Status
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Gene information
General information
TC001409 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.

NW_015451510.1: 112398..114333
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
    		TC001409
    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_07767

    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: 3 (3 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (9 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
    • >TC001409 RA
      MIEFTEDWL MHKSILGEG AYGEVKLIV NKHTNEKVA 
CKIINYGKK DDVQVNINK EVIIHKMLN HENIIKYFG 
RRREPLREY IYLEYASRG ELFQMIEPD VGMPSSLAQ 
LYMKQLLNG LHYLHNLGI VHRDIKPEN LLINDDGVL 
KISDFGMAT LFRCKGKER LLDRRCGTK PYCAPEILL 
RPYRAQPAD IWSCGIVLI AMLTGELPW SDTFSEEFV 
NYKNDNYIT VTPWSKLGN ATLSLIRKI LAIEPNKRL 
TIQEILKHP WMKYNFDDQ KTDVVDDSN LNPVKRFNS 
MMETETRVH RTNPIVILS QPTPAVRPP SIDQLVTDL 
RTNRELVCF SQPTHNDDM LLSSQIQFN ETPLTKDNF 
NNLVKRMTR FYVTTNYEK TLEVLCSVL DTFHYNWQI 
DGNGAVTIS TVDIMKNQL MFKTNVIEI QGKILVDFR 
LSKGCGIEF KKKFKKLKE CLDDIVEKN E
    CDS sequence
    • >TC001409 RA
      atgatcgag tttacggag gactggctc atgcacaag 
agcatcctg ggcgagggg gcttacgga gaagtcaag 
ctgattgtt aacaaacac accaacgag aaggtcgct 
tgcaagata atcaactac gggaaaaag gacgatgtg 
caggttaac atcaacaaa gaagtgatc atacacaag 
atgctgaac cacgagaac ataatcaag tattttggg 
cgacggagg gagcctctg agggagtac atctacctg 
gagtacgcc tccagaggc gagctcttc cagatgatt 
gagcctgac gtaggcatg ccgtcctcc ctggcccaa 
ctttacatg aagcagcta ttgaacggg ttacactac 
ttgcacaac ttggggatc gtgcaccgc gacatcaaa 
cccgaaaat ctcctaatc aacgacgac ggagtgttg 
aaaattagt gatttcgga atggcaact ttgttcagg 
tgtaagggc aaagagcgg cttttggat cgccgctgt 
ggcacgaag ccttactgc gcccctgaa atactacta 
aggccctat cgggcccaa cctgccgac atttggagc 
tgtggcatc gttttaata gcaatgttg accggagaa 
ttgccttgg agcgacaca tttagcgaa gaattcgtc 
aattataag aacgataat tacatcaca gtcacaccc 
tggagcaaa ctgggcaat gccacgctc agtctgatc 
cgaaaaatc ctggcaatt gagccaaat aagcgactg 
acgattcag gaaatcctg aagcacccc tggatgaag 
tacaacttt gacgaccaa aaaaccgat gtcgtggac 
gattccaat ttgaatccc gttaagcgt ttcaattcg 
atgatggag actgaaact cgcgtgcat cgcaccaat 
ccgattgtg atattgtct cagccgact ccagccgtg 
cgtccgccg tctatagac cagctggtg actgatctc 
aggacaaac cgcgaactt gtgtgcttc tcgcagccc 
actcataac gacgatatg cttctgagc tcccaaatt 
caattcaat gagactcca ctcaccaaa gataacttt 
aataatcta gttaagaga atgacgaga ttttatgtt 
accactaat tacgagaaa actttggaa gttttgtgc 
tctgttcta gatactttt cattataat tggcagatt 
gatggcaac ggagctgtc acgatttca actgttgat 
attatgaaa aatcaactc atgtttaag acgaacgtc 
atcgaaata caggggaaa attctagtg gatttccgc 
ctatcaaag ggctgtggt atcgaattt aaaaagaag 
ttcaaaaaa ctgaaagag tgccttgac gatattgtt 
gaaaaaaat gaataa
    mRNA sequence
    • >TC001409 RA
      tgtcacacc cgcgaaatc gattacagt tgacatgtc 
cgatcttga ggtgtcaat aaattccat gacacgatc 
aagttgtct cgatgtctt ttgtttttt gtgaggtac 
agcccgaag tcgccattg tttggcttt ctgaacaac 
tcaattaac actatcttt actggtttt gtttgttca 
agtcgtttg ttaataatt aattagtgt ttggaagaa 
aatgatcga gtttacgga ggactggct catgcacaa 
gagcatcct gggcgaggg ggcttacgg agaagtcaa 
gctgattgt taacaaaca caccaacga gaaggtcgc 
ttgcaagat aatcaacta cgggaaaaa ggacgatgt 
gcaggttaa catcaacaa agaagtgat catacacaa 
gatgctgaa ccacgagaa cataatcaa gtattttgg 
gcgacggag ggagcctct gagggagta catctacct 
ggagtacgc ctccagagg cgagctctt ccagatgat 
tgagcctga cgtaggcat gccgtcctc cctggccca 
actttacat gaagcagct attgaacgg gttacacta 
cttgcacaa cttggggat cgtgcaccg cgacatcaa 
acccgaaaa tctcctaat caacgacga cggagtgtt 
gaaaattag tgatttcgg aatggcaac tttgttcag 
gtgtaaggg caaagagcg gcttttgga tcgccgctg 
tggcacgaa gccttactg cgcccctga aatactact 
aaggcccta tcgggccca acctgccga catttggag 
ctgtggcat cgttttaat agcaatgtt gaccggaga 
attgccttg gagcgacac atttagcga agaattcgt 
caattataa gaacgataa ttacatcac agtcacacc 
ctggagcaa actgggcaa tgccacgct cagtctgat 
ccgaaaaat cctggcaat tgagccaaa taagcgact 
gacgattca ggaaatcct gaagcaccc ctggatgaa 
gtacaactt tgacgacca aaaaaccga tgtcgtgga 
cgattccaa tttgaatcc cgttaagcg tttcaattc 
gatgatgga gactgaaac tcgcgtgca tcgcaccaa 
tccgattgt gatattgtc tcagccgac tccagccgt 
gcgtccgcc gtctataga ccagctggt gactgatct 
caggacaaa ccgcgaact tgtgtgctt ctcgcagcc 
cactcataa cgacgatat gcttctgag ctcccaaat 
tcaattcaa tgagactcc actcaccaa agataactt 
taataatct agttaagag aatgacgag attttatgt 
taccactaa ttacgagaa aactttgga agttttgtg 
ctctgttct agatacttt tcattataa ttggcagat 
tgatggcaa cggagctgt cacgatttc aactgttga 
tattatgaa aaatcaact catgtttaa gacgaacgt 
catcgaaat acaggggaa aattctagt ggatttccg 
cctatcaaa gggctgtgg tatcgaatt taaaaagaa 
gttcaaaaa actgaaaga gtgccttga cgatattgt 
tgaaaaaaa tgaataatt ctagttcct tgtttttgt 
atttttata ttaaatgat taaaaaata ttattcgaa

    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