Status
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Gene information
General information
TC012300 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: 3902122..3903890
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
    		TC012300
    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
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_07598

    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 larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     head appendages position irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    head irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    head not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    thorax irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    thorax not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    abdomen irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    abdomen not present - 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: % (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
    • >TC012300 RA
      MFKYLSVFV IIGFIFFIQ CSKNEDNDV FVPTKEWQT 
VRKGQKIPK GLHVRINLE TGETEAKLL DEAPEDKTR 
ALSALPPEN PKSTLGEAV TDTYTPDEL KKIKNEFRS 
YDEIKKTLG DLKLTPKMD AEIIADLLQ RHQEVVDKT 
ELLKILEDL DFLAHQYDN AREFVKQNG FREMIYKNL 
NSTDSEVKK ETLKLMTAL MQNNVNPKI HALESGAVG 
VLLRLVNFE SDLGVKTRA LSALGALLR SFPAAQRKF 
VESGGLSVL SKFFDSDDI KLQIKLVTM ISDLLVEHE 
YSVVDENLS KYYVKFDLT KRILEHDWC KKLNKLLLG 
LLITDKDDH DSVEKCLTA MHSLRAHCG DKYEKDLIT 
NLRKRYDSL LKSDGVEDQ TFYKGLKDL CDEILYHVN 
NSVKTEL
    CDS sequence
    • >TC012300 RA
      atgttcaaa tatctcagt gtttttgta ataattgga 
tttattttt ttcatccag tgtagcaaa aatgaagac 
aatgatgtt tttgttcca accaaagag tggcaaacg 
gttagaaaa ggtcaaaag atccccaaa ggactccac 
gttaggata aacctcgag accggagag accgaggcg 
aaactgtta gacgaggcc ccggaggat aaaaccagg 
gccttatcg gccttgccc ccagaaaac cctaaatcc 
acccttggg gaggccgtt acagacact tacacccca 
gacgagtta aaaaaaatc aaaaacgaa ttccgcagt 
tacgatgag attaagaaa actctcggc gatttgaag 
ctgacgccg aaaatggac gcggaaata atcgcggat 
ttgttgcaa agacaccag gaggtggtg gacaaaacc 
gagttgttg aaaatcctc gaggatctg gattttctg 
gcacaccag tacgacaac gcgcgcgag ttcgtcaaa 
caaaacggc ttccgggaa atgatttac aaaaatttg 
aattccacc gattcggag gttaaaaaa gagacgcta 
aaactgatg actgccttg atgcagaac aacgtgaac 
ccgaaaatc cacgcgctt gagagcggc gcagttggg 
gttttgcta cgtctagtc aattttgag tcagatttg 
ggggtgaaa acgcgggct ttgagtgcg ctgggggcg 
ctcttgcgg tcctttccg gccgctcaa cgcaagttc 
gttgaaagc ggggggctg tcggtgttg agcaagttt 
ttcgatagt gacgatatc aagctgcaa attaagttg 
gtcacgatg atttcggat ctgttggtc gagcacgaa 
tattcagtc gttgatgag aacttgagc aagtattac 
gtgaaattt gacttgacc aagcgcata ctcgagcat 
gattggtgc aaaaagttg aataagctg ctgttaggg 
ttgttgata actgataag gacgatcac gattcagtc 
gagaagtgt ctcacggcc atgcattcc ttgcgggcg 
cattgtggc gacaagtac gagaaagac ttgatcacg 
aatctgaga aaacgctac gattctttg ctaaagtct 
gacggtgtc gaggaccag actttttac aaaggtcta 
aaagacctt tgtgatgaa attttgtac catgtaaat 
aatagtgta aagactgaa ctgtaa
    mRNA sequence
    • >TC012300 RA
      tgcctgaaa cccactaga gtgcagaac aatgttcga 
tgaattacg tgtccccta aacgaaaat gttcaaata 
tctcagtgt ttttgtaat aattggatt tattttttt 
catccagtg tagcaaaaa tgaagacaa tgatgtttt 
tgttccaac caaagagtg gcaaacggt tagaaaagg 
tcaaaagat ccccaaagg actccacgt taggataaa 
cctcgagac cggagagac cgaggcgaa actgttaga 
cgaggcccc ggaggataa aaccagggc cttatcggc 
cttgccccc agaaaaccc taaatccac ccttgggga 
ggccgttac agacactta caccccaga cgagttaaa 
aaaaatcaa aaacgaatt ccgcagtta cgatgagat 
taagaaaac tctcggcga tttgaagct gacgccgaa 
aatggacgc ggaaataat cgcggattt gttgcaaag 
acaccagga ggtggtgga caaaaccga gttgttgaa 
aatcctcga ggatctgga ttttctggc acaccagta 
cgacaacgc gcgcgagtt cgtcaaaca aaacggctt 
ccgggaaat gatttacaa aaatttgaa ttccaccga 
ttcggaggt taaaaaaga gacgctaaa actgatgac 
tgccttgat gcagaacaa cgtgaaccc gaaaatcca 
cgcgcttga gagcggcgc agttggggt tttgctacg 
tctagtcaa ttttgagtc agatttggg ggtgaaaac 
gcgggcttt gagtgcgct gggggcgct cttgcggtc 
ctttccggc cgctcaacg caagttcgt tgaaagcgg 
ggggctgtc ggtgttgag caagttttt cgatagtga 
cgatatcaa gctgcaaat taagttggt cacgatgat 
ttcggatct gttggtcga gcacgaata ttcagtcgt 
tgatgagaa cttgagcaa gtattacgt gaaatttga 
cttgaccaa gcgcatact cgagcatga ttggtgcaa 
aaagttgaa taagctgct gttagggtt gttgataac 
tgataagga cgatcacga ttcagtcga gaagtgtct 
cacggccat gcattcctt gcgggcgca ttgtggcga 
caagtacga gaaagactt gatcacgaa tctgagaaa 
acgctacga ttctttgct aaagtctga cggtgtcga 
ggaccagac tttttacaa aggtctaaa agacctttg 
tgatgaaat tttgtacca tgtaaataa tagtgtaaa 
gactgaact gtaaatacc actttgtta tataatata 
tttattttt cttaaataa taattttta aaaact

    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