Status
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Gene information
General information
TC006543 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_007423.3: 11267690..11269943
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
    		TC006543
    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
    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
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_04166

    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: 2 (3 dpi)
    Days post injection

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

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

    larval musculature fluorescence decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 50
     larva partially everted (inside-out) - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): less than 30%
    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
    • >TC006543 RA
      MGETTVVQG VGKCPKLPW MVEFHSTAD GKIFNNQLD 
AAFAPTFLE HLARLQEKS RVRRKRLTQ FSVIIPPRI 
SIEHIEEFL KAGMTVALI RMDYFTVDE IEEMVAMIR 
NVVDDFGKK IGRVYPIAI GLDVSEQEI KTGKLLKPL 
KEIELEKGQ TTKIVAKPE FANRVSKEF IYVNYENIA 
DVVKPGDSL IIGDDNIRM SAIEVARDI INCIIEKAG 
LLTDNLSVK LPNVPITLP KTESHEKLI QIKEKCEID 
IVFVGPSKL DMVKETLGP TVLIIAKLE YASSVDFFD 
SLVKKSDGV IIDGEKLMA TSKERVFLV QKSVIANCN 
KLGKPVLAA INCHAVTKS IVNDIANTV IDGIDGLLL 
PPDPDLIES ISLICKAAE GAVYQKRLF DDLVSLKPP 
PIEPIISIA ISAVEASFK SNAAAIILI TTTGRSAKL 
ISSFRPRCP VIALTRFGR IAKQLMIYK GVIPIFYVQ 
KTGDTFKEN VEKSIQLGM TFGKVNGYI RMGDAVVVV 
FGTRNNVGF KNCMEVVFA SEYDTIPDD DEDL
    CDS sequence
    • >TC006543 RA
      atgggcgag accacggtc gtccaaggc gtcggcaag 
tgccccaaa ctgccctgg atggtggaa ttccactca 
accgccgac ggaaaaatc ttcaacaat cagctggac 
gcggcgttc gcgcccacg tttctggaa cacttggcc 
cgccttcag gagaaaagc cgcgtgcgg aggaagcga 
ttgacccaa ttttcggtc ataatcccg cccaggatt 
tccatcgaa cacatcgag gagttccta aaggcggga 
atgaccgtc gctttgatc cgaatggac tatttcacc 
gtggacgag atcgaggag atggtggcg atgatcagg 
aacgtggtg gacgacttt ggcaaaaaa atcggacgg 
gtctacccc attgccatc ggcttggac gtctcggaa 
caggagatc aagaccggg aaactgctc aaaccactg 
aaagagatt gaactggaa aaagggcaa accaccaaa 
attgtggcc aagcccgag ttcgccaac cgggtcagc 
aaggagttt atttacgtc aattatgag aacattgcc 
gatgttgtc aagcctggg gatagtctg atcatcggt 
gatgataac attaggatg tcggcgatt gaagttgcc 
agggatatt atcaattgt atcatcgag aaagctggg 
cttttaacc gacaatctc tcggttaag ttacccaac 
gttcccata actttaccc aagactgaa tcgcacgaa 
aagttgatt caaatcaag gaaaaatgc gaaattgat 
attgttttc gtgggaccg tctaaactg gacatggtt 
aaagaaact ttaggcccc actgtcctc attatcgcc 
aaacttgag tacgcgtcc tctgttgat ttcttcgac 
tctttggtg aaaaaatcc gatggtgtt ataatcgac 
ggcgagaaa cttatggca acgtccaaa gaacgtgtt 
tttttggtc caaaaatca gtcattgcc aattgcaat 
aaactgggc aagcctgtc ctagcggcg atcaattgc 
cacgcagtc accaaatcg atagtcaac gacattgcc 
aacaccgta atcgacgga atcgacggc ttgttgcta 
cccccagac cccgactta atcgagtcc atttcacta 
atttgtaaa gctgcagaa ggtgccgtt taccagaaa 
cgccttttc gatgacctg gttagtctg aaaccgcct 
cccattgaa ccaatcatc tcaatagcc atatcagcc 
gtcgaagct tcgttcaaa agtaacgcg gctgcgatt 
attctgatt acgacgacg ggacgttcg gcgaaattg 
