Status
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Gene information
General information
TC003789 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: 17101708..17129664
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
    		TC003789
    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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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_07032

    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: 1 (3 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 3 (9 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection

    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 20
     maxilla number increased - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    mandible not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    mandible potentially transformed - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    labrum size decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    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
    • >TC003789 RA
      MPFISKDWR SPGEAWVKT QEGWEKKKV LENCKAIKQ 
SGAEEPSTY GNTETAIQP HCHITIKST KEIAGFNEL 
NEAVKKLDF MSAVRDVRR FNYICALLG LLIGQQMTA 
LSGCAQKVL LAMLEEVAS QAVASQHNP RNFRQLLKN 
LRSLSEAER SSCWGGLLG SQVLWSEHT AKIERILKM 
AANMQICEL SPESRPQLL QLPEECIRE IILRLSDHR 
DLTASAQTC EQMATIVGE QRVWRELTK FHFTPHQIE 
LVLPKNGEK VDWKDVYHS LKKSFGLSE DRQYAEMLS 
LCRYCRCLF WRSSGHPCI ADQCPEFRA RLQEAGGIT 
PPSPVPPSA FLKFFSL
    CDS sequence
    • >TC003789 RA
      atgcctttt atatcgaag gattggcgg tcaccgggg 
gaagcctgg gtcaaaaca caggaagga tgggagaag 
aaaaaagtg ctggaaaac tgcaaagcc atcaaacaa 
agtggcgca gaagaacct tctacgtac ggtaacacc 
gaaactgcc atccaaccc cattgccac attacaata 
aaatccaca aaagaaata gctggattt aacgaacta 
aacgaggct gtaaaaaaa ctggacttc atgagcgct 
gtgagagac gtccgccgc ttcaactac atttgcgct 
ttactaggc ttactcatc ggtcaacaa atgaccgca 
ctgtcgggc tgcgcccaa aaagtgctt ttagccatg 
ttggaagaa gtcgcaagc caggcggta gcaagccaa 
cacaatccc cgaaatttc agacaactg ctcaaaaat 
ttaagatcg ttgagtgag gccgaacgc tcctcctgc 
tggggcggc ctcctcggc tcccaagtg ctgtggagc 
gaacacacg gcgaaaatt gaacgcatc ctcaaaatg 
gcagctaat atgcaaatc tgcgaactc agcccggag 
tcgaggccg caattgttg cagctgccg gaggagtgc 
atccgggag attattcta agattgtcg gatcataga 
gacttgaca gctagtgcc caaacgtgc gagcaaatg 
gccacaatt gtgggcgag cagcgcgtc tggagagag 
ttaaccaag ttccacttt acacctcat caaatagag 
ctagtttta ccaaaaaac ggcgagaaa gttgactgg 
aaggatgtt tatcactca ctcaaaaag tccttcgga 
ttaagcgaa gaccgtcag tacgcagaa atgctgtcg 
ttgtgtaga tactgtcga tgcctgttt tggcggtct 
tccggtcat ccgtgcata gccgatcag tgcccggaa 
ttccgggcg agacttcaa gaagcggga ggaattact 
ccgcccagt cctgttcct ccttcggcc tttctgaag 
tttttctcc ttgtag
    mRNA sequence
    • >TC003789 RA
      tttgtttgt tgaaaactt aaataattc catttcaaa 
atctttcaa aatactcct aattaaagt aacaagcat 
ccgttcgtt tattacgcg ataataaag cgtattact 
cagttcact gccttcata accacgtta ttaaattta 
gggtaaaac actccaaag tcgtttatg taagtgttt 
agcatatcc taggttatt attaaattt gaagacgca 
gtgagtgtt ccttccacc tacttcact tgaagagaa 
aggtgaacg aactacgct aaaagtaaa tgtttaatg 
actaaaacc atgattcgt ccaatcaac tcggctcgc 
cataacaaa aacacatgg ttcaatttg gaactgctg 
gagaagaca ttcatctca ggcagcagg aaacgacca 
