Status
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Gene information
General information
TC008777 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_007422.5: 9817333..9819237
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
    		TC008777
    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_01413

    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 embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg not developed/not fertilized - Penetrance (percentage of animals/eggs on slide): less than 30%

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

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

    larval musculature random not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    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
     embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    cuticle remnants with unidentifyable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

    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
    • >TC008777 RA
      MFKLFFLLL IISFCSAFD FIFQPGPLV PASKGEIWP 
KPQHENKLD DGFFSLLPT FFHFNPIGN ICNTLTEAL 
DRYRKLIIF NNRRIKEVY YKARSCYEG GDQNFLGYL 
TSVEVELTG ACNDEEYPS FEMKEEYVV NVTSTVQRI 
SSDTIWGIL RGLETFSQL IYLTDDYSC HRIGTTSIH 
DYPRFAHRG LLLDTSRHY IPKEHILKL IETMSYNKL 
NVFHWHITD DYSFPYVSK AFPQMSNKG AFHPTLMIY 
EQDFVSEVQ EYARKRGIR VLAEFDTPG HTLSWGLGN 
PDLLTDCHN VPQLKWGPI NPIKNTTYD FIFKLFEEI 
KSVFKDEYT HLGGDEVDF SCWKSNPEI NQWMAEHQM 
EGDYVALQS HYIQKLINH VDSLGLNSI VWEEVFTNG 
VQLPKSTVV NVWISDDPK TTLKQVTEA GHPTIISSY 
WYLDILKTG GDWLKFYNA DPQDFDGTD EQKRLVLGG 
EACMWSEVV DEYNLEPRV WPRASVAAE RFWSPPDTP 
KSAQNLGEL WTIASRLQE QTCRMNRRG VAAQPPSGP 
SVCF
    CDS sequence
    • >TC008777 RA
      atgttcaaa ctatttttc cttttactc ataatttca 
ttttgttcg gctttcgat ttcattttc caacccggc 
ccacttgtt ccggcttcg aaaggcgaa atatggcca 
aagccccaa catgaaaat aaattagac gatggattc 
ttctctttg ttaccaaca ttctttcat ttcaatcca 
atcggaaac atctgtaac acgttaact gaagctttg 
gacagatac agaaagttg atcatattt aacaatcgc 
cgaataaag gaggtttat tacaaagcg cgcagttgc 
tacgaaggc ggagatcaa aattttttg ggctatttg 
acaagcgtg gaagttgaa ttgactggt gcttgtaac 
gatgaagag tacccctca tttgagatg aaagaagaa 
tatgttgta aacgtaacg tcaacagtg caaagaatt 
tcctcagac actatatgg ggaatactt cgggggctc 
gaaactttc tcacaattg atatacttg acagacgat 
tacagttgt cacagaatt ggaacaact tcaattcac 
gattacccc agatttgcc catcgcgga ctacttttg 
gacacttcc cgtcattac atcccaaaa gagcacatt 
ttgaagtta atcgagaca atgtcttac aacaaatta 
aatgttttc cactggcat atcactgac gattacagt 
tttccctac gtcagtaaa gctttcccg caaatgagc 
aataaggga gcattccat ccgactctc atgatttac 
gagcaagac tttgtaagc gaagtgcaa gagtatgct 
cgaaaacgc ggaattcgt gttttggca gagttcgat 
acccctggc cataccctt tcttggggt ctgggaaac 
ccagacttg ctcaccgat tgccacaac gtaccccaa 
cttaagtgg ggacccatc aaccccatt aaaaacacc 
acctacgac ttcattttc aaactattc gaagaaatc 
