Status
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Gene information
General information
TC006460 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: 9948551..9962505
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
    		TC006460
    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_01051

    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: 40.0% (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

    adult lethality - Number of animals showing the phenotype: 2 (9 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg not developed/not fertilized - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    embryo/egg with embryonic tissue, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): more than 80%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     egg without cuticle embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): more than 80%
    larva dorsal not closed - Penetrance (percentage of animals/eggs on slide): less than 30%

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

    posterior terminus not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 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: 30.0% (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: 3 (11 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC006460 RA
      MPNKLSQYE DIPFSHRPP HYLHELPIE DEERLGKLF 
KQLDKDGNG KIDIHDLSE ALKEHGVHH HYAEKFFQN 
SRSKSGDLS LADFIYYVR EHEKNLRLH FSHIDRNKD 
GRIDLDELI KAFSDLGIP LDTMEAKKL LQRMDQDGS 
LNISYDEWR DFLLLAPNS QDIHQLISY WRHSTCLIY 
LVIVEKNCD RKMYEQELA PASIPDVLE DCIYLFREL 
IKYLDIGED MNVPDDFTQ SEMQTGMWW RHLAAGGIA 
GAVSRTCTA PLDRLKVFL QVQPTKQRI GDCFNYMLK 
EGGVTGLWR GNGINVVKI APESAIKFA AYEQIKRLI 
KGDSKTGLS IYERFCAGA LAGGISQTA IYPLEVMKT 
RLALRKTGQ YKSIMDAAF KIYHLEGIG SFYRGYIPN 
ILGIIPYAG IDLAVYETL KKKYLKTHS NLEQPSFWM 
LLACGSVSS TLGQMCSYP LALVRTRLQ AQVAHPSMD 
PSAITMTGV FKTILEKEG VLGLYRGIT PNFIKVMPA 
VSISYVVYE YSSRLLGVN MT
    CDS sequence
    • >TC006460 RA
      atgccgaat aaactgtcg cagtacgaa gacattccc 
ttttctcat cgtcctcca cactacctg catgagcta 
ccaatcgaa gatgaggaa cgtctcggg aaactcttc 
aagcaactg gacaaagac ggaaacggc aagattgac 
atccacgac ttgagcgaa gctctcaaa gaacacggt 
gtccaccat cactacgct gagaaattt ttccaaaat 
tctcgatcg aaaagtgga gacttgtcg ctggccgac 
ttcatctac tacgttcga gaacatgag aaaaatctc 
cgactccac ttttcccac attgatagg aacaaagat 
ggtaggatt gatctggac gagctcatc aaagcgttc 
agcgatctg gggattccc ctggacacc atggaagcg 
aagaaactc ttacagagg atggatcag gatggcagt 
ctcaatatt agctatgat gagtggagg gactttctc 
ctcctcgcc cccaacagc caagatatt caccagctg 
atcagctat tggagacat tcaacgtgt ttaatttat 
ttagtaatt gttgaaaaa aattgtgat agaaaaatg 
tacgaacag gagttagcg ccggcgtcc ataccggac 
gtcctggag gactgcatt tatttattt agggaattg 
atcaagtac ctggacatc ggggaggat atgaacgtc 
cctgatgat ttcacacag agtgaaatg cagacaggg 
atgtggtgg aggcattta gctgcggga ggaatcgcc 
ggagcggtt tccaggact tgtaccgcc cccttggac 
aggctcaag gtgttcctt caggtccaa ccgacgaag 
cagcgaatc ggcgactgt ttcaattac atgctgaaa 
gagggtggt gtcacaggt ctatggcgg ggcaacggc 
atcaacgtg gtgaaaatc gcccccgag tcggcgatc 
aaatttgca gcctacgaa cagatcaaa cgactgatc 
aaaggcgat tccaagaca ggactcagc atttacgag 
cggttttgt gcgggggct ttagctggg ggtattagt 
