Status
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Gene information
General information
TC012299 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_007424.3: 3887772..3890028
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
    		TC012299
    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
    You may enter your name. The contact information can help us to clarify any questions. If you agree, we may show your name on this page to honor your contribution.
    Email
    We will use your email address only for possible questions regarding this annotation. We will never show your address or give it away.
    Publish name
    If you have entered your name and agree by marking the checkbox. we might show your name on this page to honor your contribution.
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_01964

    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: 40.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 4 (3 dpi)
    Days post injection

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

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 80%
    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): more than 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: % (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
    • >TC012299 RA
      MDLVTQTSL EALLLKATN SQNQNIDTA AVEAFCALV 
NKEKDGAHI GVKVIANRL PSGNEKELL QTLNILDTC 
MSKCGTAFQ SEVGKFRFL NEMIKLVSP KYLGSQTPL 
VVKQKVLQL MYIWTLDYP KETKIKEAY DMLRKQGVI 
KEIPNPNIV QNANIPRKK AANSVFQDE EKSKILQKL 
LQSKDPEDI QAANWLIKS MVKEDDKRA ELKSRRVSE 
LESVQNNVR LLNEMLDSY KPGISSADE LDLIKELHQ 
SCERLRPNL MKLTAETQQ NEEILGDVL QASDELSQV 
FGKYNRIIV QGVSVVDDG SNALLDFEG ADEAQCRNS 
DTKEIDVLC DIFNASNIP DSADILKPV SVLTCDKNE 
NGKEVNKFK ALEELDVLS EHFIKENLP TSRQGTFNN 
RQDKIPMNL LTKLSETKP VQSNGKNES ISESLSLDL 
SYLISKPKD EPKTNTMEN STDDCLVDI ADEKMLEAG 
ETPQRKPSL TDPAKNEIK LNDIFIKLE DIKPSPVPP 
LTILNERNG ITITLHFVK DQPRDDVHV FVVTTINKN 
EMPLTNYLF QAVVPKGCK VKLQPPSAT TLPAYNPFL 
PPSAITQIM LIANPDDVQ VFLKFFVSF VMDEETCTE 
IGEVETLPM
    CDS sequence
    • >TC012299 RA
      atggatttg gtgactcaa actagtctc gaagccctg 
cttttaaaa gccacaaac tcccaaaac caaaacatt 
gacaccgcc gctgttgag gccttctgc gcccttgta 
aacaaagag aaagatggg gcacacatc ggggttaaa 
gtgatagca aaccggctt ccttcaggt aacgagaaa 
gagctgctc caaacgctc aacatcctg gatacgtgc 
atgagcaaa tgtggcaca gctttccag tcagaagtc 
ggcaaattc cggtttctg aacgaaatg attaagcta 
gtttcgccc aaatatctg gggtcgcag acgccgctc 
gtggtgaag caaaaagtg ctgcaactg atgtacatt 
tggacactg gactacccc aaagaaacg aagataaag 
gaagcgtac gatatgctg cgaaagcag ggcgttatc 
aaggaaatc ccgaacccc aacatagta caaaacgcc 
aacattccg aggaaaaag gccgcgaat tccgtgttc 
caagacgag gagaaatca aaaattttg caaaagctg 
ctgcaaagt aaagacccc gaggacatc caagccgcc 
aattggctc attaaaagt atggtcaag gaggacgat 
aaaagggcg gaattgaag agccggcgc gtttccgag 
cttgagtca gtacaaaac aatgtgaga ttattgaat 
gaaatgctc gattcgtac aaaccgggc atttcttcc 
gccgatgag ctggacctt attaaagag ctgcatcaa 
agttgtgag cgtctgaga ccaaattta atgaaacta 
accgcagag acacaacaa aatgaagaa atcttaggt 
gatgttttg caagcaagc gatgagttg agccaagtt 
tttggcaag tataacagg attattgtg cagggagtt 
agtgtcgtg gacgatggc agcaatgcc ttgcttgat 
tttgagggc gcagacgag gctcagtgt cggaactct 
gataccaaa gaaattgac gttttatgt gatattttc 
aacgcttca aacattccg gactctgct gatattttg 
