Status
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Gene information
General information
TC009315 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_007422.5: 276096..281293
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
    		TC009315
    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
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    Email
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_01526

    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: 2 (3 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 3 (9 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
     labium partially not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    head not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    thorax cuticle dorsal structure irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    legs shortened - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    thorax not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen segment number decreased # of remaining segments - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen not present - 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): 50% - 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: 30.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 70.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality early (L5/6) - Number of animals showing the phenotype: 3 (11 dpi)
    Days post injection

    adult lethality immediately after eclosion - Number of animals showing the phenotype: 1 (16 dpi)
    Days post injection

    eclosion not fulfilled (not completely eclosed) - Number of animals showing the phenotype: 4 (16 dpi)
    Days post injection


    adult lethality - Number of animals showing the phenotype: 2 (19 dpi)
    Days post injection

    adult nutritional state bad (cachectic) - Number of animals showing the phenotype: 2 (22 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (22 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 2 (41 dpi)
    Days post injection

    Pupal morphology
    oblique dorsal thoracic muscles partially rounded - Number of animals showing the phenotype: 6

    Comment: in some cases both oblique muscles are rounded and in other cases only the outer or the inner oblique muscle is rounded
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC009315 RA
      MGKRRRLNK FISKWIKSD LPEDRSTVL LLGVTRIPT 
SPLPARRPC TLPLDPSQT LEISSQKSS SAQSRRTSF 
STRRRHTRS SSIKRRPGD DSKCSSSSW ENPNDHDDE 
LTSPSSNCV SGYENAAST TETVMDRSV DSIGTCSLD 
VEASADLSD WSEASSGGT LRSASIRTP TSEPHLPSY 
LSLACTVNG YSTTTNYDP VRLARSRDT SPHRLDNDN 
LTPKNPPTT YSIQNNLLS PPNLVPLPT HIKPKMTDH 
TITHHHHYQ STKTMTFQK HTESHHFTS KVYTKDTID 
ACYDHKKLT NKCMPKMNG QSKMNVVET KSFIEQRVE 
RLYGPGALA QGFFVSKKQ KHESECENS YVEENGIES 
PMKQSNSSP ALPVLRHLR PEFRAQLPI LSPRKGVEN 
SMQKSCTVP TLKDEVKVN GHSKQIAAS EGDNVAKMT 
IKEETGEKD GHHFLKILQ NETNRLLQL ADKVEMELS 
NTELSEEII GKIHSASGK ARLLVSQKM QQFKGLCTN 
NITQGENEA FPTTNEDLQ GFWDMVMLQ VDQVDALFK 
EIELLKANN WQEVKPSQP VNNVTNGKA KKIVNRVKA 
TSQASEEAR KKREAQRKQ MIEERRKAM KAQKPVESI 
EIFVPESS
    CDS sequence
    • >TC009315 RA
      atgggtaaa cgtcgacgt ttgaataag ttcatcagt 
aaatggatc aagagtgac ctcccggag gatcgctca 
acggtgctg ctgctcggc gtcaccagg ataccgacc 
tctccgtta ccggcccgt cgtccctgc acccttcct 
ctcgaccca tcccaaacc cttgagatc agctcccaa 
aaatcgtca agtgcacag tcacgtcgg acgtcgttt 
tcgacaaga cgacgacat actaggagt tcgtcgatc 
aaacgacgg cccggcgac gattcaaaa tgctcctca 
tcctcatgg gagaatccc aacgaccac gacgacgaa 
ctcacgtcg ccgtcttct aattgcgta tccggttat 
gaaaacgct gcttccacc accgaaacg gtgatggac 
cgatctgtc gactctatc gggacttgc tctctagac 
gttgaagct tcggctgat ctttcagac tggtctgaa 
gcctcatct ggtggcacc ctccggagc gctagcatc 
agaaccccc acatctgag ccccattta ccttcatat 
ctcagtcta gcctgcact gtaaacggc tattccacc 
acaaccaac tacgaccca gtacgtctt gctcgttcc 
agagacact tctccccat cgtctcgat aatgacaat 
ttgacacca aaaaatcca ccaacaact tattccatc 
cagaacaat cttctttca cccccaaat ctcgtccct 
ttaccaacc cacatcaag cccaaaatg accgaccat 
accatcacc catcatcat cactaccaa tcaaccaag 
accatgacg ttccaaaaa cacaccgaa tctcaccat 
