Status
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Gene information
General information
TC004397 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_007425.3: 7156013..7159157
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
    TC004397
    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_09840

    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: 10.0% (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


    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 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
    • >TC004397 RA
      MSTPSRESL SQNEAVQVI VRCRPMNSQ EKQADCNRV 
      VNVYSNRGV IEVENPKAR SENERKKIF TYDAVYDWN 
      ASQQCLYDE TVRPLVSSV LEGYNGCVF AYGQTGTGK 
      TYTMEGLDC EEQWGVIPR AFQQIWTHI NRTTGLEFL 
      VTVRYLEIY MEDIRDLLK IKNSKSLEL REITGKGVC 
      VTHLHSQTC QSADDMLRA MRVGNKNRT SGATNMNEH 
      SSRSHAIFQ IVIEMAELH SKKVKVGKL NLVDLAGSE 
      RQSKTGATG ERFKEATKI NKALSSLGN VIYALAENS 
      QHIPYRDSK LTRLLQDSL GGNSKTIMI ANIGPANCN 
      YEETIITLR YAYRAKSIK NQPIKNEDI KDAKLLALQ 
      EEIERLKRL IEMKSNGGG EVDDSEVVL EESETSDDE 
      DSKKDESKK KLELGKMEV DELAKKLET LEKQMVHGG 
      KNIVDSVNE NEVRLEQQK LEIAARKKR EIEMQQKIE 
      LEEETCIEL KQVFASLQQ QVDFKKDKL KRLYAKLQS 
      IRQEIKDNH KIYMNDRRE IEEANDEAS MQLRQRFLI 
      IDNFVPPEE RSRLINLAQ FDEDKDNWV LKKEKIDAI 
      TMERPLGHC YRRPISEYA ITTGQVVPK YRGENVLDL 
      KLDMPLRIT QDYVSPNIC PQIKATVTN MILHDVENN 
      VIVVKALPH TVSARNTSK LEHEGKYKQ ATKFVIDMQ 
      NYRTKKSSE PVH
    CDS sequence
    • >TC004397 RA
      atgtcaacg cctagtaga gaatctctt tcgcaaaat 
      gaagccgtt caagtgatt gtccgttgt cggcctatg 
      aactcgcaa gagaaacaa gccgattgt aatcgtgtt 
      gttaacgtt tactcaaat cggggtgtc attgaggtt 
      gaaaacccc aaagctagg agtgaaaat gaacgtaag 
      aaaatcttt acatatgac gctgtttac gactggaat 
      gcatctcaa cagtgtctt tacgacgag acagtgcgt 
      cctcttgtc tcgtcagtc cttgaaggt tacaacggt 
      tgtgtgttt gcttatggt caaactggc actgggaag 
      acatacacc atggaagga cttgactgt gaggaacaa 
      tggggtgtt atcccaaga gccttccag caaatttgg 
      actcatatt aaccggacc acaggtctt gaattttta 
      gtaacagtt cgctacttg gaaatatac atggaggac 
      atcagagat ttgttgaaa atcaaaaac tcgaaatcg 
      ttggaactt cgggaaatc accggaaaa ggtgtatgt 
      gtgacacat cttcactca caaacgtgt caaagtgcc 
      gacgatatg ttgcgagca atgcgagtg ggtaataaa 
      aatcgcact agcggtgca acgaatatg aatgaacac 
      agttcacga tcgcatgcg atttttcaa attgttatc 
      gaaatggct gaattacat tcgaagaaa gtcaaagtt 
      ggtaaattg aatctagtc gacttggct ggtagtgaa 
      agacagtcg aaaactgga gctacaggt gaacgattt 
      aaagaagcg acgaaaatc aacaaggcc ttgtccagt 
      ttaggcaac gtgatttat gcattagct gaaaattcc 
      caacatata ccgtatcga gattcgaaa ttgacacga 
      cttttacag gattcttta ggtgggaat agtaaaact 
      ataatgatt gcgaatatt ggaccagct aattgtaat 
      tatgaggag actataatt acgttaaga tatgcttat 
      cgggcaaaa tcgatcaaa aatcaacca attaaaaat 
      gaggatatt aaagatgcg aaattgttg gctcttcag 
      gaagaaatc gagcgattg aaacgtttg attgaaatg 
      aaatcgaac ggtggtggt gaggtagac gactctgaa 
      gtggttttg gaggaaagc gaaacgtcg gatgatgaa 
      gatagcaaa aaagatgaa agtaagaaa aaactagaa 
      ttgggtaaa atggaagtg gatgaattg gctaaaaag 
      ctggaaacg ttggaaaaa cagatggta catggagga 
      aaaaatatc gtagacagt gtgaacgaa aacgaggtt 
      agattggag caacaaaaa ctggaaatt gccgctaga 
      aaaaaacgt gaaatcgaa atgcaacaa aaaatcgaa 
      ctggaggaa gaaacctgc atcgaattg aagcaagtt 
      tttgcaagt cttcaacaa caagtcgat tttaagaaa 
      gacaaactg aaacgactc tacgccaag cttcaatca 
      attcgtcaa gaaattaaa gataatcac aagatttac 
      atgaacgat cggcgcgaa attgaagaa gcaaacgat 
      gaagcctcc atgcaattg aggcaacgt tttctcatc 
