Status
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Gene information
General information
TC000804 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_007417.3: 5875019..5877189
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
    		TC000804
    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_09610

    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: 20.0% (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 embryonic tissue, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    larval musculature pattern irregular - 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): more than 80%
    cuticle remnants with some identifiable segments - 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
    • >TC000804 RA
      MLVLRNVLS LSLVLGLAT SATLFQDAP VVQLENGQV 
RGRVDTTVG EGRTYYSFR GIPFAEPPI GDLRFEPPV 
PKSNWDGVW DATEDRSDC VQGSNTVMG SEDCLFINV 
YTPKQPSSS CELLPTMVW IYGGGFEGG SSSYNLYGP 
DYLLEKDVV VVTFNYRLG VLGFLSTGD DVAPGNNGL 
KDQVLALQW VRDNIKNFC GNPEQVTLA GQSAGSASV 
AYHLQSPLS EGLFHRAIL QSGVSLSLW AYSRRVPQV 
VGQLAQALE IDNSTSRSI VDSLKQLNT TYLQTKASA 
TISEALISN NPRDGFAMG PVSEHDHPG AFFSGRSHE 
LLSNKKFHK VPIVIGFNS LEGTFNFEL LFRLYLVKF 
DLDNTMLLP IDMNIDSSK KSEAAKKLK QHYFGWKPV 
SMANVELMK FLSDDQFGR SITEFGRLL KDDAPVYFY 
RFSYEGGLW GNYNRTNSG VTHSEELGY YWVSNHQPS 
SDHDFVIRT RMVKLWTNF IKYANPTPE QDPVLQDII 
WKPFNNSLS FVDIGEHLV VGESPEQEH MGFWDSFYG 
QYGNPPYTT Y
    CDS sequence
    • >TC000804 RA
      atgttagtc ctaagaaac gtactttct ctttccctt 
gttttgggt cttgcgact agtgccact ttgtttcaa 
gatgctcca gtagtacaa cttgaaaat ggtcaagtg 
agaggaaga gtggacaca acagtggga gaaggccga 
acttattat tctttccga ggaattccc tttgccgag 
cctccaatt ggcgatctc cgatttgaa ccccctgtc 
cctaaaagc aactgggat ggcgtctgg gacgccaca 
gaagaccga tcagattgt gttcaaggc tcaaacact 
gtgatgggt tccgaggat tgtctcttc ataaatgtt 
tacacgcca aagcaacca tcgtcctcg tgtgagttg 
cttcccacc atggtctgg atttacggt ggtgggttt 
gaaggaggc tcctcctct tacaacctc tacgggcct 
gactatctt ctcgagaag gatgttgtt gttgttacg 
ttcaattac cgtttagga gttttggga tttctgagt 
actggtgac gacgtagct cctgggaat aacggtctc 
aaagaccag gtcctggcc cttcagtgg gtgagagac 
aacataaag aatttctgt gggaaccct gaacaggtc 
actcttgct ggccaaagt gccggatct gcgtcagtg 
gcctatcac ctccaatca cccttatct gaaggactt 
ttccatagg gctatacta cagtcaggt gtgtctcta 
agtctgtgg gcttacagt cgacgagtt cctcaagtt 
gttggccaa ctggcccaa gctttggaa attgataac 
tcaacaagt cgctcgatt gttgacagt ttgaagcaa 
cttaacacc acctacctc caaactaaa gcgtctgcg 
accatatcc gaagcccta atctcgaac aatcccaga 
gacgggttt gccatgggc cctgtgagt gagcatgac 
caccctggt gcattcttt tccggaaga agccacgaa 
ctactatcc aataaaaaa ttccataaa gtaccaata 
gtcattggg ttcaattct ctggaaggg acatttaat 
ttcgaactt cttttccgt ctctatctg gtcaaattt 
gatctcgac aataccatg ttgttgcca attgacatg 
