Status
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Gene information
General information
TC003287 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: 793873..795429
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
    TC003287
    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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    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_09728

    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: 10.0% (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


    Fertility
    mature egg deposition blocked number 1st lateral oviduct: 5 number 2nd lateral oviduct: >5 - Number of animals showing the phenotype: 4
    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: < 20 embryo/egg with embryonic tissue potentially present, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    embryo/egg not developed/not fertilized - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 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: % (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
    • >TC003287 RA
      MQISVHKNR IYQYMAALT GTLGIVSSE MHYGWPSPT 
      LPILLNGTD KLQMDETEG SWLTIMPLV GAILGAIIT 
      GLVIDILGR KRLILLSSI PFFISWITI GFAETSVLL 
      HVARFLAGL TDGLSFTAV PMFLGEIAE PSIRGLLSS 
      MCPVSIVIG LLLINILGS YLTISTTAF VSSIIPVIL 
      LVTFVWIPE SPYFLLMRG RYDDARSSL QKFRGSTDV 
      ETELERLAK AVKEQNEST GKFVDLVTC PSNRKAVFI 
      ALGLRSVQQ LTGITAVTF YCKRVFEKS SNFIAPEVA 
      TIIYFTVQL VLSAISCLM VDISGRRPL LIISLAGTA 
      VTLLINGTY LYIKNCTEV DTKDFDFVL LATLLCFIV 
      IFSLGLQTI PLLIMSEMF PTNVKAFAL CLADVYFSV 
      IASVISKFF HGTSNAFGM HVPFYTFTV CCVFGLVFI 
      VLWVPETKG RTLEDIQRF LKGEIKM
    CDS sequence
    • >TC003287 RA
      atgcaaatc tcggtgcac aagaaccga atctaccaa 
      tacatggcc gctctcaca ggtactttg ggcatcgtc 
      tccagcgag atgcactac ggctggccc tcccccaca 
      ctccccatc ctcctcaac ggcaccgac aaactccaa 
      atggacgaa acggaaggc tcctggctc acgatcatg 
      cctctggtg ggcgccatc ctcggagcc atcatcaca 
      ggcctggtg attgacatc cttggccga aaacgcctc 
      attctcctg tcttcaatc ccgtttttc atctcctgg 
      attaccatc ggctttgcg gaaacgtcg gttttgtta 
      cacgtggcg aggtttcta gctgggtta accgatggg 
      ttatccttc acagcggtg cccatgttc ctgggggag 
      attgcggaa cccagcatt cgtgggctc ttaagttcc 
      atgtgtccc gtatccatc gtaatcgga ctccttcta 
      atcaatatt ttagggagt tatctcact atttccaca 
      actgcgttt gtttcatca attattccg gtgattctt 
      ttggttacg tttgtgtgg atccccgaa agtccctac 
      tttttgcta atgcgaggt cggtatgac gatgccagg 
      tcaagtctc cagaaattc cggggaagt accgatgtt 
      gaaaccgaa ctagaacga ctagccaaa gctgtgaag 
      gaacaaaac gaatccacc ggaaaattt gtagacttg 
      gtcacttgt cccagtaac cggaaggcg gtttttatc 
      gcgttgggg ctccggagt gtgcaacaa ttgaccgga 
      atcacagct gtgactttc tactgcaag cgagtgttt 
      gagaaaagt agcaacttt atcgcccct gaagtcgca 
      actattatt tatttcacc gttcagttg gttttgtcg 
      gcaatttcg tgccttatg gtggatatt tcaggccga 
      aggcctctc ctaattatc tcactagca ggcacagca 
      gtgacgctc ctaatcaac ggtacttat ctctacatc 
      aagaactgc actgaagtc gataccaaa gactttgat 
      ttcgttctt ttggcaact cttttgtgc tttattgta 
      atttttagc ttgggcttg caaactatt ccgttactt 
      atcatgtcg gagatgttt ccgaccaat gttaaggct 
      ttcgccctg tgcctggct gatgtttat ttcagtgtg 
      attgcaagt gtgatttct aagtttttc cacgggacg 
      agtaacgcg ttcggaatg catgtgccg ttttatact 
      tttacggtt tgttgtgtc tttgggttg gtttttatc 
      gtactgtgg gttcccgag actaaaggg cgaaccctt 
      gaagatatc cagcggttt ctcaagggg gagattaaa 
      atgtag
    mRNA sequence
    • >TC003287 RA
      tccatctat ttaagagag ccacccgga gtcaattga 
      gcagttgtc cgatgatgc caattaact caaccaaac 
      tcatgtgat acaaaaatg caaatctcg gtgcacaag 
      aaccgaatc taccaatac atggccgct ctcacaggt 
      actttgggc atcgtctcc agcgagatg cactacggc 
      tggccctcc cccacactc cccatcctc ctcaacggc 
      accgacaaa ctccaaatg gacgaaacg gaaggctcc 
      tggctcacg atcatgcct ctggtgggc gccatcctc 
      ggagccatc atcacaggc ctggtgatt gacatcctt 
      ggccgaaaa cgcctcatt ctcctgtct tcaatcccg 
      tttttcatc tcctggatt accatcggc tttgcggaa 
      acgtcggtt ttgttacac gtggcgagg tttctagct 
      gggttaacc gatgggtta tccttcaca gcggtgccc 
      atgttcctg ggggagatt gcggaaccc agcattcgt 
      gggctctta agttccatg tgtcccgta tccatcgta 
      atcggactc cttctaatc aatatttta gggagttat 
      ctcactatt tccacaact gcgtttgtt tcatcaatt 
      attccggtg attcttttg gttacgttt gtgtggatc 
      cccgaaagt ccctacttt ttgctaatg cgaggtcgg 
      tatgacgat gccaggtca agtctccag aaattccgg 
      ggaagtacc gatgttgaa accgaacta gaacgacta 
      gccaaagct gtgaaggaa caaaacgaa tccaccgga 
      aaatttgta gacttggtc acttgtccc agtaaccgg 
      aaggcggtt tttatcgcg ttggggctc cggagtgtg 
      caacaattg accggaatc acagctgtg actttctac 
      tgcaagcga gtgtttgag aaaagtagc aactttatc 
      gcccctgaa gtcgcaact attatttat ttcaccgtt 
      cagttggtt ttgtcggca atttcgtgc cttatggtg 
      gatatttca ggccgaagg cctctccta attatctca 
      ctagcaggc acagcagtg acgctccta atcaacggt 
      acttatctc tacatcaag aactgcact gaagtcgat 
      accaaagac tttgatttc gttcttttg gcaactctt 
      ttgtgcttt attgtaatt tttagcttg ggcttgcaa 
      actattccg ttacttatc atgtcggag atgtttccg 
      accaatgtt aaggctttc gccctgtgc ctggctgat 
      gtttatttc agtgtgatt gcaagtgtg atttctaag 
      tttttccac gggacgagt aacgcgttc ggaatgcat 
      gtgccgttt tatactttt acggtttgt tgtgtcttt 
      gggttggtt tttatcgta ctgtgggtt cccgagact 
      aaagggcga acccttgaa gatatccag cggtttctc 
      aagggggag attaaaatg taggctaaa gtgtgtcaa 
      gtacaaatt gatcgaata aaattttct acaagtt
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY