Status
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Gene information
General information
TC002813 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_007418.3: 9247405..9249175
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
    		TC002813
    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_07983

    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: 2 (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): more than 80%

    embryo/egg with embryonic tissue potentially present, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): less than 30%

    larval musculature random 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%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     cuticle remnants with unidentifyable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

    larva everted (inside-out) - Penetrance (percentage of animals/eggs on slide): less than 30%

    labrum size decreased - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    labrum complete not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    labrum position irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    head not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    thorax not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    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
    • >TC002813 RA
      MHTIFTEHQ NAYYRPGGG YSTAAAAVT ATANPYAYE 
QYSRYGYAA WHHQQHQLS TAKDMVKPP YSYIALIAM 
AIQNAPDKK ITLNGIYQF IMERFPYYR ENKQGWQNS 
IRHNLSLNE CFVKVPRDD KKPGKGSYW TLDPDSYNM 
FDNGSYLRR RRRFKKKDA LREKEEAIK RQQLDSNVT 
AKRDEKPLE EAKKLECKP KREPAELTQ CKYNDVKSV 
IVHQEHVIS EAMAMDSAA AFTVDSLMT TREQHAYGN 
SGRLHTSGG MYYCPSATP QQYIGDEAA PRYSPWYSP 
ETSPESGYR DMIFDSSAA PSCQLAGFR HSGVSPSPP 
NYRTAAAYY QQDCVGQKY
    CDS sequence
    • >TC002813 RA
      atgcatacg attttcacc gaacatcag aatgcctac 
taccggccc gggggcggc tatagcacc gccgccgcc 
gcggtgacc gccaccgcg aacccctac gcctacgag 
cagtactcc cgttatggc tacgccgca tggcaccac 
caacaacac caattatcc accgccaag gacatggtc 
aaaccgccg tattcctac atcgcgctc atcgccatg 
gccatccag aacgccccc gacaagaaa atcaccctc 
aacggcatc taccagttc ataatggag cgctttccc 
tactaccgc gagaacaaa caaggctgg cagaactca 
atccgtcac aacctcagc ctgaacgaa tgtttcgtc 
aaagtccca cgggacgac aaaaagccg ggaaaaggg 
agctactgg acccttgac ccagactcc tacaacatg 
ttcgacaac ggctcgtac ctgcgccgc cggcggcgc 
ttcaagaag aaggacgcc ctccgcgag aaggaggaa 
gccatcaag cgccaacag ctcgactcc aacgtcacc 
gccaagcgc gacgaaaaa ccgctggag gaggcgaaa 
aagctcgag tgcaagccc aagcgcgag cccgcggag 
ctcacccag tgcaagtac aacgacgtc aagtcggtc 
atcgtgcac caggagcac gtcatcagc gaggccatg 
gcgatggac tcggcggcg gccttcacc gtcgactcg 
ctgatgacg acgcgggag cagcacgcc tacggcaac 
tccgggcgc ctgcacacc tccggaggg atgtactac 
tgccccagt gccactccg cagcagtac atcggggac 
gaggccgcg ccgaggtac agcccctgg tacagcccg 
gaaacgtcc ccggagtcc ggctacagg gatatgatt 
ttcgacagc agtgcggcg cccagctgt caattggcg 
gggtttagg cactccggg gtctcgcca agtccgcct 
aattataga acggcggcg gcttactac caacaggac 
tgtgtggga cagaaatac tga
    mRNA sequence
    • >TC002813 RA
      aactgtttt cactagtaa catcgtgtc tcggcaaga 
agcaacata ctctgtttt tacttaatc tttgtgtaa 
actgcccca tgttgtgta tcataatat taagtgaac 
gcaaacttg ttttcggaa gattgattg gaatgaaaa 
cacaaaacg cactatact gttgaaata acaagactg 
ttttcgttt tagaaaact ctcggcctt ttgtcttgt 
ttgttgttt ttgcgtgta aacatgcat acgattttc 
accgaacat cagaatgcc tactaccgg cccgggggc 
ggctatagc accgccgcc gccgcggtg accgccacc 
gcgaacccc tacgcctac gagcagtac tcccgttat 
ggctacgcc gcatggcac caccaacaa caccaatta 
tccaccgcc aaggacatg gtcaaaccg ccgtattcc 
tacatcgcg ctcatcgcc atggccatc cagaacgcc 
cccgacaag aaaatcacc ctcaacggc atctaccag 
ttcataatg gagcgcttt ccctactac cgcgagaac 
aaacaaggc tggcagaac tcaatccgt cacaacctc 
agcctgaac gaatgtttc gtcaaagtc ccacgggac 
gacaaaaag ccgggaaaa gggagctac tggaccctt 
gacccagac tcctacaac atgttcgac aacggctcg 
tacctgcgc cgccggcgg cgcttcaag aagaaggac 
gccctccgc gagaaggag gaagccatc aagcgccaa 
cagctcgac tccaacgtc accgccaag cgcgacgaa 
aaaccgctg gaggaggcg aaaaagctc gagtgcaag 
cccaagcgc gagcccgcg gagctcacc cagtgcaag 
tacaacgac gtcaagtcg gtcatcgtg caccaggag 
cacgtcatc agcgaggcc atggcgatg gactcggcg 
gcggccttc accgtcgac tcgctgatg acgacgcgg 
gagcagcac gcctacggc aactccggg cgcctgcac 
acctccgga gggatgtac tactgcccc agtgccact 
ccgcagcag tacatcggg gacgaggcc gcgccgagg 
tacagcccc tggtacagc ccggaaacg tccccggag 
tccggctac agggatatg attttcgac agcagtgcg 
gcgcccagc tgtcaattg gcggggttt aggcactcc 
ggggtctcg ccaagtccg cctaattat agaacggcg 
gcggcttac taccaacag gactgtgtg ggacagaaa 
tactgaggg tacgcgtat catctcaat atcaagact 
gatgtttga aggttttgt gcgattccg gcctccaag 
gaattccag tagtgcatg gtggaaatt atagaggtg 
taggagagg tttagtgag acgattttt cactttcct 
acaggtctg taatttttt ttcattcga aatcgtttg 
gctttgttt cgttccaac ggcagctgg ttttattta 
tgtgatatg ttgatagtg taatttcgt tttttcgaa 
aatttatat ttttttatt attaggaat ggtgtttct 
ttttttgta ttatactca taggttcct ataaagatt 
ttaaccatt ccccgatga atttgcggc atttatcgg 
ttatcaact ttatagaaa gtaattacc ttacgtgtc 
cggtgtaca tatttattt gtaaaataa tgtagatgt 
attattacc cactgtatg tgttgaaag cacgtatgt 
atattattt attgacttt aaagaaata aatcacacc 
attgtgg

    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