Status
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Gene information
General information
TC000393 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_007417.3: 12164000..12168837
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
    		TC000393
    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_06806

    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: 30.0% (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

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

    Adult morphology
    prothoracic odoriferous glands colour darker - Number of animals showing the phenotype: 4 (13 dpi)
    Days post injection


    abdominal odoriferous glands colour darker - Number of animals showing the phenotype: 5 (13 dpi)
    Days post injection


    abdominal odoriferous glands content fragmented - Number of animals showing the phenotype: 5 (13 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
    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
    • >TC000393 RA
      MGLDFIEGQ GEDFERALE STGFGKFHF ALLTICGLI 
YLNTAVGIT IISFVLPSA TCDFEMSSS DKGWLTAAP 
MLGMVIGSY FWGCLADTK GRKTVLIGA LLMDGCCGL 
LSSISQVYW LFMLFRFLN GFAITGAMG ICFPYLGEF 
QPGKYRETI LCWMELFWT LGVIVLPGI AWIIIPMEF 
VYQTDNFKF ASWNLFVAT CSIPSLFIG LWLFFFPES 
PKFLLECGE AEEALEVLK DMYASNTGD SAANFPVIS 
LREKVRTMS VVSQQSTRS IRSLRIRKP KELKLLLRE 
IWEQTKALC KPPHLRYTI ITCLIQFGL TTSYYTLMI 
WFPELFYRF EEFENLHPN EKATVCEVS SVVVPVNMT 
TPSHEEFCG EPIADSVFL HTLIIGLAC IPTSFWLPL 
CVHRLGAKF FLVFSLLVA GAVTFGLYF VNSATSNLV 
LSCIFEALT SLGISTVYC VMVDLFPTN LRVMAAALS 
LTFGRGGAL IGNLLFGFL IDLNCVVPI VLFAAMLLG 
SGLLCLMLP NTGQGALD
    CDS sequence
    • >TC000393 RA
      atgggatta gacttcatc gagggccaa ggcgaagac 
ttcgaaagg gcgctcgag agcacaggt ttcggaaaa 
tttcatttc gccttgttg acaatatgt ggtttaatt 
tatttgaac accgccgtt ggaataaca ataatctcg 
ttcgttctg ccatcggcg acatgcgac ttcgagatg 
tcctcttcg gacaaagga tggctgaca gccgccccc 
atgcttggt atggtgatt ggctcgtat ttctgggga 
tgcctggct gacaccaaa ggacgcaaa acagtatta 
atcggtgcc ttgctcatg gacggctgc tgcggcctc 
ttgtcgagc atttcccaa gtctattgg ctgttcatg 
ctgttcaga ttcctaaac ggatttgcc ataacaggt 
gcaatgggc atctgtttt ccctacttg ggcgaattc 
cagcccggc aagtaccgc gagacgatc ttatgttgg 
atggaactc ttctggact ctcggcgtc attgtcctg 
ccgggaatc gcctggatc ataattcct atggaattt 
gtataccaa actgataat tttaagttt gctagttgg 
aacttgttc gttgccacg tgctcgatc ccgagcctt 
ttcatcgga ctttggctg tttttcttc ccggaaagt 
cccaagttt ctgctggag tgtggcgaa gccgaggag 
gctctcgaa gtcctcaag gatatgtac gcaagtaac 
acgggagac agcgctgcc aattttccg gtgattagt 
ttaagagaa aaagttcgc acaatgagt gtggtgtct 
caacaatcc acgcgcagt attcgtagc ttaaggatc 
cgaaagccg aaagaactt aaactgctt ttgagagaa 
atctgggag cagaccaag gccttgtgc aagccgccg 
catctcaga tataccata attacgtgt ctgatccaa 
ttcggccta actacaagt tactacact ttgatgatt 
tggttcccg gagcttttc taccggttt gaagagttc 
gaaaatctt catccgaac gaaaaagcc acagtgtgt 
gaagtctcc tcggtcgtg gttcctgtc aatatgacc 
acaccatcg cacgaggaa ttctgtggg gaaccaatc 
gccgattcc gtttttctt cacactcta attatcgga 
cttgcttgt attccgaca agcttttgg ttgccgttg 
tgcgtgcac aggctgggg gctaaattt ttcttagtt 
ttcagtcta cttgttgct ggagctgtg acttttggt 
ttgtacttc gtcaactca gcaacgtca aacctggtc 
ctttcgtgt atttttgaa gctctgacc agtttggga 
atcagcacc gtttattgt gtcatggtg gacttgttc 
ccaaccaac ttgagggta atggctgct gctttgtcg 
