Status
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Gene information
General information
TC001885 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_007416.3: 489352..491825
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
    		TC001885
    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_00308

    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)

    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 embryo/egg with embryonic tissue, no cuticle, but muscle fluorescence - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    larval musculature irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 50
     remarks - cuticles: eggs lost,
    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: 10.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 10.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality early (L5/6) - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection

    pupal molt delayed (still larva) - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection

    adult lethality immediately after eclosion - Number of animals showing the phenotype: 1 (16 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC001885 RA
      MWDSISTDS CDVCQCPPR SKRGDDSCL DKENIQQAL 
SPVKIEELS FYGNSSPPA IICSGTSPN HCNHNIITR 
RPLEDHDPN SRDSGYVAN YNEGKFSTY ASPTRGSFE 
LASIGSMED EFFEDFSDI EPLEDNLPQ DFGKLITGP 
INFQNRKET PTSPRDLVI RPLFRRALS LQTERTPPS 
RVRSCLFKT TESRPFKRP EPPQGFESP NSKKQKIED 
EEAAVPVAR PVLQRCVSA TEESIKFAV QRSFVEPDL 
IGDFSKTFC LPLTQGRHQ DLKCITADT LAKLIRGDF 
SGNVASYKV IDCRYPYEY KGGHIDGAI NVYTKEQCM 
ELLTNVASA SKEPRKRSN ILVFHCEFS SKRGPDLYR 
YLREQDRQL NQDVYPSLH YPEVYLLEG GYKKFFEEY 
SDLCVPIAY TEMLHPEYE NELRHFRLK SKTWNADTR 
QRSGCRHNL KRLGL
    CDS sequence
    • >TC001885 RA
      atgtgggat tcgataagc acggattct tgtgatgtc 
tgccagtgc cccccaaga tcgaaacga ggggacgat 
tcttgtttg gataaagaa aatattcag caagcgtta 
agtccggtc aaaatagaa gagttatcg ttttacgga 
aattcgagt cctccggca ataatctgc tccgggact 
tcaccgaat cactgcaac cacaatata ataactcgg 
cgccccctt gaggaccac gaccccaat tcgcgcgat 
tccggttac gttgctaat tacaatgag ggtaaattc 
tcgacttat gcttccccg actcggggg tcgttcgaa 
ctggcctcg atcgggtcc atggaggac gagtttttc 
gaggatttt tccgatatt gagcccttg gaggacaac 
ttgccgcag gatttcggg aaattgatc actggaccg 
atcaatttc cagaaccgg aaagagaca ccgacttcg 
ccgagggat ctagtaatt cggccctta tttcgaagg 
gctttgtcc ttgcaaact gaaaggacg ccgccaagc 
agggtcagg tcttgcctc ttcaaaaca acagaatct 
cgcccgttt aagagacca gaaccgccg caaggattc 
gaaagccca aattcgaaa aaacagaaa attgaggat 
gaggaagcc gctgttcca gtcgcaagg cctgtgctt 
cagagatgc gtgtctgcg acggaggag agtataaag 
tttgcggtc cagaggtca ttcgtggag ccagacctc 
atcggtgac ttcagcaag acgttttgt ttgccctta 
acgcaaggc cgtcatcag gacttgaag tgcatcact 
gctgacact ttggccaaa ctaatccgt ggtgacttt 
agcggaaac gtcgcctct tacaaagtt atcgattgc 
cggtaccct tacgagtac aagggtggc catattgac 
ggcgccatt aacgtctac accaaggag cagtgcatg 
gaactatta actaacgtc gcctctgcg agcaaggag 
