Status
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Gene information
General information
TC009425 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_007422.5: 1398749..1405987
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
    		TC009425
    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 *
    {{ blurReferenceResult }}
    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_04631

    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: 0.0% (includes death as pupa, adult)

    Fertility
    mature egg deposition blocked number 1st lateral oviduct: 4 number 2nd lateral oviduct: - Number of animals showing the phenotype: 1
    mature egg deposition blocked number 1st lateral oviduct: 2 number 2nd lateral oviduct: - Number of animals showing the phenotype: 1
    mature egg deposition blocked number 1st lateral oviduct: 3 number 2nd lateral oviduct: - Number of animals showing the phenotype: 1
    ovary without detectable defects - Number of animals showing the phenotype: 1
    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: < 50 larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 20
     larva appendages partially shortened - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    maxillary palp shortened - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    labium shortened - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    legs shortened - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    legs coxa size decreased - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    legs trochanter size decreased - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    legs femur size decreased - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    legs tibiotarsus size decreased - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    legs femur potentially fused - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    legs tibiotarsus potentially fused - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    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: 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

    adult lethality - Number of animals showing the phenotype: 4 (41 dpi)
    Days post injection

    Adult morphology
    elytra not closed - Number of animals showing the phenotype: 7


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC009425 RA
      MGDYQVTGV QQDAMGAVQ LELGGNPNA LALRRPFDP 
LAHDLEASF RLTRFADLK GRGCKVPQE VLNKLVEGL 
QQDYNTAAE HEHAHFMHM AIPRIGIGL DCSVTPVRH 
GGLCLVQTT DFFYPLVDD PYMMGKIAC ANVLSDLYA 
MGVTECDNM LMLLGVSTK MTEKERDVV IPLIMRGFK 
DSALEAGTT VTGGQTVVN PWCTIGGIA TTVCQPNEY 
IVPDNAVVG DVLVLTKPL GTQVAVNAH QWLDQPERW 
NRIKLVVSE EDVRKAYHR AMDSMARLN RIASRLMHK 
YNAHGATDV TGFGLLGHA QTLASHQKN EVSFVIHNL 
PVIAKMAAV AKACGNMFQ LLQGHSAET SGGLLICLP 
REQAAAYCK DIEKQEGYQ AWIIGIVEK GNRTARIID 
KPRVIEVPA KE
    CDS sequence
    • >TC009425 RA
      atgggtgat taccaagtg actggggtc cagcaggat 
gcgatgggg gctgtccag ctggagctg ggtggaaat 
ccgaatgct cttgctttg cggcggcct tttgaccct 
ttggcgcac gacttggag gccagtttc cggctaacg 
cgctttgcc gacctcaag ggacgtggc tgcaaggtg 
ccccaggag gtgctcaac aagctggtg gaggggctc 
cagcaggac tacaacacg gccgccgaa cacgaacat 
gcccacttt atgcatatg gccataccc cgcatcggc 
atcggactc gattgctcg gtgacgccg gtgcgccat 
gggggcctg tgcttggtc cagacgaca gacttcttc 
tacccactg gtggacgac ccgtacatg atggggaag 
atcgcttgt gccaatgtc ctgagtgac ttgtatgcc 
atgggggtg acagagtgc gacaatatg ctgatgttg 
ttgggggtc agtacgaag atgactgaa aaggagcga 
gatgttgtg attccccta attatgaga ggtttcaaa 
gattctgcc ctggaagct ggaacaact gtaacaggt 
ggacaaacc gttgtgaat ccctggtgt acgattggt 
