Status
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Gene information
General information
TC009378 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: 1207296..1240327
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
    		TC009378
    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
    We will use your email address only for possible questions regarding this annotation. We will never show your address or give it away.
    Publish name
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_08594

    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
    number of eggs/embryos/larvae on slide: > 50 embryo/egg with embryonic tissue potentially present, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): 30% - 50%

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

    affected eggs/embryos/larvae - 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%
    cuticle remnants with some identifiable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

    thorax segment number decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    legs podomer number decreased - Penetrance (percentage of animals/eggs on slide): less than 30%
    thorax number decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    abdomen segment number decreased - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen number decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    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: % (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
    • >TC009378 RA
      MDCSVSQAG SILPTLHQP CSPEHHSHH PNDLRTSPG 
SVDCYSSEG DHPLALCLP NSQTLVQAS RTPPPPWSI 
PTKKGTPGL ICVVCGDTS SGKHYGILA CNGCSGFFK 
RSVRRKLIY RCQAGTGRC IVDKAHRNQ CQACRLKKC 
LAMGMNKDA VQNERQPRN TATIRPETL RDMSAEQER 
ALREAAVAV GVFGPPVPL TMALTSARY SHNLLPSVP 
PPLPNREPT PTKDTSDND EESIDVTNE EEDTPSSGC 
GVSSSSGPL RPEPQPALT SGLYPSTHE TIYETSARL 
LFMAVKWAK NLPSFASLP FRDQVILLE EAWSELFLL 
NAIQWCMPL DVSASPLFN VNEHVKNGH SATDVRILA 
DTLMRFKAI HVDPAEFAC LKAIVLFRS ETRGLKDPS 
QIENLQDQA QVMLWQHCR TQLPGQVAR FGRLLLMLP 
LLRIVPASR VEAVFFQKT IGNTPMEKV LCDMYKN
    CDS sequence
    • >TC009378 RA
      atggattgt tcagtgtca caagcaggt tcgattctg 
ccaacccta caccagccg tgttcaccg gaacatcac 
tcacatcac cctaacgat ttgagaaca tcaccagga 
agcgtcgac tgttacagc tcggagggc gatcatccc 
ttggccctt tgcttgccc aactcccaa acgttggtg 
caagcgtcc aggactcca cctcctcca tggagcatc 
ccgaccaag aaagggaca ccgggatta atttgcgtg 
gtgtgtggg gacaccagt tccgggaaa cactacggg 
attctggca tgtaatggg tgttctggg ttcttcaaa 
aggtcggtc cggaggaaa ttgatttac agatgtcaa 
gccggaacc ggtcgctgc atagtggac aaagcccac 
cggaaccag tgccaagct tgccgcctg aaaaaatgc 
ctagcgatg ggaatgaac aaagacgcc gttcaaaat 
gaaaggcaa ccaaggaat acagccacc attcgacca 
gaaactctg cgagacatg agcgctgaa caggagcgg 
gctctgcga gaggccgca gtggctgtg ggggtgttt 
ggccccccg gttccgctg accatggcc ctgacctct 
gcccgctat tcgcacaat ttgctgccc tcagtgccg 
cccccgttg cccaaccga gagcccacc cccacaaaa 
gacaccagt gacaacgat gaagaaagt atagacgtc 
acaaatgaa gaggaagac accccaagc tccggctgc 
