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Gene information
General information
TC013541 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_007420.3: 8260870..8264073
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
    		TC013541
    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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    Publish name
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_11025

    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)

    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 20
    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
    • >TC013541 RA
      MKSNYFNVQ IIALFMLSL IPWPGPTVF KISCPRDNA 
RIVRKIIQN KWIPILEKY KVSLPIECP FHPIRDIFG 
PQQAAKQQH RPSQWTCGL CGKSFFEEK YLDMHFDNR 
HKGFINMAE DAVCLADYC DIMRCDVLI TQDPKTVYP 
DTVNTDIEI WREASSYTK ALATSGPRE VAKYTFKDG 
IYPHLQKSG KATKPTKHC QKNEAPEAP NSNEERQSA 
GDDDKLQNS SNNVCQNDL VDSALPAPD NRQQRIAEL 
QKLKANCKP EELQKIKTK CEILVRDCI AGLLIQLSV 
KDFKEVEDE LNRAVCWYL TCDRYWEDT QGDIRSFPW 
GLLCMIIMV LSLGICMCY YIIWVLFDT DDVSVASAS 
MTDRSTPSP AHVHRHEPP PQADGHQIY TEDYYLAPD 
KDNEYIYVT YPPDLKRRL LESCYNRTT RL
    CDS sequence
    • >TC013541 RA
      atgaagtcc aattatttc aacgtgcag ataattgcg 
ttgtttatg ctttcgttg atcccatgg ccggggccc 
acagttttc aaaatctcg tgtccgcga gataatgcc 
cgaatcgtg cggaaaata atccagaac aaatggata 
ccgatttta gaaaaatac aaagtcagt ctgcccatc 
gagtgcccc ttccacccc attagggac atcttcggg 
ccccagcag gccgccaaa cagcagcac cggccctcg 
caatggacg tgcggcctc tgcggcaag tcgtttttc 
gaggagaaa tacctggac atgcatttc gacaatcgc 
cataagggt ttcataaat atggccgaa gacgccgtg 
tgccttgca gactactgc gacattatg agatgtgac 
gtcttgata acgcaagac cccaaaacc gtctatcca 
gacaccgtc aacacggat atagaaatc tggcgcgaa 
gcttcctcg tacaccaaa gccttggcg acgtccggc 
ccacgcgaa gtcgccaaa tacaccttc aaggatggg 
atttacccc catctgcaa aaaagcgga aaagcaacg 
aagcccacc aagcattgc cagaagaat gaagcaccg 
gaagcgcct aatagcaac gaagagcgc caatctgca 
ggcgacgac gataaattg cagaatagt tcgaataat 
gtgtgtcaa aatgatttg gtggattcg gctttgccg 
gcaccggac aacaggcag cagagaata gccgaactg 
caaaagttg aaagcgaat tgtaaaccg gaagaactg 
cagaaaatt aagacgaag tgcgagatt ttggtgcgc 
gattgcatc gcggggctg ctaattcaa ctctcggtg 
aaagatttt aaagaagtt gaagacgag ttaaacagg 
gctgtctgt tggtacttg acgtgtgac cggtactgg 
gaggatacg cagggggat atccgcagc ttcccttgg 
ggtttgctc tgtatgata ataatggtt ctgtccctc 
ggcatctgc atgtgttac tacatcatt tgggtcttg 
ttcgacacc gatgacgtc agtgttgct agtgctagt 
atgaccgat agatcgacg ccttcgccg gctcatgtc 
catcggcat gagcctcca ccacaggca gacggtcac 
caaatttac acagaggat tattacctg gctccagat 
aaagataac gaatacata tacgtaact tatcctcct 
gatttaaaa cgacggctt ttagaaagc tgctacaat 
