Status
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Gene information
General information
TC008419 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_007419.2: 10034631..10036279
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
    		TC008419
    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
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    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_04484

    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: 3 (3 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 larval musculature irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     head capsule not present - Penetrance (percentage of animals/eggs on slide): more than 80%

    mandible not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    head appendages size decreased - Penetrance (percentage of animals/eggs on slide): more than 80%
    head appendages partially not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    Comment: maxilla and labium seem to be less affected than the other head appendages.
    prothorax partially 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%
    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: 30.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 30.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 3 (11 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC008419 RA
      MKDIYTVLL ALPLILHNF EITCAPVED DSLILVHVI 
FRHGNRTPS LEEMYPKDP YRNEKYFPF GLGQLTNVG 
KKREFMIGK ALRNRYNKF LGPYYYPEI VEARSTDYN 
RTKMSLELA LAGLFPPRG EEVWNYWLN WQPVPYNYV 
PQANDNVLL GTLCPNFVK KTKEYLQSG REQTELAKY 
REVLDYISE NAGFNVTSF LDVYSLYFG LTTEAEWGF 
ELPEWTQKV YPEPITQLA INEYYTQTA TTELMQMSA 
GYFLQKVIQ DSYSKINNT NSDRKIYMY AAHENNIAD 
LLILLGVFE PPHIPNYGA YVLLELHSV NNKYGIRIF 
YENYQETRP QLLKVPNCD SFCKIDQFA SLYEEYMPD 
PDLCYSV
    CDS sequence
    • >TC008419 RA
      atgaaagac atttacacg gtcttgctg gcactgcct 
ttaattttg cacaacttt gaaatcact tgtgctcca 
gttgaagac gacagccta attctggtc catgtcatt 
ttcaggcat gggaatcga accccatcc cttgaagaa 
atgtacccc aaagacccc taccgaaac gaaaagtac 
ttcccgttt gggttagga caactcact aatgtcggc 
aaaaaacgc gaattcatg attgggaaa gccctcagg 
aaccgatac aataaattt ttagggccg tactactat 
cccgaaatt gtcgaagcg cgaagtacc gactacaac 
aggactaag atgtcgctg gagctcgcc cttgcaggg 
ctgtttccg ccaaggggc gaagaagtt tggaattat 
tggttaaac tggcagccg gttccctac aattacgtc 
cctcaagcc aacgataac gttttgctc gggacattg 
tgcccaaac tttgtgaaa aaaaccaag gagtacctg 
caatctggt cgcgaacag accgaactt gccaaatat 
cgagaagtt ttggactac atttcggaa aacgcagga 
ttcaatgtt acaagtttt ctggacgtg tacagttta 
tatttcggg ttgacaacc gaggcagag tggggtttc 
gaattaccc gaatggacc caaaaagtt taccctgaa 
ccgatcaca caattggcc ataaatgag tactacact 
cagaccgca accaccgaa ctgatgcaa atgtcggct 
ggctatttc ctgcaaaaa gtaatccaa gattcctat 
tccaaaatc aacaacacc aactccgac cggaaaatc 
tacatgtac gcggcccac gagaacaat attgcggac 
cttttgatt ttgttgggg gtgtttgag cctccccac 
ataccgaat tatggggcc tacgtgctt ttggagctt 
cacagtgtg aataacaag tacgggatt aggatattt 
tacgaaaat taccaagag actaggcca caactcttg 
aaggttcca aattgcgac agtttttgc aaaatcgac 
cagtttgcg agtttgtac gaagaatac atgcctgat 
cctgattta tgttacagt gtgtaa
    mRNA sequence
    • >TC008419 RA
      ctttattca ctcgcttgg cgaaattca aaacagtga 
actacaaat tgcacattc gaaaaagtc attcaaggt 
atcaggcac atagtaatt aatatttgc gttaattgg 
cttcagttc ctttgcaaa atgaaagac atttacacg 
gtcttgctg gcactgcct ttaattttg cacaacttt 
gaaatcact tgtgctcca gttgaagac gacagccta 
attctggtc catgtcatt ttcaggcat gggaatcga 
accccatcc cttgaagaa atgtacccc aaagacccc 
taccgaaac gaaaagtac ttcccgttt gggttagga 
caactcact aatgtcggc aaaaaacgc gaattcatg 
attgggaaa gccctcagg aaccgatac aataaattt 
ttagggccg tactactat cccgaaatt gtcgaagcg 
cgaagtacc gactacaac aggactaag atgtcgctg 
gagctcgcc cttgcaggg ctgtttccg ccaaggggc 
gaagaagtt tggaattat tggttaaac tggcagccg 
gttccctac aattacgtc cctcaagcc aacgataac 
gttttgctc gggacattg tgcccaaac tttgtgaaa 
aaaaccaag gagtacctg caatctggt cgcgaacag 
accgaactt gccaaatat cgagaagtt ttggactac 
atttcggaa aacgcagga ttcaatgtt acaagtttt 
ctggacgtg tacagttta tatttcggg ttgacaacc 
gaggcagag tggggtttc gaattaccc gaatggacc 
caaaaagtt taccctgaa ccgatcaca caattggcc 
ataaatgag tactacact cagaccgca accaccgaa 
ctgatgcaa atgtcggct ggctatttc ctgcaaaaa 
gtaatccaa gattcctat tccaaaatc aacaacacc 
aactccgac cggaaaatc tacatgtac gcggcccac 
gagaacaat attgcggac cttttgatt ttgttgggg 
gtgtttgag cctccccac ataccgaat tatggggcc 
tacgtgctt ttggagctt cacagtgtg aataacaag 
tacgggatt aggatattt tacgaaaat taccaagag 
actaggcca caactcttg aaggttcca aattgcgac 
agtttttgc aaaatcgac cagtttgcg agtttgtac 
gaagaatac atgcctgat cctgattta tgttacagt 
gtgtaaaaa taaataaat ttaccaacc tgcccactt 
gttttgtga gtgtcgata aggaaggat ttgctccgt 
ttgcttaat tttgcggtt gagacgaaa gtaaacaaa 
tccagacaa gatgaacat catgcttca agataaaaa 
acctaaagc taacacaga caattaata aatcgtaaa 
ttataat

    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