Status
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Gene information
General information
TC006223 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: 5355468..5359392
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
      		TC006223
      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_04092

      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: 30.0% (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

      Fertility
      ovary without detectable defects - Number of animals showing the phenotype: 4
      Analysis of larval stage 1 cuticle
      number of eggs/embryos/larvae on slide: < 20
       antenna cuticularisation decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%

      antenna shape irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%
      affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - 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: 0.0% (includes death as larva, prepupa, pupa)
      Lethalities 22 days after larval injection: 0.0% (includes death as larva, prepupa, pupa, adult)

      Fertility
      egg production: number no/almost no eggs -
      vitellogenic egg chamber number increased - Number of animals showing the phenotype: 4

      mature egg number increased - Number of animals showing the phenotype: 4

      Comment: In each ovariole there is not more than one old follicle/mature egg, hence not held egg.
      RNAi sequence
      Primers
      Left: Right:
      Protein sequence
      • >TC006223 RA
        MWWLWKSTN NLPEATGPF TPGCMDVML DYSHEGIFM 
RLYYPTNEA KKDPRNFHR WVPWIPSAN YFIGLSKVL 
MIFPFIIRF VYWWCHTNI VPALYGSRP KTDQKLKCI 
VLSHGLGGY RSLYSNTCC ELASRGFLV AALEHRDGS 
SCYTYYYKS EEDARNQRP TNIEYEPFV LGKTHHKQR 
RRQVEHRAK ECGKVADFF ADLNSGKVP HNVICDVPT 
RRQIDFDLA DFVGKLDLT TLTIAGHSF GGATALLTL 
DQRREFKHG ILLDPWMYP IKDEGLEAK ITQPLIFIN 
TQTFHIMSN VSSMAKFLT SDDRTMFTI LHTTHENQT 
DSALVVGYW LNWFMKKLD PLVALKINN SLILEFLDK 
WVKCPSDVS DCREYLQEQ GSNLDKVLL ALGFKLKIV 
ALLFN
      CDS sequence
      • >TC006223 RA
        atgtggtgg ttgtggaaa agtacgaat aatttacct 
gaagccacg gggcctttt acgccgggc tgcatggac 
gtcatgctc gactatagc cacgagggc attttcatg 
cgtctctac taccccaca aacgaggcc aagaaagat 
ccaaggaat ttccaccgt tgggtccct tggatcccc 
tcagcgaac tactttata ggcctttca aaagtgtta 
atgatcttt cctttcata atccgattc gtgtactgg 
tggtgtcac acaaacatc gtccccgcc ttatatgga 
agtcgcccg aaaaccgac caaaaactg aaatgtatt 
gtcttatct cacggtttg ggtggttac aggtcattg 
tacagcaac acatgctgc gaattagcc tcgagaggg 
tttttagtg gcggctttg gagcacagg gacggctcc 
tcctgttac acctactac tacaaatcg gaggaagac 
gcccgaaat cagcgcccg accaacatc gagtacgag 
ccctttgtc ttgggcaaa acgcaccac aagcagcgg 
aggcgccag gtggagcac agagccaag gagtgcgga 
aaagtcgcc gactttttc gctgactta aacagcggg 
aaagtgccc cacaatgtg atttgtgac gtccccaca 
cggcgccaa attgacttc gatttggcc gattttgtc 
ggaaaactg gacttgaca acgctcaca atagcagga 
cattcgttc ggcggagct acggccctt ttgactttg 
gaccaaaga agggagttc aagcacggg attttgctg 
gacccttgg atgtatccg atcaaggac gagggtttg 
gaggcgaaa ataacccaa cctttgatt tttatcaac 
actcagacg ttccacatc atgagcaat gtcagttcc 
atggcgaaa ttcctaacg agcgacgac cggacaatg 
ttcacgatt ttgcatact actcacgaa aatcagact 
gattcggct ctagttgtg ggttattgg ctcaattgg 
ttcatgaag aagttggac cctttggtt gcgctcaaa 
attaacaat agtctaatt ctcgaattt ttggataag 
tgggttaaa tgtccgagt gatgttagc gattgtcgg 
gagtatctc caggagcaa ggatcgaat ctagacaag 
gtcttactc gcccttggc tttaaatta aaaattgtt 
gctttattg tttaattaa
      mRNA sequence
      • >TC006223 RA
        agtgtttag aatacaaag aaagtgcaa gaagttctg 
tcaaagcca aagcgtaac aaactttcg agctgtcat 
aacctaact ttttggtat ttggctaat aattgggac 
ttggggggt tactgagac ttgtgatta attaaaatg 
tggtggttg tggaaaagt acgaataat ttacctgaa 
gccacgggg ccttttacg ccgggctgc atggacgtc 
atgctcgac tatagccac gagggcatt ttcatgcgt 
ctctactac cccacaaac gaggccaag aaagatcca 
aggaatttc caccgttgg gtcccttgg atcccctca 
gcgaactac tttataggc ctttcaaaa gtgttaatg 
atctttcct ttcataatc cgattcgtg tactggtgg 
tgtcacaca aacatcgtc cccgcctta tatggaagt 
cgcccgaaa accgaccaa aaactgaaa tgtattgtc 
ttatctcac ggtttgggt ggttacagg tcattgtac 
agcaacaca tgctgcgaa ttagcctcg agagggttt 
ttagtggcg gctttggag cacagggac ggctcctcc 
tgttacacc tactactac aaatcggag gaagacgcc 
cgaaatcag cgcccgacc aacatcgag tacgagccc 
tttgtcttg ggcaaaacg caccacaag cagcggagg 
cgccaggtg gagcacaga gccaaggag tgcggaaaa 
gtcgccgac tttttcgct gacttaaac agcgggaaa 
gtgccccac aatgtgatt tgtgacgtc cccacacgg 
cgccaaatt gacttcgat ttggccgat tttgtcgga 
aaactggac ttgacaacg ctcacaata gcaggacat 
tcgttcggc ggagctacg gcccttttg actttggac 
caaagaagg gagttcaag cacgggatt ttgctggac 
ccttggatg tatccgatc aaggacgag ggtttggag 
gcgaaaata acccaacct ttgattttt atcaacact 
cagacgttc cacatcatg agcaatgtc agttccatg 
gcgaaattc ctaacgagc gacgaccgg acaatgttc 
acgattttg catactact cacgaaaat cagactgat 
tcggctcta gttgtgggt tattggctc aattggttc 
atgaagaag ttggaccct ttggttgcg ctcaaaatt 
aacaatagt ctaattctc gaatttttg gataagtgg 
gttaaatgt ccgagtgat gttagcgat tgtcgggag 
tatctccag gagcaagga tcgaatcta gacaaggtc 
ttactcgcc cttggcttt aaattaaaa attgttgct 
ttattgttt aattaataa acgttgatt tggtttatt 
agtcgttt

      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