Status
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Gene information
General information
TC015653 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_007421.3: 4179504..4199966
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
    		TC015653
    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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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_08539

    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: 40.0% (includes death as pupa, adult)

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

    adult lethality - Number of animals showing the phenotype: 1 (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): 30% - 50%

    affected eggs/embryos/larvae - 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
     larva completeeverted (inside-out) - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    larva partiallyeverted (inside-out) - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    larva dorsalbent - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    larva circumference decreased - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    Comment: the not everted part as well as the "bent" larvae
    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
    • >TC015653 RA
      MRRNALGRS PSQCLLCGD GFGMLGAQK VLCIDCRRL 
VCQKCAIET YTKAARNYW LCMICAETR EIWKKSGAW 
FFKSIPKYI LPAEKNQNY RHSLGKIGR NSKGNYRDE 
DSSSDEERK IWTRIQRRN SSTESTHDG HESVQDVAT 
MSTHKRQSS ASESQQSKE MESLKGLGS LNLSETKVW 
DQAEGSELS RRESTVSRS LSEWNWSDS RSEDRVSPS 
TSSVSSSIF KSNLEEHKP SDHSLGTIE LSLTYDPIT 
STLHCTVYR AKNLIPMDI NGLSDPFCK LNILPNAKP 
STRLRTKTV HKTRNPEFN ENLTFYDIS ESDLSKKAL 
HVLVVDDDK FGHDYMGET RIGLAKLKQ QNTIYVAAS 
LEEMRHEQK GPLPAPELN QWFDDLWSR GQILLSLCY 
STKRRALLV MVCRCANLL PMDNNGFSD PFVKLQLRP 
DPCHRKHKT SIKWKNLNP VYNEEFAFE TRPTELATQ 
SLYITVYDK DYGKSNDYL GGLILGGTG SKGLRLKQW 
LDMIRYPDH RHEAWHNLT EEILD
    CDS sequence
    • >TC015653 RA
      atgcgtcgc aacgccctg gggcgcagc ccctctcag 
tgtctcctc tgcggcgat ggttttgga atgttgggg 
gcccagaaa gtgctctgt atcgactgt cgccgtcta 
gtgtgccaa aaatgtgcc attgaaacg tatactaaa 
gcagcacgt aactattgg ttgtgtatg atttgtgcc 
gaaacgcgc gaaatttgg aaaaaatca ggcgcttgg 
tttttcaaa agcatcccc aaatatata cttccggcg 
gaaaaaaac caaaattac agacacagt ctggggaaa 
attggtcga aattcgaag gggaattac cgggatgaa 
gacagctcg tcggatgag gagaggaaa atttggacg 
aggatacag aggaggaat tctagtacg gaaagcact 
catgatggc cacgagtcc gtccaagac gtcgccacg 
atgtcgaca cacaagaga caatccagc gctagcgag 
tcgcaacaa agcaaagag atggaatca ttaaaaggc 
ttaggttcg ctgaattta agcgaaacg aaggtttgg 
gatcaggct gagggatcc gagctatcc cggagggaa 
tccacagtt agcagatcc ttatcagag tggaattgg 
agcgacagc aggagcgag gatcgagtt tcgccgagt 
acttcaagt gtgagcagc agcatattt aaaagcaac 
ctggaggag cacaaaccc tccgaccac tccctcggc 
accatcgag ctctccctc acctacgac cccatcacc 
tccaccctc cattgcacc gtctaccgt gccaaaaac 
ctcatcccc atggacatc aacggcctc tcggacccc 
ttctgcaaa ctgaacatc ctccccaac gccaagccc 
