Status
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Gene information
General information
TC011313 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_007425.3: 3177794..3180627
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
    		TC011313
    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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    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_05012

    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 embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg not developed/not fertilized - Penetrance (percentage of animals/eggs on slide): more than 80%

    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: 30.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 40.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 3 (11 dpi)
    Days post injection

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 1 (16 dpi)
    Days post injection

    Fertility
    egg production: number <50% of expected -
    vitellarium not present - Number of animals showing the phenotype: 3

    previtellogenic egg chamber not present - Number of animals showing the phenotype: 3
    vitellogenic egg chamber not present - Number of animals showing the phenotype: 3
    tropharium size shortened - Number of animals showing the phenotype: 3
    tropharium shape irregular - Number of animals showing the phenotype: 3
    fertility after larval injection decreased (no living offspring) -
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC011313 RA
      MTTIGDAAL ENRENIPLQ KGRKSATFC SCSEDYLSG 
SKFINVAFG TLTVIITAA LLLQIYYGD YQVVPHGSV 
ATDSLECSK IGTQILKKG GNSVDAAIA SVFCLAVVT 
PHLTSLDGE GQLLVYNHR ARLIPDVIE FNVGNNDAE 
HLLPRLVLG LAFVHQQYG TVPWKELVQ PAAELARRG 
FLIPKMLVQ AIKQAKAED LYGRLEPGQ MLQLENLSN 
TLAQIANIP EKELYSFVK PENQPRYSP ALKLTFNAY 
DIYVPDRPS LGPALLTYL KQLESFNFT KTDTTRTEY 
IYRLAETAQ NLYNDLNLT SKYHTGTST NVAVMDLND 
NYVSFTTGL YALFGTGEM TTGGYTLDV HPKATPCSR 
LPVIITDAQ AICGRRLLL GANDLSTAS QLVMSLLVA 
QENITNAVE APRFHILDN GGVGIESAH SPAFTDDVL 
KYLETLTTS PVLVPEPYM SSNIVEKVK DELNSHSDS 
RGGGIASRF
    CDS sequence
    • >TC011313 RA
      atgacaaca atcggagat gctgcctta gaaaatagg 
gaaaatata ccgttgcag aaaggtcgc aaaagcgcg 
actttctgc tcgtgcagt gaggactat ttgagtggt 
tccaagttt ataaatgtg gcttttggg actttaaca 
gtaataatc acagcggct ttgttacta caaatttat 
tacggtgac tatcaggtg gtcccccat ggcagtgtt 
gccactgac agccttgaa tgctcaaaa ataggcact 
caaattttg aaaaagggc ggcaattcc gtcgatgct 
gcaatagcg agtgttttt tgcctcgcc gttgtcact 
ccacacttg acaagtttg gacggagaa ggccaactt 
ctcgtctat aatcaccgg gcaaggctt atcccggac 
gtgattgaa ttcaatgtt ggcaacaat gacgcggaa 
catttgcta ccaaggctg gtcctgggg ctggctttt 
gtgcaccaa cagtacggc acagtgccc tggaaggag 
ctggtacag cctgcggca gagctagcc agacggggg 
tttctcata cccaaaatg ttggtccag gcgatcaaa 
caggccaaa gccgaggat ttgtacggc aggcttgag 
ccgggacaa atgctacaa ctcgagaat ttgagcaat 
actttggcc caaatcgcc aacatcccc gagaaagaa 
ctgtacagt ttcgtcaaa cctgaaaac cagcccagg 
tattccccc gccctcaaa ctcacattc aacgcctac 
gacatatac gtaccggat cgcccctcc ctaggcccc 
gccctcttg acttacctc aaacaactg gaaagtttc 
aatttcacc aaaactgac accactcgc actgaatac 
atctaccga ttggccgaa acggcccaa aacctctac 
aacgacctc aacctgacc tccaaatac cacacgggg 
acgtcaacc aacgtcgct gtcatggac ctgaacgac 
aactacgtg tcattcacc acagggttg tacgccctc 
ttcggcacg ggcgagatg accactggg ggctacacc 
ctcgacgtc caccccaaa gccacgcct tgctcccgc 
ctacctgtc ataatcacc gacgctcag gccatttgt 
gggcggcgc ctcttgctg ggagccaat gacctctca 
acggcgtcg caactcgtg atgtcattg ctcgtcgcc 
caggaaaat atcaccaat gcggtcgaa gcgccgcgg 
tttcatatc ctggacaac gggggcgtg ggcatcgag 
agcgcgcac tcgccggcg ttcactgac gacgtcctc 
aagtatctc gaaacgttg acgacgagc ccggtcctg 
gtgcccgag ccctacatg agcagcaac atcgtggag 
aaggtcaag gacgagctc aactcgcac tcggacagt 
cgaggtggg ggcattgcg agcaggttt taa
    mRNA sequence
    • >TC011313 RA
      atccaataa gaaatgtga aaggaggcg tgaccgaaa 
caaacgaaa cgagtcgac ttcgcgatt cgtacttaa 
gtaggtaaa taagtaaag ttcagtgta cttaattga 
ttacagttc ggcgaaaaa aagaaaaaa aattgttta 
tttatagtt tttaaatta ttgggcgtg tttgatgga 
aaatgacaa caatcggag atgctgcct tagaaaata 
gggaaaata taccgttgc agaaaggtc gcaaaagcg 
cgactttct gctcgtgca gtgaggact atttgagtg 
gttccaagt ttataaatg tggcttttg ggactttaa 
cagtaataa tcacagcgg ctttgttac tacaaattt 
attacggtg actatcagg tggtccccc atggcagtg 
ttgccactg acagccttg aatgctcaa aaataggca 
ctcaaattt tgaaaaagg gcggcaatt ccgtcgatg 
ctgcaatag cgagtgttt tttgcctcg ccgttgtca 
ctccacact tgacaagtt tggacggag aaggccaac 
ttctcgtct ataatcacc gggcaaggc ttatcccgg 
acgtgattg aattcaatg ttggcaaca atgacgcgg 
aacatttgc taccaaggc tggtcctgg ggctggctt 
ttgtgcacc aacagtacg gcacagtgc cctggaagg 
agctggtac agcctgcgg cagagctag ccagacggg 
ggtttctca tacccaaaa tgttggtcc aggcgatca 
aacaggcca aagccgagg atttgtacg gcaggcttg 
agccgggac aaatgctac aactcgaga atttgagca 
atactttgg cccaaatcg ccaacatcc ccgagaaag 
aactgtaca gtttcgtca aacctgaaa accagccca 
ggtattccc ccgccctca aactcacat tcaacgcct 
acgacatat acgtaccgg atcgcccct ccctaggcc 
ccgccctct tgacttacc tcaaacaac tggaaagtt 
tcaatttca ccaaaactg acaccactc gcactgaat 
acatctacc gattggccg aaacggccc aaaacctct 
acaacgacc tcaacctga cctccaaat accacacgg 
ggacgtcaa ccaacgtcg ctgtcatgg acctgaacg 
acaactacg tgtcattca ccacagggt tgtacgccc 
tcttcggca cgggcgaga tgaccactg ggggctaca 
ccctcgacg tccacccca aagccacgc cttgctccc 
gcctacctg tcataatca ccgacgctc aggccattt 
gtgggcggc gcctcttgc tgggagcca atgacctct 
caacggcgt cgcaactcg tgatgtcat tgctcgtcg 
cccaggaaa atatcacca atgcggtcg aagcgccgc 
ggtttcata tcctggaca acgggggcg tgggcatcg 
agagcgcgc actcgccgg cgttcactg acgacgtcc 
tcaagtatc tcgaaacgt tgacgacga gcccggtcc 
tggtgcccg agccctaca tgagcagca acatcgtgg 
agaaggtca aggacgagc tcaactcgc actcggaca 
gtcgaggtg ggggcattg cgagcaggt tttaagcac 
gagccaaag acgagtgac taatttatt gtactcttg 
gaaataaat aaagcgggt tatt

    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