ctaacgttt ggtcgagga ggtgctctt attggtaat 
ctcttgttc ggctttctc attgatttg aactgcgtc 
gtccctatt gtattattc gcagctatg ttattagga 
agcggcttg ttgtgtcta atgttgcca aacacgggc 
cagggagcg ttggactag
    mRNA sequence
    • >TC000393 RA
      gctgaattt aagacccag atgtgcgct ttaacgtct 
agtaaatta tccacgaga cgatttaac aattcgaat 
aaaagtagc gagaaagaa attagaacg caataattt 
tctccgtga gcataaagt attttaatg gaacattaa 
tgtggtcca aattactac tccataaca caggtgaca 
tgtgtaaac ttaattaat gggattaat ttaaccatc 
gattatttc tatttttag ttgaacttg tcactagac 
ccatcattt ttattatac gactgccac aagcacgga 
tgtcacgag aaagaaaac ttaatccgt cttaagccg 
ccttaaagt ctctaaatt aataagcgc gagtgcgag 
tcgagtgat gggtaaaaa ccccaaccg atgcaaaaa 
tcgaaaata accaatctg ggagtagat gaacttgag 
ataatgact gataatgga catttgacc aatgaaaat 
cggtattat gcgaaggta acgtactgc gggatatga 
tatttacaa tcgcggcta aataatatt attgtactg 
tgagtttct tcgagtgac acctgtaat tattcggat 
tttgtattg gagcgtttg ctgcgacac caacatggg 
attagactt catcgaggg ccaaggcga agacttcga 
aagggcgct cgagagcac aggtttcgg aaaatttca 
tttcgcctt gttgacaat atgtggttt aatttattt 
gaacaccgc cgttggaat aacaataat ctcgttcgt 
tctgccatc ggcgacatg cgacttcga gatgtcctc 
ttcggacaa aggatggct gacagccgc ccccatgct 
tggtatggt gattggctc gtatttctg gggatgcct 
ggctgacac caaaggacg caaaacagt attaatcgg 
tgccttgct catggacgg ctgctgcgg cctcttgtc 
gagcatttc ccaagtcta ttggctgtt catgctgtt 
cagattcct aaacggatt tgccataac aggtgcaat 
gggcatctg ttttcccta cttgggcga attccagcc 
cggcaagta ccgcgagac gatcttatg ttggatgga 
actcttctg gactctcgg cgtcattgt cctgccggg 
aatcgcctg gatcataat tcctatgga atttgtata 
ccaaactga taattttaa gtttgctag ttggaactt 
gttcgttgc cacgtgctc gatcccgag ccttttcat 
cggactttg gctgttttt cttcccgga aagtcccaa 
gtttctgct ggagtgtgg cgaagccga ggaggctct 
cgaagtcct caaggatat gtacgcaag taacacggg 
agacagcgc tgccaattt tccggtgat tagtttaag 
agaaaaagt tcgcacaat gagtgtggt gtctcaaca 
atccacgcg cagtattcg tagcttaag gatccgaaa 
gccgaaaga acttaaact gcttttgag agaaatctg 
ggagcagac caaggcctt gtgcaagcc gccgcatct 
cagatatac cataattac gtgtctgat ccaattcgg 
cctaactac aagttacta cactttgat gatttggtt 
cccggagct tttctaccg gtttgaaga gttcgaaaa 
tcttcatcc gaacgaaaa agccacagt gtgtgaagt 
ctcctcggt cgtggttcc tgtcaatat gaccacacc 
atcgcacga ggaattctg tggggaacc aatcgccga 
ttccgtttt tcttcacac tctaattat cggacttgc 
ttgtattcc gacaagctt ttggttgcc gttgtgcgt 
gcacaggct gggggctaa atttttctt agttttcag 
tctacttgt tgctggagc tgtgacttt tggtttgta 
cttcgtcaa ctcagcaac gtcaaacct ggtcctttc 
gtgtatttt tgaagctct gaccagttt gggaatcag 
caccgttta ttgtgtcat ggtggactt gttcccaac 
caacttgag ggtaatggc tgctgcttt gtcgctaac 
gtttggtcg aggaggtgc tcttattgg taatctctt 
gttcggctt tctcattga tttgaactg cgtcgtccc 
tattgtatt attcgcagc tatgttatt aggaagcgg 
cttgttgtg tctaatgtt gccaaacac gggccaggg 
agcgttgga ctaggatca ctttagttt ttaatattt 
tttcaatta tataacttt gtgataatt gtactttat 
tgacaacaa aatacctga atcgcattc gatttttta 
ggtttaaat gtacgtaca ataatgtaa aatgataat 
tatttttgt taggagaat gttttattt atagttaac 
ttatttact tgtaaactt gtaagatat ttatttata 
tttatttta tatagaaat acagcactt ttctgagcg 
agattgttg tttctgagg gaggttgta gggacaagt 
gccttagat aggactcta tttttttaa taattattg 
ttttaccag catttaggc ccaaacctt cgaaagatt 
tcacaaagt atttcacgc ctaagtttg tgttatcaa 
gtgtacatt cttatttta gtttatctt tatcaactg 
tattacccc aaaacacga ataaaaatt ttacccata 
a

    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