ttcacctca aaagtctac acaaaggat accatcgac 
gcttgctac gaccacaag aaactcacc aataaatgc 
atgccaaaa atgaacgga cagagcaaa atgaatgtt 
gttgaaaca aaatcgttc attgagcag agagttgag 
aggttgtac ggacctggg gctctagct cagggattt 
ttcgtctca aagaagcaa aaacatgaa tcggaatgt 
gagaattct tatgtggaa gaaaacgga attgaatcg 
ccaatgaaa cagagtaat agtagtcca gctttgcca 
gttttgaga catttgaga cctgaattt cgggcacaa 
ttaccgatt ttgagtccg aggaaaggg gtcgagaat 
tcaatgcag aaaagttgt actgtacct acgttgaaa 
gatgaggtt aaagttaat gggcatagt aagcaaatt 
gcggcaagt gaaggggat aatgttgcc aagatgacc 
attaaggaa gaaacaggt gaaaaggac ggtcaccac 
tttttgaaa atcctgcag aacgaaacg aaccgactt 
ttacaactg gctgacaaa gtagaaatg gaattatcc 
aacactgaa ctgtctgaa gaaatcatc gggaaaatt 
cattcggct tcggggaaa gccagactt ttagtatca 
cagaaaatg caacagttc aaaggacta tgcacgaat 
aacatcaca cagggtgaa aatgaagct tttcccacc 
actaatgag gacttgcaa ggcttttgg gacatggtg 
atgcttcag gtcgaccaa gtggatgct ctcttcaag 
gaaatcgag ttgctgaag gccaacaat tggcaagag 
gtgaagcca tcacaacct gtcaataat gtgaccaat 
ggcaaagca aagaaaata gtgaataga gtaaaagca 
acgtcacag gcgagcgaa gaagctcga aagaaacgc 
gaagcccaa cgaaaacag atgattgaa gagaggaga 
aaggcaatg aaagcccaa aaaccagta gaaagtatt 
gaaatattc gtgcctgaa tctagctga
    mRNA sequence
    • >TC009315 RA
      cgttctaaa atcagttta ttcgaatca tgctttgag 
ctagatgtg atgtaggta cacacaaaa tggatcggc 
agttttgtg gtttaaatt ttcgtttga aaatgggta 
aacgtcgac gtttgaata agttcatca gtaaatgga 
tcaagagtg acctcccgg aggatcgct caacggtgc 
tgctgctcg gcgtcacca ggataccga cctctccgt 
taccggccc gtcgtccct gcacccttc ctctcgacc 
catcccaaa cccttgaga tcagctccc aaaaatcgt 
caagtgcac agtcacgtc ggacgtcgt tttcgacaa 
gacgacgac atactagga gttcgtcga tcaaacgac 
ggcccggcg acgattcaa aatgctcct catcctcat 
gggagaatc ccaacgacc acgacgacg aactcacgt 
cgccgtctt ctaattgcg tatccggtt atgaaaacg 
ctgcttcca ccaccgaaa cggtgatgg accgatctg 
tcgactcta tcgggactt gctctctag acgttgaag 
cttcggctg atctttcag actggtctg aagcctcat 
ctggtggca ccctccgga gcgctagca tcagaaccc 
ccacatctg agccccatt taccttcat atctcagtc 
tagcctgca ctgtaaacg gctattcca ccacaacca 
actacgacc cagtacgtc ttgctcgtt ccagagaca 
cttctcccc atcgtctcg ataatgaca atttgacac 
caaaaaatc caccaacaa cttattcca tccagaaca 
atcttcttt cacccccaa atctcgtcc ctttaccaa 
cccacatca agcccaaaa tgaccgacc ataccatca 
cccatcatc atcactacc aatcaacca agaccatga 
cgttccaaa aacacaccg aatctcacc atttcacct 
caaaagtct acacaaagg ataccatcg acgcttgct 
acgaccaca agaaactca ccaataaat gcatgccaa 
aaatgaacg gacagagca aaatgaatg ttgttgaaa 
caaaatcgt tcattgagc agagagttg agaggttgt 
acggacctg gggctctag ctcagggat ttttcgtct 
caaagaagc aaaaacatg aatcggaat gtgagaatt 
cttatgtgg aagaaaacg gaattgaat cgccaatga 
aacagagta atagtagtc cagctttgc cagttttga 
gacatttga gacctgaat ttcgggcac aattaccga 
ttttgagtc cgaggaaag gggtcgaga attcaatgc 
agaaaagtt gtactgtac ctacgttga aagatgagg 
ttaaagtta atgggcata gtaagcaaa ttgcggcaa 
gtgaagggg ataatgttg ccaagatga ccattaagg 
aagaaacag gtgaaaagg acggtcacc actttttga 
aaatcctgc agaacgaaa cgaaccgac ttttacaac 
tggctgaca aagtagaaa tggaattat ccaacactg 
aactgtctg aagaaatca tcgggaaaa ttcattcgg 
cttcgggga aagccagac ttttagtat cacagaaaa 
tgcaacagt tcaaaggac tatgcacga ataacatca 
cacagggtg aaaatgaag cttttccca ccactaatg 
aggacttgc aaggctttt gggacatgg tgatgcttc 
aggtcgacc aagtggatg ctctcttca aggaaatcg 
agttgctga aggccaaca attggcaag aggtgaagc 
catcacaac ctgtcaata atgtgacca atggcaaag 
caaagaaaa tagtgaata gagtaaaag caacgtcac 
aggcgagcg aagaagctc gaaagaaac gcgaagccc 
aacgaaaac agatgattg aagagagga gaaaggcaa 
tgaaagccc aaaaaccag tagaaagta ttgaaatat 
tcgtgcctg aatctagct gaaatttat ccaaatttt 
agaagtttt atatttatt acctacaga ataatattt 
tgtgaaatt cctttaaga tctgtggtg tatggtgtt 
ttttgaaaa ttttgttgt gacctgcac tgaataatt 
catgttaag actgagttt gaaattttt tatcataat 
actaaaata ataaccaaa taactaagt actctgctg 
gtacattcc cagtgcttt tataaaaca ggtgtattt 
tttcttgta atttttacc atttgcatg ccgatttgt 
tatgtaatg ttattgtat agttaaatt ttttattac 
agttgggtt tctttcctc acactaaat attttataa 
tttgcgaaa tcaaatata agtaagaag taccattta 
ttatattcg aattgtatt tatacacac aataaattt 
tcaactttt accaacact tggcgcttg taatcacca 
cctgtcatt aattcttac aagttcttt taacttaaa 
tttgaacat tttg

    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