Status
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Gene information
General information
TC000541 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: 10007207..10009128
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
    		TC000541
    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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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_03036

    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 embryo/egg with embryonic tissue, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    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
     embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    larva partially dorsalnot closed - Penetrance (percentage of animals/eggs on slide): less than 30%

    head capsule decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    head capsule irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    head bristle irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    Comment: The irregular head bristle pattern is potentially due to the decreased head capsule (secondary defect).
    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
    • >TC000541 RA
      MSRDESFVA VKNTAESMV PSIGSDDED SFVVLETSN 
SISESLSCS PPRDEILPP IRTNKVHEM ENLIRMKIS 
QITVDPLPE LPAAVDAIV PSVASIAIS PDSSYEEIQ 
KQVEELIKE NEKLKNIIA QNNMSMKAQ YTRFLAYRD 
EVTNVMKSY KDKFNDAKM CIDKYKEEN AKLVSDVEV 
YINLKKLHE EEILNLKLK LKELENLTN GPNFSVVDT 
RKLAMMKDL ELKQEEIER LTQKLVNVP NLEQELQTK 
QQQIDDFKL DILAAKNRE SDLIDEIQS MKTTTTDLQ 
SKLDNLTKE NAKLVQSST AAQTYDQLL KLKETEILK 
LKEEQQRTA FVESTLSDE IKTLKSQLK ELQDKYNPR 
LAEDYAQSR AQLSVAQRT ITALEQERE QKIKEIEDL 
RKLLQENTS ANDEMFALK EQIEVYKND FEAEKKSKL 
AMKQEKDQV VEDLQNLQT RNKQLQNEV ERLRARNEP 
PRAEGYQCP KCSFGFNNY QSLENHVHR CLDLDGFP
    CDS sequence
    • >TC000541 RA
      atgagtcgt gacgagtcc ttcgttgct gtgaaaaac 
actgcagag tccatggtt ccgtcaatc gggtccgat 
gatgaagat tcatttgtc gttttggaa acttcaaat 
tccatcagc gaaagtttg tcttgcagc cctccaagg 
gacgaaatc ttgccccca ataaggaca aataaggtt 
cacgaaatg gaaaatcta atcaggatg aaaatatca 
caaattacc gttgatccg ttgccagaa ttaccagca 
gctgttgat gcgattgtg ccctcagtt gcaagtatt 
gcaatatcg ccggattcg tcgtatgaa gagattcaa 
aaacaagtg gaagaactg attaaggaa aacgaaaag 
ttgaagaat atcatcgca caaaataac atgagtatg 
aaggcgcag tatacgagg tttttggcc tacagggat 
gaggtcacc aatgtgatg aagtcctac aaagataag 
ttcaacgat gccaaaatg tgcatagat aagtataaa 
gaagaaaat gcaaagttg gttagtgac gttgaagtt 
tacatcaat cttaaaaag ctccatgaa gaagaaatc 
ttgaatttg aaactgaag cttaaggaa ttggaaaat 
ttgaccaac ggccccaac ttttcagtt gttgacaca 
aggaaatta gcaatgatg aaggattta gaactgaaa 
caggaagaa attgaaaga ctgacgcaa aaattggtg 
aatgtaccg aaccttgaa caggaatta caaaccaag 
cagcaacaa attgacgac tttaaactg gatattctc 
gccgcaaaa aatcgcgaa agcgaccta attgacgaa 
atccagtca atgaagaca acaaccacc gacctccaa 
tcaaaattg gataattta acaaaagaa aacgcaaaa 
ctcgtccaa tcatcgacg gcagcccaa acctacgac 
cagctcctc aaactgaaa gaaacggaa atcttgaaa 