ggtattgcc acaactgtc tgtcaaccg aatgaatat 
atcgtgccg gataatgcc gttgttgga gatgtgctc 
gtactcacc aagccactt ggaacgcaa gtggccgtc 
aacgcacac cagtggttg gaccagccc gagcgctgg 
aaccgaata aagttagtt gtaagtgaa gaggacgtg 
cgtaaagcg tatcatcgt gcaatggac tcgatggcg 
cggttgaat cgcatcgct agcagattg atgcataaa 
tataatgcc catggagct acagatgtg acaggcttt 
ggtctgtta ggtcacgca caaacgtta gcttcgcat 
cagaagaac gaggtttcg ttcgttatt cataacttg 
cccgtaatt gcgaaaatg gcagccgta gccaaggct 
tgcggtaac atgttccaa cttttgcaa ggacattcg 
gctgaaacg tcaggagga cttttgatc tgtttgccg 
cgagaacaa gcggccgct tattgtaaa gatatagaa 
aaacaagaa ggttatcaa gcttggatc attgggatt 
gttgaaaag gggaaccga actgctagg attattgat 
aagcctcgg gttattgaa gttccggct aaagaataa
    mRNA sequence
    • >TC009425 RA
      gttctgtga aacatttaa aatttattc aatgtgatg 
atgatgcgt aaattaaca aagttattt acgaaaata 
ttttacctt aggcacctg aaaaatcga taaatcatt 
tgttaagag ctttatctg accacacag tcgacattt 
cttcatttt tacaacgaa tttacaaaa aaatttgtc 
aatttgata actccagtg acagtccta tgacagtcc 
cagtctacc gtgctgcca tctatctac ttgctccaa 
cgttagatt caaataaaa tggcgactc agtttacct 
gtctgtcta atatcgtgg ttgaccgtt gacagttga 
cagttaaca ccgcagcag caactaaca attttcagt 
atttcaatt ttcagtgca ttacacgtt attctacgg 
tgcatcata ggtgtttaa tcgttgtta ataggtcac 
agtgtggca cttacaccc cgggggctc ttttttgcg 
tggcttgtt tgggttttg tttgtttga aatcgaacc 
gttgttgaa aattttgac aacctcgtg aatagttgc 
gcatcgcga acggaccaa tgggatggt tgctcggtt 
ctggtcatg cgcagaacc ggtgggctg tggaggaag 
aggtagcca ttttgtgag cgtcggttg attgtttga 
gaaacgctc tgttgacga gctagtgtt tttaacacg 
ctagtaccc agcataaag tttcaaagc cggtatggg 
tgattacca agtgactgg ggtccagca ggatgcgat 
gggggctgt ccagctgga gctgggtgg aaatccgaa 
tgctcttgc tttgcggcg gccttttga ccctttggc 
gcacgactt ggaggccag tttccggct aacgcgctt 
tgccgacct caagggacg tggctgcaa ggtgcccca 
ggaggtgct caacaagct ggtggaggg gctccagca 
ggactacaa cacggccgc cgaacacga acatgccca 
ctttatgca tatggccat accccgcat cggcatcgg 
actcgattg ctcggtgac gccggtgcg ccatggggg 
cctgtgctt ggtccagac gacagactt cttctaccc 
actggtgga cgacccgta catgatggg gaagatcgc 
ttgtgccaa tgtcctgag tgacttgta tgccatggg 
ggtgacaga gtgcgacaa tatgctgat gttgttggg 
ggtcagtac gaagatgac tgaaaagga gcgagatgt 
tgtgattcc cctaattat gagaggttt caaagattc 
tgccctgga agctggaac aactgtaac aggtggaca 
aaccgttgt gaatccctg gtgtacgat tggtggtat 
tgccacaac tgtctgtca accgaatga atatatcgt 
gccggataa tgccgttgt tggagatgt gctcgtact 
caccaagcc acttggaac gcaagtggc cgtcaacgc 
acaccagtg gttggacca gcccgagcg ctggaaccg 
aataaagtt agttgtaag tgaagagga cgtgcgtaa 
agcgtatca tcgtgcaat ggactcgat ggcgcggtt 
gaatcgcat cgctagcag attgatgca taaatataa 
tgcccatgg agctacaga tgtgacagg ctttggtct 
gttaggtca cgcacaaac gttagcttc gcatcagaa 
gaacgaggt ttcgttcgt tattcataa cttgcccgt 
aattgcgaa aatggcagc cgtagccaa ggcttgcgg 
taacatgtt ccaactttt gcaaggaca ttcggctga 
aacgtcagg aggactttt gatctgttt gccgcgaga 
acaagcggc cgcttattg taaagatat agaaaaaca 
agaaggtta tcaagcttg gatcattgg gattgttga 
aaaggggaa ccgaactgc taggattat tgataagcc 
tcgggttat tgaagttcc ggctaaaga ataagtaca 
tttcaatat tccaagtat tgatgttta tgactggcc 
gttaatttt ctagctgcc taggtcata agcgctatg 
aataacagt ttcaaccta aagtcgttt attttcaaa 
tatttttcc aagatgttc aaagaagtg catgtttat 
gaatactat ttttgttgt tgaatactg ttaccattc 
gcttcttgt agtttcaat attttccct taaagcagt 
ttataaaga tttatttag cttttgtta tcaaattta 
tttagtgat gcattttcc actaaaact aatctcaga 
ttctcgtta gtagactat gtatcttgt acaaaattt 
cgtttcgta tttatgttt cgtcataga gttttagaa 
ataggtaaa agtcgtatt ggtattttg tataataat 
ttttcaaat aattaagta ttctactga cactgtgca 
gtttttctt ccagttccc ccacacaaa acaaaag

    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