Status
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Gene information
General information
TC005884 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_007423.3: 6023275..6028671
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
    		TC005884
    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_04029

    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)

    adult lethality immediately after eclosion - 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

    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 50
     head capsule size decreased - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    head appendages shape irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    head irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    legs podomer shortened - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    thorax irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    abdomen segment number decreased - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    abdomen irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): 50% - 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: 20.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 30.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection

    eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 1 (16 dpi)
    Days post injection

    Fertility
    egg production: number no/almost no eggs -
    egg chamber number decreased - Number of animals showing the phenotype: 3

    tropharium shape irregular -

    mature egg not present -

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC005884 RA
      MSELVVGID LGTTNSCIA VERNGKIEV IPNREGNRT 
TLSYVYYGE DSILVGKTA KYMASANPS NGIYEIKRL 
IGCLHDDPD IESERKSLN YELVRGTNG EILIQVEQN 
SEKFHTLPE EVCARILHR LKIDAEMYL GQKVSKAVV 
TVPAYFNNN QRAATRDAA RIAGFEVLK LVNEPSAAA 
LAYVRENRI KNGRVILIY DLGGGTFDV SIVRTENGT 
IKVLSVDGD THLGGQDFL NRLVDHVVD YVQTKHGIK 
VRENKRLMM NILNSCEKT KKILTSANR TVIPLEFSG 
HFDQLEVTR EQFEELNRD LFAKTVKIL DNCIRNRRM 
SKEEIDEVL LVGGSSRIP RIETLLKAY FDKPIQRNI 
NADEAIAIG AALEAHHFA QTHHNSLLI DVLPLSIGT 
VFDEETIFF NFARNTPLP ANSKHVHVF KNRKQKNCI 
LSVYEGGHL DCNKNVLLG AHEIKWTAT TKKNRNVEI 
TMQINNYGI IWVTARGES IKTFSIALN KGRLEDDEI 
RKLSRGLQV S
    CDS sequence
    • >TC005884 RA
      atgtctgaa ttggtggtc ggaattgac ttaggaaca 
acgaattct tgtattgcc gttgaacga aacggtaaa 
atcgaggta ataccgaat cgcgaaggc aacagaacc 
acgttatcg tacgtttat tatggcgaa gacagcatc 
cttgttggc aaaacggcc aaatacatg gccagcgcc 
aatccatca aacggcatt tacgagatc aaaagactg 
atcggctgt ttgcacgac gaccctgat atcgaatcc 
gagcgcaaa tcgctaaat tatgagttg gtccgcggc 
accaacggc gagattttg atccaagtc gagcaaaac 
tcggagaaa tttcacact ttaccggag gaagtgtgc 
gccaggatc ctccaccgt ctgaaaatc gacgctgaa 
atgtacctt ggacagaaa gtgagcaaa gcggtggtc 
accgtcccc gcgtacttc aacaacaat caaagggca 
gcgactcgg gacgccgcc agaatcgcc ggcttcgaa 
gtgctgaag ctggtgaac gaacctagt gctgccgct 
ctggcctac gtccgcgaa aatcgcatc aaaaacggc 
cgagttatc ctaatttac gacctgggt ggtggcacc 
tttgatgtg tccattgtc cggacagag aacggaaca 
atcaaagtg ctatcagtc gacggtgac acgcatcta 
ggaggccag gattttctg aaccgcctt gtagaccac 
gtggtcgat tacgtgcaa accaaacac gggataaaa 
gtgcgcgaa aacaaacgc ttgatgatg aacattttg 
aattcgtgc gagaaaacc aaaaaaatt ctgacaagt 
gcaaaccga accgtcatc ccgctggaa ttcagcggc 
