Status
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Gene information
General information
TC003642 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: 10268953..10274969
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
    		TC003642
    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
    {{ goGene }}
    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_00596

    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: 0.0% (includes death as pupa, adult)

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg with embryonic tissue, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): more than 80%

    embryo/egg not developed/not fertilized - 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): more than 80%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     egg without cuticle embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): more than 80%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - 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: 30.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 40.0% (includes death as larva, prepupa, pupa, adult)

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

    adult lethality - Number of animals showing the phenotype: 1 (19 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC003642 RA
      MLGRQKLKY EAVDSDDEP PSDFEEKKR GFFNNNCFW 
SSLFTSVLI GTYYIPSIC LTFYQRWLF QTFHFPLVT 
VLVHMIVKF LLAALIRAV LERRQGKQR VMLEWREYL 
VAVAPMGVF SGLDIGFSN WGLELIKVS LYTMTKSTT 
VVFILGFSM LFKLEKKSW SLALIVGMI TTGLILFTY 
KATQFDTLG FLLLLLASM SSGVRWTCV QLLLQKSKI 
GMRNPIDMI YHMQPWMII SVLPFAIWM EGPSVVKNC 
QLIRTTDTS IIITMIFKI LLGAFIAFF MEVCEVLVV 
GYTSSLTLS IAGVVKEVF ILVLAVEWN GDQLSPINV 
VGLLICLSG ITCHVFHKL RNTPKVARV YEVHDERRE 
LGEHLIVSE DGHVSSDND EKNDTQVLF DILRNRDR
    CDS sequence
    • >TC003642 RA
      atgttgggc cgtcaaaaa ttaaaatac gaagctgtg 
gacagcgac gatgagccc ccgagtgat ttcgaggaa 
aagaaacgt ggttttttc aacaataat tgcttttgg 
tccagttta tttacaagt gttttgatt ggaacttac 
tacattcct tccatatgt ttgacgttc tatcagcga 
tggcttttc cagacattc cattttccg ttagtcacg 
gttttggtt catatgatt gtcaaattt ctactagct 
gcgctaatc agggctgtg ttggagcga agacagggc 
aaacaaagg gttatgttg gagtggagg gagtatctg 
gtcgcagtg gcccccatg ggggtcttc agtggccta 
gacataggc ttctctaat tggggctta gaactcatt 
aaagtctca ttatataca atgaccaag tccacgaca 
gttgtgttt attttggga ttttcgatg ctatttaag 
cttgaaaaa aagtcatgg agtcttgcc cttatcgtt 
gggatgatc acaacggga ttaatcctc tttacttac 
aaagcgacc caatttgac actttgggc tttttgttg 
cttttattg gcctcgatg tctagtgga gtgagatgg 
acttgcgtc caactcctc ctccagaag tccaaaatc 
gggatgaga aaccccatc gatatgatc taccacatg 
cagccgtgg atgatcatc tcagtccta ccatttgcc 
atatggatg gaaggcccc tcagttgta aaaaattgc 
caactgata cgcaccaca gacacctca ataataatc 
acaatgatt ttcaaaatt ttactcggg gcctttatc 
gcatttttc atggaagtg tgcgaagtc ctagtggtg 
ggctacacc tcaagtctc acgctctcc atcgctgga 
gttgttaaa gaagtgttt atcctagtc ttagccgta 
gaatggaac ggggaccaa ctatcgccc atcaacgtt 
