Status
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Gene information
General information
TC006729 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: 13445643..13449934
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
    		TC006729
    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_09406

    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: 20.0% (includes death as pupa, adult)

    adult lethality - Number of animals showing the phenotype: 1 (9 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection

    Fertility
    ovary without detectable defects - Number of animals showing the phenotype: 4
    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: < 50 larval musculature thinner - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    Comment: best to be seen on the dorsal side
    larval musculature fluorescence decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    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
    • >TC006729 RA
      MSNNTAPDS WESQADSAS PNTSPSHNA DVTAKFSTL 
NVNAVEFVP SFAKPAANA DEASPTSEA SPEHAPILN 
GTSAESAER VEVKEPPPI PPADGDASP GDGGTWEDV 
VVEDNDPLI TPEADDDEP SSEEAPIKI PKKKTVKEE 
VLKDKKEHV NVVFIGHVD AGKSTIGGQ IMALTGMVD 
KRTLEKYER EAREKSRES WYLSWALDT NQEERDKGK 
TVEVGRAFF ETEKKHFTI LDAPGHKSF VPNMIGGAA 
QADLAVLVI SARKGEFET GFDRGGQTR EHAMLAKTA 
GVKYLVVLV NKMDDPTVN WDEARYNEC RDKILPYLK 
KLGFNYNKD LFFLPCSGQ TGQGLKDQV DESICPWYR 
GPAFIPFID DLPSLNRKI DGPFIMPIV DKYKDMGTV 
LMGKVESGE CRKGQSLVI MPNRTPVTV DMLLSDDDE 
VNRIVPGEN VKVKVKGVE EEDVSPGFV LCDAVNPIH 
TGRVFDAQL VILEHKSII CAGYSAVMH IHCAAEEVT 
VKALICLVD KKTGEKSKT RPRFVKQDQ VAIMRIECA 
GVICLEPFK LFPQMGRFT LRDENKTIA IGKVLKLIE
    CDS sequence
    • >TC006729 RA
      atgtcgaat aacacagcc ccggacagt tgggaatct 
caggccgac tccgcgtcg cccaacacc tcccccagt 
cacaatgca gatgtgaca gcaaaattt tccacgttg 
aacgtgaac gctgttgaa ttcgtgcct tcatttgca 
aagcctgca gccaacgct gacgaggcc tcgccgacg 
tccgaggcc tcccccgaa cacgccccc atcctcaac 
ggaacgagc gctgagtcc gcagagcgg gtggaggtg 
aaggagccc ccgcccatc ccccccgcg gacggggac 
gcatccccc ggcgacggg ggcacctgg gaggacgtc 
gtcgtcgag gacaacgac cccctcatc acgcccgag 
gccgacgac gacgagccc tcctccgag gaggccccc 
atcaaaata cccaagaag aagaccgtc aaggaggag 
gtgctcaaa gacaagaag gaacacgtt aacgtggtt 
tttatcggg catgtggac gcggggaaa tcgaccatt 
ggggggcaa attatggcg ctgacgggc atggtggac 
aagcgaacg ctggaaaag tacgaaagg gaagccagg 
gagaaaagt cgggagtcg tggtacttg tcatgggcc 
cttgacacg aaccaagaa gaaagggac aagggcaag 
acggtggaa gtgggtcgg gcgtttttc gaaacggag 
aagaaacac tttacgatt ttggacgcg ccagggcat 
aagagtttt gttccgaat atgattggc ggagcggct 
caggccgat ttggccgtt ttggttatt tcggccagg 
aaaggggag tttgagacg gggtttgac cgaggtggt 
cagacgaga gaacacgca atgttggcc aaaacggcc 
ggtgttaaa tatttggtc gtgcttgtc aataaaatg 
gacgatccg actgttaac tgggatgaa gctagatac 
aacgaatgc agagacaaa attttaccc tatcttaaa 
aaacttgga tttaactat aataaggat ctgttcttt 
ttgccctgt tcgggacag acgggacaa gggctcaag 
gatcaagtg gatgagtcg atctgtccc tggtataga 
gggccggct ttcattccc ttcatcgac gacctgccg 
tcactcaat cgaaaaatc gacggcccc ttcataatg 
ccaatagta gacaaatac aaagacatg ggaacagtt 
cttatgggg aaagtggaa tcgggtgaa tgtcgaaaa 
ggacaaagt ctcgtcatt atgccaaac aggactccc 
gtcactgtc gatatgttg ctctctgac gacgacgaa 
gtcaatcgt atcgtaccc ggtgaaaat gtcaaagtt 
aaagtaaaa ggtgttgaa gaagaagac gttagtcca 
ggttttgta ctttgcgat gccgtcaat ccgatccac 
accggtaga gtatttgat gctcagctt gtgattttg 
gaacacaag tcgatcatt tgcgctggc tatagtgcc 
gttatgcac attcattgc gccgccgaa gaagtcacc 