tgcgcacac tcctgctgc ctgctgtag aatcagctg 
attgcgcag aaaaccaga atcgcgttt ccataatca 
aacgagcga ctgtcaaag tgttgtgta tatttacat 
cagctgttt ggctgaacc gtttaaaaa ataatgcct 
tttatatcg aaggattgg cggtcaccg ggggaagcc 
tgggtcaaa acacaggaa ggatgggag aagaaaaaa 
gtgctggaa aactgcaaa gccatcaaa caaagtggc 
gcagaagaa ccttctacg tacggtaac accgaaact 
gccatccaa ccccattgc cacattaca ataaaatcc 
acaaaagaa atagctgga tttaacgaa ctaaacgag 
gctgtaaaa aaactggac ttcatgagc gctgtgaga 
gacgtccgc cgcttcaac tacatttgc gctttacta 
ggcttactc atcggtcaa caaatgacc gcactgtcg 
ggctgcgcc caaaaagtg cttttagcc atgttggaa 
gaagtcgca agccaggcg gtagcaagc caacacaat 
ccccgaaat ttcagacaa ctgctcaaa aatttaaga 
tcgttgagt gaggccgaa cgctcctcc tgctggggc 
ggcctcctc ggctcccaa gtgctgtgg agcgaacac 
acggcgaaa attgaacgc atcctcaaa atggcagct 
aatatgcaa atctgcgaa ctcagcccg gagtcgagg 
ccgcaattg ttgcagctg ccggaggag tgcatccgg 
gagattatt ctaagattg tcggatcat agagacttg 
acagctagt gcccaaacg tgcgagcaa atggccaca 
attgtgggc gagcagcgc gtctggaga gagttaacc 
aagttccac tttacacct catcaaata gagctagtt 
ttaccaaaa aacggcgag aaagttgac tggaaggat 
gtttatcac tcactcaaa aagtccttc ggattaagc 
gaagaccgt cagtacgca gaaatgctg tcgttgtgt 
agatactgt cgatgcctg ttttggcgg tcttccggt 
catccgtgc atagccgat cagtgcccg gaattccgg 
gcgagactt caagaagcg ggaggaatt actccgccc 
agtcctgtt cctccttcg gcctttctg aagtttttc 
tccttgtag ttgccttcg tccaattaa tttattatg 
cttctgttg cattgtgat acataactg tgtattttt 
aggggccgc tatctcatg tagatatat cgaatttac 
aaattcata tttttacgt acctactct atagtgtgt 
aattttaca agatatcaa atatcggta aggatatat 
ttttcattg ggaaaatag cttgagtga taagtggct 
gatattttg ctttaaaga aacgaagtc tgaagtgat 
tattttttc aaatagatg taactctca gtgacgatg 
tttgttcgc caacaaaca gcaaacggt gtgacttta 
tagtgatat acaggctgt ctcagctaa cactttcga 
gcttaatat ctcagttat ttatcaacg aattgttat 
gaaatttag aatgcacat attttagga ggtggtctt 
tcaattagg ggcaaaaat gacctcaag ttaaaaaat 
gaaatttta aaacacatt tcttttatt taaaattaa 
gccaaatta ccgttggat cattaaacc ccgaaaaat 
aaatggcta cccaaaaaa ttaaccaaa tcgctcggc 
tgatccaag aaaaaaatt aaattttgt tggtaaaaa 
cttaatcca aattttgat aataatttg ggcagtcac 
cgtttgaaa caattgatg aagcgtttc tatgcggca 
ttttgtgta ccactgaaa aaaactgtc aaaagtgtg 
gcgctgtca gaaaagtaa aattgtttt aatttgatg 
aaattactt taaaaacca acaacagtg gctgaaatt 
tctgtgttg ttgaaaaag aaatcagta ttcgcctat 
ggaaagtgt cgttggcct ttttgtgaa atgttattt 
atgaaactt aaagttcaa agaatcgtc aataatttg 
aagacacag gaagcgaac ctgaactaa atggagtga 
ggacaaaac acgtcactg gaaacgaag caatagttg 
gggctgtaa ttcaagctt ttgaagaga atccaatca 
gcagtgtac gaaacattt ccaaagtct cgaatgttc 
aagtgtcta gaatttttc agttgttgt tcagtcttt 
tagtctttt ttgaaagat ttaaagcat ccagtacca 
aaagtaagt caaaaatat tgtttttta actttgtat 
aggtgagag ataattgtg aaatgtctc ttgcgtgac 
agttacgtt tctgcgagt aggattgac caaaattca 
atggtagtg ttcatttgt ttcatagag atctaggct 
tttgcattt gtttaacag tttgtttct catttttca 
cgcgaaaca gatgtcttt cacgaacga gttttttct 
gacagcatt tttcactga cgataattt ttttaatat 
aagtcttac aaggct

    If you use iBeetle-Base, please cite: Dönitz J et al.: Expanded and updated data and a query pipeline for iBeetle-Base,
    Nucleic Acids Res. 2018 Jan 4;46(D1):D831-D835. doi: 10.1093/nar/gkx984.

    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY