Status
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Gene information
General information
TC003028 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: 3935892..3945333
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
    		TC003028
    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_03487

    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: 2 (3 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 larval musculature dorsal partiallynot present - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    Comment: longitudinal ventral muscles are affected the most. irregularities of the lateral muscles possibly due to defect in the ventral and dorsal muscles. leg muscles normal
    larval musculature ventral mostlynot present - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    larval musculature sometimesrounded - Penetrance (percentage of animals/eggs on slide): less than 30%
    larval musculature ventral sometimesshortened - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    larval musculature dorsal mostlyshortened - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    larval musculature lateral slightlypattern irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
    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: 100.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 3 (11 dpi)
    Days post injection

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 7 (16 dpi)
    Days post injection


    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 3 (19 dpi)
    Days post injection
    Comment: died with pupal and adult features

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC003028 RA
      MVIVANEPY AETEPMLKT VSSEETPET KFRRNSYAE 
AYKNITSSM KADQLQIED PNLACKLLS TAVNLKNMP 
LAKQCIEIL DRKLDRSNV LSIFSHLSQ CKMPSSNPN 
DFEPSAPPI VENENLRDK DWVQELTDN LRHNCLLEI 
DKNADYVMK QNEVLDLSY NDLLAIITR DTLEVRNEG 
LVYATVLKW ATKECHRRT LQPHMVNIK AVVRELRYA 
PRYGLMSRK EFCSRTIYG EKGPTRSDI LEEKEWRKI 
QFYIKEKSK SRPVEELPH KMSQPRVIG TEKPKLLSS 
QSSIRAMDC PRKKNTRCS SSTTCDRFL LNFLTCWSA 
IFD
    CDS sequence
    • >TC003028 RA
      atggtgatt gtagcgaac gaaccgtac gcagaaacc 
gaaccaatg ctgaagacg gtctcttcc gaggaaacc 
cccgaaacg aaatttaga cgaaactcc tatgccgaa 
gcttacaaa aacatcacc agttcgatg aaagcggac 
caactgcag atcgaggac cccaatctc gcctgcaag 
ctgctgtcc acagcagtc aacctgaag aacatgcct 
ctggcgaag cagtgcatc gagatcctg gaccggaag 
ctcgaccgc agcaacgtc ctctccata ttctcgcac 
ttgtcccag tgcaagatg ccgagctcg aatccgaac 
gacttcgag ccgtcggcg ccccccatc gtggagaac 
gagaatctg agagacaaa gactgggtg caagaactg 
acggataat ctgcgacac aactgccta ctagaaatc 
gacaagaac gccgactat gtgatgaag cagaacgaa 
gtcctggac ttgtcctac aatgacctg ctggccatc 
atcaccaga gacacgctg gaggtgcgc aacgagggc 
ctggtgtac gccacggtg ctcaagtgg gccaccaag 
gagtgccac aggcggacg ctgcagccc cacatggtc 
aacatcaag gccgtggtg cgcgagctg cgctacgcc 
cccaggtac ggtctcatg agcaggaag gagttctgc 
agccggaca atttacggg gagaaaggg cctacgagg 
agcgacatc ctggaggag aaggagtgg cgcaaaatt 
cagttttac atcaaggag aagagcaag agtcggccg 
gtggaggag ttgcctcat aaaatgtcc cagccgcga 
gtcatcggg acggaaaaa ccgaaactt ttgagttcc 
cagagcagt attagggcg atggattgt ccacggaag 
aagaacact cggtgcagt agtagcaca acttgcgac 
aggtttctt ttgaacttt ttgacttgt tggtctgcc 
attttcgac taa
    mRNA sequence
    • >TC003028 RA
      gcaagctca gttgaaacc caccacata gtgaagtgt 
gtcgcttta gcgacccca acaatcacc attgatatt 
atcagtttt cagtgcctt tttaactgg tgactcatc 
acgtaaatg ttcatagac tttatgaaa aatggtgat 
tgtagcgaa cgaaccgta cgcagaaac cgaaccaat 
gctgaagac ggtctcttc cgaggaaac ccccgaaac 
gaaatttag acgaaactc ctatgccga agcttacaa 
aaacatcac cagttcgat gaaagcgga ccaactgca 
gatcgagga ccccaatct cgcctgcaa gctgctgtc 
cacagcagt caacctgaa gaacatgcc tctggcgaa 
gcagtgcat cgagatcct ggaccggaa gctcgaccg 
cagcaacgt cctctccat attctcgca cttgtccca 
gtgcaagat gccgagctc gaatccgaa cgacttcga 
gccgtcggc gccccccat cgtggagaa cgagaatct 
gagagacaa agactgggt gcaagaact gacggataa 
tctgcgaca caactgcct actagaaat cgacaagaa 
cgccgacta tgtgatgaa gcagaacga agtcctgga 
cttgtccta caatgacct gctggccat catcaccag 
agacacgct ggaggtgcg caacgaggg cctggtgta 
cgccacggt gctcaagtg ggccaccaa ggagtgcca 
caggcggac gctgcagcc ccacatggt caacatcaa 
ggccgtggt gcgcgagct gcgctacgc ccccaggta 
cggtctcat gagcaggaa ggagttctg cagccggac 
aatttacgg ggagaaagg gcctacgag gagcgacat 
cctggagga gaaggagtg gcgcaaaat tcagtttta 
catcaagga gaagagcaa gagtcggcc ggtggagga 
gttgcctca taaaatgtc ccagccgcg agtcatcgg 
gacggaaaa accgaaact tttgagttc ccagagcag 
tattagggc gatggattg tccacggaa gaagaacac 
tcggtgcag tagtagcac aacttgcga caggtttct 
tttgaactt tttgacttg ttggtctgc cattttcga 
ctaaagtac tattttgta atctacgga tttttccga 
aatagcact agccatgtc ttgtgatta ccacgtatt 
taatgataa ttaaacgac ggaaggact atcgaaata 
tttagatat gatattcat gtgattctt cttttagct 
ttagttggc tcattgtac gaaccgagt actatttta 
agtacaatt gttgtgttc cgtttttct aattttatt 
gctttaagt ctgtgatgt gtttatagt ttttaatat 
cgttgtttt tcttattat atgattatt atataattg 
aaatttgat atttatggc agaatttta ggctgggcc 
taggcttgt tttatataa agtttctat cactgttgg 
aatttaaat caattatac taatataaa tgtatttta 
tcaagatga aagaagata ggctaagag agatgttgg 
tgttagaaa agtgttgtt accatctgt ttggataga 
tggctgttg attggtaaa ataggccag ttctgttag 
ctgtaacca tattttaag tcaaatttg attgccata 
ttttctcgc ataatacac gtatttctg tatc

    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