Status
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Gene information
General information
TC000687 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: 7589176..7591303
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
    		TC000687
    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_00154

    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: 20.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 1 (3 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection

    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     abdomen partially circumference decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    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
    • >TC000687 RA
      MPSNNTKVV KSPTENMLL SPAETPSQV VPEKVKMKK 
QLGLLEGVA IILGIIFGS GIFISPKGI IQEVNSVGF 
SLVVWVLCG LLSMIGALC YAELGTTIP KSGGDYAYI 
YEAFGPLPS FLYLWAANL IFVPTTNAI MGLTFAKYV 
IQPFFRSCD LPEDGATVV AACTICFLT FLNGYNVKA 
TTRVQNVFM FCKIGALVL VIIIGVVWM GFGHVENFQ 
RPFEGTTTN VGKMSKAFY SGIFSYSGW NYLNFMTEE 
LKNPYVNLP RAIYLSIPL VTLIYVLAN MAYLSVLTP 
DAMISSDAI AVTFGNNVL GSWAWIIPV MVAISAFGG 
LSVHIMTSS RMLYVGARN GHFPTMLSH LNIQKCSPM 
PSLAFLNIL SLFMLCTND IHTLITYCT IVESFFVML 
SVSGLLYLR WKKPEIARP IKVNIVVPI IFVLICLFL 
IILPCFEAP YEVLGGVLI TLSGVPVYF RAVRQNKPL 
LPQSFMAKM TEICQKIFI SAHEDEDVE E
    CDS sequence
    • >TC000687 RA
      atgccttca aacaatacc aaagtagtg aaatcacca 
acagaaaac atgctccta tcacccgcc gaaacccca 
tctcaggtg gtgccagaa aaagtcaaa atgaagaag 
cagttaggc ttgcttgaa ggagtcgcg attattttg 
gggatcata tttgggtca gggattttt atttcgcca 
aaggggata atccaggaa gtaaattca gtcggattc 
tcgctagtt gtgtgggtt ctttgtgga ttattatca 
atgattggg gccctgtgt tatgccgag ttgggcaca 
actataccc aaatcaggg ggcgactat gcctacatc 
tatgaggct ttcggcccc ttaccttca tttttgtat 
ttgtgggcg gcaaactta atttttgta cccacaact 
aacgcaatc atgggcctc acgtttgcc aaatacgtg 
attcaacct ttcttccgc tcgtgcgat ttaccagag 
gatggagcc acagttgtg gccgcttgt acaatttgc 
ttccttact tttttgaac ggttataac gtgaaagcc 
accacgagg gtgcaaaat gtgttcatg ttttgcaaa 
attggggcg cttgtactt gtcattatt attggggtc 
gtgtggatg ggctttgga cacgtggag aattttcag 
aggcccttt gagggaacg actaccaac gtgggcaaa 
atgtccaaa gctttctac tcgggaatt ttctcatac 
tcgggctgg aattatttg aattttatg acggaggaa 
ctgaagaat ccttacgtt aatcttcca cgagcaatt 
tatctttca atacctcta gttacactg atttatgtt 
ttggcaaac atggcctat ttgtcagtc ctaacaccg 
gacgctatg atatcttca gatgccata gctgtgact 
tttggtaac aatgtgttg gggagctgg gcttggatt 
atcccagtg atggtcgcg atctcggcc tttggaggc 
ctcagtgtt cacatcatg acatcctca cgcatgttg 
tatgtgggt gccagaaat ggccacttt cccacaatg 
ctctctcat ttgaacatt caaaagtgt tcaccaatg 
ccttcgctc gcatttctt aacatcctt tctctcttc 
atgctgtgc actaacgac atccataca cttatcacg 
tactgcact attgtggaa tcatttttc gtcatgttg 
tccgtgtcg ggacttttg tacttgagg tggaagaaa 
ccagaaatc gcaagacca atcaaagtc aatatcgta 
gttccaatt atcttcgtc ttaatttgt ctgtttctt 
atcatttta ccgtgtttt gaagctccc tatgaggtg 
ttagggggc gtgttaatc accttgtcg ggagtacct 
gtttatttt agggccgtc agacaaaat aagccttta 
ttaccgcaa agcttcatg gccaaaatg actgaaata 
tgtcaaaaa atatttatt tctgctcat gaggatgaa 
gacgtggag gagtaa
    mRNA sequence
    • >TC000687 RA
      caacatgcg cccaagcaa ctaacctga aaaatgcac 
gtgtgctat ttgtagcat tgcattggt tttgtttcc 
gttaaaata gcagtatta tacgaatct ctagcaaga 
acaaactgg taaaagtaa aatttctag tcaatacaa 
aaaattacc aaaaatgcc ttcaaacaa taccaaagt 
agtgaaatc accaacaga aaacatgct cctatcacc 
cgccgaaac cccatctca ggtggtgcc agaaaaagt 
caaaatgaa gaagcagtt aggcttgct tgaaggagt 
cgcgattat tttggggat catatttgg gtcagggat 
ttttatttc gccaaaggg gataatcca ggaagtaaa 
ttcagtcgg attctcgct agttgtgtg ggttctttg 
tggattatt atcaatgat tggggccct gtgttatgc 
cgagttggg cacaactat acccaaatc agggggcga 
ctatgccta catctatga ggctttcgg ccccttacc 
ttcattttt gtatttgtg ggcggcaaa cttaatttt 
tgtacccac aactaacgc aatcatggg cctcacgtt 
tgccaaata cgtgattca acctttctt ccgctcgtg 
cgatttacc agaggatgg agccacagt tgtggccgc 
ttgtacaat ttgcttcct tactttttt gaacggtta 
taacgtgaa agccaccac gagggtgca aaatgtgtt 
catgttttg caaaattgg ggcgcttgt acttgtcat 
tattattgg ggtcgtgtg gatgggctt tggacacgt 
ggagaattt tcagaggcc ctttgaggg aacgactac 
caacgtggg caaaatgtc caaagcttt ctactcggg 
aattttctc atactcggg ctggaatta tttgaattt 
tatgacgga ggaactgaa gaatcctta cgttaatct 
tccacgagc aatttatct ttcaatacc tctagttac 
actgattta tgttttggc aaacatggc ctatttgtc 
agtcctaac accggacgc tatgatatc ttcagatgc 
catagctgt gacttttgg taacaatgt gttggggag 
ctgggcttg gattatccc agtgatggt cgcgatctc 
ggcctttgg aggcctcag tgttcacat catgacatc 
ctcacgcat gttgtatgt gggtgccag aaatggcca 
ctttcccac aatgctctc tcatttgaa cattcaaaa 
gtgttcacc aatgccttc gctcgcatt tcttaacat 
cctttctct cttcatgct gtgcactaa cgacatcca 
tacacttat cacgtactg cactattgt ggaatcatt 
tttcgtcat gttgtccgt gtcgggact tttgtactt 
gaggtggaa gaaaccaga aatcgcaag accaatcaa 
agtcaatat cgtagttcc aattatctt cgtcttaat 
ttgtctgtt tcttatcat tttaccgtg ttttgaagc 
tccctatga ggtgttagg gggcgtgtt aatcacctt 
gtcgggagt acctgttta ttttagggc cgtcagaca 
aaataagcc tttattacc gcaaagctt catggccaa 
aatgactga aatatgtca aaaaatatt tatttctgc 
tcatgagga tgaagacgt ggaggagta atttttgta 
ttgtttagg tagtttcgt taaaaaaaa 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