Status
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Gene information
General information
TC003998 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: 28917148..28921285
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
    		TC003998
    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
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    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_03667

    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: 50.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 4 (3 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection

    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%

    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: 80.0% (includes death as larva, prepupa, pupa, adult)

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

    eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 5 (16 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC003998 RA
      MELDYQMAL ILQHRFEQE AGQTEQSDS ELAKQLQEQ 
FEQEAAVEQ PPSSLVYHQ PKKGSDSTK SLIDPSWEL 
VDPTPDIHN LFIAFDQRF FWNKLVAVC VSWSKKMTS 
CAGICSYSG RGGLCSITL SEPLLKLRP RKDLVETLL 
HEMIHAYLF VTHNNRDRD GHGPEFHKH MYRINNEAG 
TSITVYHNF HDEVRLYQQ HWWRCDGPC QHRKPFFGM 
VRRATNRAP GPNDRWWAE HLRTCGGTF IKVKEPEKK 
KQEKKNETK SVKSKDIRD FMGGNVKGF KDLKNGVVR 
GKSNSSSTI VVTKNTKTS ETTFKPTIF NASTSTILK 
TETNSFRAS TSTKPSDDY VAVRNHWAN KFNNANKRQ 
SSEESSTVS KIPKLFGSS PTSTQKNPN SGEFCECPV 
CNQRVLMAD LNQHLDQCL LKSPEERDA ESVDLTDSF 
HEEEDTKEC PLCTKEIVT SKFDTHVEK CLMEVYNGV 
EEKLAVPKA QEETVSCLA CGKKIVKSE LNSHLDECM 
VDIFDDEES KDKEVCDKN NSQFNCPFC LKLVEESEM 
KEHIDGCLM ADNLAEAFA DDDF
    CDS sequence
    • >TC003998 RA
      atggagctg gactaccaa atggcgctc attttgcag 
cacaggttt gaacaagaa gctgggcaa accgaacag 
tctgattct gagttggcc aaacaattg caagaacag 
ttcgaacag gaggctgca gttgaacag cccccttct 
agtcttgtc tatcaccag cctaaaaag gggtccgac 
tcgaccaaa tcactcata gacccctca tgggagctc 
gtggacccc acccccgac atacacaac ctgttcata 
gcttttgac caacgtttt ttttggaat aaattggtg 
gcggtttgt gtctcttgg agcaagaaa atgacttcg 
tgtgctggc atttgctcg tatagtggc agagggggg 
ctttgtagt atcaccttg agtgaaccg ttacttaaa 
ttaaggccc aggaaagac ttagttgag actcttctt 
catgaaatg attcacgct tatttattt gtaacccat 
aataataga gacagggat gggcacggg cccgagttt 
cataaacac atgtaccgg atcaataac gaggcaggg 
actagtatt accgtttac cataacttc catgatgaa 
gttcgttta tatcagcaa cactggtgg cgctgtgac 
ggaccttgt cagcaccgg aagcccttt tttggcatg 
gtcagaagg gccacaaat agggctccg gggcccaat 
gataggtgg tgggcagag catttaagg acttgcggt 
ggaaccttt attaaagtc aaagaaccg gaaaagaag 
aaacaggag aagaagaat gaaacgaaa agtgtgaag 
agtaaagat attagagat tttatgggt ggtaatgtt 
aaaggtttc aaagacttg aaaaatggc gttgttagg 
ggaaaaagc aactcatca agcactata gtagtcact 
aaaaacact aaaactagt gaaactact ttcaaaccg 
acgattttt aatgccagt actagtact attttgaag 
actgaaaca aatagcttt cgtgctagt actagtact 
aaaccgagt gatgattat gtagctgtt cgaaatcat 
