Status
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Gene information
General information
TC001300 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: 14170145..14171338
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
    		TC001300
    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
    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
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_03167

    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: 60.0% (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: 3 (9 dpi)
    Days post injection

    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
    • >TC001300 RA
      MRLFNILFC LYFAFVRSV FGQTDDCVC VPFYLCTNG 
TLNTNGENI IDIRINAND CPSYLDFCC PTKEVLEKP 
KPKSPVIPP GCGHRNRNG VQYSITGAT DNEAQFGEF 
PWVVAILRK DNETLSLQC GGSLIHPQV VLTAAHCVH 
FVEQMVVRA GEWDSKTTQ EPLKHQDVK VSSAKVHPD 
FNSKNLKND IALLFLETP VSLDDNHIG LACLPRQNN 
ALSSNGCYV NGWGKNKFG KDAVFQNIL KKIQLPVVA 
HEQCQDAFR KTRLGKYFI LNESFVCAG GEEGKDACT 
GDGGGPLVC PSEEGRYEQ VGIVSWGIG CGEKGVPGA 
YTNVGRFKN WIKKQTQTR SFTIQ
    CDS sequence
    • >TC001300 RA
      atgcgactt ttcaacatt ttattttgc ctgtatttt 
gcatttgta agatcagtg tttgggcaa actgacgat 
tgcgtttgt gtccccttt tatttatgt acaaatggc 
acacttaac accaacgga gagaacatt atcgacatc 
agaatcaac gcaaacgac tgccccagt tatctagac 
ttctgttgt cccaccaaa gaagtcctt gagaaacct 
aagcccaaa tccccagtt atcccacct ggttgcggt 
caccgcaac cgcaacggc gtccagtac agtataaca 
ggagccaca gacaacgaa gcccagttt ggggaattc 
ccctgggtg gttgcaatt ttgcgcaaa gacaacgaa 
actctctcc ctccaatgt ggaggatcc ttaatccac 
ccacaagtg gtcctgacc gccgcccat tgtgtccac 
tttgtggaa caaatggta gtgcgagct ggggaatgg 
gacagtaaa acgacccaa gaacccttg aaacaccaa 
gacgtgaag gtgtcttca gccaaagtc caccccgac 
ttcaacagc aaaaatctc aaaaacgac atcgcgctc 
ctatttctt gaaactccc gtgagcttg gacgacaac 
cacattggt cttgcttgc ctcccgaga caaaataac 
gcactgtca tcaaatggt tgttacgtg aacggttgg 
gggaaaaac aaatttggg aaagacgcg gtctttcaa 
aacattctc aaaaaaatc caactgccg gttgttgca 
catgagcag tgccaggac gccttcagg aaaacaaga 
ctgggaaag tattttatc ctcaatgag agtttcgtt 
tgtgcaggt ggtgaggaa ggcaaggat gcgtgtacg 
ggagatggg ggcggtcct ctagtctgt ccaagtgag 
gaagggagg tacgaacaa gttgggatt gtgtcgtgg 
ggtatcggg tgtggggaa aaaggggta ccgggggct 
tacaccaac gttggccgc ttcaaaaat tggataaaa 
aagcaaacg cagacgagg agtttcaca attcagtga
    mRNA sequence
    • >TC001300 RA
      atactttag taaagcaaa tttaacgag ttacgtgta 
aaaatgcga cttttcaac attttattt tgcctgtat 
tttgcattt gtaagatca gtgtttggg caaactgac 
gattgcgtt tgtgtcccc ttttattta tgtacaaat 
ggcacactt aacaccaac ggagagaac attatcgac 
atcagaatc aacgcaaac gactgcccc agttatcta 
gacttctgt tgtcccacc aaagaagtc cttgagaaa 
cctaagccc aaatcccca gttatccca cctggttgc 
ggtcaccgc aaccgcaac ggcgtccag tacagtata 
acaggagcc acagacaac gaagcccag tttggggaa 
ttcccctgg gtggttgca attttgcgc aaagacaac 
gaaactctc tccctccaa tgtggagga tccttaatc 
cacccacaa gtggtcctg accgccgcc cattgtgtc 
cactttgtg gaacaaatg gtagtgcga gctggggaa 
tgggacagt aaaacgacc caagaaccc ttgaaacac 
caagacgtg aaggtgtct tcagccaaa gtccacccc 
gacttcaac agcaaaaat ctcaaaaac gacatcgcg 
ctcctattt cttgaaact cccgtgagc ttggacgac 
aaccacatt ggtcttgct tgcctcccg agacaaaat 
aacgcactg tcatcaaat ggttgttac gtgaacggt 
tgggggaaa aacaaattt gggaaagac gcggtcttt 
caaaacatt ctcaaaaaa atccaactg ccggttgtt 
gcacatgag cagtgccag gacgccttc aggaaaaca 
agactggga aagtatttt atcctcaat gagagtttc 
gtttgtgca ggtggtgag gaaggcaag gatgcgtgt 
acgggagat gggggcggt cctctagtc tgtccaagt 
gaggaaggg aggtacgaa caagttggg attgtgtcg 
tggggtatc gggtgtggg gaaaaaggg gtaccgggg 
gcttacacc aacgttggc cgcttcaaa aattggata 
aaaaagcaa acgcagacg aggagtttc acaattcag 
tgatttgtt taaatgcgc atgcgatta atgtggatg 
ttaataaaa ataaaatga ttatcatat a

    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