ccgcgcaaa aggagcaat atcctggtt ttccattgc 
gagttttcg agcaagcgg ggtccagat ttatatcgg 
tatttgcgt gagcaggac cgccagctc aaccaggac 
gtctaccct tcgttgcac taccccgaa gtctaccta 
cttgagggt ggctataag aagttcttc gaggaatat 
tccgacctc tgcgttcct atagcctac acggagatg 
ctgcacccg gaatatgag aatgagttg cgacatttc 
cggctcaaa tccaaaacc tggaatgct gatacgcgt 
caacggtcc gggtgccgt cacaatttg aaaagacta 
ggactgtaa
    mRNA sequence
    • >TC001885 RA
      aggataaag actgaggta ggctacctt cacttccaa 
gtcgcgttt gtgtggtgt gcgaggacg tatcgtcct 
ggtttgagt gcttgttgc ttgtgttag attttaaga 
cgttttaag gatatttca ccgctttct tccgacaat 
gtgggattc gataagcac ggattcttg tgatgtctg 
ccagtgccc cccaagatc gaaacgagg ggacgattc 
ttgtttgga taaagaaaa tattcagca agcgttaag 
tccggtcaa aatagaaga gttatcgtt ttacggaaa 
ttcgagtcc tccggcaat aatctgctc cgggacttc 
accgaatca ctgcaacca caatataat aactcggcg 
cccccttga ggaccacga ccccaattc gcgcgattc 
cggttacgt tgctaatta caatgaggg taaattctc 
gacttatgc ttccccgac tcgggggtc gttcgaact 
ggcctcgat cgggtccat ggaggacga gtttttcga 
ggatttttc cgatattga gcccttgga ggacaactt 
gccgcagga tttcgggaa attgatcac tggaccgat 
caatttcca gaaccggaa agagacacc gacttcgcc 
gagggatct agtaattcg gcccttatt tcgaagggc 
tttgtcctt gcaaactga aaggacgcc gccaagcag 
ggtcaggtc ttgcctctt caaaacaac agaatctcg 
cccgtttaa gagaccaga accgccgca aggattcga 
aagcccaaa ttcgaaaaa acagaaaat tgaggatga 
ggaagccgc tgttccagt cgcaaggcc tgtgcttca 
gagatgcgt gtctgcgac ggaggagag tataaagtt 
tgcggtcca gaggtcatt cgtggagcc agacctcat 
cggtgactt cagcaagac gttttgttt gcccttaac 
gcaaggccg tcatcagga cttgaagtg catcactgc 
tgacacttt ggccaaact aatccgtgg tgactttag 
cggaaacgt cgcctctta caaagttat cgattgccg 
gtaccctta cgagtacaa gggtggcca tattgacgg 
cgccattaa cgtctacac caaggagca gtgcatgga 
actattaac taacgtcgc ctctgcgag caaggagcc 
gcgcaaaag gagcaatat cctggtttt ccattgcga 
gttttcgag caagcgggg tccagattt atatcggta 
tttgcgtga gcaggaccg ccagctcaa ccaggacgt 
ctacccttc gttgcacta ccccgaagt ctacctact 
tgagggtgg ctataagaa gttcttcga ggaatattc 
cgacctctg cgttcctat agcctacac ggagatgct 
gcacccgga atatgagaa tgagttgcg acatttccg 
gctcaaatc caaaacctg gaatgctga tacgcgtca 
acggtccgg gtgccgtca caatttgaa aagactagg 
actgtaaat atcgaatcc cagtgccaa aatttgtga 
gatagtaca aaatacaag tgcgcggac ttgtttgcc 
aaatgatat gtacaaagt aatgtgcta tattagcat 
gtatcctga agacttagt cttcttagt gtatattac 
aactgtata taagagagt acctaaata gcttgctcc 
agagtagtt gagatgaga tctttcctt ttgcaatgc 
taaaccacc aaagttttc tttttgtta tttagacag 
tcgacggat catcctggt cccccttta atttatttt 
ttatgtgca atttgaaca gcaataacg atgtgatgt 
tgcatttct ttaccagta cattatgct tccttgctg 
ttgcgctgg tgtttgttt gcagatttt ttatgttca 
ttttattag tttagtata gtctaagtg tcagtattg 
tttttgtat ccttcagca tattcaaat gtgttcgaa 
tgcaacggc tggggattt tatactact tgaatgtga 
tttgttcac tatttggac ggactgatg cttacccat 
ccgttgcat catagattt ttaaagtga tacttaata 
ttatagatc tgtacaata ttttaatat ttttataac 
ttatgataa tacattttt gttccacat

    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