gtcaaggcc ttaatttgt ctcgtggac aagaagact 
ggtgaaaag agtaaaacg cggcccagg tttgtgaag 
caagatcag gtagccata atgcgaata gaatgcgca 
ggtgtgatt tgcctggag ccctttaaa ttgttccct 
caaatgggc cgttttacg ctcagagat gaaaataaa 
acaattgcc atcggaaag gtactgaag ttaatcgag 
taa
    mRNA sequence
    • >TC006729 RA
      acaaagtaa ttagggcct tttcggata aaccgcgtc 
acgtgtgga tattagaaa aagaatttt gtattttgg 
gtcagtaac tggggacgg tggtggttg tgttattgt 
taggggcga gttcttgtc atttgtgat gacagtcgg 
ccattagtt tccggtggc agtgagtga acgcacgcg 
gatatttag agcagctga aagctcgag ttttattaa 
ttttccccg taaaagaac cgccccaag tgcacaaaa 
tgtcgaata acacagccc cggacagtt gggaatctc 
aggccgact ccgcgtcgc ccaacacct cccccagtc 
acaatgcag atgtgacag caaaatttt ccacgttga 
acgtgaacg ctgttgaat tcgtgcctt catttgcaa 
agcctgcag ccaacgctg acgaggcct cgccgacgt 
ccgaggcct cccccgaac acgccccca tcctcaacg 
gaacgagcg ctgagtccg cagagcggg tggaggtga 
aggagcccc cgcccatcc cccccgcgg acggggacg 
catcccccg gcgacgggg gcacctggg aggacgtcg 
tcgtcgagg acaacgacc ccctcatca cgcccgagg 
ccgacgacg acgagccct cctccgagg aggccccca 
tcaaaatac ccaagaaga agaccgtca aggaggagg 
tgctcaaag acaagaagg aacacgtta acgtggttt 
ttatcgggc atgtggacg cggggaaat cgaccattg 
gggggcaaa ttatggcgc tgacgggca tggtggaca 
agcgaacgc tggaaaagt acgaaaggg aagccaggg 
agaaaagtc gggagtcgt ggtacttgt catgggccc 
ttgacacga accaagaag aaagggaca agggcaaga 
cggtggaag tgggtcggg cgtttttcg aaacggaga 
agaaacact ttacgattt tggacgcgc cagggcata 
agagttttg ttccgaata tgattggcg gagcggctc 
aggccgatt tggccgttt tggttattt cggccagga 
aaggggagt ttgagacgg ggtttgacc gaggtggtc 
agacgagag aacacgcaa tgttggcca aaacggccg 
gtgttaaat atttggtcg tgcttgtca ataaaatgg 
acgatccga ctgttaact gggatgaag ctagataca 
acgaatgca gagacaaaa ttttaccct atcttaaaa 
aacttggat ttaactata ataaggatc tgttctttt 
tgccctgtt cgggacaga cgggacaag ggctcaagg 
atcaagtgg atgagtcga tctgtccct ggtatagag 
ggccggctt tcattccct tcatcgacg acctgccgt 
cactcaatc gaaaaatcg acggcccct tcataatgc 
caatagtag acaaataca aagacatgg gaacagttc 
ttatgggga aagtggaat cgggtgaat gtcgaaaag 
gacaaagtc tcgtcatta tgccaaaca ggactcccg 
tcactgtcg atatgttgc tctctgacg acgacgaag 
tcaatcgta tcgtacccg gtgaaaatg tcaaagtta 
aagtaaaag gtgttgaag aagaagacg ttagtccag 
gttttgtac tttgcgatg ccgtcaatc cgatccaca 
ccggtagag tatttgatg ctcagcttg tgattttgg 
aacacaagt cgatcattt gcgctggct atagtgccg 
ttatgcaca ttcattgcg ccgccgaag aagtcaccg 
tcaaggcct taatttgtc tcgtggaca agaagactg 
gtgaaaaga gtaaaacgc ggcccaggt ttgtgaagc 
aagatcagg tagccataa tgcgaatag aatgcgcag 
gtgtgattt gcctggagc cctttaaat tgttccctc 
aaatgggcc gttttacgc tcagagatg aaaataaaa 
caattgcca tcggaaagg tactgaagt taatcgagt 
aaatcgtcg ctagattag attgtaaaa cttgacatt 
ttaaccaac tcgcaatcg actggtgga catttttcc 
gaggtgacc accacacaa tgttcattt tgtattgtc 
ggtgaccac gaagagact ctagatcgg tgctacaaa 
cagtagcgt gtgaaaatg atgaatttt ttaattaat 
taattaatg ttttctttt ttgtatatt tagtctggt 
gtaatggta taattttcc ttttagata tgttttgta 
catttctaa ttttaattt attaaatta aggggtgta 
ttattattt tagcgatcg aaattgtgt ggtgtacat 
cattgttat taaaagagt tcttttgaa tcgatgtac 
tccttttgt tcgacagcc tggtgcttt atttatatt 
ttcgagacg agtgaaggt atttgacca cggcctatc 
accacctga tgcgttgtt gactgagag aacaaagtg 
tgcagtaaa taccttcaa gctcccggt tttatttac 
aacacgcct tttcaaaga gttcgctct agctttgac 
agttccatt gtaaataaa gagtttata agggtcacc 
atgtggcca aacttaata aatttatgc ttatgttgt 
attgcaaat tctttctgt taattaagt tgtgtttta 
ctctttatt aataattat ataagtaac caagaaatg 
ttgctatca attttatat attcaataa aatgtaaat 
tggact

    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