Status
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Gene information
General information
TC009492 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: 320125..324834
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
    		TC009492
    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_04645

    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: 0.0% (includes death as pupa, adult)

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 larval musculature dorsal partiallyorientation irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): less than 30%
    thorax segment posterior fused - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    abdomen segment number decreased - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    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: 30.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 40.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 3 (11 dpi)
    Days post injection

    adult nutritional state - Number of animals showing the phenotype: 1 (22 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC009492 RA
      MMEEMFTEL PVPLLSTAA IIRHHTRYQ PYQRLHQPQ 
HFHTPVQEL HALQQPDHG TTHISCLYP EILAIIFSY 
LEVRDKGRV AQVCTAWRD AAYNKSVWR GVEAKLHLR 
RANPSLFAS LVKRGIKRV QVLSLRKSL RDVIQGIPN 
LESLNLRGC YNVGDVGIS HAFVADSPT LTELDLSLC 
KQVTDTSLT RIAQHLKNL EVLELGGCS NVTNSGLML 
IAWGLKKLK RLNLRSCWH VGDQGIQHL ASGNPSLEH 
LGLQDCQKL SDEALKHAT GLTSLISIN LSFCVSITD 
SGLKHLAKM TNLRELNLR SCDNISDTG MAFLAEGGS 
RISSLDVSF CDKIGDQAL VHISQGLFN LRNLLMSAC 
QLSDEGLAK IANSLHDLE TLNIGQCSR VTDKGLTTI 
AESLLRLKC IDLYGCTRI TTVGLERIM KLPQLSVLN 
LGLWHVR
    CDS sequence
    • >TC009492 RA
      atgatggag gagatgttc actgagttg cccgtcccc 
ttgctgtcc acagcggcc atcatccgc caccacacc 
agataccag ccctaccaa aggctgcac cagccccag 
cacttccac acgcccgtc caggagctc cacgcgctg 
caacaacca gaccatggc accacgcac atctcctgt 
ctctatcca gagatcttg gccatcatc ttcagctac 
ctggaggtg cgcgacaag ggccgcgtg gcgcaggtt 
tgcactgcg tggcgcgac gccgcttac aacaagtcc 
gtgtggcgc ggcgtcgaa gccaaactc cacctccgt 
cgcgctaac ccttcacta ttcgcttcg ctggtgaaa 
cgcggtatc aaacgtgtt caggtcctg tccctacgt 
aaatccctc cgggacgtc atccagggc atccctaac 
ttggagtct ttgaacctc cgtggttgt tacaacgtg 
ggggacgtg ggcatatcc cacgcattt gtggcagac 
tcacccacc ctcaccgaa ctggacctc tccctctgc 
aagcaagtc accgacacg tccctcaca cgcatcgcc 
caacacttg aagaacttg gaggtgctg gaactgggc 
ggttgctcc aacgtcacc aactccggc ctgatgctc 
atcgcctgg ggcctcaag aagctcaaa agactgaat 
ttacgctcg tgctggcac gtgggggac caaggaatc 
caacacttg gcttcgggg aatccatcg ctcgagcac 
ttggggctc caagactgt cagaaactc tccgacgag 
gctctcaaa cacgccacc ggcttgact tccctcatc 
tcaatcaat ctgagtttt tgtgttagt ataacggac 
agcgggtta aaacaccta gccaaaatg acgaattta 
cgcgagttg aatttgcgt tcgtgtgat aatatttcc 
gacacggga atggcgttc cttgcagaa ggcgggtcg 
agaatttcg tctttggac gtatcattt tgtgacaaa 
atcggtgac caagcgcta gtgcacatt tcacaagga 
ctgttcaat ttgcgaaat ttgttaatg agtgcgtgt 
caactctcg gatgaaggt ctggcgaaa atcgcgaat 
tcgctccat gacctggag acgctcaac atcggacag 
tgcagtcgt gtgacggat aagggctta acaaccatt 
