Status
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Gene information
General information
TC016023 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.

NW_015451234.1: 0..5413
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
    		TC016023
    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_05943

    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: 60.0% (includes death as pupa, adult)

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

    adult lethality - Number of animals showing the phenotype: 3 (9 dpi)
    Days post injection

    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): less than 30%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): less than 30%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 20
     head size decreased - Penetrance (percentage of animals/eggs on slide): more than 80%

    head appendages partially not present - Penetrance (percentage of animals/eggs on slide): more than 80%

    thorax mostly not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    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
    • >TC016023 RA
      MLPTVQKIK MAQWGTTSE SGILRKNKP KENHDDLLV 
FGYACKLFR DDEKASYID KGHHLIPWM GDDSLKIDR 
YDCRGALSD ISPFEASRE GFDAMRWLG LSDSERKLE 
QLCDKERYY SLHINEEEE QMYKEEEQK RQKANEFQY 
SYDVPANPA PESAPTVAE PEEEDEEYV PSPHLDVPV 
DIAIPKTVK ENIRIEKTA LFVCKQGPQ MEILIKAKQ 
ADNPQFGFL NQGHNLYKY YRHVLAAIK SGRYQVTST 
TKKEEKREE PPEASSTDD HYLHPSLIS TSSSQPDVQ 
TTIPTIPYK PSANCSYSQ LVNRIQGNS QSEGAKPPE 
MTYDQQQYY QYYYAAQYY EYYKQLAQY QQGNGQGAS 
IQPPETHLD PSVQTYIQQ MAYAQYMHN QSSSTNPYA 
QIVSNVSKE MSNPYPTDE KVPKTTEPD AESVETPKS 
TLLLLAQYG SDSEPEEDD SFKTPTGEV QIVIDKMAT 
YVAKNGVQF EEIVKAKGD PRFEFLNES HEFYKYYKN 
KIKLITEGE GSGDKGAGT PPKPKEKKV IAPCASG
    CDS sequence
    • >TC016023 RA
      atgttgcca accgtacaa aaaatcaaa atggcgcag 
tggggcaca acttcagag tcgggtatt ttgcgcaaa 
aacaagccg aaagagaac cacgacgat cttttagtg 
ttcggttat gcgtgtaaa ttgttccgc gatgacgaa 
aaggcctcc tacatcgat aaaggccac catcttatc 
ccgtggatg ggagacgac agtctcaaa attgataga 
tatgactgt cggggcgcc ctgtcggac atatcaccg 
tttgaggcg agtcgggag ggttttgac gccatgcgg 
tggttgggt ttgagtgac tctgagagg aaacttgag 
cagttgtgt gataaggaa cggtactat tcgttacat 
atcaatgaa gaagaggag caaatgtac aaggaggag 
gagcagaag agacagaaa gcgaatgag tttcagtac 
agttatgac gtcccggcg aacccggcg ccagagagc 
gcccccacg gtggcagag cccgaggag gaggacgag 
gagtacgtc ccgtcaccg catttggac gtgccagtt 
gatattgca ataccaaaa accgtcaaa gaaaatatt 
cggatcgag aaaacggcg cttttcgta tgtaaacaa 
gggccccaa atggaaatc ctaatcaag gccaaacaa 
gctgataat ccacaattt ggttttctg aaccaggga 
cacaacttg tacaagtat taccggcac gtgttggcg 
gctatcaaa agtggccgg tatcaagtt acttcaacc 
acaaaaaaa gaggaaaag cgtgaagag ccgcctgaa 
gcaagttcg accgatgat cactacctt cacccaagc 
ttaatatcg acgtcaagc agccaaccg gatgtacaa 
actacaata ccgacaata ccgtacaag ccttcggcc 
aattgttcc tattcacag ttggttaac aggatccag 
ggaaacagc caatcggaa ggcgccaag ccgccggaa 