gttggcttg cttatttgt ctctctgga atcacgtgc 
catgttttc cacaagttg aggaacact ccgaaggtg 
gcacgtgtg tatgaggtg cacgacgag cgacgcgag 
ctgggtgag catttaata gtcagtgaa gatggacac 
gtgtcgagt gataacgac gagaagaac gacacgcaa 
gtactgttc gatattttg cgcaatcgg gacaggtag
    mRNA sequence
    • >TC003642 RA
      tcaaacgtc actcggtcc tgtcaactt gtcacaaaa 
cagaaaaaa agtgaaata aaccaaaaa aagtgcatt 
tattccacg tctacggaa aatgtgacc ttatcatgg 
attttccgc gccacgaaa ccttatctt cgcccacaa 
accacagta aaatcccta tcaacatgt aaacaagat 
gttgggccg tcaaaaatt aaaatacga agctgtgga 
cagcgacga tgagccccc gagtgattt cgaggaaaa 
gaaacgtgg ttttttcaa caataattg cttttggtc 
cagtttatt tacaagtgt tttgattgg aacttacta 
cattccttc catatgttt gacgttcta tcagcgatg 
gcttttcca gacattcca ttttccgtt agtcacggt 
tttggttca tatgattgt caaatttct actagctgc 
gctaatcag ggctgtgtt ggagcgaag acagggcaa 
acaaagggt tatgttgga gtggaggga gtatctggt 
cgcagtggc ccccatggg ggtcttcag tggcctaga 
cataggctt ctctaattg gggcttaga actcattaa 
agtctcatt atatacaat gaccaagtc cacgacagt 
tgtgtttat tttgggatt ttcgatgct atttaagct 
tgaaaaaaa gtcatggag tcttgccct tatcgttgg 
gatgatcac aacgggatt aatcctctt tacttacaa 
agcgaccca atttgacac tttgggctt tttgttgct 
tttattggc ctcgatgtc tagtggagt gagatggac 
ttgcgtcca actcctcct ccagaagtc caaaatcgg 
gatgagaaa ccccatcga tatgatcta ccacatgca 
gccgtggat gatcatctc agtcctacc atttgccat 
atggatgga aggcccctc agttgtaaa aaattgcca 
actgatacg caccacaga cacctcaat aataatcac 
aatgatttt caaaatttt actcggggc ctttatcgc 
atttttcat ggaagtgtg cgaagtcct agtggtggg 
ctacacctc aagtctcac gctctccat cgctggagt 
tgttaaaga agtgtttat cctagtctt agccgtaga 
atggaacgg ggaccaact atcgcccat caacgttgt 
tggcttgct tatttgtct ctctggaat cacgtgcca 
tgttttcca caagttgag gaacactcc gaaggtggc 
acgtgtgta tgaggtgca cgacgagcg acgcgagct 
gggtgagca tttaatagt cagtgaaga tggacacgt 
gtcgagtga taacgacga gaagaacga cacgcaagt 
actgttcga tattttgcg caatcggga caggtagtc 
gcgagtttt cttcatgac tggatagta cttaaggaa 
atgtgggtg tgagtcacc cagattttt taatttaat 
acttttata acaacataa gattatgtt ttgtgatat 
tgtgtaatt taaggctaa gtgtatgtg tgacaatgt 
gattgtttt ttattgagt gaggggtaa ggttgcgat 
gtcgctaaa gttacgtct ttttttaat tattcttct 
actggacga ttttaaaag ccggtaata aaattttcg 
aatctccct taaaaaaaa tttcttgtc cattttggt 
gaaactttg gacaatttt aaggaagtt ttgagctcc 
acctgtgta aaatgttcc gaggagttg ataaaatta 
gacatttta cgagttatg aatggattt aactttaac 
acaagtgca ttagctcat actccaaac atgcactat 
tatccgaac acttcataa taattattt tttcaaaaa 
ttgaatata ctttgaata gacttatac tgtatattt 
tgttataca tgaagtact agcgagttt ataaaataa 
atctttaaa tagtgaaat atttaaggt agtacttta 
ataagcatt tacttttta ttactacta attactagt 
aattttcgt actcaagtc ttaatagct gttagctat 
tcggccgtt attatatat atttttttg aaaatggct 
taattttta aatatcaac ttaatgtca aacgctcaa 
ggcaatcta atagttgct gccatgtta cactcattg 
gtcacaagt tgtcctcat ggtcaccac actgcattc 
ccattggtc acaagcctg ataatcaaa aatctgtat 
ggtaaaaaa ttttcatta aagtacaga ttacagaca 
ttttatcaa ccaaataaa gcatgggag tagaa

    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