gctgagtcg ctcctgaga ctaaagtgc atcgatttg 
tacggatgc accaggata acgacggta ggacttgaa 
cgaattatg aaattgccg cagttgagt gtcctcaat 
ttggggctg tggcatgtt aggtga
    mRNA sequence
    • >TC009492 RA
      ggtcacgtg gtgcgcact cggaccaat ggcagcact 
cgcaactcg tttcgtctg ttctccagt ttggtcgcc 
aacagtttg aaatgagtc gttgtagag gtgagaagg 
cgcccgtgc tccgagtcg tggtgcgca cgtagtggt 
tccgactat gatggagga gatgttcac tgagttgcc 
cgtcccctt gctgtccac agcggccat catccgcca 
ccacaccag ataccagcc ctaccaaag gctgcacca 
gccccagca cttccacac gcccgtcca ggagctcca 
cgcgctgca acaaccaga ccatggcac cacgcacat 
ctcctgtct ctatccaga gatcttggc catcatctt 
cagctacct ggaggtgcg cgacaaggg ccgcgtggc 
gcaggtttg cactgcgtg gcgcgacgc cgcttacaa 
caagtccgt gtggcgcgg cgtcgaagc caaactcca 
cctccgtcg cgctaaccc ttcactatt cgcttcgct 
ggtgaaacg cggtatcaa acgtgttca ggtcctgtc 
cctacgtaa atccctccg ggacgtcat ccagggcat 
ccctaactt ggagtcttt gaacctccg tggttgtta 
caacgtggg ggacgtggg catatccca cgcatttgt 
ggcagactc acccaccct caccgaact ggacctctc 
cctctgcaa gcaagtcac cgacacgtc cctcacacg 
catcgccca acacttgaa gaacttgga ggtgctgga 
actgggcgg ttgctccaa cgtcaccaa ctccggcct 
gatgctcat cgcctgggg cctcaagaa gctcaaaag 
actgaattt acgctcgtg ctggcacgt gggggacca 
aggaatcca acacttggc ttcggggaa tccatcgct 
cgagcactt ggggctcca agactgtca gaaactctc 
cgacgaggc tctcaaaca cgccaccgg cttgacttc 
cctcatctc aatcaatct gagtttttg tgttagtat 
aacggacag cgggttaaa acacctagc caaaatgac 
gaatttacg cgagttgaa tttgcgttc gtgtgataa 
tatttccga cacgggaat ggcgttcct tgcagaagg 
cgggtcgag aatttcgtc tttggacgt atcattttg 
tgacaaaat cggtgacca agcgctagt gcacatttc 
acaaggact gttcaattt gcgaaattt gttaatgag 
tgcgtgtca actctcgga tgaaggtct ggcgaaaat 
cgcgaattc gctccatga cctggagac gctcaacat 
cggacagtg cagtcgtgt gacggataa gggcttaac 
aaccattgc tgagtcgct cctgagact aaagtgcat 
cgatttgta cggatgcac caggataac gacggtagg 
acttgaacg aattatgaa attgccgca gttgagtgt 
cctcaattt ggggctgtg gcatgttag gtgaaacgt 
atttgttga aatttgcgc cctctgaat gaaacgagt 
cgagatgac caaaaatgc attcattcc caaatctcg 
accggttca agacggtgg cggttttat gctgtgata 
gattttaaa cgaatgacg taaagttcg actaaagtg 
aaattaaac gtaagcatc gtaaacaat gagaactga 
ttttctatg gtggtgccg ccaaaatga agcacatgc 
tagttacag ggaataatt cacatgaat tcgaccgaa 
caacttttt tgatactag tttattaaa acgttggtc 
tgtttactc tttgttatt tttctactt aaatgttag 
cacttctaa gtcgctatc aactttttt tttaatgaa 
aagctatgt ttttcacta cgtttttgg attatttga 
gttatttta agggaattt ttatcagct gtccccata 
tctaaattt aatcgtttt cgagatatt taagaattt 
ttggaaatg tttgaatta caccgttca cttagatgt 
tcacattca tagtaattt tatttaaag gaggatttt 
attgcagac gagtgtaat taaacgaaa aattccaaa 
tagtgaata tttgcttca ttttgtgca caccaccca 
agatttgac actgctaca agccttgga atttttttc 
ataccttca ctagcacgt agcaccaca aatttgcaa 
tattataca tcgaattgt gattagttt gtttcgaaa 
aatgtgata gcggttaaa caatcattt tcgaaaacg 
ttaagtttg aatttcgcc tctttgtta gcatcaggt 
ttttgttca atttttgct tgttccgtg ttttttttt 
tgtggtgca gagacaatt tttcaaact gtaaaaatg 
tacagtgat cattatagt atttgtaaa taaacgtaa 
agttatcaa tatttgtta ctattacgt tatgttttt 
ataaattaa acaaattta aacttaata aagttttta 
tcaacaa

    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