atgacctac gaccagcag cagtattat cagtattac 
tacgcagct cagtactat gagtattac aagcagctg 
gcgcagtac cagcaaggg aatggacaa ggtgcgagc 
attcaaccg cctgagacg cacttggac cccagcgtt 
caaacctac atccaacag atggcgtac gctcaatac 
atgcacaac caatcatca agcaccaat ccctacgcc 
cagatcgtc tcgaacgtt agtaaagaa atgtcaaat 
ccgtatcca acggacgaa aaagtgcca aaaacaaca 
gaaccggac gccgaaagc gtcgaaacg cccaaaagt 
acgctcctt ctactagct cagtatggt tccgattcg 
gaaccggaa gaagacgac agttttaaa accccaacc 
ggggaagta cagatcgtg attgacaaa atggcaacg 
tacgtggcc aaaaacggc gtccagttt gaggaaatt 
gtcaaggct aagggggat ccccgattt gagtttctc 
aacgaaagt catgaattt tataagtat tacaagaat 
aagatcaag ttgattacg gagggcgag ggcagcggg 
gacaagggg gcggggacg cctcccaaa cccaaggag 
aaaaaagtt atagcaccc tgcgcttcc ggttga
    mRNA sequence
    • >TC016023 RA
      tattcgtaa aattgtcca ttatttggt tttgcgtat 
tgttggttg ccggggcaa ccggcattg tttgtaaaa 
aatgttgcc aaccgtaca aaaaatcaa aatggcgca 
gtggggcac aacttcaga gtcgggtat tttgcgcaa 
aaacaagcc gaaagagaa ccacgacga tcttttagt 
gttcggtta tgcgtgtaa attgttccg cgatgacga 
aaaggcctc ctacatcga taaaggcca ccatcttat 
cccgtggat gggagacga cagtctcaa aattgatag 
atatgactg tcggggcgc cctgtcgga catatcacc 
gtttgaggc gagtcggga gggttttga cgccatgcg 
gtggttggg tttgagtga ctctgagag gaaacttga 
gcagttgtg tgataagga acggtacta ttcgttaca 
tatcaatga agaagagga gcaaatgta caaggagga 
ggagcagaa gagacagaa agcgaatga gtttcagta 
cagttatga cgtcccggc gaacccggc gccagagag 
cgcccccac ggtggcaga gcccgagga ggaggacga 
ggagtacgt cccgtcacc gcatttgga cgtgccagt 
tgatattgc aataccaaa aaccgtcaa agaaaatat 
tcggatcga gaaaacggc gcttttcgt atgtaaaca 
agggcccca aatggaaat cctaatcaa ggccaaaca 
agctgataa tccacaatt tggttttct gaaccaggg 
acacaactt gtacaagta ttaccggca cgtgttggc 
ggctatcaa aagtggccg gtatcaagt tacttcaac 
cacaaaaaa agaggaaaa gcgtgaaga gccgcctga 
agcaagttc gaccgatga tcactacct tcacccaag 
cttaatatc gacgtcaag cagccaacc ggatgtaca 
aactacaat accgacaat accgtacaa gccttcggc 
caattgttc ctattcaca gttggttaa caggatcca 
gggaaacag ccaatcgga aggcgccaa gccgccgga 
aatgaccta cgaccagca gcagtatta tcagtatta 
ctacgcagc tcagtacta tgagtatta caagcagct 
ggcgcagta ccagcaagg gaatggaca aggtgcgag 
cattcaacc gcctgagac gcacttgga ccccagcgt 
tcaaaccta catccaaca gatggcgta cgctcaata 
catgcacaa ccaatcatc aagcaccaa tccctacgc 
ccagatcgt ctcgaacgt tagtaaaga aatgtcaaa 
tccgtatcc aacggacga aaaagtgcc aaaaacaac 
agaaccgga cgccgaaag cgtcgaaac gcccaaaag 
tacgctcct tctactagc tcagtatgg ttccgattc 
ggaaccgga agaagacga cagttttaa aaccccaac 
cggggaagt acagatcgt gattgacaa aatggcaac 
gtacgtggc caaaaacgg cgtccagtt tgaggaaat 
tgtcaaggc taaggggga tccccgatt tgagtttct 
caacgaaag tcatgaatt ttataagta ttacaagaa 
taagatcaa gttgattac ggagggcga gggcagcgg 
ggacaaggg ggcggggac gcctcccaa acccaagga 
gaaaaaagt tatagcacc ctgcgcttc cggttgaag 
aaagtgacg aagaagaga agctcacga ctgaaacaa 
ctgattcag ttacaaaag aagcagaat tgtcaaatg 
atacgtcgg agtctagtc acaaaaacg gggttttt

    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