aaacctgtt tcagtatta acttgtgat aaaaacgaa 
aatgggaaa gaggtgaat aaattcaaa gccttggaa 
gagttggac gttttgagc gaacacttt attaaggaa 
aatctccca actagcaga caaggcact tttaataat 
aggcaagac aaaatccca atgaatctc cttacaaag 
ctatctgag acgaaacca gttcagagt aacggaaag 
aacgaatcg attagtgaa tctctaagt ctagatttg 
agttattta ataagcaaa ccaaaagac gaaccaaaa 
acaaacaca atggaaaat tccactgat gactgtttg 
gtggacata gctgacgag aaaatgctg gaagctggg 
gaaaccccc caacgaaag cccagctta actgacccg 
gcaaaaaat gaaataaaa ctgaacgac atttttatc 
aaattggaa gatatcaag ccaagtccc gtcccacct 
ctcacgatt ttaaacgag aggaacgga atcacaata 
accctgcat ttcgtgaaa gaccagccc cgagacgac 
gtgcatgtc tttgttgtg accacaatt aacaaaaac 
gagatgcct ttgactaac tacctgttc caggctgtg 
gtacctaag ggctgcaaa gtcaaactg caacctccc 
tcagcaacc accctcccg gcttacaac ccgttcctg 
cccccttct gccataacg caaatcatg ctgatcgca 
aatcctgat gatgtacaa gtttttctc aagtttttt 
gtaagtttt gtaatggac gaagagact tgtactgaa 
atcggcgag gttgaaact cttccaatg taa
    mRNA sequence
    • >TC012299 RA
      tgacgttta agtgacatg aaaataaaa tgattgaaa 
caatttaaa aacccataa aatggattt ggtgactca 
aactagtct cgaagccct gcttttaaa agccacaaa 
ctcccaaaa ccaaaacat tgacaccgc cgctgttga 
ggccttctg cgcccttgt aaacaaaga gaaagatgg 
ggcacacat cggggttaa agtgatagc aaaccggct 
tccttcagg taacgagaa agagctgct ccaaacgct 
caacatcct ggatacgtg catgagcaa atgtggcac 
agctttcca gtcagaagt cggcaaatt ccggtttct 
gaacgaaat gattaagct agtttcgcc caaatatct 
ggggtcgca gacgccgct cgtggtgaa gcaaaaagt 
gctgcaact gatgtacat ttggacact ggactaccc 
caaagaaac gaagataaa ggaagcgta cgatatgct 
gcgaaagca gggcgttat caaggaaat cccgaaccc 
caacatagt acaaaacgc caacattcc gaggaaaaa 
ggccgcgaa ttccgtgtt ccaagacga ggagaaatc 
aaaaatttt gcaaaagct gctgcaaag taaagaccc 
cgaggacat ccaagccgc caattggct cattaaaag 
tatggtcaa ggaggacga taaaagggc ggaattgaa 
gagccggcg cgtttccga gcttgagtc agtacaaaa 
caatgtgag attattgaa tgaaatgct cgattcgta 
caaaccggg catttcttc cgccgatga gctggacct 
tattaaaga gctgcatca aagttgtga gcgtctgag 
accaaattt aatgaaact aaccgcaga gacacaaca 
aaatgaaga aatcttagg tgatgtttt gcaagcaag 
cgatgagtt gagccaagt ttttggcaa gtataacag 
gattattgt gcagggagt tagtgtcgt ggacgatgg 
cagcaatgc cttgcttga ttttgaggg cgcagacga 
ggctcagtg tcggaactc tgataccaa agaaattga 
cgttttatg tgatatttt caacgcttc aaacattcc 
ggactctgc tgatatttt gaaacctgt ttcagtatt 
aacttgtga taaaaacga aaatgggaa agaggtgaa 
taaattcaa agccttgga agagttgga cgttttgag 
cgaacactt tattaagga aaatctccc aactagcag 
acaaggcac ttttaataa taggcaaga caaaatccc 
aatgaatct ccttacaaa gctatctga gacgaaacc 
agttcagag taacggaaa gaacgaatc gattagtga 
atctctaag tctagattt gagttattt aataagcaa 
accaaaaga cgaaccaaa aacaaacac aatggaaaa 
ttccactga tgactgttt ggtggacat agctgacga 
gaaaatgct ggaagctgg ggaaacccc ccaacgaaa 
gcccagctt aactgaccc ggcaaaaaa tgaaataaa 
actgaacga catttttat caaattgga agatatcaa 
gccaagtcc cgtcccacc tctcacgat tttaaacga 
gaggaacgg aatcacaat aaccctgca tttcgtgaa 
agaccagcc ccgagacga cgtgcatgt ctttgttgt 
gaccacaat taacaaaaa cgagatgcc tttgactaa 
ctacctgtt ccaggctgt ggtacctaa gggctgcaa 
agtcaaact gcaacctcc ctcagcaac caccctccc 
ggcttacaa cccgttcct gcccccttc tgccataac 
gcaaatcat gctgatcgc aaatcctga tgatgtaca 
agtttttct caagttttt tgtaagttt tgtaatgga 
cgaagagac ttgtactga aatcggcga ggttgaaac 
tcttccaat gtaaagcat tttaatttt agtgtaatt 
aaatcgtgc ttaagtca

    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