atttcctcc ttcaggccc aggtgccca gtcatcgcc 
ctgaccagg ttcgggcgc atcgccaaa cagctcatg 
atctacaaa ggcgtgatc ccgattttc tacgtccag 
aagacgggc gatacgttc aaggagaac gtggagaag 
agcatccag ctggggatg acgtttggc aaagtgaac 
ggctacatc aggatgggg gacgcggtc gtggttgtg 
ttcgggacg cggaataac gtggggttc aagaactgc 
atggaggtg gtgttcgcg tctgaatac gacacgatt 
cccgacgac gacgaagac ttgtag
    mRNA sequence
    • >TC006543 RA
      tttgacaac atttgacac gaaccgatc aaaattctc 
agtaaaaat gggcgagac cacggtcgt ccaaggcgt 
cggcaagtg ccccaaact gccctggat ggtggaatt 
ccactcaac cgccgacgg aaaaatctt caacaatca 
gctggacgc ggcgttcgc gcccacgtt tctggaaca 
cttggcccg ccttcagga gaaaagccg cgtgcggag 
gaagcgatt gacccaatt ttcggtcat aatcccgcc 
caggatttc catcgaaca catcgagga gttcctaaa 
ggcgggaat gaccgtcgc tttgatccg aatggacta 
tttcaccgt ggacgagat cgaggagat ggtggcgat 
gatcaggaa cgtggtgga cgactttgg caaaaaaat 
cggacgggt ctaccccat tgccatcgg cttggacgt 
ctcggaaca ggagatcaa gaccgggaa actgctcaa 
accactgaa agagattga actggaaaa agggcaaac 
caccaaaat tgtggccaa gcccgagtt cgccaaccg 
ggtcagcaa ggagtttat ttacgtcaa ttatgagaa 
cattgccga tgttgtcaa gcctgggga tagtctgat 
catcggtga tgataacat taggatgtc ggcgattga 
agttgccag ggatattat caattgtat catcgagaa 
agctgggct tttaaccga caatctctc ggttaagtt 
acccaacgt tcccataac tttacccaa gactgaatc 
gcacgaaaa gttgattca aatcaagga aaaatgcga 
aattgatat tgttttcgt gggaccgtc taaactgga 
catggttaa agaaacttt aggccccac tgtcctcat 
tatcgccaa acttgagta cgcgtcctc tgttgattt 
cttcgactc tttggtgaa aaaatccga tggtgttat 
aatcgacgg cgagaaact tatggcaac gtccaaaga 
acgtgtttt tttggtcca aaaatcagt cattgccaa 
ttgcaataa actgggcaa gcctgtcct agcggcgat 
caattgcca cgcagtcac caaatcgat agtcaacga 
cattgccaa caccgtaat cgacggaat cgacggctt 
gttgctacc cccagaccc cgacttaat cgagtccat 
ttcactaat ttgtaaagc tgcagaagg tgccgttta 
ccagaaacg ccttttcga tgacctggt tagtctgaa 
accgcctcc cattgaacc aatcatctc aatagccat 
atcagccgt cgaagcttc gttcaaaag taacgcggc 
tgcgattat tctgattac gacgacggg acgttcggc 
gaaattgat ttcctcctt caggcccag gtgcccagt 
catcgccct gaccaggtt cgggcgcat cgccaaaca 
gctcatgat ctacaaagg cgtgatccc gattttcta 
cgtccagaa gacgggcga tacgttcaa ggagaacgt 
ggagaagag catccagct ggggatgac gtttggcaa 
agtgaacgg ctacatcag gatggggga cgcggtcgt 
ggttgtgtt cgggacgcg gaataacgt ggggttcaa 
gaactgcat ggaggtggt gttcgcgtc tgaatacga 
cacgattcc cgacgacga cgaagactt gtagtaata 
aattgtttt gaactttct ggcttttaa tttggcgga 
aaaggtcac atgtcaagt taacgtttc aatcagagg 
accctcggt gcagttacg acaaccaca ataaaattc 
ctaaaccgt gacaaagct ggttgccat tatcattca 
tgttttaat atggggatg acatatgtg acgtgggaa 
atttgtcaa gtcgaacaa gtctgtccg attttgttt 
aatttcgct taaaacgat ttttcaaag tctggtggc 
ggttttcta aagaaagta aaactggaa ataatcaat 
tcatttcgg agtttaaaa ctgaataag tgagtgcgt 
caacagtcc atcaccgcg tttattgtg acaacttgg 
gctagttta acctacttt caaaccaac tttacgact 
cggcccagc caaaagtgt cccaaattc tggtttatg 
gttgaccta atgaaatag aaattttcc cgaaactgt 
caagacggc cataaatct agtttcgtt ttcaatggt 
ctgatttta cgagctaat tgggcgcta ctgggaatt 
tgttcaaga atcatcttt cacttttaa caacaaaaa 
gaactaaac aatcctgca aaca

    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