Status
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Gene information
General information
TC009549 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_007422.5: 2314036..2316010
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
    		TC009549
    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_01574

    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

    Analysis of embryonic musculature and early development
    embryo/egg with embryonic tissue potentially present, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    embryo/egg with embryonic tissue, no cuticle, but muscle fluorescence - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    larval musculature irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): more than 80%

    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     cuticle remnants - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    head complete not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    head not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    thorax not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - 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: 0.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 0.0% (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC009549 RA
      MDNVLLPTE IEFYIETMV PQDIRHVGN KQWLEWHQR 
LQKLNQQAL IEASQMREE HVKETLITF QKTPVLVHE 
AVLINIWKH KVLPQMLKL DPNPQNTFM GYTILYHEA 
VCVALLELV MYHGNCCDS LGDFSGDLL DYACGTTSQ 
LLAIAKEPS HELLKQLED LKFDIGIRC LSIIRYMAE 
NLDRLPLST TSRMYTTCD IPILFAQIL TTRPWIRDG 
KQYSAGRWM DWDGEALGQ AEAQVWLTL RQLLLDPAC 
REYYTVTEA RRAQLAKLM MLLTPVLMD QLAPLVELK 
QWLSHVTMG EQVAKGSRP VLLETVLEV KERIVAQAG 
GKWKKLAKE QLPVVFCND QKTLMECAQ TLSDAYNTD 
LIEKFEVKE KASCQQCGK SAIQRH
    CDS sequence
    • >TC009549 RA
      atggacaac gtgctgctc ccaactgag atcgagttt 
tacatcgag acgatggtg ccccaagac atacgacac 
gtcggaaac aaacagtgg ttggagtgg caccaaaga 
ctgcaaaaa ctgaaccaa caagcccta attgaagcc 
tcacaaatg cgcgaagaa cacgtcaag gaaacactc 
atcacgttc caaaaaacc ccagttttg gtacacgaa 
gccgttttg atcaacatc tggaaacac aaagtgttg 
ccccagatg ctaaaactt gacccaaac ccgcagaac 
accttcatg ggctacacc atcctgtac catgaagcc 
gtctgtgtg gctttactg gaactggta atgtaccat 
gggaactgt tgcgattct ttgggcgac ttttcgggg 
gatttactc gactatgcc tgcggtacc acctcacaa 
ctcctggca attgcaaaa gaaccatct cacgaatta 
ttaaaacaa ctggaagac ttgaaattc gatatcggg 
attcgctgt ctgtccatc attcgctac atggccgaa 
aacttagac cggcttccg ctcagtacc acctcccgg 
atgtacaca acgtgtgat atccccatc ctgtttgcg 
caaattttg accacccgg ccctggatt agagacggg 
aagcagtac tctgccggg aggtggatg gactgggac 
ggggaggct ttaggccag gcggaggcg caagtctgg 
ttgactttg cgtcagttg ttgctggat ccagcctgt 
cgcgagtat tataccgtt acggaggcg aggagggcg 
cagttggcc aagctgatg atgctgttg acgccggtt 
ttgatggat cagttggca ccgctggtg gagttgaag 
cagtggttg tcgcacgtg acgatgggg gagcaagtg 
gcgaagggc tcaaggccc gtgttgttg gagacggtc 
ttggaggtg aaggagcgg attgtggcg caggccggg 
ggcaagtgg aagaagttg gcgaaggag cagttgccg 
gtggtgttt tgtaacgat cagaagacg ctaatggag 
tgtgcacag acgctaagt gacgcttac aacaccgat 
ttgattgag aaattcgaa gtgaaggaa aaggcctca 
tgccaacaa tgcggcaaa agcgccatt cagcgtcac 
tga
    mRNA sequence
    • >TC009549 RA
      tagtgacaa aaatggaca acgtgctgc tcccaactg 
agatcgagt tttacatcg agacgatgg tgccccaag 
acatacgac acgtcggaa acaaacagt ggttggagt 
ggcaccaaa gactgcaaa aactgaacc aacaagccc 
taattgaag cctcacaaa tgcgcgaag aacacgtca 
aggaaacac tcatcacgt tccaaaaaa ccccagttt 
tggtacacg aagccgttt tgatcaaca tctggaaac 
acaaagtgt tgccccaga tgctaaaac ttgacccaa 
acccgcaga acaccttca tgggctaca ccatcctgt 
accatgaag ccgtctgtg tggctttac tggaactgg 
taatgtacc atgggaact gttgcgatt ctttgggcg 
acttttcgg gggatttac tcgactatg cctgcggta 
ccacctcac aactcctgg caattgcaa aagaaccat 
ctcacgaat tattaaaac aactggaag acttgaaat 
tcgatatcg ggattcgct gtctgtcca tcattcgct 
acatggccg aaaacttag accggcttc cgctcagta 
ccacctccc ggatgtaca caacgtgtg atatcccca 
tcctgtttg cgcaaattt tgaccaccc ggccctgga 
ttagagacg ggaagcagt actctgccg ggaggtgga 
tggactggg acggggagg ctttaggcc aggcggagg 
cgcaagtct ggttgactt tgcgtcagt tgttgctgg 
atccagcct gtcgcgagt attataccg ttacggagg 
cgaggaggg cgcagttgg ccaagctga tgatgctgt 
tgacgccgg ttttgatgg atcagttgg caccgctgg 
tggagttga agcagtggt tgtcgcacg tgacgatgg 
gggagcaag tggcgaagg gctcaaggc ccgtgttgt 
tggagacgg tcttggagg tgaaggagc ggattgtgg 
cgcaggccg ggggcaagt ggaagaagt tggcgaagg 
agcagttgc cggtggtgt tttgtaacg atcagaaga 
cgctaatgg agtgtgcac agacgctaa gtgacgctt 
acaacaccg atttgattg agaaattcg aagtgaagg 
aaaaggcct catgccaac aatgcggca aaagcgcca 
ttcagcgtc actgactgg cccgttcac aaggaaatt 
tgcaataaa acgca

    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