Status
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Gene information
General information
TC004160 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_007416.3: 1820729..1823443
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
    TC004160
    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
    If you have entered your name and agree by marking the checkbox. we might show your name on this page to honor your contribution.
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_08283

    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 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
    • >TC004160 RA
      MTTKPILNC FILLIVCCS SAFAQVGDT CVVKSTGVR 
      GVCRISSNC PIVEEQAQN GISPTICGY YQLTVPIVC 
      CEESPFVQP NDDTLLNPE PNLSNQQPS YSNSNSREP 
      SYSNSNSRE PSYSNSNSR EPSYSNSNS REPSYSNSN 
      SREPSYSNS NSREPSYSN SNSREPSYS NSNNRQPSP 
      SQNREPNPN IFPAGEPDA VIYPDSDNQ PSRPQVTHT 
      SKSEQKCQE YSKAITGVV QAIPLVTNT EVVSYSFVK 
      CDYNGVALI VGGKPASAG EFPFMAAIG FYVDNKVEW 
      RCGGTLISE EYVLTAAHC TYTRDGDTP KIVRLGDLD 
      LSRDDDGSV HTDYNVRNI VVHPRYRYP LKYNDIALI 
      QLSTTVRFT KFIRPACLY TKSQVELPQ AIATGWGKT 
      DYAAAEISD KLMKVSLNI YSNDRCAQT YQTSKHLPQ 
      GIKSNMICA GELRGGQDT CQGDSGGPL LITKKGNQC 
      KFYVIGVTS FGKSCGQAN TPAIYTRVS EYVPWIEKT 
      IW
    CDS sequence
    • >TC004160 RA
      atgacaaca aaacctata cttaactgt tttatattg 
      ttaattgtt tgttgctct tctgcgttt gcgcaagtg 
      ggagatacc tgcgtagta aaatccaca ggcgttcga 
      ggggtttgc aggatatcc tcaaactgc cccattgtc 
      gaagaacaa gcacaaaac ggaattagc ccgacaata 
      tgtgggtac tatcaactg acagtcccc atcgtctgc 
      tgcgaggaa agccccttc gtccaacca aacgacgat 
      acgttactg aatccagaa cccaacctg agtaaccag 
      caaccgagc tactccaac tccaacagc cgggaacca 
      agctactca aactccaac agccgggaa ccgagctac 
      tctaattcc aacagccgg gaaccgagc tactccaat 
      tccaacagc cgggaaccg agctactcc aattccaac 
      agccgggaa ccgagctac tccaattcc aacagccgg 
      gaaccgagc tactccaat tccaacagc cgggaaccg 
      agctactcc aactccaac aaccggcag ccaagtccc 
      tcccaaaac cgggaaccg aatccgaac atatttcca 
      gctggtgag ccggacgct gtgatatat cctgattcg 
      gacaatcag ccgtcgcgg ccccaagtg actcataca 
      agtaaaagc gagcaaaag tgccaagag tacagtaaa 
      gccataact ggtgtcgtt caagcgatt cctttagtg 
      actaatact gaggtggtt agctatagc tttgtcaag 
      tgtgactac aatggtgta gcgttgatc gtcgggggc 
      aagcctgcc tccgctggg gaattcccg tttatggcg 
      gccatcggt ttttacgtg gataacaaa gtggagtgg 
      cgctgcggg ggcacgctg atcagtgag gagtatgtt 
      ttaaccgcc gcccactgc acttacacc cgcgatggg 
      gacacgccg aagattgtt cgattggga gaccttgac 
      ttatcccgc gatgacgac ggctccgta cacactgac 
      tacaacgta cggaacatt gtagtgcat cctcggtac 
      cgctacccc ctcaaatac aacgacatt gccctcatc 
      cagctgtcc acaacagtc agattcacg aaattcatc 
      cgacctgcg tgtctttac accaaatcg caggtggag 
      ctcccgcaa gccatagcg accggctgg ggcaaaacg 
      gactacgcc gctgccgag ataagcgac aagttgatg 
      aaagtctcg ctaaatatt tacagcaat gaccgatgt 
      gcccagacg taccagacc agcaaacac ttgccacaa 
