Status
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Gene information
General information
TC003819 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_007418.3: 21552531..21558248
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
    		TC003819
    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_02725

    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: 0.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 0.0% (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC003819 RA
      MNIPTCLVG SFCLLTLAE CMTNMTLKR TVEDDYYMN 
YDYEISNDS FNSELKVDS FLLPNPENI DSKYAVDVL 
PNVELPDDS LSDTDLKDH DFIDNLMYV YYGSHNKNG 
HSYGPEVII VGSVLSCAA QLLTIFFVL LKKNLNGKK 
EMKNLFLHM MGSFCFSNL LFMLGVYAI KNSVKCLMV 
AFLLHYLHL LTAFWMFLY CYYIYKRFS SSGVPKNKY 
FFSVGYGVP LVFSLLSYV VSPYSFETK RFCFMSVQK 
GMIINYMLP ISLLIVITT IYSLNGIRK INIELSKLE 
FSSSVESLN ALKNELDVV MNDKKQECA DEEVVSLRE 
SKTCLKLMC VVQTGYDIV WFIVVLALE SNSENNSMS 
IVYSVTSCL LNWYIFIKA KSFLPNIMH VSRSIDNVL 
LHQEQQATN AHKENSSLS RRGSSDSVP LLVNSENCT 
EMRELRLEY ISTISN
    CDS sequence
    • >TC003819 RA
      atgaacatt ccgacatgt cttgtgggt agtttttgt 
ttgttaact cttgcagaa tgcatgaca aatatgact 
ttaaagcgc accgtcgaa gacgattat tacatgaat 
tatgactac gaaatttcg aacgactcg ttcaattcc 
gagctgaaa gttgattcc tttctgttg ccaaatccc 
gaaaatatt gactcaaaa tatgcagtt gacgtgctc 
cccaatgtt gaactcccc gatgattcg ctctcagac 
accgacttg aaagaccac gatttcatc gataattta 
atgtacgtt tattacggc tctcataat aagaacgga 
cacagttat gggcctgag gtgataatt gttggctca 
gtgctcagc tgcgctgct cagctactg acgattttt 
ttcgttcta ctcaagaag aatttgaat gggaaaaag 
gagatgaaa aatttgttc ttgcacatg atgggctcg 
ttctgtttc tccaatttg ctcttcatg ttaggtgtc 
tatgcgata aaaaattcg gttaagtgt ttgatggta 
gccttcctc ttgcactac ttgcattta cttacagcg 
ttttggatg ttcttgtat tgttattat atctacaag 
cgattctct agtagtggt gtcccgaaa aataaatat 
tttttctcg gtgggttat ggggttcca ctcgttttt 
agtcttctt tcatatgtg gtgtcgccg tacagtttc 
gaaacgaag cgattttgc ttcatgtca gtacaaaaa 
ggaatgata ataaactat atgcttcca atatctcta 
ctaatcgtt ataacaacg atctactcg ctcaatggt 
ataagaaaa ataaatata gaattgtcc aaattagag 
tttagtagt tcagtcgag tcattaaac gctttaaag 
aacgaactg gacgttgta atgaacgac aagaaacag 
gaatgtgca gacgaagaa gtcgtcagt ttaagggaa 
tcgaagact tgcttgaaa ctgatgtgt gtggtgcaa 
actggatac gatatagtg tggttcatt gtagttctg 
gctcttgag agcaacagt gaaaataac agtatgtcg 
attgtatat tcggttact tcgtgttta ctgaactgg 
tacatcttc attaaagct aaatctttt cttccaaat 
attatgcac gtttctcgt tcaattgac aatgttctt 
ctacaccag gagcagcaa gcgacaaat gcacataag 
gagaattcg tcgttgtcg aggagaggg tcttccgac 
agtgttcct cttttggta aattcggaa aattgtacc 
gaaatgaga gaactgcgc cttgaatac attagtact 
ataagcaac taa
    mRNA sequence
    • >TC003819 RA
      caatggatg aactcggga tatttgctc aatttccct 
cccgaattt tgttatgaa cattccgac atgtcttgt 
gggtagttt ttgtttgtt aactcttgc agaatgcat 
gacaaatat gactttaaa gcgcaccgt cgaagacga 
ttattacat gaattatga ctacgaaat ttcgaacga 
ctcgttcaa ttccgagct gaaagttga ttcctttct 
gttgccaaa tcccgaaaa tattgactc aaaatatgc 
agttgacgt gctccccaa tgttgaact ccccgatga 
ttcgctctc agacaccga cttgaaaga ccacgattt 
catcgataa tttaatgta cgtttatta cggctctca 
taataagaa cggacacag ttatgggcc tgaggtgat 
aattgttgg ctcagtgct cagctgcgc tgctcagct 
actgacgat ttttttcgt tctactcaa gaagaattt 
gaatgggaa aaaggagat gaaaaattt gttcttgca 
catgatggg ctcgttctg tttctccaa tttgctctt 
catgttagg tgtctatgc gataaaaaa ttcggttaa 
gtgtttgat ggtagcctt cctcttgca ctacttgca 
tttacttac agcgttttg gatgttctt gtattgtta 
ttatatcta caagcgatt ctctagtag tggtgtccc 
gaaaaataa atatttttt ctcggtggg ttatggggt 
tccactcgt ttttagtct tctttcata tgtggtgtc 
gccgtacag tttcgaaac gaagcgatt ttgcttcat 
gtcagtaca aaaaggaat gataataaa ctatatgct 
tccaatatc tctactaat cgttataac aacgatcta 
ctcgctcaa tggtataag aaaaataaa tatagaatt 
gtccaaatt agagtttag tagttcagt cgagtcatt 
aaacgcttt aaagaacga actggacgt tgtaatgaa 
cgacaagaa acaggaatg tgcagacga agaagtcgt 
cagtttaag ggaatcgaa gacttgctt gaaactgat 
gtgtgtggt gcaaactgg atacgatat agtgtggtt 
cattgtagt tctggctct tgagagcaa cagtgaaaa 
taacagtat gtcgattgt atattcggt tacttcgtg 
tttactgaa ctggtacat cttcattaa agctaaatc 
ttttcttcc aaatattat gcacgtttc tcgttcaat 
tgacaatgt tcttctaca ccaggagca gcaagcgac 
aaatgcaca taaggagaa ttcgtcgtt gtcgaggag 
agggtcttc cgacagtgt tcctctttt ggtaaattc 
ggaaaattg taccgaaat gagagaact gcgccttga 
atacattag tactataag caactaaag cgctgcaat 
attattcga acgtagaca ttgtatact cactagtca 
gaataatgt ttatttttt cttttcaga gtaaattgt 
tgaaaagtt actctttgg accagtttg tcgtttttg 
tggtctgag ggatggttc tttattcta acgtaattt 
taagacatc ggcctatat cagtattag aagttctta 
cttcttacc tctatttct actgtaaac aatgttcta 
aaaaagcac aagttgtcc gtgtaagca accaaaaat 
aaatgttgt ttatctaa

    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