Status
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Gene information
General information
TC002777 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_007418.3: 11605182..11608993
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
    		TC002777
    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_09013

    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: 20.0% (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: 1 (9 dpi)
    Days post injection

    Fertility
    mature egg not present - Number of animals showing the phenotype: 2

    vitellogenic egg chamber late number decreased - Number of animals showing the phenotype: 3
    vitellogenic egg chamber potentially structure degenerated - Number of animals showing the phenotype: 1

    yolk deposition irregular - Number of animals showing the phenotype: 3

    yolk ectopically earlypresent - Number of animals showing the phenotype: 2

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: < 50 larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): more than 80%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 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): 30% - 50%
    cuticle remnants strongly fragmented (cuticle crumbs) - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    larva segment number decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    larva appendages shape irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    larva bristle mostly not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    larva potentially everted (inside-out) - Penetrance (percentage of animals/eggs on slide): less than 30%

    head appendages shape swollen - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    legs segment number decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    legs pretarsus present - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    legs segment potentially fused - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    abdomen segment sometimesnumber decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    abdomen segment shape irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    abdomen tracheal opening mostly not present - 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
    • >TC002777 RA
      MSYQDEEEG GAFDGHASS FPKDFGYGA FDGDHDVNL 
SASGEQKPR ILLMGLRRS GKSSIQKVV FHKMSPNET 
LFLESTNKI VKDDINNSS FVQFQIWDF PGQIDFFDS 
SFDSDMIFG GCGALVFVI DAQDDYMEA LNKLNLTVT 
KAYKVNPSI KFEVFIHKV DGLGDDFKM ESQRDIHQR 
ATDDLADSG YDQIHLSFH LTSIYDHSI FEAFSKVVQ 
KLIPQLPAL ENLLNILNT NSAIEKSFL FDVVSKIYI 
ATDSTPVDM QSYELCCDM IDVVIDVSW IYGQVFSVK 
EEQDPAAFD EQSSSLIKL NNGTVLYLR EVNKFLALV 
CILREDNFD HKGIIDYNF LCFREAIQQ VFELRNKCQ 
GNSLTNSAG SPIVNGNNI LGERHLSPT LTDELGSK
    CDS sequence
    • >TC002777 RA
      atgtcgtat caagatgaa gaggaaggt ggggctttt 
gatgggcat gcaagttcg tttcctaaa gattttggt 
tatggggct ttcgacggg gaccacgac gtgaacctg 
tcggcctca ggggaacag aaacctcga atacttctc 
atggggctc aggagatct gggaaatcg tcgatacag 
aaagtcgtt ttccataaa atgtcccca aacgaaact 
ctcttcctt gaaagtaca aataagata gttaaggat 
gacataaac aactccagt tttgttcag ttccaaatc 
tgggatttc cccggacag attgatttt ttcgattcg 
tcgtttgat tccgacatg atttttggc ggctgtggg 
gcgctagtt ttcgtgata gatgcccaa gacgactac 
atggaagct ctcaataaa ttaaatcta acggttaca 
aaagcctac aaagtgaac ccgtcgata aaatttgaa 
gttttcatt cataaggta gatggctta ggagatgat 
ttcaagatg gagtcgcag agggacatc catcagcga 
gccacagat gacttagcc gactctggt tatgaccaa 
atacacctc agttttcat ttgacgtcg atctacgac 
cactcgatt ttcgaagcg ttctctaaa gtagtgcaa 
aagttgatc cctcagtta ccggccttg gaaaacttg 
ctcaatatt ttaaacacg aattcagcg attgaaaaa 
tcgtttttg ttcgatgtg gtttcaaaa atctacatt 
gcgaccgat tcaaccccc gtcgatatg caaagctac 
gaattgtgc tgcgatatg atcgacgtt gtgattgac 
gtttcgtgg atttatggt caagttttc agtgtcaaa 
gaggaacaa gacccggcc gccttcgac gagcagagt 
tctagtctt attaagtta aataacggt actgttctt 
tatttgagg gaagtcaac aaattcctg gctctagtc 
tgtattttg cgagaggac aatttcgac cacaaagga 
atcatcgac tacaatttt ttgtgcttt cgggaggcg 
atccagcaa gtgtttgaa ttgcgaaat aagtgccaa 
ggtaactcg ttaactaat tccgcaggc agccctata 
gttaatgga aacaatatt ttgggagag aggcattta 
agtcccaca ctaactgat gaactaggt agtaaataa
    mRNA sequence
    • >TC002777 RA
      acgattttg atggcgtcg caagtgtca tatgatgtc 
aaaagttta catttttcc acattttga taatttatg 
cgatgtgta atcaccgtg gcttttaaa tcaacacaa 
acccaaaca tttctcgca aaattcaac aatgtcgta 
tcaagatga agaggaagg tggggcttt tgatgggca 
tgcaagttc gtttcctaa agattttgg ttatggggc 
tttcgacgg ggaccacga cgtgaacct gtcggcctc 
aggggaaca gaaacctcg aatacttct catggggct 
caggagatc tgggaaatc gtcgataca gaaagtcgt 
tttccataa aatgtcccc aaacgaaac tctcttcct 
tgaaagtac aaataagat agttaagga tgacataaa 
caactccag ttttgttca gttccaaat ctgggattt 
ccccggaca gattgattt tttcgattc gtcgtttga 
ttccgacat gatttttgg cggctgtgg ggcgctagt 
tttcgtgat agatgccca agacgacta catggaagc 
tctcaataa attaaatct aacggttac aaaagccta 
caaagtgaa cccgtcgat aaaatttga agttttcat 
tcataaggt agatggctt aggagatga tttcaagat 
ggagtcgca gagggacat ccatcagcg agccacaga 
tgacttagc cgactctgg ttatgacca aatacacct 
cagttttca tttgacgtc gatctacga ccactcgat 
tttcgaagc gttctctaa agtagtgca aaagttgat 
ccctcagtt accggcctt ggaaaactt gctcaatat 
tttaaacac gaattcagc gattgaaaa atcgttttt 
gttcgatgt ggtttcaaa aatctacat tgcgaccga 
ttcaacccc cgtcgatat gcaaagcta cgaattgtg 
ctgcgatat gatcgacgt tgtgattga cgtttcgtg 
gatttatgg tcaagtttt cagtgtcaa agaggaaca 
agacccggc cgccttcga cgagcagag ttctagtct 
tattaagtt aaataacgg tactgttct ttatttgag 
ggaagtcaa caaattcct ggctctagt ctgtatttt 
gcgagagga caatttcga ccacaaagg aatcatcga 
ctacaattt tttgtgctt tcgggaggc gatccagca 
agtgtttga attgcgaaa taagtgcca aggtaactc 
gttaactaa ttccgcagg cagccctat agttaatgg 
aaacaatat tttgggaga gaggcattt aagtcccac 
actaactga tgaactagg tagtaaata aattaaata 
aatgtaaga aataaaaaa atgtacata ggtacgatg 
tgcctttta tttttgtgt acgacttgt tatttttat 
gtttatcgt ttcatatat tttaaaaag tctaaatgt 
atatatagc gtctttcca tgtatcatt ttaagtttt 
gtaagcaca catgttaaa ccaatcgaa acctactct 
cagctaagc tttgtttca ataaattct ttattaccg 
aattgttgt tttcttgaa actaaacca cgaccataa 
gt

    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