Status
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Gene information
General information
TC009249 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: 2493847..2496134
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
    		TC009249
    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_06264

    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

    Fertility
    mature egg deposition blocked number 1st lateral oviduct: number 2nd lateral oviduct: -

    Comment: Mature eggs seem to be stored in the egg chamber and not able to get into oviduct. Potentially held egg.
    lateral oviduct potentially irregular - Number of animals showing the phenotype: 4
    vitellogenic egg chamber late number increased - Number of animals showing the phenotype: 4

    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)

    potentially confused/crosscontaminated with: adults of..., iB # (comma separated)
    Pupal morphology
    oblique dorsal thoracic muscles shortened - Number of animals showing the phenotype: 10

    longitudinal dorsal thoracic muscles not present - Number of animals showing the phenotype: 10

    Comment: Eye and mandible well-developed unlike muscle pattern.
    potentially confused/crosscontaminated with: adults of..., iB # (comma separated)
    Adult morphology
    prosternal process potentially shortened - Number of animals showing the phenotype: 10


    elytra dorsal not closed - Number of animals showing the phenotype: 3


    elytra potentially surface irregular - Number of animals showing the phenotype: 10


    potentially confused/crosscontaminated with: adults of..., iB # (comma separated)
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC009249 RA
      MLDGWYCRS MANAASLAE EEERSQEES 
KFKKEYKFL KRKFHNLVY ENEALMQAL 
RAAQKRLLS VTRDRTFLL DRLLLHEKV 
DNSTSESEE TDSSDDGEP LKVEPPAKK 
RKLENSFNN GPGKVLPTV KKKRNPAPR 
PAKAIPHHT LVHMPGGST GNILSDGHM 
TPEEVERHL QAQNYVELV PERAPPTVP 
TEMFSNEPS LDSESNDIG ELETSPSNM 
GEELSIDMI PE
    CDS sequence
    • >TC009249 RA
      atgctggac gggtggtat tgccgttca atggcgaac 
gcggcgagc ctggccgaa gaggaggag cggtcccag 
gaggagtcc aagttcaaa aaagagtac aaattcctc 
aaacgcaag ttccacaat ctagtttac gaaaatgag 
gctctcatg caagcgctc cgcgccgcc cagaagcgc 
ctcctttcg gtgacacgc gaccgaacg tttctcctg 
gaccgcctc ctcctgcac gaaaaggtg gacaactcc 
acgtcggaa tcggaagaa acagactct tcggacgac 
ggggagccc ctcaaagtc gagcctccg gccaaaaag 
agaaaattg gaaaattcg ttcaataac gggccgggc 
aaagtgtta ccaacggtg aaaaagaag cgaaacccg 
gcccccagg cccgccaag gccatacca caccacacg 
ttagtgcac atgccgggg ggctccact gggaatatt 
ttatccgat gggcacatg acccccgag gaggtggaa 
aggcattta caggcacaa aattatgtg gaattggtg 
cccgaaagg gcgcccccc accgtcccc acggaaatg 
ttcagtaat gagccctca cttgacagt gaatcaaac 
gatattggc gagctcgag acttcaccc agtaacatg 
ggagaggag ctaagcatt gatatgata ccagaataa
    mRNA sequence
    • >TC009249 RA
      aaacgcgtg gttgtttaa tgcaagttt tgaccaaaa 
cgccgccaa ttgtggcgg taaaacttg caaagtgtg 
gctctgtca ttaataaat ttgttcggt ttttgcgat 
ttttggcca ttctggtga ctggggtgc cgcccgatt 
ggcaatagt cgtaacctc aaactgtca ctgtaatta 
acaaaacaa acaataatt ttgcgataa aattgttaa 
caatgctgg acgggtggt attgccgtt caatggcga 
acgcggcga gcctggccg aagaggagg agcggtccc 
aggaggagt ccaagttca aaaaagagt acaaattcc 
tcaaacgca agttccaca atctagttt acgaaaatg 
aggctctca tgcaagcgc tccgcgccg cccagaagc 
gcctccttt cggtgacac gcgaccgaa cgtttctcc 
tggaccgcc tcctcctgc acgaaaagg tggacaact 
ccacgtcgg aatcggaag aaacagact cttcggacg 
acggggagc ccctcaaag tcgagcctc cggccaaaa 
agagaaaat tggaaaatt cgttcaata acgggccgg 
gcaaagtgt taccaacgg tgaaaaaga agcgaaacc 
cggccccca ggcccgcca aggccatac cacaccaca 
cgttagtgc acatgccgg ggggctcca ctgggaata 
ttttatccg atgggcaca tgacccccg aggaggtgg 
aaaggcatt tacaggcac aaaattatg tggaattgg 
tgcccgaaa gggcgcccc ccaccgtcc ccacggaaa 
tgttcagta atgagccct cacttgaca gtgaatcaa 
acgatattg gcgagctcg agacttcac ccagtaaca 
tgggagagg agctaagca ttgatatga taccagaat 
aataataat ttataaagc aaacagtgt ataaagtaa 
tttattcgc cgctgtcag tactttcat actgactat 
cgtcactat cctcactta gttcgacac tgacgttat 
tttcttgca tccgaacgt atttttcga tggtttctt 
gcagtcttc gatcgccta agactctac tttcttgca 
acttggctt tcagttctt ggtctttgt tggctgggt 
cttcgttga gcgcaataa agccgcagt ggacttcgt 
acagttctt tctttcgtt tcatttgaa gcaaatttc 
ccattttag tgaaacaat tcttgcttt cctccctta 
tctcatttt ccgacaaac ccaaattgt gttcgttga 
cacacttcc ttatacact tttcaatgt cgcgatacg 
tcgggaaat tattacgtt tgtacgact ttgtaaccg 
cccgattta tttcgttat agttcgagt gaacgaatt 
taattttct cgtgcaaaa gccgcccag caaacggat 
ttcgttgca aaagctcgc agtacttct tataaactt 
tgctcagtc tgtcggtat aacggtcca gcttcatgt 
aggtcgaat cctcctcat cgttaaaat ccacttcgg 
cctcctcca acctcttga taaccctca acaattttt 
tcaaagtct tctccaact tgcggattt tgtggagat 
tctcctccg ggacttcga cactgtcgc ccttgatgt 
ggtccaaca aatacgagt agagcctct ggaagctca 
ccaccgctt cgggggcag aggctttgg cgctctccg 
tgaagtcct gcaaggttt tatggaagc tggggtcct 
ggtggattt cctcgcact tgttgaagc ttttgcgca 
ttttttggt acttgggga agacccgat cggcgtatt 
tcgaccctt tcattgatt tggtgcaaa cgtcgagga 
actcctcca caagggtgt gcgcttccg aagccttgg 
aggttgagg gtctgatga ttatttcga aattttggg 
gctcagtct tcggttctg gggtgacct ggagcgggt 
cctccgtct ccgattcgg agcccacaa ccaggcatt 
cgccattgg tcgattttt caactttgg ggcttgtct 
cagcgattt tttcggcaa tttgaggct catcgtcga 
tgaggttaa ctatattgg tttcgttct ctttgccta 
aaaaaaaaa aaaaacatt taggaaacg gggactgta 
acggaaaat gattcactt ttttcgtgg attacgatg 
gttatgttg ttttcctcc ttgtaattg attttgagc 
ttcgt

    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