Status
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Gene information
General information
TC009740 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: 7138571..7141297
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
    		TC009740
    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_02848

    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: 40.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 1 (3 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 3 (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): 50% - 80%
    larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    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
     embryo/egg without visible larval cuticle in cuticle preparation - 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%
    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 early (L5/6) - Number of animals showing the phenotype: 3 (11 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC009740 RA
      MILLPESLS AMQKYEKLE KIGEGTYGT VFKAKNRET 
HEIVALKRV RLDDDDEGV PSSALREIC LLKELKHKN 
IVRLYDVLH SDKKLTLVF EHCDQDLKK YFDSLNGDI 
DLDVVKSFM YQLLRGLAF CHSHNVLHR DLKPQNLLI 
NKNGELKLA DFGLARAFG IPVKCYSAE VVTLWYRPP 
DVLFGAKLY TTSIDMWSA GCIFAELAN AGRPLFPGS 
DVDDQLRRI FKLLGTPTE ETWSGMTQL PDYKPFPLY 
QPNMSLSQV VPKLGNRGR DLLQRLLVC NPMGRMSAD 
DAMAHAYFS DLNPAIKND RC
    CDS sequence
    • >TC009740 RA
      atgattctg ctacccgag agcctttcc gcgatgcag 
aaatatgaa aagttggag aaaatcggc gaaggcact 
tacggcacc gtctttaag gcaaaaaac cgcgaaacc 
cacgaaatc gtagctctc aaaagggtg cgcttggac 
gacgatgac gagggggtg ccttcctca gctttacgg 
gaaatatgc ttactgaag gaactcaaa cacaaaaac 
atcgtccgt ttatatgat gttctccac agtgataag 
aaattgact ctagttttt gaacactgt gatcaagat 
ctcaagaag tatttcgat agcttgaac ggtgatatt 
gacttagac gtagttaaa tccttcatg taccagtta 
ctaagaggt ctagcgttc tgccatagt cataatgtg 
ttacacaga gacctgaaa ccacaaaat ttgctcatt 
aacaaaaac ggcgagttg aagttggcc gactttggg 
ctggctagg gcgttcgga atcccggtg aagtgttac 
tcggccgaa gtggtcacc ttgtggtac cggcccccg 
gatgtcttg tttggggcc aaactgtac accacttcc 
attgacatg tggtcagcg gggtgtatt tttgcggaa 
ttggcaaat gccggtcga cccttattc ccgggttcc 
gatgttgat gaccagttg agacggatt tttaaatta 
ctagggacc cccactgaa gaaacttgg agcggaatg 
actcaactt cccgattat aaaccgttt ccgctctat 
cagcctaac atgagttta tctcaggtt gtgcctaaa 
ttagggaac agaggtaga gatcttctg cagagacta 
ctagtttgt aaccccatg ggaaggatg tccgcagac 
gacgctatg gcgcacgct tatttcagt gatttaaat 
ccagcaatt aaaaatgac cgatgctaa
    mRNA sequence
    • >TC009740 RA
      caagtgtca aaaacatca aaacaaaca taacctcca 
aatagtgcc gaaaacctg aattcggtg aatgattct 
gctacccga gagcctttc cgcgatgca gaaatatga 
aaagttgga gaaaatcgg cgaaggcac ttacggcac 
cgtctttaa ggcaaaaaa ccgcgaaac ccacgaaat 
cgtagctct caaaagggt gcgcttgga cgacgatga 
cgagggggt gccttcctc agctttacg ggaaatatg 