cagacggcg atttatccg ctggaggtt atgaagacg 
aggttggcg ttgcgtaaa acgggacag tataagagt 
atcatggat gctgctttt aaaatctat catctggaa 
ggcatcggt agtttttat agaggttac attccgaat 
attcttggt attataccg tatgccggt atcgatttg 
gctgtgtac gaaacgttg aaaaagaag tacttgaag 
actcattcc aatttggaa cagccgagc ttttggatg 
ttgctggcc tgtggcagc gtctcgagt actttaggg 
caaatgtgt tcttacccc ttggcgctg gtgcggacg 
aggttgcaa gcacaagtg gcgcatccg tcgatggac 
ccctctgcc atcacaatg actggggtg ttcaaaacg 
atattagag aaggaaggt gtgttgggt ttgtaccgc 
ggcataact ccgaacttt atcaaagta atgccggca 
gtaagcata agttacgtc gtttacgag tactcgagt 
cgcttactc ggagtaaat atgacgtga
    mRNA sequence
    • >TC006460 RA
      tgtcaaaaa tctcaaaca gctgtcaaa tgccgtttt 
cgcgaagtc gcattgcgg cattgcatt agttgcttt 
tccaccaaa aatcgtcat aaattagct cttggtgtt 
gcatcggga gtggttttg atgtgaaaa tgccgaata 
aactgtcgc agtacgaag acattccct tttctcatc 
gtcctccac actacctgc atgagctac caatcgaag 
atgaggaac gtctcggga aactcttca agcaactgg 
acaaagacg gaaacggca agattgaca tccacgact 
tgagcgaag ctctcaaag aacacggtg tccaccatc 
actacgctg agaaatttt tccaaaatt ctcgatcga 
aaagtggag acttgtcgc tggccgact tcatctact 
acgttcgag aacatgaga aaaatctcc gactccact 
tttcccaca ttgatagga acaaagatg gtaggattg 
atctggacg agctcatca aagcgttca gcgatctgg 
ggattcccc tggacacca tggaagcga agaaactct 
tacagagga tggatcagg atggcagtc tcaatatta 
gctatgatg agtggaggg actttctcc tcctcgccc 
ccaacagcc aagatattc accagctga tcagctatt 
ggagacatt caacgtgtt taatttatt tagtaattg 
ttgaaaaaa attgtgata gaaaaatgt acgaacagg 
agttagcgc cggcgtcca taccggacg tcctggagg 
actgcattt atttattta gggaattga tcaagtacc 
tggacatcg gggaggata tgaacgtcc ctgatgatt 
tcacacaga gtgaaatgc agacaggga tgtggtgga 
ggcatttag ctgcgggag gaatcgccg gagcggttt 
ccaggactt gtaccgccc ccttggaca ggctcaagg 
tgttccttc aggtccaac cgacgaagc agcgaatcg 
gcgactgtt tcaattaca tgctgaaag agggtggtg 
tcacaggtc tatggcggg gcaacggca tcaacgtgg 
tgaaaatcg cccccgagt cggcgatca aatttgcag 
cctacgaac agatcaaac gactgatca aaggcgatt 
ccaagacag gactcagca tttacgagc ggttttgtg 
cgggggctt tagctgggg gtattagtc agacggcga 
tttatccgc tggaggtta tgaagacga ggttggcgt 
tgcgtaaaa cgggacagt ataagagta tcatggatg 
ctgctttta aaatctatc atctggaag gcatcggta 
gtttttata gaggttaca ttccgaata ttcttggta 
ttataccgt atgccggta tcgatttgg ctgtgtacg 
aaacgttga aaaagaagt acttgaaga ctcattcca 
atttggaac agccgagct tttggatgt tgctggcct 
gtggcagcg tctcgagta ctttagggc aaatgtgtt 
cttacccct tggcgctgg tgcggacga ggttgcaag 
cacaagtgg cgcatccgt cgatggacc cctctgcca 
tcacaatga ctggggtgt tcaaaacga tattagaga 
aggaaggtg tgttgggtt tgtaccgcg gcataactc 
cgaacttta tcaaagtaa tgccggcag taagcataa 
gttacgtcg tttacgagt actcgagtc gcttactcg 
gagtaaata tgacgtgat gtaggagca ttttaggaa 
caaattatt tattattaa ttataaaat tccctctca 
ttttgtccg ggacacggg caaacgata tttctggca 
actttgatt gcttggtct atttatttg tacagatta 
ttactgtaa gaatacttg aataggctt taacaaact 
aaacttgtt gaatgtcga ttgttaata atttacgaa 
atctttttt caatctctt gacgctcat gtggcttct 
ttgacacat ttatgtaag ttttaaagt ctaaacgtt 
tctcgatgt tgttgattc taccaaaga aggcatgtt 
ctgttacta aatgacaat tttaatatt gatactgtg 
tattttcca tgattgaga ttactttag gaagaggac 
gattgtgat gtacttaat attttaata aactgg

    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