaa attgggaaa agtgcaagt gattatgat 
      tttgtgcta agtgggaaa atggctgtg aaccacggg 
      aaaatcgcg cgcgtgctt tggatctcc tgcctgctc 
      atcgtgcca tccgcgaaa ggacacata gccccagta 
      aaaaaaaac cgatttcaa gtgaccaac tcgacgcga 
      aacggcaaa ttcctcttt aaccagcta gtcggccta 
      acatcattc ctaaccggc gggaccgac tccagcgag 
      gacgacgac gacgagggc aagacgcgg aactgcact 
      tgcgaatgt ggccaaagc aaccaagag aaccgaatc 
      gttgggggg cgcccgacc gggataaac cgctacccc 
      tgggtggcc aggatcgtc tacgacggc cacttccac 
      tgcggggcc tccctgctg acagaagac tacgtcttg 
      accgctgca cactgcgtc cgacggctg aagcggtcg 
      aaaattcgc gtgattttg ggcgaccat gaccagtcc 
      accaccgag gacactccg gccaaaatg cgcgcggtt 
      tcggcggtc atcaggcac aggaacttc gaccaggag 
      tcgtacaac cacgacatc gcgctgcta aagttgcga 
      aaaccggtc gagtttacg aaaaatatc cgcccgatt 
      tgcttgccc acagggaag gatccggcg gggaaaacc 
      gggactgtg gtcggctgg ggccggact acagagggt 
      gggatgtta ccgaatgtc gtccaagaa gtacaagtg 
      ccaattcta acactgtcg cagtgtcgg gccatgaaa 
      tacagggcg tccagaatc acgtcttat atgctctgt 
      gcagggagg ggggccatg gattcctgc caaggggac 
      agtggaggc ccgcttttg gtcccaaac ggggacaag 
      ttcgaaatt gtaggtatt gtgtcgtgg ggtgttgga 
      tgcggccgc cccggatac cccggagtt tacacaaga 
      gtctcaaaa tacatcaac tggctcaag tacaacctc 
      gacgatacg tgtatatgt tcatagtgc aaataaatt 
      attttttct tct
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY