Status
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Gene information
General information
TC002458 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_007418.3: 29935883..29938021
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
    		TC002458
    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_09812

    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: 3 (3 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (9 dpi)
    Days post injection

    Fertility
    mature egg deposition blocked number 1st lateral oviduct: >5 number 2nd lateral oviduct: - Number of animals showing the phenotype: 1
    mature egg not present - Number of animals showing the phenotype: 2
    previtellogenic egg chamber number decreased - Number of animals showing the phenotype: 3

    egg chamber stage sequence irregular -
    vitellogenic egg chamber number decreased - Number of animals showing the phenotype: 3
    yolk mostly amount decreased - Number of animals showing the phenotype: 3

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: < 20 embryo/egg with embryonic tissue potentially present, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): more than 80%

    Comment: 5/5
    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 80%
    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): more than 80%
    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: % (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
    • >TC002458 RA
      MNYYQSMNH HMPHPQFHF SQPNPPPNR FIYVKHNFV 
APNPAPKVL LNPHFKKKV YVNPQFKPA QNPLPPTNA 
KPKIHINPN VLKNFAKTV NNVPKVVEP PKATTVIST 
RNKLVRIPC NKSPEIRKR RNSVHTKYK IVRSGAKTG 
SPNRFKLDK RQEKSANKT LIRSAKKRY VYVNRFLSI 
DVMAKNVLL KKNPNLSKP GFVKINGIL YKKSPNSLR 
KASDTSLLK STKSSTRRS LVKRYKLIR SSSAPSHAR 
RVKPRPNFK AKKPTPSKL RKCNIPCPI FRKYGKCPG 
KAAGTCFKL HNPDQIVLC TRFLQGACR NERCLLSHK 
VSHEKMPTC KYFLDGLCS KDNCPYLHV KISPKADIC 
RDFLEGFCK KGAECDKRH QFLCPEFEK NKKCSKRRC 
PYPHGNTVR KNSKVLNRL AKKCSTKKA KTEIVECEK 
NRYYKEKET EGGEEKVIK TVAKDRPKL GDLPAFIPL 
FEAT
    CDS sequence
    • >TC002458 RA
      atgaattat taccaatca atgaatcac catatgccc 
catccccag ttccatttc tcccaacct aacccccct 
ccgaaccgt tttatctac gtaaagcac aatttcgtt 
gccccaaac ccggccccc aaagtcctc ctcaacccc 
catttcaag aagaaagtt tacgtcaac cctcagttc 
aaaccggcc caaaacccc cttccgcca acaaacgcg 
aaaccaaaa atccacatc aacccgaac gttttgaaa 
aatttcgcc aaaactgta aacaacgtg cccaaagtt 
gtcgaaccc ccaaaagca acgactgtg atatctacc 
cgaaataaa ttagtccga attccgtgc aataaatca 
cccgaaata agaaaacgg cgcaattcc gtacataca 
aagtacaaa atcgtgcga agtggtgct aaaaccggt 
tcccccaac cgtttcaaa ctcgacaaa aggcaggaa 
aaaagtgcg aataaaacc cttattagg tcagccaaa 
aaacgctac gtttacgta aaccgcttc ctgagcatc 
gacgtaatg gccaaaaac gtgctcttg aaaaagaac 
ccgaacttg tccaagccc ggattcgtt aaaatcaac 
ggaattctg tacaaaaaa tccccgaat tccttgcgg 
aaagcctcc gacacgtcc ctgctcaaa tccacgaaa 
tctagcact cggcgaagc ctcgtcaaa cgctacaag 
ctgatcagg tctagctcc gcccctagc cacgcccgc 
agagttaag ccacgcccc aatttcaag gccaagaaa 
ccgacaccc agcaaactg cgcaagtgc aacatcccg 
tgccccatt ttccggaag tatggaaaa tgtccgggg 
aaggcagca ggcacttgt ttcaagctg cacaacccc 
gatcagatc gtcctgtgc acgaggttt ctccaaggg 
gcgtgtcgt aatgaaaga tgcctactt tcccacaaa 
gtttcgcac gaaaaaatg cccacgtgc aagtatttc 
ctcgacggg ttgtgttct aaggacaac tgtccctat 
ctccacgtg aagatcagc cccaaggcc gatatttgc 
agggacttt ttggagggt ttctgcaag aagggcgct 
gagtgcgac aaacgccac caattcttg tgtcccgaa 
ttcgagaag aacaagaag tgttcaaaa cggaggtgt 
ccatacccg catggaaac acggtaaga aaaaattct 
aaggtttta aataggctt gccaagaaa tgttcaacg 
aaaaaagca aaaacggag attgtcgag tgtgaaaaa 
aaccgctat tacaaggaa aaagaaact gaaggcggg 
gaggaaaaa gtcattaag actgtggcc aaggatagg 
ccaaaattg ggggattta ccggctttt ataccgttg 
tttgaggcc acgtga
    mRNA sequence
    • >TC002458 RA
      ttttgcgtt tttttgttt attaaaaat ttatttttt 
tatgaacgt agacgcatt tatttgtgg cgcaagcgc 
agtaaaaca aaacgtcaa aggaatgtt aaacatctg 
atctcaatt acttcagtt tttggtgag ttttgcagt 
catttgagt gaaaatcgg tgaacgagg atgttattt 
taaccgttt tacacacca gaatgaatt attaccaat 
caatgaatc accatatgc cccatcccc agttccatt 
tctcccaac ctaaccccc ctccgaacc gttttatct 
acgtaaagc acaatttcg ttgccccaa acccggccc 
ccaaagtcc tcctcaacc cccatttca agaagaaag 
tttacgtca accctcagt tcaaaccgg cccaaaacc 
cccttccgc caacaaacg cgaaaccaa aaatccaca 
tcaacccga acgttttga aaaatttcg ccaaaactg 
taaacaacg tgcccaaag ttgtcgaac ccccaaaag 
caacgactg tgatatcta cccgaaata aattagtcc 
gaattccgt gcaataaat cacccgaaa taagaaaac 
ggcgcaatt ccgtacata caaagtaca aaatcgtgc 
gaagtggtg ctaaaaccg gttccccca accgtttca 
aactcgaca aaaggcagg aaaaaagtg cgaataaaa 
cccttatta ggtcagcca aaaaacgct acgtttacg 
taaaccgct tcctgagca tcgacgtaa tggccaaaa 
acgtgctct tgaaaaaga acccgaact tgtccaagc 
ccggattcg ttaaaatca acggaattc tgtacaaaa 
aatccccga attccttgc ggaaagcct ccgacacgt 
ccctgctca aatccacga aatctagca ctcggcgaa 
gcctcgtca aacgctaca agctgatca ggtctagct 
ccgccccta gccacgccc gcagagtta agccacgcc 
ccaatttca aggccaaga aaccgacac ccagcaaac 
tgcgcaagt gcaacatcc cgtgcccca ttttccgga 
agtatggaa aatgtccgg ggaaggcag caggcactt 
gtttcaagc tgcacaacc ccgatcaga tcgtcctgt 
gcacgaggt ttctccaag gggcgtgtc gtaatgaaa 
gatgcctac tttcccaca aagtttcgc acgaaaaaa 
tgcccacgt gcaagtatt tcctcgacg ggttgtgtt 
ctaaggaca actgtccct atctccacg tgaagatca 
gccccaagg ccgatattt gcagggact ttttggagg 
gtttctgca agaagggcg ctgagtgcg acaaacgcc 
accaattct tgtgtcccg aattcgaga agaacaaga 
agtgttcaa aacggaggt gtccatacc cgcatggaa 
acacggtaa gaaaaaatt ctaaggttt taaataggc 
ttgccaaga aatgttcaa cgaaaaaag caaaaacgg 
agattgtcg agtgtgaaa aaaaccgct attacaagg 
aaaaagaaa ctgaaggcg gggaggaaa aagtcatta 
agactgtgg ccaaggata ggccaaaat tgggggatt 
taccggctt ttataccgt tgtttgagg ccacgtgac 
gaatatttc ttggcaatt ttagatttt ttatactgt 
ctttgagaa aataaaaca atgaagcaa ca

    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