Status
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Gene information
General information
TC009563 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: 2583274..2586643
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
    		TC009563
    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
    {{ goGene }}
    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_04656

    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 (11 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 larval musculature random not present - Penetrance (percentage of animals/eggs on slide): less than 30%

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

    head appendages position irregular - Penetrance (percentage of animals/eggs on slide): less than 30%
    head appendages shape irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    head appendages random not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    labrum potentially not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    antenna sometimes not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    head shape irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    head not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    thorax segment random potentiallynot present - Penetrance (percentage of animals/eggs on slide): less than 30%

    thorax shape irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    thorax not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen shape irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    abdomen not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 50% - 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: % (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
    • >TC009563 RA
      MVSNGDNWV RIFDIPDIS KHRKGFTIY KVISMLYPE 
SCPDAITKI TVWKRFNDF KKLHREIKV LHNKLNIKE 
KFPSLPTST YFKRFSDET VQERRQSIL NFLEYVGYH 
SQLFTSSEF VKFFETSHT PVDQLNGNI NAIRADLNL 
PEDPEYCIA NSDDDRTIS DTDSVTTNS DFFADSVPQ 
KTLSKSRLS LSHSHQSKN SDNISISTT TDSITLLDG 
QIYPTPPNT PSCAENYAQ YIIDASIHV NIATELENE 
KKYEDAFTA YKTAIDILL KYGKDDKNY DRRQIVRYK 
TDKYLLRAE KIYNMHLAP EVQSLKRIT ESEENGQNA 
DQYVQRPIS DLYKYKVVR VIASGMLVL HSELQQLFY 
IKVIHKTMK FLNDNLILP ENVPYMVKL CNYYNCENA 
LFLVLEYCS GKALWDYVK CRSEDPSDI FYPNEAQIL 
RQVHDMDLS DPESEHSYS DLINDYASN KGKNSTKCD 
DDDDDYVKV DPGFNRNLM DEPVPSKLP DLLRKSSRK 
FSEMSSFDD LDLAQSLLI PHENIVKWA AQLLLALEK 
VHALGVVCH DLQSRNLLI DDEGDLVLT YMCNVNDVF 
APESLQNVA PEIFSFEPV TTAADWWCY GAILYELLV 
GMPLSEIYP EGLTSHTVL KVPKYVSPE GRSLLRQLL 
TFEPQKRLG FGANGPENL KSHPFFHSV DWEQLLSKY 
NFKV
    CDS sequence
    • >TC009563 RA
      atggtgtcg aatggtgac aactgggtc cgcattttt 
gatatccct gatatcagc aagcaccgg aagggcttt 
accatctac aaagtcatc tcaatgctt tatcccgag 
tcttgcccc gacgcgata acaaaaatt accgtctgg 
aaacgtttc aatgacttt aagaagctc caccgcgaa 
atcaaagtc ttgcacaat aaattgaac atcaaagag 
aagttccct agtttgccc acctccacc tacttcaaa 
aggtttagt gacgagact gtgcaggag agaagacag 
agcattttg aattttttg gaatacgtc ggttatcac 
tctcagttg ttcacttca agcgagttt gttaagttc 
tttgaaacg agtcacacg cctgttgac caactgaac 
ggtaatatt aatgcaatt agagccgat ttaaactta 
cctgaggac cctgaatat tgcatagcc aactctgat 
gatgatcgc acgatcagc gatactgat tcagtaaca 
acaaatagc gattttttt gccgattct gtgcctcaa 
aaaaccctc tctaaatcc cgtttaagc ctcagccac 
tcgcaccaa tccaaaaat tctgataac ataagtata 
tccacgacc actgacagt ataacacta ttggacggt 
cagatttat ccaacgcct cccaatact cccagttgt 
gccgagaat tatgcacaa tatatcata gacgcttca 
attcacgta aatattgcc acggaatta gaaaacgaa 
aagaaatat gaggacgct ttcacggct tataaaacc 
gcaattgat attttgctg aaatatggg aaagacgat 
aaaaattac gataggaga caaatagtg aggtacaaa 
actgataaa tatttactg agggccgaa aaaatttat 
aacatgcat ttggccccc gaagtgcaa agtctgaag 
cgaattacc gaatcggag gaaaacggc caaaacgcc 
gatcaatac gtgcaacga cccatatcc gacttatac 
aaatataaa gtggtccgt gttatagcc tccggaatg 
