Status
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Gene information
General information
TC008188 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_007419.2: 6322580..6324644
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
    		TC008188
    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_07194

    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: 50.0% (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: 2 (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: 2
    mature egg deposition blocked number 1st lateral oviduct: 2 number 2nd lateral oviduct: - Number of animals showing the phenotype: 2
    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%

    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: < 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
    • >TC008188 RA
      MAPVDVEAP PMENQLRNL VLSGHVGFD SLPDQLVSK 
SVQNGFVFN IMCIGETGL GKSTLMDSL FNTNFEAVP 
SPHTLPTVK LKAHTYELQ ESNVRLKLT IVDTVGYGD 
QINKEDSFK AIVDYIDAQ FENYLQEEL KIKRSLTTF 
HDSRIHVCL YFICPTGHG LKSIDLVCM KKLDQKVNI 
IPIIAKADT ISKTELQKF KTKIVAELQ NNGVHIYEF 
PVDDESVAE VNGTMNSHV PFAVIGSTD FVRVGNKMV 
RARQYPWGT VQVENESHC DFVKLREML IRTNMEDMR 
EKTHCRHYE LYRRKRLEQ MGFSDVDAD NKPISFQQT 
FEAKRSNHL QELQQKEDE MRQMFVVRV KEKEAELKE 
AEKELHAKF DKLKKDHTD EKKKIEDSR KKLEDEIVE 
FNRRKAQYQ QMGTSHHTL TLGKSKKK
    CDS sequence
    • >TC008188 RA
      atggcacca gtggacgtt gaagcgcct ccgatggaa 
aatcagttg cgaaatttg gttttgtca ggccatgtg 
ggctttgat agtttgccg gatcaattg gtgtcgaaa 
agtgtccaa aacggcttt gttttcaac atcatgtgc 
atcggggaa actgggtta ggcaagtcg actctgatg 
gactcattg ttcaatacg aactttgag gcggtcccg 
agcccccat accttgccc acggtcaag ctaaaggca 
cacacttac gaattgcaa gaaagtaac gtgcgactt 
aagttaaca attgtggac actgtgggg tacggcgac 
cagatcaat aaggaggac agttttaag gcaatcgtt 
gactacatt gacgcccaa tttgagaac tacctccaa 
gaggagctc aagatcaaa cgctcgctt accacgttt 
cacgattcg cgcattcac gtctgcttg tatttcatt 
tgtcccacg ggacacggc ttgaagtca attgacctg 
gtttgcatg aaaaaactt gaccagaaa gtcaacatt 
atcccaatt atcgcaaaa gctgatacc atttcaaag 
acagagctc caaaaattc aagactaaa atcgtagca 
gagctgcaa aataatggc gtacacatt tacgaattc 
ccggttgat gatgaatca gttgctgag gtaaatggt 
accatgaac tcccatgta ccatttgcg gtgattggc 
agcactgat ttcgtccgg gttgggaat aaaatggta 
agggcccgg caatatccc tggggtacg gtgcaagtc 
gagaatgaa tcgcactgc gattttgtc aaattacgc 
gaaatgttg atcagaacg aacatggaa gatatgagg 
gagaagacg cactgtcgt cactatgaa ttgtacaga 
cgaaagcgc ttggaacag atgggtttc agtgatgtt 
gacgctgat aacaagccc atcagcttt cagcaaact 
tttgaggcc aagaggtcc aatcatttg caagagttg 
cagcaaaaa gaggacgaa atgaggcaa atgtttgtg 
gtgcgtgtg aaggaaaag gaagccgag ctgaaggaa 
gcggaaaaa gagctgcat gcgaaattc gataaattg 
aaaaaggat cacactgac gagaagaag aaaatcgag 
gacagtcgc aagaagctt gaggatgag atagttgag 
ttcaacaga cgtaaggcc cagtaccag cagatgggc 
acaagtcac cacactcta accttggga aaaagtaaa 
aagaaataa
    mRNA sequence
    • >TC008188 RA
      gaagacgtt aaagttggg tgtttgttg tgcttgttt 
atccgttcc ttcgtgact taaattata aacaaatta 
acagttaac aatggcacc agtggacgt tgaagcgcc 
tccgatgga aaatcagtt gcgaaattt ggttttgtc 
aggccatgt gggctttga tagtttgcc ggatcaatt 
ggtgtcgaa aagtgtcca aaacggctt tgttttcaa 
catcatgtg catcgggga aactgggtt aggcaagtc 
gactctgat ggactcatt gttcaatac gaactttga 
ggcggtccc gagccccca taccttgcc cacggtcaa 
gctaaaggc acacactta cgaattgca agaaagtaa 
cgtgcgact taagttaac aattgtgga cactgtggg 
gtacggcga ccagatcaa taaggagga cagttttaa 
ggcaatcgt tgactacat tgacgccca atttgagaa 
ctacctcca agaggagct caagatcaa acgctcgct 
taccacgtt tcacgattc gcgcattca cgtctgctt 
gtatttcat ttgtcccac gggacacgg cttgaagtc 
aattgacct ggtttgcat gaaaaaact tgaccagaa 
agtcaacat tatcccaat tatcgcaaa agctgatac 
catttcaaa gacagagct ccaaaaatt caagactaa 
aatcgtagc agagctgca aaataatgg cgtacacat 
ttacgaatt cccggttga tgatgaatc agttgctga 
ggtaaatgg taccatgaa ctcccatgt accatttgc 
ggtgattgg cagcactga tttcgtccg ggttgggaa 
taaaatggt aagggcccg gcaatatcc ctggggtac 
ggtgcaagt cgagaatga atcgcactg cgattttgt 
caaattacg cgaaatgtt gatcagaac gaacatgga 
agatatgag ggagaagac gcactgtcg tcactatga 
attgtacag acgaaagcg cttggaaca gatgggttt 
cagtgatgt tgacgctga taacaagcc catcagctt 
tcagcaaac ttttgaggc caagaggtc caatcattt 
gcaagagtt gcagcaaaa agaggacga aatgaggca 
aatgtttgt ggtgcgtgt gaaggaaaa ggaagccga 
gctgaagga agcggaaaa agagctgca tgcgaaatt 
cgataaatt gaaaaagga tcacactga cgagaagaa 
gaaaatcga ggacagtcg caagaagct tgaggatga 
gatagttga gttcaacag acgtaaggc ccagtacca 
gcagatggg cacaagtca ccacactct aaccttggg 
aaaaagtaa aaagaaata agcttgttg tatgtattt 
taaaatgtt tattgatta cgcaatttt atctatatt 
tattatttt aacttagtg atttttgtg cttgttctg 
tgtagttga aaaatatat ttattatgg aaattgatt 
acaactata gaccaaagt atttttaaa gtaatacag 
cgaattcgt gtcaatgta agccttgca tactgtatt 
gcgttttct ttttatatt tttatgact aaaatatag 
tttttttat tcta

    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