aaaagcgtt ttcaaagac gaatacacg caccttggc 
ggcgacgaa gtcgatttc tcttgctgg aaaagcaac 
ccagaaatc aaccaatgg atggctgag caccagatg 
gagggcgat tacgtcgcc ctgcaaagc cactacatc 
caaaaactc atcaaccac gtcgattct ttaggttta 
aactcaatt gtttgggaa gaagtgttc accaacggt 
gtccaacta cccaaatcc acagtagtc aacgtctgg 
attagcgat gacccgaaa acaaccctc aaacaagta 
acagaagct ggccatcca acaatcatc tcatcttac 
tggtatttg gatattttg aagaccgga ggtgattgg 
ttaaaattc tacaatgct gacccgcaa gactttgat 
ggtactgac gaacaaaaa agacttgtt cttggaggg 
gaggcgtgt atgtggagc gaagtcgtt gatgagtat 
aacttggag ccaagggtg tggccgaga gctagtgtg 
gcggcggag aggttttgg tcgcctcca gacactccc 
aaaagtgcg caaaattta ggagagctt tggactatc 
gctagcagg ctacaagag cagacttgc agaatgaac 
aggagaggg gtggcggca cagccgcct tcaggacca 
agtgtttgt ttttaa
    mRNA sequence
    • >TC008777 RA
      acacgatca tgatgttca aactatttt tccttttac 
tcataattt cattttgtt cggctttcg atttcattt 
tccaacccg gcccacttg ttccggctt cgaaaggcg 
aaatatggc caaagcccc aacatgaaa ataaattag 
acgatggat tcttctctt tgttaccaa cattctttc 
atttcaatc caatcggaa acatctgta acacgttaa 
ctgaagctt tggacagat acagaaagt tgatcatat 
ttaacaatc gccgaataa aggaggttt attacaaag 
cgcgcagtt gctacgaag gcggagatc aaaattttt 
tgggctatt tgacaagcg tggaagttg aattgactg 
gtgcttgta acgatgaag agtacccct catttgaga 
tgaaagaag aatatgttg taaacgtaa cgtcaacag 
tgcaaagaa tttcctcag acactatat ggggaatac 
ttcgggggc tcgaaactt tctcacaat tgatatact 
tgacagacg attacagtt gtcacagaa ttggaacaa 
cttcaattc acgattacc ccagatttg cccatcgcg 
gactacttt tggacactt cccgtcatt acatcccaa 
aagagcaca ttttgaagt taatcgaga caatgtctt 
acaacaaat taaatgttt tccactggc atatcactg 
acgattaca gttttccct acgtcagta aagctttcc 
cgcaaatga gcaataagg gagcattcc atccgactc 
tcatgattt acgagcaag actttgtaa gcgaagtgc 
aagagtatg ctcgaaaac gcggaattc gtgttttgg 
cagagttcg atacccctg gccataccc tttcttggg 
gtctgggaa acccagact tgctcaccg attgccaca 
acgtacccc aacttaagt ggggaccca tcaacccca 
ttaaaaaca ccacctacg acttcattt tcaaactat 
tcgaagaaa tcaaaagcg ttttcaaag acgaataca 
cgcaccttg gcggcgacg aagtcgatt tctcttgct 
ggaaaagca acccagaaa tcaaccaat ggatggctg 
agcaccaga tggagggcg attacgtcg ccctgcaaa 
gccactaca tccaaaaac tcatcaacc acgtcgatt 
ctttaggtt taaactcaa ttgtttggg aagaagtgt 
tcaccaacg gtgtccaac tacccaaat ccacagtag 
tcaacgtct ggattagcg atgacccga aaacaaccc 
tcaaacaag taacagaag ctggccatc caacaatca 
tctcatctt actggtatt tggatattt tgaagaccg 
gaggtgatt ggttaaaat tctacaatg ctgacccgc 
aagactttg atggtactg acgaacaaa aaagacttg 
ttcttggag gggaggcgt gtatgtgga gcgaagtcg 
ttgatgagt ataacttgg agccaaggg tgtggccga 
gagctagtg tggcggcgg agaggtttt ggtcgcctc 
cagacactc ccaaaagtg cgcaaaatt taggagagc 
tttggacta tcgctagca ggctacaag agcagactt 
gcagaatga acaggagag gggtggcgg cacagccgc 
cttcaggac caagtgttt gtttttaag ctaatgaat 
tattgtttt ttaataatt ttgaataaa atattgtta 
actca

    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