Status
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Gene information
General information
TC006564 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_007423.3: 11435389..11437749
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
    		TC006564
    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_10675

    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 with embryonic tissue, no cuticle, but muscle fluorescence - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): less than 30%
    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
    • >TC006564 RA
      MASGNNFPF VQEFVADPL DGITLLLDL LRAIQLSQS 
SGTTTTGKI PPSLQRRAL LDELSCLQC LLLCCQRYN 
EAVRKLTSS SAGLFTLAI CIMSNVTKS RILALQLLT 
KACNNGHSA VSEALATLR LRFGEPVRF RFLVGMLMS 
AGGQGELLV AGMKFLNTF LDTSGTMQK RIYIQAELE 
QAGFDIATI KKQISINSA STEQLFEEL DHWEKKFLD 
VESLSIRLE STERENDSL RDKVLLLER RVQILLEEK 
GILISLEQC LKERCSELQ EEVHSLKSE KSQKNSSCG 
SSKKKEDSP HEDEGISSS ERSLTPDEV LQRESSVYE 
LYNVQNPIM KKPSKIEEE DETTIDEVI EELRNIIND 
AETETYRTE EKKKLERKK IEEAQVASK IQMTVAIDD 
FSKEIEIVP SNLHPQPPR RTKSLVHLF IPAEDYDYG 
NKELFFENE TPYTSEEGS DSLLSASKY QLPRVEKGR 
KPVHRSESF RQAKQPQNP VSKQNSFDG GYFSVGVVA 
EDSKKIKSK SLDRIDDGL ETLVDIVVT AEHEVPKPE 
SLLNHQKKF SDEKMKMFL PKRDNDVLY YFPRIQERK 
NNTFLARGH NAGLYSGQV TRQNSVKKP EFVSGNNRG 
KVTDLPSGL Y
    CDS sequence
    • >TC006564 RA
      atggcttct ggcaacaat tttcccttc gtccaagaa 
ttcgtcgcc gatccactc gacggaatc actctcctc 
cttgacttg ctccgagca attcaattg agtcagtcg 
agtggcacc accaccacg ggcaaaatc cctccatcc 
ctccagcgg cgcgccctc ctcgacgag ctctcctgc 
ctccaatgc ctcctgctc tgctgtcaa agatacaac 
gaagcggtc cgaaaactc acatcttcc tcagccggg 
cttttcact ctagccatt tgcattatg agcaatgtg 
acgaaatcg cgaattctg gcccttcag ttactgacc 
aaggcctgt aataacggc cacagcgcg gtctccgaa 
gccctagcc acgctcagg cttaggttt ggggagccg 
gtcaggttt aggtttctg gtgggcatg ctcatgtcg 
gcagggggg caaggcgag ctgctagtg gccgggatg 
aaattcctg aatacgttc ctggacacg tccgggacc 
atgcaaaag aggatttat atccaagcc gagttggaa 
caggcaggt tttgatatc gcaacgatc aaaaaacaa 
attagtatt aattcagcc tcgactgag caacttttc 
gaggagttg gatcattgg gagaagaag tttctcgat 
gttgaaagt ctctcaatc aggcttgag agcacggaa 
cgtgaaaat gactcgttg agggataaa gtgttgttg 
ttggaacga cgagttcag attcttttg gaggaaaaa 
gggattttg atttcgctc gagcagtgt ctgaaagaa 
cgctgcagt gaattgcag gaggaagtc cattcgttg 
aagtccgaa aagtcgcaa aagaactct tcgtgtgga 
agttcgaag aagaaagaa gactctccc catgaagac 
gagggcatt tcttcatcc gagagaagc ctcacgcct 
gacgaagtc ctccagcgc gaatcctcc gtctacgag 
ctgtacaac gtccaaaac cccatcatg aagaaaccg 
tcaaaaatc gaagaagaa gacgaaaca accatcgac 
gaagtgatc gaagagtta cggaacata ataaacgac 
gcggaaacc gagacctac cgaacggaa gaaaagaag 
aaactcgaa cgcaaaaaa attgaagaa gcacaagtc 
gccagcaaa atccaaatg acggtggcc atcgacgac 
ttcagcaaa gaaatagaa atagtccct tcgaacctc 
cacccccag ccccctcga cgcaccaaa agcctcgtc 
cacttattt atcccagct gaagattac gattacggt 
aacaaggag ttatttttc gaaaacgaa acaccgtac 
actagtgaa gaaggctcc gattcgctc ctaagtgcc 
tccaagtac caactacca cgggtggaa aaggggcgc 
