Status
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Gene information
General information
TC009413 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: 1517373..1528990
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
    		TC009413
    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
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    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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    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_06270

    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)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 2 (3 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: < 50 embryo/egg not developed/not fertilized - Penetrance (percentage of animals/eggs on slide): more than 80%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 80%
    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): 50% - 80%
    affected eggs/embryos/larvae - 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: 0.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 0.0% (includes death as larva, prepupa, pupa, adult)

    Fertility
    egg production: number no/almost no eggs -
    mature egg deposition blocked number 1st lateral oviduct: 2 number 2nd lateral oviduct: - Number of animals showing the phenotype: 4

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC009413 RA
      MKYHHLVLL CVALISIFC TKSAYSKVT VLNKSGDPV 
KTTVHFTVK KSLQLKCES DETGNVVWE KGGKSVETL 
NELKGRFEL KDNKTVFTI NNLKDSDVG NYTCAVYSN 
GNKISEYTV SLHTATSSK WGVRVSKNS NVVEGEKLT 
IKCEIRGEL TLSWFYKNT TSGDNYTTL PGENGRVKL 
KDYYDEERK VNVTGGLLI IDEVDMGDR GEYICIGKS 
ADGQMFNMT STVRIKDKY AALWPFLGI CAEVFVLCA 
IIFIYEKKR NKTELEESD TDQSPEQKN TPDHGKESN 
LRHRQ
    CDS sequence
    • >TC009413 RA
      atgaagtac caccaccta gtgctgttg tgtgtcgct 
ttaatctcg atattttgc acgaaaagc gcctactcc 
aaggttacc gtattaaac aaatccgga gatcctgtg 
aagacgaca gtacatttt acggtcaag aagagtctg 
cagttgaaa tgcgaatca gacgaaact ggaaatgtc 
gtatgggaa aaaggcggt aaatccgtc gagacgctg 
aacgagttg aagggccgc ttcgaatta aaggataat 
aagacggtg ttcaccatc aacaatttg aaggattcc 
gacgtgggg aattacacg tgtgccgtg tacagcaac 
ggtaataaa atctccgaa tacaccgtc tccctgcac 
acggccacc agctccaaa tggggcgtg agggtcagc 
aagaactcc aacgtcgtc gaaggcgag aaactcacc 
atcaagtgc gaaatcagg ggcgaactc acgctcagc 
tggttctac aagaacacc accagtggt gacaactat 
accacgtta ccgggcgaa aatggacga gtcaaattg 
aaggattac tacgacgaa gaaagaaaa gtgaatgtg 
actgggggg ctgttaata atcgatgaa gttgatatg 
ggcgacaga ggtgaatac atttgtata ggaaaatcg 
gctgatggc caaatgttc aacatgacg agtacagtc 
cgcattaaa gataaatat gcggcgttg tggccattt 
ttgggtatc tgtgccgaa gtgttcgtc ctttgtgcc 
attatattt atatacgaa aagaaacgt aacaaaacg 
gaattggag gagagcgac actgatcag agccccgaa 
cagaaaaac acccccgac cacggtaaa gagtcgaac 
ttgaggcac agacagtga
    mRNA sequence
    • >TC009413 RA
      tagccgcag caactcaaa atgaagtac caccaccta 
gtgctgttg tgtgtcgct ttaatctcg atattttgc 
acgaaaagc gcctactcc aaggttacc gtattaaac 
aaatccgga gatcctgtg aagacgaca gtacatttt 
acggtcaag aagagtctg cagttgaaa tgcgaatca 
gacgaaact ggaaatgtc gtatgggaa aaaggcggt 
aaatccgtc gagacgctg aacgagttg aagggccgc 
ttcgaatta aaggataat aagacggtg ttcaccatc 
aacaatttg aaggattcc gacgtgggg aattacacg 
tgtgccgtg tacagcaac ggtaataaa atctccgaa 
tacaccgtc tccctgcac acggccacc agctccaaa 
tggggcgtg agggtcagc aagaactcc aacgtcgtc 
gaaggcgag aaactcacc atcaagtgc gaaatcagg 
ggcgaactc acgctcagc tggttctac aagaacacc 
accagtggt gacaactat accacgtta ccgggcgaa 
aatggacga gtcaaattg aaggattac tacgacgaa 
gaaagaaaa gtgaatgtg actgggggg ctgttaata 
atcgatgaa gttgatatg ggcgacaga ggtgaatac 
atttgtata ggaaaatcg gctgatggc caaatgttc 
aacatgacg agtacagtc cgcattaaa gataaatat 
gcggcgttg tggccattt ttgggtatc tgtgccgaa 
gtgttcgtc ctttgtgcc attatattt atatacgaa 
aagaaacgt aacaaaacg gaattggag gagagcgac 
actgatcag agccccgaa cagaaaaac acccccgac 
cacggtaaa gagtcgaac ttgaggcac agacagtga 
atcatccat caatccatc ttgttacca ttaccacac 
gtaaaatta aaaccaagt ttagaagtt caagttata 
gttacattc gtcatgtgt attattgaa gactattta 
actaacaag ttgtccgag atcgcactg tacaaagta 
acgtttaag gttattgtt gaagccttc gttttctcg 
gacgggtgt tgctttgag tacagtctt ttttaattg 
ttgttttcc gcgatacgg ttccgttca ggtacttac 
cttttccaa tctctagta cttaatgta gatattgta 
aaattgtta tgacgcaat cgaaagagg ctgtaatcc 
aaccgcaaa accatcatc ccattgtac ataaataaa 
ttaagaaat tgtatcctg tttatatgt attgttaaa 
tgaaattgt gtttaaaca tatggactg ttgtttttt 
ctttacgtt ttcttgtga tactttcga ttgtcaagt 
gcttaacga tccaaaggc ggcgtcttg ttatctttc 
ttcagattt tagtttggc gagattgta gttattaaa 
aaattaaag agtatcaat gtggtcttc atgtcatcg 
gtactaata gattcgagt aggctgctt ggatttcac 
cgctcagtg ctaatagtg gaagaaatt ttgtttcga 
ccaagatgg tgcccacct gtcccgggc gccatttct 
cgatgtgaa ccatttaac tcttctcta gttgactta 
ttaataaat tttaagcat aaactatat tagaatata 
aaaattatg atgacttaa aaataacgc agagcagat 
ttatttttt acttattct agagttatc tttaagtca 
ttgcctagg tttagacgt tccattcat ccgaggtga 
gactcgaac ggccactcc ttcatttac tcaactcga 
ttagttagc tctgcccat agcaacgac ggcacttcg 
agtggcacc tcaccgtaa aagcaaaca taaatcaac 
tagcattcg caattagag taaaatatt ggtgcttgc 
acaaacaaa acatcggac aggactcac tctgtcacc 
gcgttcatt aaatattta ggctgctgc tgatttttc 
tctaactta ctgtaatca tttcgtacc attttattg 
ttttcatgt aacagtcga tcattcttc cctattttt 
acttatgac ataccattt ttaaaaaaa ggtaatcac 
agattatta tgttgaaat aaactttaa ataaaatt

    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