Status
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Gene information
General information
TC012027 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: 7663820..7670525
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
    		TC012027
    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
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_05152

    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
    number of eggs/embryos/larvae on slide: > 50 embryo/egg with muscle fluorescence/pattern, but not hatched (pot. late embryonic lethality) - Penetrance (percentage of animals/eggs on slide): 30% - 50%

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

    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%
    head number decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    thorax number decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 50% - 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
    • >TC012027 RA
      MVVSDLCLS WPVVTCAAF ASILIVKLY TFLTCGYYT 
AIRKMDGKT VIITGGNGG IGKETAKEI AKRGARVIL 
ACRNLETAE KARDEIVQA SNNQNVFVK KLDLSSQKS 
IREFAEEIT RSEPKLDVL IHNAGMAAN KIQITEDNL 
ELTMATNHY GPFLLTHLL IDLLKKSAP SRIVVVASE 
LYRVVSLNL NNVNPTRSW FVPRLYYVS KYANICFTK 
ELARRLEGT GVTANCLHP GIVDTGIWE SAPVLVRWP 
LRLLIKGFF KTPLQGCQT SVYVACAEE LQGVTGKYF 
AECKERGLS RGASDENKA KKLWEISEG LVNLKPSDP 
KI
    CDS sequence
    • >TC012027 RA
      atggtagtg tccgatctg tgtttgtct tggccggtg 
gtaacgtgc gctgcattc gcgtcgatt ttaatcgta 
aaattatac acttttctc acttgcggt tattacacc 
gcaattagg aaaatggac ggcaagacg gtgattatc 
accggtggc aacggcggc atcggcaaa gaaaccgcc 
aaggaaatt gccaaaaga ggagcgcgg gttattttg 
gcttgtcgt aatctggaa acggccgaa aaggccaga 
gatgagatt gtgcaggcg tcgaacaac caaaatgtg 
tttgtgaaa aagttggat ttgtcgtcg caaaagtcg 
atcagagag tttgcagag gagatcacg cggagcgag 
cccaagttg gacgttttg atccacaac gccggaatg 
gcagcgaac aagatacag attactgaa gataatctt 
gaactgacc atggccacg aatcattac gggccgttt 
cttctcaca catctctta atcgacttg ttaaaaaaa 
tcggccccc tctcgcatc gtcgtggtg gcttccgag 
ctgtaccgc gtcgtttct ctcaacctc aacaacgtg 
aatcccacg aggtcgtgg ttcgtgcct cgcctctac 
tacgtgtcc aagtacgcc aacatttgc ttcacgaag 
gagttggca cgccgcctt gaaggcaca ggtgtgaca 
gccaactgt ctccatccc ggaatcgtg gacaccggc 
atttgggaa agtgctccg gtgctcgtc cgctggcct 
ttgcgcctc ctcatcaag ggtttcttc aaaacgccg 
cttcaaggc tgccaaacc agcgtgtac gtggcctgt 
gcggaggaa ctccaagga gtcacgggc aagtacttc 
gccgaatgc aaggagaga ggactgagt cggggggcc 
agcgacgag aacaaagcg aagaaactg tgggagatt 
tcggagggt ttggtcaat ctcaagccc agcgatccg 
aaaatttaa
    mRNA sequence
    • >TC012027 RA
      actttttgc aagaatcaa atattaatc gtcgtcatt 
aaaagaaat ttccccttg aaatggttg cgttttcaa 
acaattccc cgaagattt ctaaaatac ttagtcata 
cagcaagtg ccactgatt ggttttcac tttctttac 
ttatccatt gttaccaca gcagtgtaa gcacctgtt 
aaacgctta cgtgtgatc cccaggtta aagtcgcaa 
cctactttt ttctagtgt tttttgcat cgaggaaaa 
cccgttgat caatttgta aaccttgca tcaaggatg 
gtagtgtcc gatctgtgt ttgtcttgg ccggtggta 
acgtgcgct gcattcgcg tcgatttta atcgtaaaa 
ttatacact tttctcact tgcggttat tacaccgca 
attaggaaa atggacggc aagacggtg attatcacc 
ggtggcaac ggcggcatc ggcaaagaa accgccaag 
gaaattgcc aaaagagga gcgcgggtt attttggct 
tgtcgtaat ctggaaacg gccgaaaag gccagagat 
gagattgtg caggcgtcg aacaaccaa aatgtgttt 
gtgaaaaag ttggatttg tcgtcgcaa aagtcgatc 
agagagttt gcagaggag atcacgcgg agcgagccc 
aagttggac gttttgatc cacaacgcc ggaatggca 
gcgaacaag atacagatt actgaagat aatcttgaa 
ctgaccatg gccacgaat cattacggg ccgtttctt 
ctcacacat ctcttaatc gacttgtta aaaaaatcg 
gccccctct cgcatcgtc gtggtggct tccgagctg 
taccgcgtc gtttctctc aacctcaac aacgtgaat 
cccacgagg tcgtggttc gtgcctcgc ctctactac 
gtgtccaag tacgccaac atttgcttc acgaaggag 
ttggcacgc cgccttgaa ggcacaggt gtgacagcc 
aactgtctc catcccgga atcgtggac accggcatt 
tgggaaagt gctccggtg ctcgtccgc tggcctttg 
cgcctcctc atcaagggt ttcttcaaa acgccgctt 
caaggctgc caaaccagc gtgtacgtg gcctgtgcg 
gaggaactc caaggagtc acgggcaag tacttcgcc 
gaatgcaag gagagagga ctgagtcgg ggggccagc 
gacgagaac aaagcgaag aaactgtgg gagatttcg 
gagggtttg gtcaatctc aagcccagc gatccgaaa 
atttaaact tgtatttgt tgtggtgtt gtaataatt 
aataaattg tattcttgt tg

    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