aagcccgtc caccggtcg gagtccttc agacaagcc 
aagcagccc caaaacccc gtctcgaaa cagaacagc 
ttcgacggg ggttatttc agcgtgggg gttgtcgcc 
gaagactcg aaaaaaatc aagtcgaag agtttggac 
cgaatcgac gacggttta gagactttg gttgatatt 
gtggtcaca gcagaacac gaagtcccc aagcctgag 
tcgctcctc aaccaccag aagaagttc agtgatgag 
aaaatgaag atgtttttg cccaagcgc gacaatgac 
gtgctttat tacttcccg aggatacaa gagcggaaa 
aataacacg ttcctggcg cggggccac aacgccggg 
ttgtactcg gggcaagtg acaagacaa aactcggtg 
aagaaaccg gagtttgtc tcggggaat aaccggggg 
aaagtgacg gatttaccg tcgggactt tactga
    mRNA sequence
    • >TC006564 RA
      aaagaaaaa gccatggct tctggcaac aattttccc 
ttcgtccaa gaattcgtc gccgatcca ctcgacgga 
atcactctc ctccttgac ttgctccga gcaattcaa 
ttgagtcag tcgagtggc accaccacc acgggcaaa 
atccctcca tccctccag cggcgcgcc ctcctcgac 
gagctctcc tgcctccaa tgcctcctg ctctgctgt 
caaagatac aacgaagcg gtccgaaaa ctcacatct 
tcctcagcc gggcttttc actctagcc atttgcatt 
atgagcaat gtgacgaaa tcgcgaatt ctggccctt 
cagttactg accaaggcc tgtaataac ggccacagc 
gcggtctcc gaagcccta gccacgctc aggcttagg 
tttggggag ccggtcagg tttaggttt ctggtgggc 
atgctcatg tcggcaggg gggcaaggc gagctgcta 
gtggccggg atgaaattc ctgaatacg ttcctggac 
acgtccggg accatgcaa aagaggatt tatatccaa 
gccgagttg gaacaggca ggttttgat atcgcaacg 
atcaaaaaa caaattagt attaattca gcctcgact 
gagcaactt ttcgaggag ttggatcat tgggagaag 
aagtttctc gatgttgaa agtctctca atcaggctt 
gagagcacg gaacgtgaa aatgactcg ttgagggat 
aaagtgttg ttgttggaa cgacgagtt cagattctt 
ttggaggaa aaagggatt ttgatttcg ctcgagcag 
tgtctgaaa gaacgctgc agtgaattg caggaggaa 
gtccattcg ttgaagtcc gaaaagtcg caaaagaac 
tcttcgtgt ggaagttcg aagaagaaa gaagactct 
ccccatgaa gacgagggc atttcttca tccgagaga 
agcctcacg cctgacgaa gtcctccag cgcgaatcc 
tccgtctac gagctgtac aacgtccaa aaccccatc 
atgaagaaa ccgtcaaaa atcgaagaa gaagacgaa 
acaaccatc gacgaagtg atcgaagag ttacggaac 
ataataaac gacgcggaa accgagacc taccgaacg 
gaagaaaag aagaaactc gaacgcaaa aaaattgaa 
gaagcacaa gtcgccagc aaaatccaa atgacggtg 
gccatcgac gacttcagc aaagaaata gaaatagtc 
ccttcgaac ctccacccc cagccccct cgacgcacc 
aaaagcctc gtccactta tttatccca gctgaagat 
tacgattac ggtaacaag gagttattt ttcgaaaac 
gaaacaccg tacactagt gaagaaggc tccgattcg 
ctcctaagt gcctccaag taccaacta ccacgggtg 
gaaaagggg cgcaagccc gtccaccgg tcggagtcc 
ttcagacaa gccaagcag ccccaaaac cccgtctcg 
aaacagaac agcttcgac gggggttat ttcagcgtg 
ggggttgtc gccgaagac tcgaaaaaa atcaagtcg 
aagagtttg gaccgaatc gacgacggt ttagagact 
ttggttgat attgtggtc acagcagaa cacgaagtc 
cccaagcct gagtcgctc ctcaaccac cagaagaag 
ttcagtgat gagaaaatg aagatgttt ttgcccaag 
cgcgacaat gacgtgctt tattacttc ccgaggata 
caagagcgg aaaaataac acgttcctg gcgcggggc 
cacaacgcc gggttgtac tcggggcaa gtgacaaga 
caaaactcg gtgaagaaa ccggagttt gtctcgggg 
aataaccgg gggaaagtg acggattta ccgtcggga 
ctttactga tttaatgta aataattat ttatctgtg 
caatattag agtacacga ggttagggt ttgaggggg 
cacttgggc cgttcttgg cgagaacgg gccccaagt 
ggcggaatg tacaaaaag gggtagatt atgatctcg 
agtgtctat attttaata aaatggttc tcaaacg

    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