cttactgaa ggaactcaa acacaaaaa catcgtccg 
tttatatga tgttctcca cagtgataa gaaattgac 
tctagtttt tgaacactg tgatcaaga tctcaagaa 
gtatttcga tagcttgaa cggtgatat tgacttaga 
cgtagttaa atccttcat gtaccagtt actaagagg 
tctagcgtt ctgccatag tcataatgt gttacacag 
agacctgaa accacaaaa tttgctcat taacaaaaa 
cggcgagtt gaagttggc cgactttgg gctggctag 
ggcgttcgg aatcccggt gaagtgtta ctcggccga 
agtggtcac cttgtggta ccggccccc ggatgtctt 
gtttggggc caaactgta caccacttc cattgacat 
gtggtcagc ggggtgtat ttttgcgga attggcaaa 
tgccggtcg acccttatt cccgggttc cgatgttga 
tgaccagtt gagacggat ttttaaatt actagggac 
ccccactga agaaacttg gagcggaat gactcaact 
tcccgatta taaaccgtt tccgctcta tcagcctaa 
catgagttt atctcaggt tgtgcctaa attagggaa 
cagaggtag agatcttct gcagagact actagtttg 
taaccccat gggaaggat gtccgcaga cgacgctat 
ggcgcacgc ttatttcag tgatttaaa tccagcaat 
taaaaatga ccgatgcta aattttttt attaatttt 
gaaacgtcc attctctag tcataacca attttttta 
ttatgttta tttggagat tataattcg gtgtaaaca 
tagccatct cactttcaa taaacgtac tgaaactga 
ggtgactat ttttcatta ccattggat tttttcgtg 
atgtaaacc atttttata ttgaaataa ttgtaggaa 
taaacaact catttgaat tacattatt tacgaaccc 
ttgcgtatt ttgcgggaa aaattggag aggtgcaga 
taaaatgcg tttttttaa taatttatt acagcaata 
ctaagcaca ataacaaag attaggaga ttgacagga 
cacgtaagt acgacgaaa taagtaact gatatactt 
tggccctta gatatctgg cacacaata tgtttgcat 
ggcaattac gtatttcct atatcgaaa tataactag 
acagttcta tgtttaata aagagaaca tgcactttg 
cactgcata acaatatga aatacatgt tcgacctac 
gaggattcc ctcgggtct gagcatttt aattataca 
caaaaattc aggccggac gttttaaca ctgtaataa 
aatcgcgtg taagtaaac aaaacaaac attaaaaca 
tagcaaaat aaagcacga atctaaaac ctaacacaa 
aaacgtgaa agtatcaca cggaaatac caagagtca 
gtcttttat cacaatgta cactacaaa cttaattaa 
aattcaagt gcaatctga ccaaagcct ttaaaaata 
tttcatcca gggcgaggt tcaccagat ccgattggt 
gagactagc tctaacgat gtaacaccg ctaagtggt 
gactaagtt ttattaaac tttgattaa ggaacatta 
gttcgttta aaaagacag ttatttact tcatctaaa 
aataaagaa cataaacat tctcaaata aaacaacaa 
attgcaaat ttatcactc ggaaaatga ctaatcgac 
gtcaattca atttcagac taataaata tcttaaacc 
tacttaata atttataac atgaatttc atacaaact 
tacaaacgc cataacaac ttagatatt cctaaactg 
ccattacga aatgatttg tctttaata aatcggtat 
ttaaaacac gttcccgtt ttatcattt ttagtttag 
atccacatc ccttgagcc ttgcgttcg aaaataaaa 
caaatacaa ttctgcaag ataattcaa atttttaca 
taatgttat ctagacatt tattattaa tatctaaat 
atagcgcag tgttttaac tgcagatat tttcaatgt 
acactttaa caatttgtt acatctggg acaactttg 
tcagacgac ttctcccct aaaaaatat cttcataaa 
tacttcaac tttgtagct ccacttttg cagcagcgg 
cggcttttt gtttctcga tgtagcgtt ttctggcgc 
tctgaatca aattctctt tgcgtctgt ggagaatct 
tttcgcgct ccgacgaag acttcgaaa atctgctcc 
ccaaactgc tcgtatctt cactgaaaa agcacaatc 
ttcaatatt tctatattg gctatgcaa ccagtaaaa 
cacttctgt caagattaa taattttgt ctccatgca

    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