cgaactacc cgcttgtga
    mRNA sequence
    • >TC013541 RA
      aagtggcgt aataagtga ataattaac cgatttccg 
aaggctaaa tgaccgtga atgtcgcct agcaacttg 
cggcgacgt ccagcgtct tcggcgtcg tagcatacg 
atgctttct aaatgccac aagaaaggt agagttttc 
tttcatcct agtaccggt aaagaatat gaatgaagt 
ccaattatt tcaacgtgc agataattg cgttgttta 
tgctttcgt tgatcccat ggccggggc ccacagttt 
tcaaaatct cgtgtccgc gagataatg cccgaatcg 
tgcggaaaa taatccaga acaaatgga taccgattt 
tagaaaaat acaaagtca gtctgccca tcgagtgcc 
ccttccacc ccattaggg acatcttcg ggccccagc 
aggccgcca aacagcagc accggccct cgcaatgga 
cgtgcggcc tctgcggca agtcgtttt tcgaggaga 
aatacctgg acatgcatt tcgacaatc gccataagg 
gtttcataa atatggccg aagacgccg tgtgccttg 
cagactact gcgacatta tgagatgtg acgtcttga 
taacgcaag accccaaaa ccgtctatc cagacaccg 
tcaacacgg atatagaaa tctggcgcg aagcttcct 
cgtacacca aagccttgg cgacgtccg gcccacgcg 
aagtcgcca aatacacct tcaaggatg ggatttacc 
cccatctgc aaaaaagcg gaaaagcaa cgaagccca 
ccaagcatt gccagaaga atgaagcac cggaagcgc 
ctaatagca acgaagagc gccaatctg caggcgacg 
acgataaat tgcagaata gttcgaata atgtgtgtc 
aaaatgatt tggtggatt cggctttgc cggcaccgg 
acaacaggc agcagagaa tagccgaac tgcaaaagt 
tgaaagcga attgtaaac cggaagaac tgcagaaaa 
ttaagacga agtgcgaga ttttggtgc gcgattgca 
tcgcggggc tgctaattc aactctcgg tgaaagatt 
ttaaagaag ttgaagacg agttaaaca gggctgtct 
gttggtact tgacgtgtg accggtact gggaggata 
cgcaggggg atatccgca gcttccctt ggggtttgc 
tctgtatga taataatgg ttctgtccc tcggcatct 
gcatgtgtt actacatca tttgggtct tgttcgaca 
ccgatgacg tcagtgttg ctagtgcta gtatgaccg 
atagatcga cgccttcgc cggctcatg tccatcggc 
atgagcctc caccacagg cagacggtc accaaattt 
acacagagg attattacc tggctccag ataaagata 
acgaataca tatacgtaa cttatcctc ctgatttaa 
aacgacggc ttttagaaa gctgctaca atcgaacta 
cccgcttgt gagacctag tacgaagag atcgtttag 
ctcaatttt tatttattt tgtagactt tttaaacag 
actccatac tgaaaacat tccaaaatt ataagtagg 
ggaatactc aaatgtatt aaagtttta caaaactta 
atactttta agtaatttt ctgtttcta tctagattg 
tagtttaga cataattcg aatttggta gccaatagc 
tggactgag cctttttcc cttaaaaat actttaatt 
ttaatcgaa cagtagatg gtggcataa tttttgaac 
gtcatacat ttcgtacga aataaaatc ggaattttg 
tttcactgc ttgctgtct catgccttg accattaac 
atgaaaaaa acggaattt aaattcttg tccttgtac 
ctaagataa tccaagctg aattccatc ctacgatta 
ccaaacaaa ctcagatac aatttgtta caactaggt 
gtagtcttt agcgtaata attagcttg atgttactt 
tgtttttat tgcaacgat gtacataat gatagttgg 
ataactttt gtacatgtg aaatacttt actatgcac 
ctttttgag cattgcaat gaatgtaaa tttacatct 
ttaaaacca tgttcataa tttataaaa atgtaataa 
tattcaagg atcataata aagatttaa tattgaa
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY
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