      attgataat tttgtaccg cctgaggaa cgttcacgt 
      ttgataaac ttggcacag tttgatgaa gataaagat 
      aattgggtg ttgaaaaag gaaaagatt gatgcaatt 
      acaatggaa cggcctttg gggcattgt tatcgaagg 
      cctatctct gaatatgct attacaacg ggacaagtt 
      gtaccaaaa tatcgtggc gaaaatgtg ttagatttg 
      aaattggat atgccgtta cgtatcaca caagattac 
      gtcagtcca aatatttgt ccgcaaatt aaagccacc 
      gtcactaat atgatttta cacgacgtt gaaaacaat 
      gtcattgtt gttaaagcc ttgcctcat acggttagt 
      gcaagaaac acttccaag ttggaacat gaaggcaaa 
      tataagcag gcgacgaaa ttcgttata gatatgcag 
      aattacagg actaaaaaa tcaagtgaa ccggtccat 
      tga
    mRNA sequence
    • >TC004397 RA
      tgacaactg atacaaaaa cccaaaaat aatgatttc 
      ttcacgtta attccataa ttggtgaat ttgattaca 
      tttattgtc gtagtgtta agtaattga aaaaatgtc 
      aacgcctag tagagaatc tctttcgca aaatgaagc 
      cgttcaagt gattgtccg ttgtcggcc tatgaactc 
      gcaagagaa acaagccga ttgtaatcg tgttgttaa 
      cgtttactc aaatcgggg tgtcattga ggttgaaaa 
      ccccaaagc taggagtga aaatgaacg taagaaaat 
      ctttacata tgacgctgt ttacgactg gaatgcatc 
      tcaacagtg tctttacga cgagacagt gcgtcctct 
      tgtctcgtc agtccttga aggttacaa cggttgtgt 
      gtttgctta tggtcaaac tggcactgg gaagacata 
      caccatgga aggacttga ctgtgagga acaatgggg 
      tgttatccc aagagcctt ccagcaaat ttggactca 
      tattaaccg gaccacagg tcttgaatt tttagtaac 
      agttcgcta cttggaaat atacatgga ggacatcag 
      agatttgtt gaaaatcaa aaactcgaa atcgttgga 
      acttcggga aatcaccgg aaaaggtgt atgtgtgac 
      acatcttca ctcacaaac gtgtcaaag tgccgacga 
      tatgttgcg agcaatgcg agtgggtaa taaaaatcg 
      cactagcgg tgcaacgaa tatgaatga acacagttc 
      acgatcgca tgcgatttt tcaaattgt tatcgaaat 
      ggctgaatt acattcgaa gaaagtcaa agttggtaa 
      attgaatct agtcgactt ggctggtag tgaaagaca 
      gtcgaaaac tggagctac aggtgaacg atttaaaga 
      agcgacgaa aatcaacaa ggccttgtc cagtttagg 
      caacgtgat ttatgcatt agctgaaaa ttcccaaca 
      tataccgta tcgagattc gaaattgac acgactttt 
      acaggattc tttaggtgg gaatagtaa aactataat 
      gattgcgaa tattggacc agctaattg taattatga 
      ggagactat aattacgtt aagatatgc ttatcgggc 
      aaaatcgat caaaaatca accaattaa aaatgagga 
      tattaaaga tgcgaaatt gttggctct tcaggaaga 
      aatcgagcg attgaaacg tttgattga aatgaaatc 
      gaacggtgg tggtgaggt agacgactc tgaagtggt 
      tttggagga aagcgaaac gtcggatga tgaagatag 
      caaaaaaga tgaaagtaa gaaaaaact agaattggg 
      taaaatgga agtggatga attggctaa aaagctgga 
      aacgttgga aaaacagat ggtacatgg aggaaaaaa 
      tatcgtaga cagtgtgaa cgaaaacga ggttagatt 
      ggagcaaca aaaactgga aattgccgc tagaaaaaa 
      acgtgaaat cgaaatgca acaaaaaat cgaactgga 
      ggaagaaac ctgcatcga attgaagca agtttttgc 
      aagtcttca acaacaagt cgattttaa gaaagacaa 
      actgaaacg actctacgc caagcttca atcaattcg 
      tcaagaaat taaagataa tcacaagat ttacatgaa 
      cgatcggcg cgaaattga agaagcaaa cgatgaagc 
      ctccatgca attgaggca acgttttct catcattga 
      taattttgt accgcctga ggaacgttc acgtttgat 
      aaacttggc acagtttga tgaagataa agataattg 
      ggtgttgaa aaaggaaaa gattgatgc aattacaat 
      ggaacggcc tttggggca ttgttatcg aaggcctat 
      ctctgaata tgctattac aacgggaca agttgtacc 
      aaaatatcg tggcgaaaa tgtgttaga tttgaaatt 
      ggatatgcc gttacgtat cacacaaga ttacgtcag 
      tccaaatat ttgtccgca aattaaagc caccgtcac 
      taatatgat tttacacga cgttgaaaa caatgtcat 
      tgttgttaa agccttgcc tcatacggt tagtgcaag 
      aaacacttc caagttgga acatgaagg caaatataa 
      gcaggcgac gaaattcgt tatagatat gcagaatta 
      caggactaa aaaatcaag tgaaccggt ccattgatt 
      gaatctagt cagctttta ttttcgtac tatctatca 
      tctatacta gtcttgtcc atgtagctt aatttcgt
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY