Status
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Gene information
General information
TC015409 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_007421.3: 511641..515027
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
    		TC015409
    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
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    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
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    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_07435

    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: 30.0% (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

    adult lethality - Number of animals showing the phenotype: 1 (9 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection

    Fertility
    mature egg deposition blocked number 1st lateral oviduct: >5 number 2nd lateral oviduct: - Number of animals showing the phenotype: 2
    ovary without detectable defects - Number of animals showing the phenotype: 2
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 20
    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
    • >TC015409 RA
      MTPHALISS DFHDVIKPL INLTKIFGF LPVCSSQKG 
QKTCLNLSI NYCICGYIF SAILFSLSI LGLTEDLNS 
APIRMKNPI VKYIILIDL GEVAVTVLA GILTTPFKL 
PYFWKMLTG FGKIEQVLP PHHAPEEKK RSFWAVTIF 
LVLAASVIF FDVVVWGLS ASDLGVFFK RFLPVYVSY 
LLIFVQQIP FCFFVRVIR LKIEDLNGA FRAGLERVQ 
NGENQWISV MKVNKQPKV IQGKSALSY ERLNEFMRL 
VEEIEDVIE AINGFYGVH TLLILFSCL LHLVVTPYY 
LLIEVCNAG YLPFILLQV AWIVLHLIR LMVIVETCQ 
RCIDEYQVT TNLVLKLLT SPLLPDIKE QVEILAVQV 
SNKKIKFSS FGMLKISRS LLTSFGGAL TTFLVILFQ 
YGGIHGNVY
    CDS sequence
    • >TC015409 RA
      atgacacct cacgcttta atttcctcc gatttccac 
gacgttatc aaaccctta atcaattta acaaaaata 
ttcggtttc ctcccagtc tgctcgagc caaaagggc 
caaaaaacc tgcctcaac ctctcgatt aactactgc 
atttgtggc tacattttt agcgcaatt ctgttctcc 
ttatccatc cttggatta accgaagac ttgaactcc 
gccccaatc cgaatgaaa aaccccatc gtgaaatac 
ataatcctc atcgacctt ggcgaggtc gcggtcaca 
gttttagcc ggaattcta acaacccct ttcaaactc 
ccctacttt tggaaaatg ttgaccgga ttcggaaaa 
atcgagcaa gtgctgccg ccccaccac gccccagag 
gagaaaaag cgaagtttt tgggctgtc acgattttt 
ctggttttg gccgcaagt gtgattttt ttcgatgtg 
gtggtgtgg ggcttgagt gcgtccgat ttgggcgtt 
tttttcaaa cgctttttg cccgtgtat gtgtcgtat 
ttgctcatt tttgtgcaa caaattccg ttttgtttt 
ttcgtgcgt gttattcgc ctcaaaatt gaggatttg 
aatggggcg ttcagggcc ggactggag cgggtacaa 
aatggggaa aatcagtgg atttcggtc atgaaggtt 
aacaagcaa cccaaggtt atacagggc aaaagtgcg 
ttgagttac gaacgcttg aacgagttt atgaggctg 
gttgaggag attgaggac gtgattgag gcaattaat 
gggttttat ggcgttcac actttgttg attttattc 
agctgtctt ttgcattta gtggtcact ccgtattac 
ctgttaatt gaggtgtgt aacgctggg tatctgcct 
tttattctg cttcaagtt gcttggatt gtgctgcat 
ttgattcgt ttgatggta attgtggaa acttgccaa 
cggtgtata gacgaatat caagtcacc acaaatctg 
gttttgaaa ttattgaca agtcctcta cttccggac 
attaaggaa caagtcgaa attttggct gtgcaagtt 
tcgaacaaa aaaattaag ttttcatcg tttggtatg 
ttgaagatt agtcggtct ctgttaact tcttttgga 
ggtgccctg acgacgttt ttagtcatt ttgtttcag 
tatggtggt attcatggg aatgtttac taa
    mRNA sequence
    • >TC015409 RA
      atttatcaa aaaataatt acatcaagt gtccagtcg 
acctccagc tatgacacc tcacgcttt aatttcctc 
cgatttcca cgacgttat caaaccctt aatcaattt 
aacaaaaat attcggttt cctcccagt ctgctcgag 
ccaaaaggg ccaaaaaac ctgcctcaa cctctcgat 
taactactg catttgtgg ctacatttt tagcgcaat 
tctgttctc cttatccat ccttggatt aaccgaaga 
cttgaactc cgccccaat ccgaatgaa aaaccccat 
cgtgaaata cataatcct catcgacct tggcgaggt 
cgcggtcac agttttagc cggaattct aacaacccc 
tttcaaact cccctactt ttggaaaat gttgaccgg 
attcggaaa aatcgagca agtgctgcc gccccacca 
cgccccaga ggagaaaaa gcgaagttt ttgggctgt 
cacgatttt tctggtttt ggccgcaag tgtgatttt 
tttcgatgt ggtggtgtg gggcttgag tgcgtccga 
tttgggcgt ttttttcaa acgcttttt gcccgtgta 
tgtgtcgta tttgctcat ttttgtgca acaaattcc 
gttttgttt tttcgtgcg tgttattcg cctcaaaat 
tgaggattt gaatggggc gttcagggc cggactgga 
gcgggtaca aaatgggga aaatcagtg gatttcggt 
catgaaggt taacaagca acccaaggt tatacaggg 
caaaagtgc gttgagtta cgaacgctt gaacgagtt 
tatgaggct ggttgagga gattgagga cgtgattga 
ggcaattaa tgggtttta tggcgttca cactttgtt 
gattttatt cagctgtct tttgcattt agtggtcac 
tccgtatta cctgttaat tgaggtgtg taacgctgg 
gtatctgcc ttttattct gcttcaagt tgcttggat 
tgtgctgca tttgattcg tttgatggt aattgtgga 
aacttgcca acggtgtat agacgaata tcaagtcac 
cacaaatct ggttttgaa attattgac aagtcctct 
acttccgga cattaagga acaagtcga aattttggc 
tgtgcaagt ttcgaacaa aaaaattaa gttttcatc 
gtttggtat gttgaagat tagtcggtc tctgttaac 
ttcttttgg aggtgccct gacgacgtt tttagtcat 
tttgtttca gtatggtgg tattcatgg gaatgttta 
ctaaatagt gctaccaaa caccaaata ataaataat 
ttacatgat g

    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