cacttcgac cagttggaa gtcacacgt gaacagttc 
gaggagcta aaccgcgat ctcttcgcc aaaacggtc 
aaaatcctc gacaactgc atcaggaac cgacgaatg 
agcaaggag gaaattgac gaggttttg ctagtcgga 
ggctcctcg aggattccc cggattgaa accctcctc 
aaagcctac ttcgacaaa cccatccag cgcaacatc 
aacgccgac gaggccatc gccataggg gcggccctt 
gaagcccac catttcgcc caaacccac cacaattcg 
ctcctaatt gacgtgctt ccactttca atagggacg 
gttttcgac gaagagacc atttttttc aatttcgcg 
cgcaacacg ccgctccca gccaactcc aaacacgtc 
catgttttc aaaaatcgc aaacaaaag aactgtatt 
ttgtcggtg tacgagggg gggcatttg gattgcaat 
aaaaacgtc ctgttgggg gcgcacgaa atcaaatgg 
acggccaca acgaaaaag aacagaaat gtcgaaatt 
acgatgcaa attaacaat tatgggatt atttgggtg 
acggcgaga ggcgagtcg attaagacg ttcagcatt 
gcgctgaat aagggacga cttgaagac gacgaaatt 
cggaaattg agccgagga ttgcaagtc tcgtaa
    mRNA sequence
    • >TC005884 RA
      gtaaaaaat aattattat aataaacta caaacaagc 
tatgataac gcaattatt tcgcagaat tttgttgaa 
aacaaatgt acctgatac ctccgaaac agtgcgcac 
aacgttgta aaaataaat tgcccccgc gcaattgcc 
caacatttt aaatattta ggtatcgat aaaaatcga 
gataagata aaatcaaaa caatcaacg attaatctc 
agttttttt cgcgaaaat gtctgaatt ggtggtcgg 
aattgactt aggaacaac gaattcttg tattgccgt 
tgaacgaaa cggtaaaat cgaggtaat accgaatcg 
cgaaggcaa cagaaccac gttatcgta cgtttatta 
tggcgaaga cagcatcct tgttggcaa aacggccaa 
atacatggc cagcgccaa tccatcaaa cggcattta 
cgagatcaa aagactgat cggctgttt gcacgacga 
ccctgatat cgaatccga gcgcaaatc gctaaatta 
tgagttggt ccgcggcac caacggcga gattttgat 
ccaagtcga gcaaaactc ggagaaatt tcacacttt 
accggagga agtgtgcgc caggatcct ccaccgtct 
gaaaatcga cgctgaaat gtaccttgg acagaaagt 
gagcaaagc ggtggtcac cgtccccgc gtacttcaa 
caacaatca aagggcagc gactcggga cgccgccag 
aatcgccgg cttcgaagt gctgaagct ggtgaacga 
acctagtgc tgccgctct ggcctacgt ccgcgaaaa 
tcgcatcaa aaacggccg agttatcct aatttacga 
cctgggtgg tggcacctt tgatgtgtc cattgtccg 
gacagagaa cggaacaat caaagtgct atcagtcga 
cggtgacac gcatctagg aggccagga ttttctgaa 
ccgccttgt agaccacgt ggtcgatta cgtgcaaac 
caaacacgg gataaaagt gcgcgaaaa caaacgctt 
gatgatgaa cattttgaa ttcgtgcga gaaaaccaa 
aaaaattct gacaagtgc aaaccgaac cgtcatccc 
gctggaatt cagcggcca cttcgacca gttggaagt 
cacacgtga acagttcga ggagctaaa ccgcgatct 
cttcgccaa aacggtcaa aatcctcga caactgcat 
caggaaccg acgaatgag caaggagga aattgacga 
ggttttgct agtcggagg ctcctcgag gattccccg 
gattgaaac cctcctcaa agcctactt cgacaaacc 
catccagcg caacatcaa cgccgacga ggccatcgc 
cataggggc ggcccttga agcccacca tttcgccca 
aacccacca caattcgct cctaattga cgtgcttcc 
actttcaat agggacggt tttcgacga agagaccat 
ttttttcaa tttcgcgcg caacacgcc gctcccagc 
caactccaa acacgtcca tgttttcaa aaatcgcaa 
acaaaagaa ctgtatttt gtcggtgta cgagggggg 
gcatttgga ttgcaataa aaacgtcct gttgggggc 
gcacgaaat caaatggac ggccacaac gaaaaagaa 
cagaaatgt cgaaattac gatgcaaat taacaatta 
tgggattat ttgggtgac ggcgagagg cgagtcgat 
taagacgtt cagcattgc gctgaataa gggacgact 
tgaagacga cgaaattcg gaaattgag ccgaggatt 
gcaagtctc gtaacccac atgcgacgc ctatggctg 
ccgttggta tggaaatag cgaaaaatc catggttac 
aacgtttgt tggcatgga aatgttgaa attttgatt 
gttgatgca gtggcgtca catcctgcg ctcttatta 
tttaaataa aatataaaa tataagtgg tcgtttcag 
tagaattag ttttatccc acgcaataa tcaaaaacg 
aatgcgttt tcatttatt tttcaagaa cttgtagaa 
caaggagtt gtttgtctc gattcagct cgactgtaa 
ataaaattt tatgaaaaa t

    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