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Gene information
General information
TC006402 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: 8451309..8454852
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
      TC006402
      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
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      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_10496

      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)

      adult lethality - Number of animals showing the phenotype: 2 (9 dpi)
      Days post injection


      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
      • >TC006402 RA
        MFYVKNPSA LNKPWILSK KGDENVVAI PLEVCRLLK 
        NYHIMTIEF LYHNYRKGV KGAVLNQQR GMNFSLQIG 
        AFLRAIVQS PALILVICS RESSCYWHY HLVNHAGFD 
        VVQITSKNA DDTYESNNK IALLVTHDC LKLCEGLLD 
        CDFFSVIVE DLDQLALKR IIKRLNGTF NVGLTTRSF 
        YTHPDQKLQ WNMLNWANP GCVGKLNDF YEADNRNFE 
        RFDDNYRYW WMRLTWDFC ESFEKPTDE ETDTYERKI 
        SEWASQNDL NFPKKQSRK RKHPPKTEP PPENDSSND 
        TIINEVPID KYVKLPSMD ESPIVTSII KNFEISPEP 
        ILTRTSSLP YTQTHASYS KYEEDSVLF AFLDDKERP 
        STSKSESEE FILSLINKS EDESKDIRK KADAVLQN
      CDS sequence
      • >TC006402 RA
        atgttctac gttaaaaat ccttccgct ctcaacaag 
        ccgtggatt ttgtccaaa aaaggcgac gaaaatgtc 
        gttgcaatc ccgcttgaa gtttgcaga cttttaaaa 
        aactaccat ataatgaca attgagttt ctctaccac 
        aactaccgg aaaggggtc aagggggcg gttttgaac 
        caacagcgc gggatgaat ttcagttta cagattggg 
        gcgtttctc agagctatt gtgcaaagt ccggccctt 
        attttggtt atttgtagt agagaatcg agttgttac 
        tggcattac cacctggta aaccacgcc ggttttgac 
        gtcgttcaa ataacttca aaaaacgct gatgatact 
        tacgagagc aataacaaa atagcttta cttgtaaca 
        catgactgc ttgaaacta tgcgagggg ctactcgat 
        tgtgacttt ttttccgtc attgtggag gatttggac 
        caactcgcg ctcaaacga attattaaa agactgaat 
        gggacgttc aatgtgggg ctcacaact cggagtttt 
        tacacacat cccgatcaa aaattgcaa tggaacatg 
        ttgaactgg gccaacccc ggctgtgtc ggcaaatta 
        aacgacttc tacgaggcc gacaaccgc aatttcgaa 
        cgatttgac gacaattac cgttactgg tggatgaga 
        ctgacttgg gacttttgc gaatcgttt gaaaaaccc 
        accgacgag gaaaccgac acttacgag aggaaaata 
        tcagagtgg gcttcccaa aacgactta aactttccc 
        aaaaaacaa tcacgcaaa cgtaaacac cccccaaag 
        actgaacca cctccagag aacgacagc tccaacgat 
        acaatcatc aacgaagtg ccaattgat aaatacgtc 
        aagttgccc agcatggac gagagccct attgtcact 
        tccattatt aaaaatttt gagatttct cccgaaccg 
        attctcact cgtacgtct tcgttgcca tatactcaa 
        actcacgcg agttactcc aagtatgaa gaagatagt 
        gtgctgttt gcgtttttg gatgataag gagcggccc 
        agcacttca aaaagcgag tcagaggag ttcattctg 
        agtttgatc aacaagtcg gaagacgaa tcaaaagat 
        attcggaaa aaggctgat gctgtcttg cagaattaa
      mRNA sequence
      • >TC006402 RA
        cgagattta ctgaaattt tgtcttaaa aatgttcta 
        cgttaaaaa tccttccgc tctcaacaa gccgtggat 
        tttgtccaa aaaaggcga cgaaaatgt cgttgcaat 
        cccgcttga agtttgcag acttttaaa aaactacca 
        tataatgac aattgagtt tctctacca caactaccg 
        gaaaggggt caagggggc ggttttgaa ccaacagcg 
        cgggatgaa tttcagttt acagattgg ggcgtttct 
        cagagctat tgtgcaaag tccggccct tattttggt 
        tatttgtag tagagaatc gagttgtta ctggcatta 
        ccacctggt aaaccacgc cggttttga cgtcgttca 
        aataacttc aaaaaacgc tgatgatac ttacgagag 
        caataacaa aatagcttt acttgtaac acatgactg 
        cttgaaact atgcgaggg gctactcga ttgtgactt 
        tttttccgt cattgtgga ggatttgga ccaactcgc 
        gctcaaacg aattattaa aagactgaa tgggacgtt 
        caatgtggg gctcacaac tcggagttt ttacacaca 
        tcccgatca aaaattgca atggaacat gttgaactg 
        ggccaaccc cggctgtgt cggcaaatt aaacgactt 
        ctacgaggc cgacaaccg caatttcga acgatttga 
        cgacaatta ccgttactg gtggatgag actgacttg 
        ggacttttg cgaatcgtt tgaaaaacc caccgacga 
        ggaaaccga cacttacga gaggaaaat atcagagtg 
        ggcttccca aaacgactt aaactttcc caaaaaaca 
        atcacgcaa acgtaaaca ccccccaaa gactgaacc 
        acctccaga gaacgacag ctccaacga tacaatcat 
        caacgaagt gccaattga taaatacgt caagttgcc 
        cagcatgga cgagagccc tattgtcac ttccattat 
        taaaaattt tgagatttc tcccgaacc gattctcac 
        tcgtacgtc ttcgttgcc atatactca aactcacgc 
        gagttactc caagtatga agaagatag tgtgctgtt 
        tgcgttttt ggatgataa ggagcggcc cagcacttc 
        aaaaagcga gtcagagga gttcattct gagtttgat 
        caacaagtc ggaagacga atcaaaaga tattcggaa 
        aaaggctga tgctgtctt gcagaatta attggcatt 
        cctttggga caagactgg cgcttttat tacattttt 
        attgtggct tttattgta tttattaga ttcgtaata 
        aaccgtgcg gctttgacc atttcattt ttgtggttt 
        tgctgattc gaggacaaa tgttaagga ccaataaac 
        tggtcctta acat
      The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY