Status
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Gene information
General information
TC007099 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_007419.2: 9578553..9583281
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
    		TC007099
    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_07239

    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: 2 (9 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): more than 80%

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

    larva fragmented - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    larva partially everted (inside-out) - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    head appendages shape irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    head appendages random not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    thorax partially not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    mesothorax not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    metathorax not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    abdomen everted (inside-out) - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    affected eggs/embryos/larvae - 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: % (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
    • >TC007099 RA
      MSRLILKSG ASFAQTFQN CGFLSVFPT NFGAQKLKL 
REQRRFMSA GIVQSPLGP SKKIPNENL VEYIYKNND 
KWIEEPAMT CGVSGRSYT YGMLRMLIN RCAQALLGH 
CGMKPREVV GLLLPNIPE YAVVCHGAI EAGLVVTFV 
NPLYTPDEI KRQFENAGV KMIVTVPQL LEVALTIAP 
QLQEYRTTI CIGGEDDPS KNVNGLQSM LMAGHEAEL 
PGINPREIA ILPYSSGTT GLPKGVMLS HYNLVANLV 
QGEHPALED LETKDGKRH TMLTVLPFF HIYGFNGIL 
NLCLKNGAH IITIPRFTP EDYLKTLVE YKPSFIFVV 
PSLLLFLAS HPAVTKEHL SSIEAVQSG AAPLTEGLL 
QKFRQKVGR DDILIRQGY GMTESSPVT FCMPKLTPP 
SKIATIGLP YPGTEAKVI SLSNGEPQG THKSGELLV 
RGPQIMMGY LNNEQATAE TVDEEGWLH TGDVAYYDE 
DFYFYIVDR CKELIKVKG NQVSFF
    CDS sequence
    • >TC007099 RA
      atgtcgcgt ttaatttta aaaagtggt gcatccttc 
gcgcaaacc ttccaaaat tgtggattc ctctccgtt 
tttccgacc aacttcggg gcccaaaaa ctgaaactg 
cgtgaacag aggcgattt atgagtgct ggaatcgtc 
cagtcgcct ctgggacca agcaaaaaa ataccaaac 
gaaaacctc gtcgagtac atttacaaa aataacgac 
aaatggatc gaggagccc gccatgact tgtggcgtt 
tccgggcga agctacacc tacggaatg ctccggatg 
ctgatcaac agatgtgcc caggccctt ttgggccac 
tgcggcatg aaaccgcga gaagtcgtc ggtttgctt 
ctaccaaac attcccgaa tacgccgta gtgtgtcat 
ggggccatc gaggccgga cttgtggtc acttttgtc 
aacccttta tacactcct gatgaaatc aaacgccag 
tttgagaat gccggagtc aagatgatt gttacagtg 
cctcaattg ctagaggtg gcgttaaca atagcccca 
caattgcaa gagtatcga actacgatt tgtatcgga 
ggagaggac gatccctcg aagaacgtt aacgggctt 
cagagcatg ttaatggcg gggcatgaa gccgaactt 
cccgggatt aatcccaga gagattgcc attttgccg 
tattcgagt ggcacgacg ggattgccg aagggagta 
atgctctcg cattataat ttagtggcg aatttggtg 
caaggggaa cacccggct ttggaggac ttggaaact 
aaagatggg aaaaggcac accatgcta acagtcctt 
cccttcttc cacatttac ggcttcaat ggaattttg 
aacttgtgc ctcaaaaac ggcgctcac atcatcacc 
attccacgg tttactccc gaagattac ctcaaaacc 
ctcgtcgaa tacaaaccg agctttatt ttcgtcgtt 
ccttccctg ctcttgttc ctggcctcg catcctgcc 
gtcaccaag gaacacttg agttctatt gaagccgtc 
