Status
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Gene information
General information
TC006490 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_007423.3: 10467450..10469440
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
    		TC006490
    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
    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
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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_01055

    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: 0.0% (includes death as pupa, adult)

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 head musculature not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%

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

    leg musculature potentially mostlynot present - 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
     labrum not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    labrum partially not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    labrum position irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    head appendages shape irregular - Penetrance (percentage of animals/eggs on slide): more than 80%

    head appendages orientation irregular - Penetrance (percentage of animals/eggs on slide): more than 80%
    head capsule not present - Penetrance (percentage of animals/eggs on slide): more than 80%

    head appendages partially not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    antenna not present - Penetrance (percentage of animals/eggs on slide): more than 80%
    head not present - 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): 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
    • >TC006490 RA
      MNGDGDSES WLSGWEQQC ADSVDEQPD 
FEQSLRDES ENSHTRIWT AFQDSAAAI 
AQLYRDRVT GEPATLWLQ FQTAAGTVT 
SLYKESSEG LRKSSDLAK QCGYQKRNK 
EILNWAKRK RRLICREDL LAYLSGKLP 
PKPNHHQYH HHNHHRNIS PPPGVAPPE 
SLGLNSELH TFREALARS PLSCIARGP 
DLCAFITGE MARHCKRPA SPSDVTMDS 
PTQQKRPRY M
    CDS sequence
    • >TC006490 RA
      atgaacggt gacggtgat agtgagtct tggttatcg 
ggatgggaa cagcagtgt gccgattcg gtggacgag 
cagcccgac ttcgagcag tcccttcgt gacgaatcg 
gagaattct cacacgcga atatggact gcgttccag 
gactccgcc gcagccata gcccagctg tatcgcgat 
cgggttaca ggagagccg gcgacgctc tggttgcag 
ttccagacg gctgcgggc acggtcacc tcattatat 
aaagaatct tcagagggg ctgcggaag tcgagcgac 
ctggcgaaa cagtgcgga taccaaaaa cggaacaag 
gaaatactc aattgggcc aagcggaaa cggcgcctg 
atctgcaga gaggacctg ctcgcctac ctctccgga 
aagcttcca cccaaaccc aaccaccac cagtaccac 
caccacaac caccacagg aacatatcg ccgcctcct 
ggagtcgcg ccccctgaa tctctgggt cttaatagt 
gagttacac accttcagg gaggccttg gcgcgatcg 
cccttgtct tgcattgcc cggggccca gacttgtgc 
gcttttatc acaggggaa atggccagg cattgtaaa 
cggccggcg agtccttcc gatgtgaca atggacagt 
cctacacaa caaaaaaga cctcgatat atgtga
    mRNA sequence
    • >TC006490 RA
      agcgtttta ttccgagtt tccgttaat tttttctcc 
tctcgttgg tgccccaat cgcagtgtc gccaccaca 
cgagtccca tctgtcact tcgtcaaac atggccgtg 
tgtagctga aagttatcg cgtagtttt ccgaaattc 
cattgtgtt ccgttaatt tttggtcac aaaaacgtg 
agatgaacg gtgacggtg atagtgagt cttggttat 
cgggatggg aacagcagt gtgccgatt cggtggacg 
agcagcccg acttcgagc agtcccttc gtgacgaat 
cggagaatt ctcacacgc gaatatgga ctgcgttcc 
aggactccg ccgcagcca tagcccagc tgtatcgcg 
atcgggtta caggagagc cggcgacgc tctggttgc 
agttccaga cggctgcgg gcacggtca cctcattat 
ataaagaat cttcagagg ggctgcgga agtcgagcg 
acctggcga aacagtgcg gataccaaa aacggaaca 
aggaaatac tcaattggg ccaagcgga aacggcgcc 
tgatctgca gagaggacc tgctcgcct acctctccg 
gaaagcttc cacccaaac ccaaccacc accagtacc 
accaccaca accaccaca ggaacatat cgccgcctc 
ctggagtcg cgccccctg aatctctgg gtcttaata 
gtgagttac acaccttca gggaggcct tggcgcgat 
cgcccttgt cttgcattg cccggggcc cagacttgt 
gcgctttta tcacagggg aaatggcca ggcattgta 
aacggccgg cgagtcctt ccgatgtga caatggaca 
gtcctacac aacaaaaaa gacctcgat atatgtgaa 
aaacgtcat cagtcctgc agttttcct actcgttca 
ataggtgca gttgccttc cgttttgta tacagtttt 
tcatttgat ttttggtgc ttttaatgt ttttttaag 
tctgtgata attgcctga acttattat tttcttctg 
tttttaacg cggtaatat cggatttgg gggatagag 
gtattggtc attctttta aattaattg ttttcgcta 
caaaacgcg cgacgtgca ggaacgatg gggtaaata 
tccatcact aaatattca atgaataaa gtagtttat 
tattcatta gattgtaag gcaattaaa aataataca 
aaaaattgg ccattacga aattgtaaa taagttctt 
ctttcgtta aatacttgt tgaaaactt cttactgtt 
tttttacac ttatgagac aaatcatta tattgtaat 
atagaggtg cctcggtcg attttttat aatatgaag 
ccttccaat tttttgaga atcgatata ttcaagaca 
cagactgcc acttattat attttattt atttatatg 
gagaggttg agattgttg atatcggga atttttttt 
gaaaagata ccgagtctc aggatgcta aatacgatc 
ttcacacac gactttata ttgatttat cttgtattc 
caattgtta ttctgtata gttgcaaga ttcttattt 
tcaacaagt gttaataga ctgtacgaa tatttgcac 
atatttatt taattaaat ctagttttt taaaccttt 
gttattttg tttcggtac ttctaagat ccaattatg 
tttcgactt tttcagtga tgtaagtaa ttgttctgt 
aaattatta ttggtctaa atatattat attggtcta 
a

    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