      gggatcaag tctaacatg atctgtgca ggggagttg 
      agggggggc caggacacg tgtcagggg gactctggg 
      gggccccta cttatcacc aaaaagggc aaccaatgc 
      aagttctac gttatcggg gtcacctcg ttcgggaag 
      tcctgcgga caggccaac acgcccgcc atctacacc 
      agagtctca gaatacgtg ccatggatc gaaaaaacc 
      atctggtaa
    mRNA sequence
    • >TC004160 RA
      gtagaaagt ctaaagttt ccgtttcac gaattgtgt 
      gaggtgttt gtgagacag cgatttagt cggtttttc 
      ggtgaaaga gacgtttga tgaattttc aagatcttg 
      ttaagaatc acatcagct tataaatag taataaaac 
      atattgttt tcagttatt aatgagaca gtggtgtag 
      tcaagttag cggaataat tattgtaat ttaacgaat 
      ttatataag tttcttaat attgaggat cttcaagga 
      ttttgttat ttatgcgag cgtgtcacg gtaaaccag 
      atagcctgt ggtaaacaa taattgaag agtatattt 
      tatgaaaca agttatagt gacgccaat gactgctgg 
      taaatccag tgttattta catacatct taactaaaa 
      agaaagaaa aagacgcag aatagtttc tgaacctga 
      ggaataacg atgtcagtg ttttgaagt tcttcacaa 
      tgacaacaa aacctatac ttaactgtt ttatattgt 
      taattgttt gttgctctt ctgcgtttg cgcaagtgg 
      gagatacct gcgtagtaa aatccacag gcgttcgag 
      gggtttgca ggatatcct caaactgcc ccattgtcg 
      aagaacaag cacaaaacg gaattagcc cgacaatat 
      gtgggtact atcaactga cagtcccca tcgtctgct 
      gcgaggaaa gccccttcg tccaaccaa acgacgata 
      cgttactga atccagaac ccaacctga gtaaccagc 
      aaccgagct actccaact ccaacagcc gggaaccaa 
      gctactcaa actccaaca gccgggaac cgagctact 
      ctaattcca acagccggg aaccgagct actccaatt 
      ccaacagcc gggaaccga gctactcca attccaaca 
      gccgggaac cgagctact ccaattcca acagccggg 
      aaccgagct actccaatt ccaacagcc gggaaccga 
      gctactcca actccaaca accggcagc caagtccct 
      cccaaaacc gggaaccga atccgaaca tatttccag 
      ctggtgagc cggacgctg tgatatatc ctgattcgg 
      acaatcagc cgtcgcggc cccaagtga ctcatacaa 
      gtaaaagcg agcaaaagt gccaagagt acagtaaag 
      ccataactg gtgtcgttc aagcgattc ctttagtga 
      ctaatactg aggtggtta gctatagct ttgtcaagt 
      gtgactaca atggtgtag cgttgatcg tcgggggca 
      agcctgcct ccgctgggg aattcccgt ttatggcgg 
      ccatcggtt tttacgtgg ataacaaag tggagtggc 
      gctgcgggg gcacgctga tcagtgagg agtatgttt 
      taaccgccg cccactgca cttacaccc gcgatgggg 
      acacgccga agattgttc gattgggag accttgact 
      tatcccgcg atgacgacg gctccgtac acactgact 
      acaacgtac ggaacattg tagtgcatc ctcggtacc 
      gctaccccc tcaaataca acgacattg ccctcatcc 
      agctgtcca caacagtca gattcacga aattcatcc 
      gacctgcgt gtctttaca ccaaatcgc aggtggagc 
      tcccgcaag ccatagcga ccggctggg gcaaaacgg 
      actacgccg ctgccgaga taagcgaca agttgatga 
      aagtctcgc taaatattt acagcaatg accgatgtg 
      cccagacgt accagacca gcaaacact tgccacaag 
      ggatcaagt ctaacatga tctgtgcag gggagttga 
      gggggggcc aggacacgt gtcaggggg actctgggg 
      ggcccctac ttatcacca aaaagggca accaatgca 
      agttctacg ttatcgggg tcacctcgt tcgggaagt 
      cctgcggac aggccaaca cgcccgcca tctacacca 
      gagtctcag aatacgtgc catggatcg aaaaaacca 
      tctggtaaa atcacccac ttaacgaca ttttttatt 
      ttatcattc acatacaat acgtataga
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY