Status
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Gene information
General information
TC005310 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: 14556507..14559613
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
    		TC005310
    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_00824

    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: 50.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 5 (3 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: < 50 larval musculature irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     egg without cuticle embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): more than 80%

    cuticle remnants with some identifiable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

    appendages partially remaining - Penetrance (percentage of animals/eggs on slide): less than 30%
    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: 20.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 30.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality early (L5/6) - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (19 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC005310 RA
      MNESGNHED GEIRATRFR NLPSVNSLS QEELIVTQP 
ENTELLSSI RRRVQTSSE KIETGSLNV LSAKYESLD 
YDTCENYLL LDEERKKGY RFIVKKSLA RWFIFLLIG 
VVTALIACA IDISIEELS QLKYASLSK YVDEYVTQG 
KLHIPYFFW VLYNIIPVL IGSTLVAYV EPIAAGSGI 
PQVKCYLNG VKIPRVVRI KTLFVKSVG VVCSVVGGL 
AGGKEGPMI HSGAVVAAG LSQGKSTTF RRDFKIFKF 
FREDHEKRD FVSGGAAAG VSAAFGAPV GGVLFSLEE 
GTSFWNQSL TWRTFFASV ISTFTLNVV LSTYHGVPG 
DLSYPGLLN LGKFENFSY KVYELPIFL VMGALGGLS 
GALWNHINY KLSVFRMRY IRKRWLKVI EACIVAAVS 
ATLGFLMMF LLNDCKPLG QDPTKYPTQ LYCQDGQYN 
VLASIWFQT PEASVRSLF HDPPSTHNA TSLAFFVLV 
YFFLSSWTF GLASSNGLF IPTLLTGAA WGRLISVGL 
FRVIPDAVL IHPGKYALI GAAAQLGGV VRMTISLTV 
IIMETTGNI SFALPLILT LIAAKWTGD FFNEGIYDT 
LIQLSGVPL LPWEPPPLV HNIYASEVM SHPVVTLKC 
VENVGHIVE LLKLTTYNG FPVVDPPLT DQSEVTTYG 
RIRGLVLRS QLIVILKKK IFNENSDFW EDINAGIFR 
DEYPRYPTI EQVSVSEVE KTYSIDLRP FMNPSPYTV 
LHSASLPRM FRLFRALGL RHLPIVNDT NEVIGMVTR 
KDLARYRVW RHRGRMGVE ELLISKEI
    CDS sequence
    • >TC005310 RA
      atgaacgaa agtgggaat catgaggat ggtgaaatt 
cgagccacc agatttagg aatttgcca tcggtcaat 
tcgttgagt caagaagaa ctgattgtg acacaacct 
gaaaatacc gaattgtta tcgtcaatc agacggagg 
gtacaaact agttctgaa aaaattgaa acagggtct 
ttgaacgtg ttatcggcg aaatatgaa agccttgat 
tacgacacg tgtgagaat tatttactt ttggatgaa 
gagagaaaa aaaggttat agatttatt gtgaaaaaa 
agtttagcg agatggttt attttcctc ttaattgga 
gtggtaacc gcgttaatt gcttgtgcc atagatata 
tcaatagaa gaattatca caactgaaa tatgcctca 
ttaagcaaa tatgtggac gaatacgtc acacagggg 
