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Gene information
General information
TC003857 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: 23345271..23349865
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
    		TC003857
    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_03637

    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 larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 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: 20.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 20.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection

    Adult morphology
    abdominal odoriferous glands sometimes size increased - Number of animals showing the phenotype: 4 (22 dpi)
    Days post injection


    Fertility
    egg production: number <50% of expected -
    Comment: No ovary phenotype!
    ovary without detectable defects - Number of animals showing the phenotype: 4
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC003857 RA
      MPTPSYSHQ IVFNPLWLT LNSRGHHVT LFTTDPIKN 
ANLSNFRQI DWSFAYQLW HEKHNVSDI IRNFNTNLL 
KCLNQYVEM MNDIIIQEL EHPQVQEII NDKNEHFDL 
VVVEFLNPA MVAFSKRFN CPFIGMSPM DLTNFVHEA 
LGNPISPAL FPDFISRYD GEMNFFERV LNTFYYVGS 
KLYFKYYFY PKIDEIIKE YFGEDVPPL EQMQRNASM 
VFLNTNPII HNIRPLMSN VLMVGGGTH FEGDTPLPE 
DIQKFLDGA ENGAIYFSL GTNVKSKDL DQDTKTTFL 
QVFSELPYK VLWKFEDAK HPKIKLFIT QGGLQSLEE 
AIYNGIPII GMPVYVDQY SNVKRAIRK GMGIILDSN 
NVGKEILKK SIEDILNNE KYKKSAEKL SILLKEQPV 
SGLNQTVKW IEYVLKYKG AKFLKPAQI PTYQYLLID 
VLTFFVALF IFSAYFSFV CLKLLVKCM KERRRVKTT 
KLE
    CDS sequence
    • >TC003857 RA
      atgccaacc ccttcatac agccaccaa atcgtcttc 
aatcccctc tggctcaca ctgaactca agagggcac 
cacgtcacc ttattcacc accgatcca atcaaaaac 
gccaattta tcaaacttt cggcagatt gattggagc 
ttcgcttac caattatgg cacgaaaag cacaacgtc 
agcgacatc ataaggaac ttcaacaca aatttactc 
aagtgttta aaccagtac gtggaaatg atgaacgac 
atcatcata caagagctg gaacatccc caagtccag 
gaaatcatc aatgacaaa aacgaacac tttgatttg 
gtcgtcgtt gagttttta aatcccgca atggtggct 
ttcagtaag agatttaac tgtccgttt attggaatg 
tccccaatg gatttgacc aattttgta catgaagcc 
ttgggtaat ccaatctct ccggctttg ttcccggat 
tttatttct cgctacgat ggcgagatg aattttttt 
gagcgagtc cttaacacg ttctactac gttggaagt 
aaactctat ttcaagtat tatttttac ccgaaaatt 
gatgagatt attaaggag tattttgga gaggatgtc 
cctcctttg gaacagatg caacgcaat gccagcatg 
gtttttctg aacacgaac ccaattatt cacaacata 
aggccccta atgagcaac gtgttaatg gtaggtggg 
ggaacacat tttgaggga gatactccc ctacctgaa 
gatatacaa aaatttttg gacggggct gaaaacgga 
gcgatttat ttcagtctt gggacaaat gttaaaagc 
aaggatttg gaccaagac acgaaaaca acatttttg 
caagtattt tccgaactg ccgtataaa gtgttatgg 
aaattcgaa gacgcaaaa catccaaaa ataaaactc 
ttcattact caaggaggt ctccagtct ttagaggaa 
gcaatttac aacggaatt cccattatt gggatgcct 
gtctatgtt gatcagtat tcaaacgtt aaaagggca 
attcggaaa gggatggga attatcctt gatagtaat 
aacgtgggg aaggaaata ctgaagaag tctatcgaa 
gatatttta aataatgag aagtataaa aaatccgca 
gaaaagttg tcaatttta ttgaaagag caacccgtt 
tctgggctt aatcaaacc gtgaagtgg attgagtat 
gtcttgaaa tataaagga gcgaaattt ttgaaacca 
gctcaaatt ccaacgtat cagtatctc ctgattgat 
gtgttaaca ttttttgta gcattgttt atattctct 
gcttatttt tcgtttgtg tgtttgaaa ttacttgtc 
aagtgtatg aaagaaaga cgtagggtt aaaacaacc 
aagttagaa taa
    mRNA sequence
    • >TC003857 RA
      cgtgtatca agacaagaa atgttgcta aaacaactc 
gttctttcc ctaatttta accaactta attcctccc 
agtgccagt gaccgaatt ttagccata atgccaacc 
ccttcatac agccaccaa atcgtcttc aatcccctc 
tggctcaca ctgaactca agagggcac cacgtcacc 
ttattcacc accgatcca atcaaaaac gccaattta 
tcaaacttt cggcagatt gattggagc ttcgcttac 
caattatgg cacgaaaag cacaacgtc agcgacatc 
ataaggaac ttcaacaca aatttactc aagtgttta 
aaccagtac gtggaaatg atgaacgac atcatcata 
caagagctg gaacatccc caagtccag gaaatcatc 
aatgacaaa aacgaacac tttgatttg gtcgtcgtt 
gagttttta aatcccgca atggtggct ttcagtaag 
agatttaac tgtccgttt attggaatg tccccaatg 
gatttgacc aattttgta catgaagcc ttgggtaat 
ccaatctct ccggctttg ttcccggat tttatttct 
cgctacgat ggcgagatg aattttttt gagcgagtc 
cttaacacg ttctactac gttggaagt aaactctat 
ttcaagtat tatttttac ccgaaaatt gatgagatt 
attaaggag tattttgga gaggatgtc cctcctttg 
gaacagatg caacgcaat gccagcatg gtttttctg 
aacacgaac ccaattatt cacaacata aggccccta 
atgagcaac gtgttaatg gtaggtggg ggaacacat 
tttgaggga gatactccc ctacctgaa gatatacaa 
aaatttttg gacggggct gaaaacgga gcgatttat 
ttcagtctt gggacaaat gttaaaagc aaggatttg 
gaccaagac acgaaaaca acatttttg caagtattt 
tccgaactg ccgtataaa gtgttatgg aaattcgaa 
gacgcaaaa catccaaaa ataaaactc ttcattact 
caaggaggt ctccagtct ttagaggaa gcaatttac 
aacggaatt cccattatt gggatgcct gtctatgtt 
gatcagtat tcaaacgtt aaaagggca attcggaaa 
gggatggga attatcctt gatagtaat aacgtgggg 
aaggaaata ctgaagaag tctatcgaa gatatttta 
aataatgag aagtataaa aaatccgca gaaaagttg 
tcaatttta ttgaaagag caacccgtt tctgggctt 
aatcaaacc gtgaagtgg attgagtat gtcttgaaa 
tataaagga gcgaaattt ttgaaacca gctcaaatt 
ccaacgtat cagtatctc ctgattgat gtgttaaca 
ttttttgta gcattgttt atattctct gcttatttt 
tcgtttgtg tgtttgaaa ttacttgtc aagtgtatg 
aaagaaaga cgtagggtt aaaacaacc aagttagaa 
taaactctt ttttcgtgt acttaattt gataagat

    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