ttggttttg cattccgag ctccagcaa ctcttttat 
attaaagtt atacacaag actatgaaa tttctgaac 
gacaacttg attttgccc gagaacgtg ccttacatg 
gttaagttg tgcaattat tacaattgc gaaaacgcc 
ttgttttta gtgttagag tactgtagc ggtaaagca 
ctatgggat tacgtgaag tgcaggtct gaggaccct 
tctgatatt ttttacccg aatgaggcg caaatcctg 
cgccaagtg cacgatatg gatctttcc gatccggaa 
tcggagcat agttacagc gatttaatc aacgattac 
gcaagcaac aaaggcaaa aactcgaca aaatgcgac 
gacgacgac gatgattac gtgaaagtc gatccgggc 
tttaataga aacttaatg gacgaacct gtcccgtcc 
aaactcccc gatttatta agaaaatca tcacggaag 
ttcagcgaa atgtcgagc ttcgacgac ttggatctg 
gcacaaagt ctcctcatt ccacacgag aacatcgtc 
aagtgggcg gcgcaactc ctactagcg ttggagaaa 
gtgcacgcc ttgggagtt gtgtgccac gacttgcag 
tctcgcaat ttgttaatt gacgacgag ggcgacctg 
gtgctcacc tacatgtgt aacgtgaac gacgttttt 
gccccagaa agtttacaa aacgtagca ccggaaatt 
ttttctttc gaaccggtt acaaccgcc gccgattgg 
tggtgttat ggcgctatt ttgtacgaa cttttggtc 
ggaatgcct ttgtcagaa atttatcca gaagggtta 
acgagtcat acagttttg aaagttccc aaatatgtg 
tcaccagaa gggcggtct ttgttgagg caacttttg 
acgtttgag ccgcaaaaa cggctaggt tttggggcc 
aatggtcca gaaaattta aaatcgcat ccgtttttt 
cattcagtt gattgggaa caattgctt tcaaagtac 
aattttaaa gtctga
    mRNA sequence
    • >TC009563 RA
      tgtcacttt gacagccgc cttatcgct agcaaaaaa 
tgtgaaatt ttatcaaaa agtcaaaaa atggtgtcg 
aatggtgac aactgggtc cgcattttt gatatccct 
gatatcagc aagcaccgg aagggcttt accatctac 
aaagtcatc tcaatgctt tatcccgag tcttgcccc 
gacgcgata acaaaaatt accgtctgg aaacgtttc 
aatgacttt aagaagctc caccgcgaa atcaaagtc 
ttgcacaat aaattgaac atcaaagag aagttccct 
agtttgccc acctccacc tacttcaaa aggtttagt 
gacgagact gtgcaggag agaagacag agcattttg 
aattttttg gaatacgtc ggttatcac tctcagttg 
ttcacttca agcgagttt gttaagttc tttgaaacg 
agtcacacg cctgttgac caactgaac ggtaatatt 
aatgcaatt agagccgat ttaaactta cctgaggac 
cctgaatat tgcatagcc aactctgat gatgatcgc 
acgatcagc gatactgat tcagtaaca acaaatagc 
gattttttt gccgattct gtgcctcaa aaaaccctc 
tctaaatcc cgtttaagc ctcagccac tcgcaccaa 
tccaaaaat tctgataac ataagtata tccacgacc 
actgacagt ataacacta ttggacggt cagatttat 
ccaacgcct cccaatact cccagttgt gccgagaat 
tatgcacaa tatatcata gacgcttca attcacgta 
aatattgcc acggaatta gaaaacgaa aagaaatat 
gaggacgct ttcacggct tataaaacc gcaattgat 
attttgctg aaatatggg aaagacgat aaaaattac 
gataggaga caaatagtg aggtacaaa actgataaa 
tatttactg agggccgaa aaaatttat aacatgcat 
ttggccccc gaagtgcaa agtctgaag cgaattacc 
gaatcggag gaaaacggc caaaacgcc gatcaatac 
gtgcaacga cccatatcc gacttatac aaatataaa 
gtggtccgt gttatagcc tccggaatg ttggttttg 
cattccgag ctccagcaa ctcttttat attaaagtt 
atacacaag actatgaaa tttctgaac gacaacttg 
attttgccc gagaacgtg ccttacatg gttaagttg 
tgcaattat tacaattgc gaaaacgcc ttgttttta 
gtgttagag tactgtagc ggtaaagca ctatgggat 
tacgtgaag tgcaggtct gaggaccct tctgatatt 
ttttacccg aatgaggcg caaatcctg cgccaagtg 
cacgatatg gatctttcc gatccggaa tcggagcat 
agttacagc gatttaatc aacgattac gcaagcaac 
aaaggcaaa aactcgaca aaatgcgac gacgacgac 
gatgattac gtgaaagtc gatccgggc tttaataga 
aacttaatg gacgaacct gtcccgtcc aaactcccc 
gatttatta agaaaatca tcacggaag ttcagcgaa 
atgtcgagc ttcgacgac ttggatctg gcacaaagt 
ctcctcatt ccacacgag aacatcgtc aagtgggcg 
gcgcaactc ctactagcg ttggagaaa gtgcacgcc 
ttgggagtt gtgtgccac gacttgcag tctcgcaat 
ttgttaatt gacgacgag ggcgacctg gtgctcacc 
tacatgtgt aacgtgaac gacgttttt gccccagaa 
agtttacaa aacgtagca ccggaaatt ttttctttc 
gaaccggtt acaaccgcc gccgattgg tggtgttat 
ggcgctatt ttgtacgaa cttttggtc ggaatgcct 
ttgtcagaa atttatcca gaagggtta acgagtcat 
acagttttg aaagttccc aaatatgtg tcaccagaa 
gggcggtct ttgttgagg caacttttg acgtttgag 
ccgcaaaaa cggctaggt tttggggcc aatggtcca 
gaaaattta aaatcgcat ccgtttttt cattcagtt 
gattgggaa caattgctt tcaaagtac aattttaaa 
gtctgattt tgttaagtg ttcagtatt taggtgcgt 
tgcttatta cattccacg tgttttgtt gcttttgta 
ctaaataaa gttttgtta tctat

    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