Status
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Gene information
General information
TC009882 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: 12722727..12725561
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
    		TC009882
    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_04718

    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: 10.0% (includes death as pupa, adult)

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

    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): more than 80%

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

    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%
    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: 0.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 0.0% (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC009882 RA
      MAFQNNFKE FLKVAESDH GKEFRELQE AINRSKETA 
KEEKFNREF DRQTVDIRN FYKKIEKSD DAVEVSKGN 
RVTRTLRSS PKKPNLHKG FLQIIHHDP VFSLPIPTN 
PKFKKYSIS LRRKLLSES FTQINKCIA KLAKESLIR 
APLPSPIHP SSNYKLPET SNGIPSGGS FDDLVDQIP 
VENLYVSRS GRQVKRKIY TEQEDVDSD PDFAGIVKK 
NKAEFGDSS TKITLDLPY VPEEDLTEE KTPATCKST 
KPKIPRKNL SISARKPTS RSEAMFDKF IQGEEKRKQ 
QEAEMENFE RTLPSLEDN SEDFVIETS PVKDNEQNF 
LRRRVPPPV PGKKNKRPK KATKQEDPD AITEVVAER 
ASANLPKSA PRTRTPAKV EKPPEEKIS CPICNAEFP 
QSQIENHAS TCGIEDDIV ENLVPTSEA KALQCNICN 
KNFPANSEY EVHVRQCIA SEVLDM
    CDS sequence
    • >TC009882 RA
      atggcgttt caaaataat tttaaggag ttccttaaa 
gtcgcagag tcagatcac gggaaggaa tttagggag 
ctgcaagaa gcgattaac aggtcgaaa gaaacagca 
aaagaagag aaattcaac cgagagttt gaccgacaa 
accgtggac ataaggaac ttttataag aaaatcgaa 
aagtctgat gacgcagtt gaagtttcg aagggaaac 
agagtcacg cgaactctg cggtcttct ccaaaaaaa 
cccaatctg cataaaggg tttctgcaa atcattcac 
cacgaccct gtcttttcc ctcccaatt cccacaaac 
cccaaattt aagaagtac tccatctcg ctgcgcaga 
aaattacta tcagagtcg tttacacag attaataag 
tgcatcgcg aaattagca aaagagtct ctcataagg 
gcccctctg ccttccccc attcatcca tcaagcaat 
tacaagctg cctgaaacc agcaatgga atcccaagc 
ggtggcagc tttgatgac ctagtggat caaattcca 
gttgaaaat ctatacgtt agccgctca ggccgccag 
gttaaacga aaaatttac acagagcag gaggatgta 
gacagcgac cctgacttt gccggcatt gtaaagaaa 
aacaaagcg gaatttgga gactcaagt acaaaaatt 
acattagac cttccttac gttcctgaa gaagatctc 
actgaagaa aagacccct gctacctgc aaatccaca 
aaaccgaaa atcccacga aaaaattta tccataagc 
gccagaaag cccaccagc aggtctgag gcgatgttt 
gacaagttt atacaaggt gaggagaaa aggaagcag 
caagaagca gaaatggag aattttgaa agaacgctc 
ccatctttg gaggacaac tctgaagac ttcgtaatt 
gagacgagt ccagtcaaa gataacgaa cagaacttt 
ttgaggagg agggtgcct cccccagtt ccgggtaaa 
aaaaacaag aggccgaaa aaagccacc aaacaagaa 
gatcctgac gcaattaca gaagtcgtt gcagaaaga 
gcgagcgca aaccttccg aaaagtgca ccgagaacc 
agaactccc gcaaaagtt gaaaaaccg ccagaggaa 
aaaattagt tgtcccatt tgtaacgcg gaattccca 
cagagtcaa attgagaat cacgcctcc acgtgtggc 
attgaagac gacattgtt gaaaatctc gttcccaca 
tctgaggca aaagctttg cagtgcaac atctgcaac 
aagaatttt cctgcaaac tccgagtac gaggttcat 
gtgaggcag tgtatagcg tcggaagtg ttagacatg 
tga
    mRNA sequence
    • >TC009882 RA
      ttaacctga aaaaatgag tgcgtctgt gtttttgtg 
ttcgaaaat aattgaaat ttacattta actttggca 
attgttgtg ttattattg tagtcaaac aatggcgtt 
tcaaaataa ttttaagga gttccttaa agtcgcaga 
gtcagatca cgggaagga atttaggga gctgcaaga 
agcgattaa caggtcgaa agaaacagc aaaagaaga 
gaaattcaa ccgagagtt tgaccgaca aaccgtgga 
cataaggaa cttttataa gaaaatcga aaagtctga 
tgacgcagt tgaagtttc gaagggaaa cagagtcac 
gcgaactct gcggtcttc tccaaaaaa acccaatct 
gcataaagg gtttctgca aatcattca ccacgaccc 
tgtcttttc cctcccaat tcccacaaa ccccaaatt 
taagaagta ctccatctc gctgcgcag aaaattact 
atcagagtc gtttacaca gattaataa gtgcatcgc 
gaaattagc aaaagagtc tctcataag ggcccctct 
gccttcccc cattcatcc atcaagcaa ttacaagct 
gcctgaaac cagcaatgg aatcccaag cggtggcag 
ctttgatga cctagtgga tcaaattcc agttgaaaa 
tctatacgt tagccgctc aggccgcca ggttaaacg 
aaaaattta cacagagca ggaggatgt agacagcga 
ccctgactt tgccggcat tgtaaagaa aaacaaagc 
ggaatttgg agactcaag tacaaaaat tacattaga 
ccttcctta cgttcctga agaagatct cactgaaga 
aaagacccc tgctacctg caaatccac aaaaccgaa 
aatcccacg aaaaaattt atccataag cgccagaaa 
gcccaccag caggtctga ggcgatgtt tgacaagtt 
tatacaagg tgaggagaa aaggaagca gcaagaagc 
agaaatgga gaattttga aagaacgct cccatcttt 
ggaggacaa ctctgaaga cttcgtaat tgagacgag 
tccagtcaa agataacga acagaactt tttgaggag 
gagggtgcc tcccccagt tccgggtaa aaaaaacaa 
gaggccgaa aaaagccac caaacaaga agatcctga 
cgcaattac agaagtcgt tgcagaaag agcgagcgc 
aaaccttcc gaaaagtgc accgagaac cagaactcc 
cgcaaaagt tgaaaaacc gccagagga aaaaattag 
ttgtcccat ttgtaacgc ggaattccc acagagtca 
aattgagaa tcacgcctc cacgtgtgg cattgaaga 
cgacattgt tgaaaatct cgttcccac atctgaggc 
aaaagcttt gcagtgcaa catctgcaa caagaattt 
tcctgcaaa ctccgagta cgaggttca tgtgaggca 
gtgtatagc gtcggaagt gttagacat gtgaaatgt 
gatattgaa cattgttac aaaagtgtc atacttaag 
ccattcaaa taaaattag tcatctggt ctaactttg 
catcggctg aattgaatt gaaaccgag atgactgta 
aatattttg tgttatcat acttgtagt ttatattta 
tctaacatt ctcctagag tcagttata aagttacta 
gtgttaaaa tatttttgt attactcta atgaatatt 
atgttttct tatc

    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