Status
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Gene information
General information
TC015698 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: 5397443..5416397
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
    		TC015698
    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_05877

    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: 30.0% (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

    Fertility
    mature egg deposition blocked number 1st lateral oviduct: 2 number 2nd lateral oviduct: 3 - Number of animals showing the phenotype: 2
    ovary without detectable defects - Number of animals showing the phenotype: 2
    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg with muscle fluorescence/pattern, but not hatched (pot. late embryonic lethality) - Penetrance (percentage of animals/eggs on slide): 30% - 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): 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): 30% - 50%
    cuticle remnants with some identifiable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

    head appendages partially shape irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

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

    thorax segment number decreased - Penetrance (percentage of animals/eggs on slide): less than 30%

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

    legs femur potentially fused - Penetrance (percentage of animals/eggs on slide): less than 30%
    legs tibiotarsus potentially fused - Penetrance (percentage of animals/eggs on slide): less than 30%
    thorax not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    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)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC015698 RA
      MASRVNMRP TNKNTLLKV VILGDGGVG 
KSCLMNRFV SNQFDEHSF HTIGVEFLN 
KDIEIDGET YTLQIWDTA GQERFKTLR 
TPFYRGSDI CMLTYAVDD KHSFRNLQM 
WKNEFLYYA DVKENVQFP FIVVGNKSD 
VEQNEREVS QIEMETWCT ENGISACIE 
TSAKNASNV HDAFAIAVQ HWLKLETRA 
DKNDCIYAD TVDLTKKQS ENRTSCCIN 
TSDE
    CDS sequence
    • >TC015698 RA
      atggcttca cgagtcaac atgcgaccc accaacaag 
aacacgctg ctcaaagtg gtgattttg ggggatggg 
ggcgtcggg aagagctgt ctgatgaac aggttcgtc 
tcgaatcag ttcgacgag cactcgttt cacaccatt 
ggggtggaa ttcctgaac aaggacata gaaattgac 
ggggaaaca tacactcta cagatttgg gacactgcg 
ggacaggaa cggttcaag acgctccgg acgcccttt 
taccgaggg agcgatatc tgcatgctg acctacgca 
gtggacgac aaacacagc ttccggaac ctacaaatg 
tggaaaaac gagttcctt tattacgcc gatgttaag 
gaaaacgtc cagtttcct tttatcgtg gttggaaac 
aagtccgac gttgaacaa aatgaacgt gaggtttcg 
caaatcgaa atggagacc tggtgcacc gaaaacggc 
atttctgca tgcattgaa acgtccgcc aagaacgca 
agtaacgtc cacgatgcg tttgcaata gccgttcaa 
cattggttg aaactggag acaagagcc gataaaaac 
gactgtatc tatgccgat acggttgat ttaactaag 
aaacaatca gagaaccga acttcttgt tgtattaac 
acctctgac gagtaa
    mRNA sequence
    • >TC015698 RA
      attgtgtgg tgggggtag gtaaggtca aggcccttg 
gtcacgtgt tcaacctca aggtcattc ggcgaatca 
agtacaacg gcaccgcgt cgttggaga tccactacg 
ttggatggc gctcttgta gatgatgac gatgaacaa 
cagcacaat acaactctc accacgtca aacgattta 
acaaattta atttagaac gcgtttttt ggcgaaaaa 
ttttggggt ttcggtgat gatgatgag agaaaccac 
gacgagagc gacgatgac ggtgtctca ggtaccact 
aagcgaccg ctgggaaaa atgccgttc attcgacgc 
gaaaaatcc gcatatttg catgccata cgtaccgtt 
cttatctcg ttctcctca aatgcatcc ttggccaga 
taaatcctc gccaaaatc gattgagaa agcacaaaa 
tgttaggta atatcaatt ttcactttc acgaatcgg 
acttatgca cggggcaca ccttcggcg gagtttatt 
gacaccaga ggttcaggt aaaaccgat ttttacaca 
cactgctat tgcaggacg ttgtctcca ctgtcacgc 
gccccgaaa cgtgccccc aaacacacc aacaacccc 
aaaaacaac gcacaactg tacacagct ccaacaatc 
tcccagtcg aaaaaacga acacaaaaa atgctcaat 
tcacaatcg tctgtaaaa acaatggaa attaaaaaa 
tgacaaaca gcgccacct atcccacac ctgtcaaac 
accacgacc gccaaccta cgaaaaaga accaaacgg 
gcctcacct gaccatttc gaacgcaat taattacat 
aatcagtaa taatcgcac aatttggtc gcacccagc 
acgcaccca agcccattc aagtcccaa cggtttgac 
atttttgac acctgtcac attgacagc tgtcttact 
gactggtgg gtaagagca atttgaatc aattcccag 
atcagatga gtcacaatc gtgcaggaa agtccccaa 
aaactgata caatgttat aataaacaa attcggatg 
gcttcacga gtcaacatg cgacccacc aacaagaac 
acgctgctc aaagtggtg attttgggg gatgggggc 
gtcgggaag agctgtctg atgaacagg ttcgtctcg 
aatcagttc gacgagcac tcgtttcac accattggg 
gtggaattc ctgaacaag gacatagaa attgacggg 
gaaacatac actctacag atttgggac actgcggga 
caggaacgg ttcaagacg ctccggacg cccttttac 
cgagggagc gatatctgc atgctgacc tacgcagtg 
gacgacaaa cacagcttc cggaaccta caaatgtgg 
aaaaacgag ttcctttat tacgccgat gttaaggaa 
aacgtccag tttcctttt atcgtggtt ggaaacaag 
tccgacgtt gaacaaaat gaacgtgag gtttcgcaa 
atcgaaatg gagacctgg tgcaccgaa aacggcatt 
tctgcatgc attgaaacg tccgccaag aacgcaagt 
aacgtccac gatgcgttt gcaatagcc gttcaacat 
tggttgaaa ctggagaca agagccgat aaaaacgac 
tgtatctat gccgatacg gttgattta actaagaaa 
caatcagag aaccgaact tcttgttgt attaacacc 
tctgacgag taattttta ataatttga ctcagtttt 
gccggatgg aggttgtgt attgtctta ttccaaaga 
atagttaaa tatcaaaca ttctactaa acaaattgt 
gataactct tcttaattt ccatatttc aagtgtgta 
ggtcttaga gcattttta ttttgtaca ttctttatt 
gtactcatt gtaaatata tctcaggag caccaaatt 
atgcggcct tttgctatc agttaattt gcttcaagc 
actctgtat atattagtg ctgttagct tttgtactg 
caacgtttt gataaggca tatcaattc tcgaattgg 
aatcgttca gtatttcgg tgctgttat tatttatta 
attgtatcg gcacgttca atagatctg ttgtaaaat 
aatcaagtc gccttattt acccacgtg acctagaag 
cgccaatca gtttgtaa

    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