aaactccac atcccctac ttcttctgg gtgttatac 
aacataatc ccagtccta ataggctca actctagtt 
gcttacgtt gagcctatt gctgctggt agtggaatt 
cctcaagtg aaatgttac ctcaatggg gttaaaata 
ccccgcgtc gtacgaata aaaacacta tttgtaaaa 
agtgtaggc gttgtgtgt tcagttgtg ggtggttta 
gctgggggc aaagaagga ccaatgatt cattcagga 
gctgtcgtt gcagcggga ctttctcaa gggaaaagt 
acaacgttt aggcgagat ttcaaaata tttaaattt 
tttcgggaa gatcacgaa aaacgggac tttgtctct 
gggggcgcc gctgcggga gtttcggca gctttcgga 
gcaccagtt ggtggagtg ctttttagt ttggaagaa 
ggtacaagc ttttggaat cagagccta acatggcgc 
acttttttc gcttccgtg ataagcacc tttactcta 
aacgtagtt ttatcaact tatcacgga gttcccggt 
gatttaagc tatccagga cttttgaat ttaggcaaa 
tttgaaaac tttagttat aaagtgtac gaattacca 
attttcctc gtaatgggg gctttaggt ggattatcg 
ggggcgtta tggaatcac atcaattac aaattatca 
gtttttcga atgagatat atacgaaaa agatggtta 
aaagtaatt gaagcttgt attgtcgca gctgttagt 
gccacttta ggtttcctg atgatgttt ttactgaat 
gattgcaag cctttggga caagatccc acgaaatat 
ccaactcag ttatactgt caagatggc caatacaat 
gttttggca agcatttgg tttcaaact cctgaagcc 
tcagtccgt tctcttttt cacgatccc ccaagtacg 
cacaacgcc acctctctg gcctttttc gtcctagtt 
tatttcttt ttatcgtca tggactttt ggtcttgcc 
tcttctaat ggtcttttt ataccgact ctcctaacg 
ggggctgct tggggtcgg cttatttca gtcggacta 
tttcgagta atccccgac gctgttctc attcatccg 
gggaaatac gccctgatt ggtgcagcc gctcaatta 
ggaggcgta gtcagaatg acaattagt ttgacagtg 
attataatg gaaacgaca ggaaacatt tcctttgct 
ttgcctcta attctgaca ttaattgcg gcaaaatgg 
actggtgat tttttcaat gagggaatt tatgacaca 
cttatacaa ctcagtggt gttccgtta ctcccatgg 
gaacccccg ccactagtt cacaatatc tacgccagt 
gaggtgatg tcgcatccg gtggtcaca ctgaagtgt 
gttgagaat gtggggcat attgttgaa ttgttgaaa 
ttaacaact tataacgga tttccggtt gttgatccg 
ccactaact gatcaatcg gaagttacc acgtatggg 
agaataaga gggttagtt ttgaggtca caattaatt 
gttattttg aaaaagaag atttttaac gaaaattcg 
gacttttgg gaggatatt aatgcggga atctttcga 
gatgagtat ccccgatat ccaacaata gagcaagtg 
agtgtttcc gaagttgaa aaaacttat tctattgat 
ctgaggccg tttatgaat ccgtcacca tatacggtg 
cttcattcg gcatcacta cctcgaatg tttagatta 
ttccgagct ctcggttta cgacatttg ccgattgtt 
aatgacaca aatgaggtt ataggaatg gtaacaagg 
aaagattta gctcgttat agagtctgg agacatcgg 
ggtcgcatg ggggtagaa gaattatta atttccaaa 
gaaatatga
    mRNA sequence
    • >TC005310 RA
      tgacgttta atttttcgg agaatgcaa aataatatg 
aatacgttt ttatcgcag atgattcat ttcgtaatc 
aaatcggga cacaattca aagttataa tgcgcgtta 
ttttctaat ctgggagaa tgaacgaaa gtgggaatc 
atgaggatg gtgaaattc gagccacca gatttagga 
atttgccat cggtcaatt cgttgagtc aagaagaac 
tgattgtga cacaacctg aaaataccg aattgttat 
cgtcaatca gacggaggg tacaaacta gttctgaaa 
aaattgaaa cagggtctt tgaacgtgt tatcggcga 
aatatgaaa gccttgatt acgacacgt gtgagaatt 
atttacttt tggatgaag agagaaaaa aaggttata 
gatttattg tgaaaaaaa gtttagcga gatggttta 
ttttcctct taattggag tggtaaccg cgttaattg 
cttgtgcca tagatatat caatagaag aattatcac 
aactgaaat atgcctcat taagcaaat atgtggacg 
aatacgtca cacagggga aactccaca tcccctact 
tcttctggg tgttataca acataatcc cagtcctaa 
taggctcaa ctctagttg cttacgttg agcctattg 
ctgctggta gtggaattc ctcaagtga aatgttacc 
tcaatgggg ttaaaatac cccgcgtcg tacgaataa 
aaacactat ttgtaaaaa gtgtaggcg ttgtgtgtt 
cagttgtgg gtggtttag ctgggggca aagaaggac 
caatgattc attcaggag ctgtcgttg cagcgggac 
tttctcaag ggaaaagta caacgttta ggcgagatt 
tcaaaatat ttaaatttt ttcgggaag atcacgaaa 
aacgggact ttgtctctg ggggcgccg ctgcgggag 
tttcggcag ctttcggag caccagttg gtggagtgc 
tttttagtt tggaagaag gtacaagct tttggaatc 
agagcctaa catggcgca cttttttcg cttccgtga 
taagcacct ttactctaa acgtagttt tatcaactt 
atcacggag ttcccggtg atttaagct atccaggac 
ttttgaatt taggcaaat ttgaaaact ttagttata 
aagtgtacg aattaccaa ttttcctcg taatggggg 
ctttaggtg gattatcgg gggcgttat ggaatcaca 
tcaattaca aattatcag tttttcgaa tgagatata 
tacgaaaaa gatggttaa aagtaattg aagcttgta 
ttgtcgcag ctgttagtg ccactttag gtttcctga 
tgatgtttt tactgaatg attgcaagc ctttgggac 
aagatccca cgaaatatc caactcagt tatactgtc 
aagatggcc aatacaatg ttttggcaa gcatttggt 
ttcaaactc ctgaagcct cagtccgtt ctctttttc 
acgatcccc caagtacgc acaacgcca cctctctgg 
cctttttcg tcctagttt atttctttt tatcgtcat 
ggacttttg gtcttgcct cttctaatg gtcttttta 
taccgactc tcctaacgg gggctgctt ggggtcggc 
ttatttcag tcggactat ttcgagtaa tccccgacg 
ctgttctca ttcatccgg ggaaatacg ccctgattg 
gtgcagccg ctcaattag gaggcgtag tcagaatga 
caattagtt tgacagtga ttataatgg aaacgacag 
gaaacattt cctttgctt tgcctctaa ttctgacat 
taattgcgg caaaatgga ctggtgatt ttttcaatg 
agggaattt atgacacac ttatacaac tcagtggtg 
ttccgttac tcccatggg aacccccgc cactagttc 
acaatatct acgccagtg aggtgatgt cgcatccgg 
tggtcacac tgaagtgtg ttgagaatg tggggcata 
ttgttgaat tgttgaaat taacaactt ataacggat 
ttccggttg ttgatccgc cactaactg atcaatcgg 
aagttacca cgtatggga gaataagag ggttagttt 
tgaggtcac aattaattg ttattttga aaaagaaga 
tttttaacg aaaattcgg acttttggg aggatatta 
atgcgggaa tctttcgag atgagtatc cccgatatc 
caacaatag agcaagtga gtgtttccg aagttgaaa 
aaacttatt ctattgatc tgaggccgt ttatgaatc 
cgtcaccat atacggtgc ttcattcgg catcactac 
ctcgaatgt ttagattat tccgagctc tcggtttac 
gacatttgc cgattgtta atgacacaa atgaggtta 
taggaatgg taacaagga aagatttag ctcgttata 
gagtctgga gacatcggg gtcgcatgg gggtagaag 
aattattaa tttccaaag aaatatgac cgcttacag 
tattatgat atgataata tagtttcac gaataatta 
tgttgtcgc ttttgacaa aagaatttt atttattgt 
taattaaag actttaccc attt

    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