tcgacccgc ctccgcacc aagaccgtc cacaaaaca 
cgcaatccc gaattcaac gaaaaccta actttctac 
gacatctcc gagagcgac ctctcgaag aaggccctc 
cacgtcctg gtggtggac gacgataag ttcggacac 
gactacatg ggcgagacc aggatcgga ctggccaaa 
ctcaaacaa caaaacacc atctacgtg gccgcctct 
ctggaggag atgcgacac gagcaaaag gggccactc 
ccagcaccc gaattgaac caatggttc gacgatttg 
tggtcacgt ggacaaatc ctcctatcg ctgtgctac 
agcaccaag aggagggcg ttgctggtg atggtgtgc 
aggtgtgcc aacttactg ccaatggac aataacggg 
ttctccgac ccgtttgtt aaactgcaa ttacgacca 
gatccttgc caccgcaag cacaagact tccattaaa 
tggaaaaat cttaacccg gtttataac gaggagttt 
gcgtttgag acacgtccc acagagttg gccacgcaa 
agtctctat atcacagtc tatgataag gactatggc 
aaaagtaac gattatttg gggggtttg atcctagga 
ggcaccgga tcgaaggga ctgaggttg aaacaatgg 
ttggatatg attagatat ccggatcat agacatgaa 
gcctggcat aacttaacc gaagaaatt ctagattga
    mRNA sequence
    • >TC015653 RA
      ctcaagcaa cgaccaacg tgatttatt tcacccttt 
ttgtccatg gtaaacaat ggtcgattg tggagccaa 
cgatgctac caacagatt tgtttgtcc caatgatcg 
gcaattggc gcttcgagc caagttggg cgtctggtc 
gagcgtctg gaaaacatg cgtcgcaac gccctgggg 
cgcagcccc tctcagtgt ctcctctgc ggcgatggt 
tttggaatg ttgggggcc cagaaagtg ctctgtatc 
gactgtcgc cgtctagtg tgccaaaaa tgtgccatt 
gaaacgtat actaaagca gcacgtaac tattggttg 
tgtatgatt tgtgccgaa acgcgcgaa atttggaaa 
aaatcaggc gcttggttt ttcaaaagc atccccaaa 
tatatactt ccggcggaa aaaaaccaa aattacaga 
cacagtctg gggaaaatt ggtcgaaat tcgaagggg 
aattaccgg gatgaagac agctcgtcg gatgaggag 
aggaaaatt tggacgagg atacagagg aggaattct 
agtacggaa agcactcat gatggccac gagtccgtc 
caagacgtc gccacgatg tcgacacac aagagacaa 
tccagcgct agcgagtcg caacaaagc aaagagatg 
gaatcatta aaaggctta ggttcgctg aatttaagc 
gaaacgaag gtttgggat caggctgag ggatccgag 
ctatcccgg agggaatcc acagttagc agatcctta 
tcagagtgg aattggagc gacagcagg agcgaggat 
cgagtttcg ccgagtact tcaagtgtg agcagcagc 
atatttaaa agcaacctg gaggagcac aaaccctcc 
gaccactcc ctcggcacc atcgagctc tccctcacc 
tacgacccc atcacctcc accctccat tgcaccgtc 
taccgtgcc aaaaacctc atccccatg gacatcaac 
ggcctctcg gaccccttc tgcaaactg aacatcctc 
cccaacgcc aagccctcg acccgcctc cgcaccaag 
accgtccac aaaacacgc aatcccgaa ttcaacgaa 
aacctaact ttctacgac atctccgag agcgacctc 
tcgaagaag gccctccac gtcctggtg gtggacgac 
gataagttc ggacacgac tacatgggc gagaccagg 
atcggactg gccaaactc aaacaacaa aacaccatc 
tacgtggcc gcctctctg gaggagatg cgacacgag 
caaaagggg ccactccca gcacccgaa ttgaaccaa 
tggttcgac gatttgtgg tcacgtgga caaatcctc 
ctatcgctg tgctacagc accaagagg agggcgttg 
ctggtgatg gtgtgcagg tgtgccaac ttactgcca 
atggacaat aacgggttc tccgacccg tttgttaaa 
ctgcaatta cgaccagat ccttgccac cgcaagcac 
aagacttcc attaaatgg aaaaatctt aacccggtt 
tataacgag gagtttgcg tttgagaca cgtcccaca 
gagttggcc acgcaaagt ctctatatc acagtctat 
gataaggac tatggcaaa agtaacgat tatttgggg 
ggtttgatc ctaggaggc accggatcg aagggactg 
aggttgaaa caatggttg gatatgatt agatatccg 
gatcataga catgaagcc tggcataac ttaaccgaa 
gaaattcta gattgaatt attggacca aattgtaat 
aaatttaat caaagctt

    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