ctgaaggaa gaacaacaa cgcaccgct ttcgtcgaa 
tccaccctc agtgatgag ataaaaacc ctaaaatcg 
caacttaag gagctccaa gacaagtac aacccgcgt 
ttggccgaa gattatgcc caatcccgg gcccagttg 
agcgttgcc caaaggaca atcacagca ttggaacag 
gaaagggaa cagaagatt aaagaaatc gaagatttg 
cgtaaacta cttcaagaa aatacaagt gccaacgac 
gaaatgttc gcattgaag gaacaaatc gaagtgtat 
aagaacgat tttgaagca gagaagaag agcaaactt 
gcgatgaaa caagagaag gaccaggtt gttgaagat 
ttgcagaat ctgcaaacg aggaacaaa caactgcag 
aatgaagtg gagaggctg agggcgagg aacgagccg 
ccgagggcc gaggggtat cagtgcccc aagtgctcg 
ttcggattt aataattac cagtcattg gaaaatcat 
gttcatagg tgcttggat ttggacggt tttccctaa
    mRNA sequence
    • >TC000541 RA
      ctacagttg tgtcccaaa tgaaatttt acgtaaata 
gttatgcca caataacat ttttagagc tttaatatt 
cttaaaaaa ttaaattaa ggctaaggc gacttttta 
ttggtccgg ttggtagca gtgtcttta atcgtgtgt 
cagtagttt ggtattttc atattctat gttctaatt 
cattctatt ttgcgccgc aaatgtagt gttgtactg 
cagctgttg ttaaaactt gaaagtcat caaaaatga 
gtcgtgacg agtccttcg ttgctgtga aaaacactg 
cagagtcca tggttccgt caatcgggt ccgatgatg 
aagattcat ttgtcgttt tggaaactt caaattcca 
tcagcgaaa gtttgtctt gcagccctc caagggacg 
aaatcttgc ccccaataa ggacaaata aggttcacg 
aaatggaaa atctaatca ggatgaaaa tatcacaaa 
ttaccgttg atccgttgc cagaattac cagcagctg 
ttgatgcga ttgtgccct cagttgcaa gtattgcaa 
tatcgccgg attcgtcgt atgaagaga ttcaaaaac 
aagtggaag aactgatta aggaaaacg aaaagttga 
agaatatca tcgcacaaa ataacatga gtatgaagg 
cgcagtata cgaggtttt tggcctaca gggatgagg 
tcaccaatg tgatgaagt cctacaaag ataagttca 
acgatgcca aaatgtgca tagataagt ataaagaag 
aaaatgcaa agttggtta gtgacgttg aagtttaca 
tcaatctta aaaagctcc atgaagaag aaatcttga 
atttgaaac tgaagctta aggaattgg aaaatttga 
ccaacggcc ccaactttt cagttgttg acacaagga 
aattagcaa tgatgaagg atttagaac tgaaacagg 
aagaaattg aaagactga cgcaaaaat tggtgaatg 
taccgaacc ttgaacagg aattacaaa ccaagcagc 
aacaaattg acgacttta aactggata ttctcgccg 
caaaaaatc gcgaaagcg acctaattg acgaaatcc 
agtcaatga agacaacaa ccaccgacc tccaatcaa 
aattggata atttaacaa aagaaaacg caaaactcg 
tccaatcat cgacggcag cccaaacct acgaccagc 
tcctcaaac tgaaagaaa cggaaatct tgaaactga 
aggaagaac aacaacgca ccgctttcg tcgaatcca 
ccctcagtg atgagataa aaaccctaa aatcgcaac 
ttaaggagc tccaagaca agtacaacc cgcgtttgg 
ccgaagatt atgcccaat cccgggccc agttgagcg 
ttgcccaaa ggacaatca cagcattgg aacaggaaa 
gggaacaga agattaaag aaatcgaag atttgcgta 
aactacttc aagaaaata caagtgcca acgacgaaa 
tgttcgcat tgaaggaac aaatcgaag tgtataaga 
acgattttg aagcagaga agaagagca aacttgcga 
tgaaacaag agaaggacc aggttgttg aagatttgc 
agaatctgc aaacgagga acaaacaac tgcagaatg 
aagtggaga ggctgaggg cgaggaacg agccgccga 
gggccgagg ggtatcagt gccccaagt gctcgttcg 
gatttaata attaccagt cattggaaa atcatgttc 
ataggtgct tggatttgg acggttttc cctaaatat 
attttttga ctagtattt gtttattgt tcttatata 
aatatctaa aggaattaa taagtttaa caaggccat 
cgtaattgt ttggaaatg tattatttt gtagttact 
gttcctcgt ttacaacaa taaatacga gttaataaa 
gttcttatt tgtct

    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