Status
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Gene information
General information
TC002880 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: 7546996..7549017
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
    		TC002880
    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
    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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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_06954

    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

    adult nutritional state bad (cachectic) - Number of animals showing the phenotype: 4 (11 dpi)
    Days post injection

    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
    • >TC002880 RA
      MSLSQKHYG KVLVPWFNT AEWKAVYNL IYSETGQDW 
PKALSILKI WKLRTPLLS SGVEGTLIV LEALLVNTN 
LLSSYETSH IFCTSLVRF LNLCAANSA KQGTFYKTA 
IKNDLPKWL IGLRHDIAH SHNVPPLSM LELGLKFCL 
GWLKGKYWD VQCDNMADF VVEKATGNG IEDAFYILE 
NLGENGVHE NIKLMKKIN NFVGEAQKQ TSCKKMQEY 
VLNRLRKEI TTNKEASVG ALCKLLIDD LTILSIQIE 
IDESGVKRI PPDYLNKWN KLFGGMYEA QIMPDFIYK 
LFNFVCDDR NDLLHREVA SLWIKEIFL ALINQQNND 
KNIAVLSFS SHNNSLKDK HLVTEVLER LTPFTPNFA 
REVLIYNNA PVELIEDSL CLMSAFDTH SATTNGKIF 
TVDDLDLIE ETFNDVRDV PTQSKSRWT LIEDTSLFL 
NLPLGVLPH QDRNKSPLL DV
    CDS sequence
    • >TC002880 RA
      atgtctttg tcgcagaaa cactacgga aaagtgtta 
gtcccctgg tttaacaca gcggaatgg aaagccgtc 
tacaattta atttactcg gaaacaggc caggactgg 
ccgaaggcc ttgtccatt ttaaaaatc tggaagctc 
cgaacgccc ttattatca tcaggggtg gagggaacc 
ctcatagtc ctggaagcc cttctcgta aacacaaat 
cttctgtct tcgtacgaa actagccac attttttgc 
acctctctg gtccgtttc ttaaacttg tgtgctgcc 
aacagcgcc aaacaaggc acgttttat aaaactgcg 
ataaagaat gatttgcca aagtggctg attggtttg 
agacatgat atcgcccac agtcacaac gttccacct 
ttgtcgatg ttagaattg ggtcttaag ttttgtttg 
ggttggttg aaagggaaa tactgggac gtgcagtgt 
gacaacatg gctgatttt gtggttgag aaagcgaca 
ggcaatggt attgaggat gcgttttat attttggaa 
aatctgggc gagaatgga gtgcacgaa aatattaaa 
ttaatgaag aagattaat aatttcgtg ggggaagca 
cagaaacag accagttgc aaaaaaatg caagaatat 
gtgctaaat agattgcgg aaagaaata acaactaat 
aaagaagca agtgttggt gcactttgt aaattactg 
attgatgat cttacaatt ttgtcaatt cagatagag 
attgatgag tcaggggtt aaaagaatt ccgcctgat 
tatttaaat aaatggaat aaattattc ggtggtatg 
tacgaagca caaataatg cctgatttt atttacaaa 
ctatttaac ttcgtgtgt gacgacaga aacgatttg 
ttacacaga gaagttgca agtttatgg atcaaagaa 
attttttta gccctcatt aatcaacaa aataatgat 
aaaaatata gctgttttg tcgttctca agtcacaat 
aattctttg aaagacaaa catttagta acagaagtg 
ctggaaaga ctaacccct ttcactcca aattttgct 
agagaggtt ttaatttac aacaacgct cctgttgaa 
ttaattgag gattcactt tgcctcatg tctgcattt 
gatacacac agtgccacc actaatggg aaaattttt 
acagttgat gatttagat ttaattgaa gaaactttt 
aatgatgta agggacgtg ccaacgcaa tcaaaatcg 
cgctggact ttaattgaa gatacaagt ttgttcctt 
aatttgccc ttaggagtc ttgccccat caagacaga 
aataaaagt cctcttcta gatgtatga
    mRNA sequence
    • >TC002880 RA
      atattttta atttttcgt aaaaatgtg gtcttgtaa 
ttttgtctt caattaaac ttgagctag ttagagaca 
gttaaagag atcaacaat gtctttgtc gcagaaaca 
ctacggaaa agtgttagt cccctggtt taacacagc 
ggaatggaa agccgtcta caatttaat ttactcgga 
aacaggcca ggactggcc gaaggcctt gtccatttt 
aaaaatctg gaagctccg aacgccctt attatcatc 
aggggtgga gggaaccct catagtcct ggaagccct 
tctcgtaaa cacaaatct tctgtcttc gtacgaaac 
tagccacat tttttgcac ctctctggt ccgtttctt 
aaacttgtg tgctgccaa cagcgccaa acaaggcac 
gttttataa aactgcgat aaagaatga tttgccaaa 
gtggctgat tggtttgag acatgatat cgcccacag 
tcacaacgt tccaccttt gtcgatgtt agaattggg 
tcttaagtt ttgtttggg ttggttgaa agggaaata 
ctgggacgt gcagtgtga caacatggc tgattttgt 
ggttgagaa agcgacagg caatggtat tgaggatgc 
gttttatat tttggaaaa tctgggcga gaatggagt 
gcacgaaaa tattaaatt aatgaagaa gattaataa 
tttcgtggg ggaagcaca gaaacagac cagttgcaa 
aaaaatgca agaatatgt gctaaatag attgcggaa 
agaaataac aactaataa agaagcaag tgttggtgc 
actttgtaa attactgat tgatgatct tacaatttt 
gtcaattca gatagagat tgatgagtc aggggttaa 
aagaattcc gcctgatta tttaaataa atggaataa 
attattcgg tggtatgta cgaagcaca aataatgcc 
tgattttat ttacaaact atttaactt cgtgtgtga 
cgacagaaa cgatttgtt acacagaga agttgcaag 
tttatggat caaagaaat ttttttagc cctcattaa 
tcaacaaaa taatgataa aaatatagc tgttttgtc 
gttctcaag tcacaataa ttctttgaa agacaaaca 
tttagtaac agaagtgct ggaaagact aaccccttt 
cactccaaa ttttgctag agaggtttt aatttacaa 
caacgctcc tgttgaatt aattgagga ttcactttg 
cctcatgtc tgcatttga tacacacag tgccaccac 
taatgggaa aatttttac agttgatga tttagattt 
aattgaaga aacttttaa tgatgtaag ggacgtgcc 
aacgcaatc aaaatcgcg ctggacttt aattgaaga 
tacaagttt gttccttaa tttgccctt aggagtctt 
gccccatca agacagaaa taaaagtcc tcttctaga 
tgtatgaag tttataaat ataattttt gctgattt

    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