Status
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Gene information
General information
TC005107 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.

NW_015450592.1: 6175..10351
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
    		TC005107
    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_03907

    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

    Fertility
    previtellogenic egg chamber not present - Number of animals showing the phenotype: 4

    vitellogenic egg chamber number decreased - Number of animals showing the phenotype: 4
    egg chamber potentially fused - Number of animals showing the phenotype: 3
    tropharium potentially shape irregular - Number of animals showing the phenotype: 3
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 20
     egg without cuticle embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): more than 80%
    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): more than 80%
    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: 100.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 100.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 10 (11 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC005107 RA
      MCDIKRRLS QMDDFNEKM FEGKPWAEK LLSESIKLT 
KKAVANWCH IVCKIGEAE VDLDDYVTI FLQQIETLY 
EDLIADVDT IHEKSLDKI MKLLEKLEN LCRDLHVPI 
PTFNYEGVP LSEVRLQIV QKVDEFEAL AQIRRREFS 
ELQQKELKL CACLGRAPR LLPGAPLPL PPELEELKA 
YVENLETEA MEREEVFFQ LKEKIVEIV SELEMCPNL 
EFEKDILNL SNTQVRITD AEMEQLRQF HDQLVKRLA 
DVTEEVEEL RSRIDDLWK KLEVDLVER DDFRARHVG 
HSLKTLEAL KEELNRLKA MKKAKLQSF ILKQRDELE 
EWWEKCHCT QKQRDDFTF YYSDCFTED LFDIHEREI 
EKWKNYHEE NSEIFALLK EFKTLWTEQ IELESNSKG 
ANRYKNRGG QLLIEERKR NKLKKRLPV VEDKLRSLA 
QAYLVRNGQ EFETFGQTI DDYIQQLHE NKERDFKQK 
LSAKKQLRE QQPSCSSRL PTTPRHCSK RKVTATPAT 
EPSKKAKLA VLKKVSKTG LPKFNTSKT KNNRRRSSA 
HKQRLRSRL FKSSDKENQ SNVSTTYHD FEKEISARD 
ACRSTIGGT IGLQVTNPE GIRIKQENF AIPSGIAPL 
PRTPRPKNP SKF
    CDS sequence
    • >TC005107 RA
      atgtgcgac ataaagcgc cggctgtct caaatggac 
gatttcaac gaaaaaatg tttgagggc aagccgtgg 
gccgaaaaa ctgttatct gaatcgata aaattgaca 
aaaaaggca gtggcgaac tggtgccac atcgtgtgt 
aaaatcggc gaagccgag gtagacctg gacgattat 
gtgacaatt ttcctccaa caaatcgaa accctttac 
gaagacctg atcgccgat gtggacaca atccacgag 
aaaagtctc gataaaata atgaaactg ttggagaaa 
ctcgaaaat ctctgtcgc gacctccac gtcccaatc 
cccactttc aactacgaa ggggttcct ctgagtgag 
gtgcgcctc caaatcgtc caaaaggtg gacgaattc 
gaggctttg gcccagatt cgccgacgg gagtttagc 
gagttgcag cagaaagag ctcaaactg tgtgcctgt 
ctggggcgg gccccccga ctgctcccc ggggcccca 
ctcccgttg ccccccgag ctggaggag ttgaaggcc 
tatgtcgag aacctggag acggaggcg atggaacgg 
gaggaggtt ttcttccaa ctgaaggaa aaaatcgtc 
gagattgtc tccgaacta gagatgtgc cctaatcta 
gagttcgag aaggatatt ttgaatttg tccaatacc 
caagtgcgc ataaccgac gcagaaatg gagcagttg 
cggcagttc cacgaccag ttggtcaag cgcctcgct 
gacgtgacc gaggaggtt gaagagttg aggagcagg 
atcgacgat ttatggaaa aaattggag gttgatttg 
gtggagcgt gatgatttc cgggcgaga cacgtgggg 
cactcgttg aagacgctg gaggcgctt aaagaggag 
ttgaatagg ttgaaggcg atgaaaaag gccaagctt 
cagagtttc attttaaag caacgagat gagctcgaa 
gaatggtgg gaaaagtgt cactgtaca caaaaacaa 
cgcgatgat tttacgttt tactactcc gattgtttt 
accgaagat ttgttcgat atacatgag cgtgaaatc 
gagaaatgg aagaattat cacgaggag aactctgaa 
atctttgca cttctcaag gagtttaag acgttgtgg 
acggaacag atcgagcta gaatcgaat tctaaaggt 