tgggccaac aaattcaat aatgccaat aaaagacaa 
tcatccgaa gaatcatca actgtttcc aaaattccg 
aaattgttt gggtcttcg cctactagc acccaaaaa 
aatcccaat tctggtgaa ttttgtgaa tgtcctgtt 
tgtaatcaa agggtgctg atggctgat ttgaaccaa 
catctcgat cagtgtttg cttaaatca ccggaagaa 
agagatgca gaaagtgtt gatcttact gattctttc 
catgaggag gaagataca aaagaatgt ccactttgt 
accaaagaa attgtaact tccaaattt gacactcat 
gttgaaaag tgcctaatg gaggtttat aacggagtt 
gaggaaaag ttggctgtt ccaaaagcc caagaagaa 
acggtttcg tgtttggct tgtggtaaa aaaatcgta 
aaaagtgaa cttaattcg catttggat gagtgtatg 
gttgatatt ttcgatgat gaggaaagt aaagataag 
gaagtttgt gataagaat aattcgcag tttaattgt 
ccattttgt ttgaaactg gtggaagag agcgaaatg 
aaggaacat attgatggg tgtttgatg gctgataat 
ctcgccgag gcttttgca gatgatgat ttttga
    mRNA sequence
    • >TC003998 RA
      attttacag ctaaaacgc ctcaagaca acgatcagg 
ggccgtttt tgaggttag gatggagct ggactacca 
aatggcgct cattttgca gcacaggtt tgaacaaga 
agctgggca aaccgaaca gtctgattc tgagttggc 
caaacaatt gcaagaaca gttcgaaca ggaggctgc 
agttgaaca gcccccttc tagtcttgt ctatcacca 
gcctaaaaa ggggtccga ctcgaccaa atcactcat 
agacccctc atgggagct cgtggaccc cacccccga 
catacacaa cctgttcat agcttttga ccaacgttt 
tttttggaa taaattggt ggcggtttg tgtctcttg 
gagcaagaa aatgacttc gtgtgctgg catttgctc 
gtatagtgg cagaggggg gctttgtag tatcacctt 
gagtgaacc gttacttaa attaaggcc caggaaaga 
cttagttga gactcttct tcatgaaat gattcacgc 
ttatttatt tgtaaccca taataatag agacaggga 
tgggcacgg gcccgagtt tcataaaca catgtaccg 
gatcaataa cgaggcagg gactagtat taccgttta 
ccataactt ccatgatga agttcgttt atatcagca 
acactggtg gcgctgtga cggaccttg tcagcaccg 
gaagccctt ttttggcat ggtcagaag ggccacaaa 
tagggctcc ggggcccaa tgataggtg gtgggcaga 
gcatttaag gacttgcgg tggaacctt tattaaagt 
caaagaacc ggaaaagaa gaaacagga gaagaagaa 
tgaaacgaa aagtgtgaa gagtaaaga tattagaga 
ttttatggg tggtaatgt taaaggttt caaagactt 
gaaaaatgg cgttgttag gggaaaaag caactcatc 
aagcactat agtagtcac taaaaacac taaaactag 
tgaaactac tttcaaacc gacgatttt taatgccag 
tactagtac tattttgaa gactgaaac aaatagctt 
tcgtgctag tactagtac taaaccgag tgatgatta 
tgtagctgt tcgaaatca ttgggccaa caaattcaa 
taatgccaa taaaagaca atcatccga agaatcatc 
aactgtttc caaaattcc gaaattgtt tgggtcttc 
gcctactag cacccaaaa aaatcccaa ttctggtga 
attttgtga atgtcctgt ttgtaatca aagggtgct 
gatggctga tttgaacca acatctcga tcagtgttt 
gcttaaatc accggaaga aagagatgc agaaagtgt 
tgatcttac tgattcttt ccatgagga ggaagatac 
aaaagaatg tccactttg taccaaaga aattgtaac 
ttccaaatt tgacactca tgttgaaaa gtgcctaat 
ggaggttta taacggagt tgaggaaaa gttggctgt 
tccaaaagc ccaagaaga aacggtttc gtgtttggc 
ttgtggtaa aaaaatcgt aaaaagtga acttaattc 
gcatttgga tgagtgtat ggttgatat tttcgatga 
tgaggaaag taaagataa ggaagtttg tgataagaa 
taattcgca gtttaattg tccattttg tttgaaact 
ggtggaaga gagcgaaat gaaggaaca tattgatgg 
gtgtttgat ggctgataa tctcgccga ggcttttgc 
agatgatga tttttgatt gttaattat ttttgtttt 
tttttatgc caaatatac atacttttt ctaa

    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