cagtcagga gcggccccc ttgactgaa ggtctcttg 
caaaaattc agacagaag gtgggaaga gacgatatt 
ctgataaga caaggttac ggcatgacg gagagttcg 
ccggttact ttctgtatg cccaagttg acgccaccg 
tcgaaaatt gcaacgatt ggacttcct tatcccggg 
acggaagca aaagttatt agtttgtca aatggggaa 
ccgcagggg acacacaag tcgggtgaa ttgctagtg 
agggggcca cagattatg atggggtac ttgaacaac 
gaacaagcc actgcggag actgtcgat gaggaaggg 
tggctccat acaggggat gtggcctat tacgacgaa 
gatttctac ttttacatt gtcgatagg tgcaaggaa 
ctcatcaaa gtcaagggc aatcaagta agttttttt 
taa
    mRNA sequence
    • >TC007099 RA
      tactttgtg taaaaagtg atatacgtc agtgttgga 
taaataaga aacacgtgt gtttggcat cttttggtc 
tgatttacc atcaatcaa actttgcac caaacaatt 
aatgataat ggaaatggc gcaaacaaa acgattcaa 
tgcaatgta aagtcctta ttcattctt tgcggccaa 
tctagggct tattacaat aagtgaaag cgtcagaaa 
gttaccgct gctattttt ctcggcgtt cagccgctt 
gtttgatca gaaatatcc gaatggtga gaagttgga 
ctttgaatc attggactc cgtacaagt tatctattt 
tattttaat taaatgtac tcgcggatc cattcaaaa 
caatcatag gtgcaataa agacaacac ggttgcggt 
gtgctcaaa accagtgcg agtgttaat taacccacc 
ttcaagatt tttcactat tttccaagg tagcacacc 
tatttttac cggggaata aatatgtcg cgtttaatt 
ttaaaaagt ggtgcatcc ttcgcgcaa accttccaa 
aattgtgga ttcctctcc gtttttccg accaacttc 
ggggcccaa aaactgaaa ctgcgtgaa cagaggcga 
tttatgagt gctggaatc gtccagtcg cctctggga 
ccaagcaaa aaaatacca aacgaaaac ctcgtcgag 
tacatttac aaaaataac gacaaatgg atcgaggag 
cccgccatg acttgtggc gtttccggg cgaagctac 
acctacgga atgctccgg atgctgatc aacagatgt 
gcccaggcc cttttgggc cactgcggc atgaaaccg 
cgagaagtc gtcggtttg cttctacca aacattccc 
gaatacgcc gtagtgtgt catggggcc atcgaggcc 
ggacttgtg gtcactttt gtcaaccct ttatacact 
cctgatgaa atcaaacgc cagtttgag aatgccgga 
gtcaagatg attgttaca gtgcctcaa ttgctagag 
gtggcgtta acaatagcc ccacaattg caagagtat 
cgaactacg atttgtatc ggaggagag gacgatccc 
tcgaagaac gttaacggg cttcagagc atgttaatg 
gcggggcat gaagccgaa cttcccggg attaatccc 
agagagatt gccattttg ccgtattcg agtggcacg 
acgggattg ccgaaggga gtaatgctc tcgcattat 
aatttagtg gcgaatttg gtgcaaggg gaacacccg 
gctttggag gacttggaa actaaagat gggaaaagg 
cacaccatg ctaacagtc cttcccttc ttccacatt 
tacggcttc aatggaatt ttgaacttg tgcctcaaa 
aacggcgct cacatcatc accattcca cggtttact 
cccgaagat tacctcaaa accctcgtc gaatacaaa 
ccgagcttt attttcgtc gttccttcc ctgctcttg 
ttcctggcc tcgcatcct gccgtcacc aaggaacac 
ttgagttct attgaagcc gtccagtca ggagcggcc 
cccttgact gaaggtctc ttgcaaaaa ttcagacag 
aaggtggga agagacgat attctgata agacaaggt 
tacggcatg acggagagt tcgccggtt actttctgt 
atgcccaag ttgacgcca ccgtcgaaa attgcaacg 
attggactt ccttatccc gggacggaa gcaaaagtt 
attagtttg tcaaatggg gaaccgcag gggacacac 
aagtcgggt gaattgcta gtgaggggg ccacagatt 
atgatgggg tacttgaac aacgaacaa gccactgcg 
gagactgtc gatgaggaa gggtggctc catacaggg 
gatgtggcc tattacgac gaagatttc tacttttac 
attgtcgat aggtgcaag gaactcatc aaagtcaag 
ggcaatcaa gtaagtttt ttttaatta gctcaaaag 
gtaagtaca gattttatc accactaat aagtggata 
agcgcaaat cttacgaat tcgcgtcta ttcaaagtt 
aatttacaa caaaatgta gccaaaaag gacaagact 
ctgctctac ttgttagat ttaaactaa ctgtagaac 
gtagggaaa agaatcata attattaca catacatat 
tacgttacc ttaaataca aggtgttta aacgtaatt 
tacgcctat aaaatgcaa tcagcaata catataatt 
taagaat

    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