gctaatcgg tacaagaac cgcggaggg caattgttg 
attgaggaa aggaaacgt aataagctc aaaaaacga 
cttccagta gttgaggat aagctccga agtttggct 
caagcgtat ttggtccga aatgggcaa gaattcgag 
acgtttggg caaacaatc gacgactac attcaacaa 
ctgcacgaa aataaagaa cgggatttt aaacagaaa 
ctgagtgcc aagaaacaa ctgcgtgag caacagccg 
tcctgttcg agcagactg cccacaact ccacgccac 
tgctccaaa cgcaaagtc acagcgact ccagcgaca 
gaaccctcc aaaaaagca aaacttgcg gttttgaaa 
aaggtctca aagactggc ttacccaaa ttcaacaca 
tcaaaaact aagaataat cgtcggcgg tcctctgca 
cataaacaa cgactgaga agccgacta tttaagagc 
tcggataag gaaaatcag agtaatgtt tcgaccaca 
taccacgat tttgagaaa gaaatatcg gcaagagat 
gcgtgcagg agtaccatc ggtggaacg attggtcta 
caggttaca aatccagag gggattcgc ataaagcag 
gaaaacttt gccattccc agtggcatt gctcccttg 
cccaggaca ccaaggccc aaaaatccg agcaaattt 
taa
    mRNA sequence
    • >TC005107 RA
      taaacagtg acactgaag gacgttaaa acgaattta 
aaacttgtt accgtcctt tttatgtct ttaacgttt 
cactgtgtt tgtcagtaa aagtttcca agtttttaa 
gaaatatgt gcgacataa agcgccggc tgtctcaaa 
tggacgatt tcaacgaaa aaatgtttg agggcaagc 
cgtgggccg aaaaactgt tatctgaat cgataaaat 
tgacaaaaa aggcagtgg cgaactggt gccacatcg 
tgtgtaaaa tcggcgaag ccgaggtag acctggacg 
attatgtga caattttcc tccaacaaa tcgaaaccc 
tttacgaag acctgatcg ccgatgtgg acacaatcc 
acgagaaaa gtctcgata aaataatga aactgttgg 
agaaactcg aaaatctct gtcgcgacc tccacgtcc 
caatcccca ctttcaact acgaagggg ttcctctga 
gtgaggtgc gcctccaaa tcgtccaaa aggtggacg 
aattcgagg ctttggccc agattcgcc gacgggagt 
ttagcgagt tgcagcaga aagagctca aactgtgtg 
cctgtctgg ggcgggccc cccgactgc tccccgggg 
ccccactcc cgttgcccc ccgagctgg aggagttga 
aggcctatg tcgagaacc tggagacgg aggcgatgg 
aacgggagg aggttttct tccaactga aggaaaaaa 
tcgtcgaga ttgtctccg aactagaga tgtgcccta 
atctagagt tcgagaagg atattttga atttgtcca 
atacccaag tgcgcataa ccgacgcag aaatggagc 
agttgcggc agttccacg accagttgg tcaagcgcc 
tcgctgacg tgaccgagg aggttgaag agttgagga 
gcaggatcg acgatttat ggaaaaaat tggaggttg 
atttggtgg agcgtgatg atttccggg cgagacacg 
tggggcact cgttgaaga cgctggagg cgcttaaag 
aggagttga ataggttga aggcgatga aaaaggcca 
agcttcaga gtttcattt taaagcaac gagatgagc 
tcgaagaat ggtgggaaa agtgtcact gtacacaaa 
aacaacgcg atgatttta cgttttact actccgatt 
gttttaccg aagatttgt tcgatatac atgagcgtg 
aaatcgaga aatggaaga attatcacg aggagaact 
ctgaaatct ttgcacttc tcaaggagt ttaagacgt 
tgtggacgg aacagatcg agctagaat cgaattcta 
aaggtgcta atcggtaca agaaccgcg gagggcaat 
tgttgattg aggaaagga aacgtaata agctcaaaa 
aacgacttc cagtagttg aggataagc tccgaagtt 
tggctcaag cgtatttgg tccgaaatg ggcaagaat 
tcgagacgt ttgggcaaa caatcgacg actacattc 
aacaactgc acgaaaata aagaacggg attttaaac 
agaaactga gtgccaaga aacaactgc gtgagcaac 
agccgtcct gttcgagca gactgccca caactccac 
gccactgct ccaaacgca aagtcacag cgactccag 
cgacagaac cctccaaaa aagcaaaac ttgcggttt 
tgaaaaagg tctcaaaga ctggcttac ccaaattca 
acacatcaa aaactaaga ataatcgtc ggcggtcct 
ctgcacata aacaacgac tgagaagcc gactattta 
agagctcgg ataaggaaa atcagagta atgtttcga 
ccacatacc acgattttg agaaagaaa tatcggcaa 
gagatgcgt gcaggagta ccatcggtg gaacgattg 
gtctacagg ttacaaatc cagagggga ttcgcataa 
agcaggaaa actttgcca ttcccagtg gcattgctc 
ccttgccca ggacaccaa ggcccaaaa atccgagca 
aattttaat taatcgact gttacattt tgtttttgt 
attattttt acgcacatg tacttaaaa ggagtttag 
tttttaaat tacgtccat ttgtttttt atttaaagg 
tgctcctct attatatgt tacaaatta ctaaatata 
tttattgca tgact

    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