ggcgtctcc tccagcagc ggccccctt cggccggag 
ccccagcca gccctaaca tcaggcctc tacccctca 
acccacgaa accatctac gaaacctcg gctcgactt 
ctcttcatg gcggtcaaa tgggccaaa aacttgccc 
agcttcgcc agtttacca tttcgcgat caagtaatt 
ttactggaa gaagcctgg agcgagctc ttcctcctc 
aacgccatc cagtggtgc atgcccctg gacgtgtca 
gccagcccc ctcttcaac gtgaacgaa cacgtgaag 
aacggccac tccgccacc gacgtccgc attctggcc 
gacactctg atgcgtttc aaggcaatt cacgtcgat 
ccggccgaa tttgcctgc ttgaaagcc atagttctg 
ttcagatca gaaacgaga gggttgaaa gatccaagc 
cagatcgaa aacttgcaa gaccaggct caggtgatg 
ttgtggcag cattgtcgg acacagctt cctggccag 
gtggcaagg ttcggtcga ctccttctg atgttgcca 
ctgcttcgg atagtgccg gcgtccagg gtcgaagct 
gtgtttttt caaaaaact atagggaat actccgatg 
gagaaggtt ttgtgcgat atgtacaaa aattga
    mRNA sequence
    • >TC009378 RA
      accctcggc gatagcaaa catcaagtg accactgat 
tgtactgat aagggctat cacagtgtt gcaattagt 
aaatctctg gccgattta gtgaatttt gtatttttt 
ttaaacaca gaactgttc aataaatta attaaattt 
tacgtgtcg tgttttgag ataaatgaa ccgtaaata 
agttagaaa tacctaaaa gttggtctt cgacgggcg 
ccatggatt gttcagtgt cacaagcag gttcgattc 
tgccaaccc tacaccagc cgtgttcac cggaacatc 
actcacatc accctaacg atttgagaa catcaccag 
gaagcgtcg actgttaca gctcggagg gcgatcatc 
ccttggccc tttgcttgc ccaactccc aaacgttgg 
tgcaagcgt ccaggactc cacctcctc catggagca 
tcccgacca agaaaggga caccgggat taatttgcg 
tggtgtgtg gggacacca gttccggga aacactacg 
ggattctgg catgtaatg ggtgttctg ggttcttca 
aaaggtcgg tccggagga aattgattt acagatgtc 
aagccggaa ccggtcgct gcatagtgg acaaagccc 
accggaacc agtgccaag cttgccgcc tgaaaaaat 
gcctagcga tgggaatga acaaagacg ccgttcaaa 
atgaaaggc aaccaagga atacagcca ccattcgac 
cagaaactc tgcgagaca tgagcgctg aacaggagc 
gggctctgc gagaggccg cagtggctg tgggggtgt 
ttggccccc cggttccgc tgaccatgg ccctgacct 
ctgcccgct attcgcaca atttgctgc cctcagtgc 
cgcccccgt tgcccaacc gagagccca cccccacaa 
aagacacca gtgacaacg atgaagaaa gtatagacg 
tcacaaatg aagaggaag acaccccaa gctccggct 
gcggcgtct cctccagca gcggccccc ttcggccgg 
agccccagc cagccctaa catcaggcc tctacccct 
caacccacg aaaccatct acgaaacct cggctcgac 
ttctcttca tggcggtca aatgggcca aaaacttgc 
ccagcttcg ccagtttac catttcgcg atcaagtaa 
ttttactgg aagaagcct ggagcgagc tcttcctcc 
tcaacgcca tccagtggt gcatgcccc tggacgtgt 
cagccagcc ccctcttca acgtgaacg aacacgtga 
agaacggcc actccgcca ccgacgtcc gcattctgg 
ccgacactc tgatgcgtt tcaaggcaa ttcacgtcg 
atccggccg aatttgcct gcttgaaag ccatagttc 
tgttcagat cagaaacga gagggttga aagatccaa 
gccagatcg aaaacttgc aagaccagg ctcaggtga 
tgttgtggc agcattgtc ggacacagc ttcctggcc 
aggtggcaa ggttcggtc gactccttc tgatgttgc 
cactgcttc ggatagtgc cggcgtcca gggtcgaag 
ctgtgtttt ttcaaaaaa ctataggga atactccga 
tggagaagg ttttgtgcg atatgtaca aaaattgaa 
tttaatgtt gttggcgtt taatgtttt caacgaatt 
gttttgtaa gaaaatgaa cgaaaaagc gcacctagg 
actaatttt attcaaatt ttggcacta atttatatt 
cgatcaagc aagctcact ttgactgac gcgttcatg 
tgttaaatt atagaaaat atttaggat gtgtatatt 
actgtttct tatttcatc gaactttgg tgttacgtg 
tatataaac aaaatatat cctgtcttc gtaa

    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