Status
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Gene information
General information
TC000081 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: 11381978..11393199
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
    		TC000081
    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_06977

    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: 60.0% (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

    adult lethality - Number of animals showing the phenotype: 2 (9 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: < 50 larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    larval musculature thinner - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 50% - 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): 30% - 50%
    larva bristle number increased - Penetrance (percentage of animals/eggs on slide): less than 30%

    gena triplet bristle duplicated - Penetrance (percentage of animals/eggs on slide): less than 30%

    thorax bristle random number increased - Penetrance (percentage of animals/eggs on slide): less than 30%
    legs cuticle shape irregular - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen bristle random number increased - Penetrance (percentage of animals/eggs on slide): less than 30%

    posterior terminus shape irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    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
    • >TC000081 RA
      MNDFVLENT IPNTTDILG IQPRYHLRS GFAGLQISD 
ENTRSIRTM PNIFAKSNR KFATAIRNA FKEAETIKD 
TAIKNCWNT ITATDLECI LCSRCIFDP ITTACGHTF 
CKGCLTRVL DHGLSCPLC MASLSLKDY SRGITVVLD 
QAIRFLLPR EHNERLLID LKEAQMLNR NSDIPVFIC 
TNAFPGVAC PLYVYEPRY RLLVRRCLL SPTRRFAMA 
AKEDSGEKF VSYGTVLEV KDAVSLEDG SFILTTVGV 
RRFRVLSRG EQDGYDTAK IQVIKDTVV SSDKLPELI 
ALHHKVYTK ASKWITSLT PKVLAEVER LIGKMPRVE 
KNWLSLPDG PSWTWWLMP ILPLSSQLQ VVFLSTTNL 
EKRLRAIDK MLERMEIRM KSLERNTCP LSEDASDSC 
DSERTIEIP LNN
    CDS sequence
    • >TC000081 RA
      atgaatgat tttgtttta gaaaacaca atccccaac 
accaccgac attctaggc atccaaccc cgctaccac 
ctccgttcc ggctttgca ggtttacaa atcagcgac 
gaaaacacg agaagtatt agaacaatg cccaacatt 
ttcgcaaaa tcaaaccga aaatttgcc actgcgata 
cgaaacgcc ttcaaagaa gccgaaacg atcaaagat 
acagccatc aaaaactgc tggaacact ataacagca 
accgacttg gaatgcatc ctttgtagt cgctgtatt 
ttcgatccc attaccacg gcttgcgga cacacgttt 
tgcaagggt tgtttgacc cgggttttg gaccatgga 
ctgtcttgc cccctctgt atggcgtcg ttgagcctg 
aaggactat tcccgaggg atcactgtg gtcctggac 
caggccatc aggttcctg ctcccgagg gaacacaat 
gaacggctt ttaatcgac ttgaaggag gcgcaaatg 
ctcaatcga aattctgat attcctgtg tttatttgc 
acgaatgcg ttccccgga gtggcgtgc cctttgtac 
gtgtacgag cctcggtac cgcctcctg gtgcggagg 
tgtttgttg tcgccgacg cgccgtttt gcaatggct 
gcgaaggaa gacagtgga gagaagttt gtttcgtat 
ggaacggtt ctggaagtg aaagatgcc gtttcgttg 
gaggatggc agttttatt ttgactacg gtgggagtg 
cggaggttt cgcgtcctg agtcgagga gaacaggac 
ggctacgac accgctaag atccaggtg atcaaggac 
accgtcgtc tcctccgac aagctcccc gagctcatt 
gccctccac cacaaggtc tacaccaag gcatcgaag 
tggatcacc tccttaacg cccaaagtc ctggccgaa 
gtcgaacgg ctcatcggc aaaatgccg cgggttgag 
aaaaactgg ctcagtctc ccagacggg ccctcctgg 
acgtggtgg ttgatgcct atcctccct cttagttcg 
caattacaa gtcgttttc ctgagcacg accaacctg 
gagaagcgt ctgcgtgcc atcgacaag atgctcgaa 
aggatggaa atccggatg aagtctctg gagcgcaac 
acttgtccc ttgtccgaa gatgcgagc gattcgtgc 
gattcggaa cgaacgatc gaaatccct ctaaataac 
taa
    mRNA sequence
    • >TC000081 RA
      ctcgtatgg tgctaggaa acgttcagt attgtttaa 
aaatgaatg attttgttt tagaaaaca caatcccca 
acaccaccg acattctag gcatccaac cccgctacc 
acctccgtt ccggctttg caggtttac aaatcagcg 
acgaaaaca cgagaagta ttagaacaa tgcccaaca 
ttttcgcaa aatcaaacc gaaaatttg ccactgcga 
tacgaaacg ccttcaaag aagccgaaa cgatcaaag 
atacagcca tcaaaaact gctggaaca ctataacag 
caaccgact tggaatgca tcctttgta gtcgctgta 
ttttcgatc ccattacca cggcttgcg gacacacgt 
tttgcaagg gttgtttga cccgggttt tggaccatg 
gactgtctt gccccctct gtatggcgt cgttgagcc 
tgaaggact attcccgag ggatcactg tggtcctgg 
accaggcca tcaggttcc tgctcccga gggaacaca 
atgaacggc ttttaatcg acttgaagg aggcgcaaa 
tgctcaatc gaaattctg atattcctg tgtttattt 
gcacgaatg cgttccccg gagtggcgt gccctttgt 
acgtgtacg agcctcggt accgcctcc tggtgcgga 
ggtgtttgt tgtcgccga cgcgccgtt ttgcaatgg 
ctgcgaagg aagacagtg gagagaagt ttgtttcgt 
atggaacgg ttctggaag tgaaagatg ccgtttcgt 
tggaggatg gcagtttta ttttgacta cggtgggag 
tgcggaggt ttcgcgtcc tgagtcgag gagaacagg 
acggctacg acaccgcta agatccagg tgatcaagg 
acaccgtcg tctcctccg acaagctcc ccgagctca 
ttgccctcc accacaagg tctacacca aggcatcga 
agtggatca cctccttaa cgcccaaag tcctggccg 
aagtcgaac ggctcatcg gcaaaatgc cgcgggttg 
agaaaaact ggctcagtc tcccagacg ggccctcct 
ggacgtggt ggttgatgc ctatcctcc ctcttagtt 
cgcaattac aagtcgttt tcctgagca cgaccaacc 
tggagaagc gtctgcgtg ccatcgaca agatgctcg 
aaaggatgg aaatccgga tgaagtctc tggagcgca 
acacttgtc ccttgtccg aagatgcga gcgattcgt 
gcgattcgg aacgaacga tcgaaatcc ctctaaata 
actaactaa ctaaaaaat caattggct gtggcttgg 
tccaaatgt gatcgggga acggatgga aaaatatac 
agaaaaatt ccctattga cctaatgta caatcattt 
ttacgtagg aaatttttt gaatattta ctgtagatt 
ggtaggaca aattctgat tattgaatg gtttacgaa 
atgatattt gtgatatgt ttcataagc gaccaaaaa 
tttattatt tatttttat atcgtatga ttttctaag 
gttttttat tggttttcc tactgaact acactgtct 
cggagttat tttttaatt cttttacat tgtttcgtg 
ctaggagta atgtgtcta ggttttaat cgcattatc 
gtaatttat ttctgttta gctaaggaa tatgcttga 
taatattta tttcataat tttataatt gttgtaatt 
taatgacta ttttaaacg ataaaccaa tgaagtttt 
taaatattt attttgtca atgtgatat tacattatt 
atttattat actttccca aactatttt acggaataa 
ataaatttg aaatca

    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