aatattgac agcagcaag aaatcggaa gctgccaaa 
aaattaaag caacattat ttcggctgg aagcctgtt 
agtatggcc aacgtcgag ttgatgaag ttcctcagc 
gatgaccaa tttgggcga tctattaca gaatttggc 
cggcttttg aaagatgac gcccctgta tatttctac 
cggttttca tacgagggg ggattgtgg ggtaattac 
aaccgaact aactcaggt gtaacacat agtgaagaa 
ttgggttac tactgggtt tccaatcat caaccatcg 
tctgatcac gattttgtt atacgcact agaatggta 
aagttgtgg actaacttt atcaaatat gcgaatccc 
actccggag caagaccct gtgttgcaa gatattatc 
tggaaaccc tttaataat agtttgtct tttgtggat 
attggagaa catttggtt gttggtgaa tctccagaa 
caggaacat atggggttc tgggatagc ttttatggg 
caatatgga aacccacct tatactacg tattga
    mRNA sequence
    • >TC000804 RA
      cttatttag tccagtaag taaaatgtt agtcctaag 
aaacgtact ttctctttc ccttgtttt gggtcttgc 
gactagtgc cactttgtt tcaagatgc tccagtagt 
acaacttga aaatggtca agtgagagg aagagtgga 
cacaacagt gggagaagg ccgaactta ttattcttt 
ccgaggaat tccctttgc cgagcctcc aattggcga 
tctccgatt tgaaccccc tgtccctaa aagcaactg 
ggatggcgt ctgggacgc cacagaaga ccgatcaga 
ttgtgttca aggctcaaa cactgtgat gggttccga 
ggattgtct cttcataaa tgtttacac gccaaagca 
accatcgtc ctcgtgtga gttgcttcc caccatggt 
ctggattta cggtggtgg gtttgaagg aggctcctc 
ctcttacaa cctctacgg gcctgacta tcttctcga 
gaaggatgt tgttgttgt tacgttcaa ttaccgttt 
aggagtttt gggatttct gagtactgg tgacgacgt 
agctcctgg gaataacgg tctcaaaga ccaggtcct 
ggcccttca gtgggtgag agacaacat aaagaattt 
ctgtgggaa ccctgaaca ggtcactct tgctggcca 
aagtgccgg atctgcgtc agtggccta tcacctcca 
atcaccctt atctgaagg acttttcca tagggctat 
actacagtc aggtgtgtc tctaagtct gtgggctta 
cagtcgacg agttcctca agttgttgg ccaactggc 
ccaagcttt ggaaattga taactcaac aagtcgctc 
gattgttga cagtttgaa gcaacttaa caccaccta 
cctccaaac taaagcgtc tgcgaccat atccgaagc 
cctaatctc gaacaatcc cagagacgg gtttgccat 
gggccctgt gagtgagca tgaccaccc tggtgcatt 
cttttccgg aagaagcca cgaactact atccaataa 
aaaattcca taaagtacc aatagtcat tgggttcaa 
ttctctgga agggacatt taatttcga acttctttt 
ccgtctcta tctggtcaa atttgatct cgacaatac 
catgttgtt gccaattga catgaatat tgacagcag 
caagaaatc ggaagctgc caaaaaatt aaagcaaca 
ttatttcgg ctggaagcc tgttagtat ggccaacgt 
cgagttgat gaagttcct cagcgatga ccaatttgg 
gcgatctat tacagaatt tggccggct tttgaaaga 
tgacgcccc tgtatattt ctaccggtt ttcatacga 
ggggggatt gtggggtaa ttacaaccg aactaactc 
aggtgtaac acatagtga agaattggg ttactactg 
ggtttccaa tcatcaacc atcgtctga tcacgattt 
tgttatacg cactagaat ggtaaagtt gtggactaa 
ctttatcaa atatgcgaa tcccactcc ggagcaaga 
ccctgtgtt gcaagatat tatctggaa accctttaa 
taatagttt gtcttttgt ggatattgg agaacattt 
ggttgttgg tgaatctcc agaacagga acatatggg 
gttctggga tagctttta tgggcaata tggaaaccc 
accttatac tacgtattg atttcaaat tgttgacat 
ttctgtaaa aatcgcaag tctaataaa ataataaaa 
acgcc

    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