Status
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Gene information
General information
TC000817 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: 6214296..6216401
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
    		TC000817
    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
    If you have entered your name and agree by marking the checkbox. we might show your name on this page to honor your contribution.
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_03082

    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)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 2 (3 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 larval musculature irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    abdomen musculature random irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    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
    App. 50 larvae on slide.
    larva partially dorsalnot closed - Penetrance (percentage of animals/eggs on slide): 30% - 50%

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

    abdomen segment number decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    affected eggs/embryos/larvae - 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: % (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
    • >TC000817 RA
      MISSALVWG FLYDTLGRK RLLMVGFFL DTVFVFISG 
FSQSKTILM ICKFFGGFI INGPFAALT AYISEFHCS 
KYRARMQLV LGTIFSCGS VTLPVLAWA VLPQNYYFS 
LFNKTLEFH SWNIYLFIC GFPALFSTV IFIFMPESP 
KFLMTVGQN DKALKVFQK IYSVNSRNP PETYPIRQL 
VDEIEVKKN SQSKHTTHV TANRNKIQA LREGWQQLK 
PLFFPPHLA NIILVCLLQ TLFTMSLNT LRLWLPQIF 
QAINDYKYY HNDSSADLC KMLDMIQPA STLGECVVN 
LNNSSVYIN TIIISSVSA SSYIFAGYF INILGKKKL 
MSVLGGSCA FSIYFSTNT AMTVAFASI FIASSSVAT 
NVVLAVCID LFPTTLRTM TLSLSMMLA RSGAMIGNL 
VFPLLLQTG CAPPFFTIG SLIFVCAFI AMLLPNTDL 
KALE
    CDS sequence
    • >TC000817 RA
      atgatttcg agtgccttg gtttgggga tttctttat 
gacacttta gggaggaaa agactgttg atggttggc 
ttcttccta gacactgtt tttgtcttc atcagcggt 
ttctcccaa agcaaaaca attctaatg atttgtaaa 
ttttttggc ggctttata ataaacggc ccgtttgct 
gctctaaca gcctatatt tctgagttc cattgttcc 
aaatataga gcaagaatg cagctagta cttggaact 
atttttagt tgtgggagc gttacttta cctgtcttg 
gcctgggct gtcttgccc caaaattac tacttttca 
ctttttaac aaaacactt gaatttcat tcctggaac 
atttatctt ttcatttgt ggctttccc gccctgttc 
agtaccgta atatttatt ttcatgccc gaaagtccg 
aaatttctg atgacggtg ggccaaaac gacaaggca 
ctcaaagtg tttcaaaaa atctacagt gtaaatagc 
aggaatcca cctgaaacc tatccaatt aggcaacta 
gttgacgaa attgaagtt aagaaaaac agtcaaagt 
aagcacaca actcacgtg acagccaac aggaacaag 
atacaagct ctcagagaa gggtggcaa caactaaaa 
cccttattt ttcccgcca catttagca aacattatc 
cttgtgtgt ctcctccaa actttattt acaatgagt 
ttgaacact ttgcggctt tggttgccg caaattttt 
caagccatc aatgactac aagtattat cacaacgat 
tctagtgcc gatctttgc aaaatgctg gacatgatc 
cagccagcc agtacttta ggcgaatgc gttgttaac 
ctcaacaat tcctcagtt tatatcaac acaataatt 
atttcgtct gtgagtgct agtagctac atcttcgcc 
ggctatttc atcaacatc ctcggaaag aaaaaactg 
atgagtgtt ttgggagga tcgtgtgct ttttcaatc 
tacttttcc acgaacaca gcaatgacg gtggctttt 
gcttcaatt tttatcgca tcgtcaagt gtggcaact 
aatgtagtt ctagccgtt tgcatagac ttgtttccg 
actacttta agaacaatg acactatcg ttatcaatg 
atgttggct cgaagtggg gcaatgatt gggaatttg 
gtcttcccc ttgttactc caaacagga tgtgctcct 
ccgttcttc acaatcggt tctctaatt tttgtatgt 
gctttcatc gcaatgctg ctaccaaac actgaccta 
aaggccttg gagtaa
    mRNA sequence
    • >TC000817 RA
      tcggtcatg tattcatta aaaatctgt cgtcacaat 
gaaagaaaa acatagcac ggccaaaaa tatctacgt 
agttcccat agatgacga aactaaagc aaaagctac 
agaaccggc tgattttga aacggcaat ttcggccac 
tggcttcgg atactacaa tttatttct gatccttat 
ctcaattcc tgcaggatg gtcttctat ctttgaaac 
gaccacaat gtcgtatgt atttgcagc cgcacagtg 
tgaccttga cttgagttt agatgataa aggaatgtt 
aaacgcaat tacttactt aggcacgta acaattaac 
ataactaat agataacga ctgatcttc aggaatgat 
ttcgagtgc cttggtttg gggatttct ttatgacac 
tttagggag gaaaagact gttgatggt tggcttctt 
cctagacac tgtttttgt cttcatcag cggtttctc 
ccaaagcaa aacaattct aatgatttg taaattttt 
tggcggctt tataataaa cggcccgtt tgctgctct 
aacagccta tatttctga gttccattg ttccaaata 
tagagcaag aatgcagct agtacttgg aactatttt 
tagttgtgg gagcgttac tttacctgt cttggcctg 
ggctgtctt gccccaaaa ttactactt ttcactttt 
taacaaaac acttgaatt tcattcctg gaacattta 
tcttttcat ttgtggctt tcccgccct gttcagtac 
cgtaatatt tattttcat gcccgaaag tccgaaatt 
tctgatgac ggtgggcca aaacgacaa ggcactcaa 
agtgtttca aaaaatcta cagtgtaaa tagcaggaa 
tccacctga aacctatcc aattaggca actagttga 
cgaaattga agttaagaa aaacagtca aagtaagca 
cacaactca cgtgacagc caacaggaa caagataca 
agctctcag agaagggtg gcaacaact aaaaccctt 
atttttccc gccacattt agcaaacat tatccttgt 
gtgtctcct ccaaacttt atttacaat gagtttgaa 
cactttgcg gctttggtt gccgcaaat ttttcaagc 
catcaatga ctacaagta ttatcacaa cgattctag 
tgccgatct ttgcaaaat gctggacat gatccagcc 
agccagtac tttaggcga atgcgttgt taacctcaa 
caattcctc agtttatat caacacaat aattatttc 
gtctgtgag tgctagtag ctacatctt cgccggcta 
tttcatcaa catcctcgg aaagaaaaa actgatgag 
tgttttggg aggatcgtg tgctttttc aatctactt 
ttccacgaa cacagcaat gacggtggc ttttgcttc 
aatttttat cgcatcgtc aagtgtggc aactaatgt 
agttctagc cgtttgcat agacttgtt tccgactac 
tttaagaac aatgacact atcgttatc aatgatgtt 
ggctcgaag tggggcaat gattgggaa tttggtctt 
ccccttgtt actccaaac aggatgtgc tcctccgtt 
cttcacaat cggttctct aatttttgt atgtgcttt 
catcgcaat gctgctacc aaacactga cctaaaggc 
cttggagta atcttaaag actgtgaaa ctgtgaaag 
actttttta ttaatacaa aatacagta agat

    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