Status
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Gene information
General information
TC000469 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_007417.3: 10911650..10913437
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
    		TC000469
    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
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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_10526

    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)

    Fertility
    mature egg deposition blocked number 1st lateral oviduct: number 2nd lateral oviduct: - Number of animals showing the phenotype: 3

    ovary without detectable defects - Number of animals showing the phenotype: 1
    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
    • >TC000469 RA
      MDLIFGLMT IAAIYLWVL FMDRFFKSC SHYGYIQFL 
KGTGLEIKL FQFSWTTTA FNKLLLKWG SHNTKFLNL 
WFNLGLCVS LVLLPASIY LLLVAFFQN FLSSASGEE 
SIIQPVVPG INLPASEMG YYSLTLLIS SVLHELGHA 
LGAVQEDVN VINVGANVI FILPVAYVN LNSDKLFSL 
NPWKRLKIL CAGVWHNLL IALVAYLLY TSLPSVFSP 
FFNFGKGVV VTEFEAKSP IFGNRGLNV GDLILKIND 
CEVDDENAW YKCLVALRT KKPAFCIEG DVVRDLDES 
VHLKHSESG IVSCCHSEN KGKLCFEYL DSKDSILEL 
PPYACLPGR PAIEASTNF CISDPHVCP KDTYCFRPI 
LTNNTNLFK IKRVNKNDV IYIGPVSDL VRTVTVSSY 
VPKYSFLGT RIPDVTTKF LGYLAMFSM GLALVNILP 
CLFMDGQHI TNTLFHIIF ASHLRTTHI KIISGVVTA 
SFTLLLVIH CVIVIWTRL N
    CDS sequence
    • >TC000469 RA
      atggacttg atttttggc ttaatgaca atagcggcg 
atttactta tgggttctc ttcatggac aggtttttt 
aaatcatgt tctcattac ggatacatc caatttctt 
aaaggaacg ggcctggag atcaaattg ttccagttt 
tcgtggacc acgacagcc tttaataaa ttgctgctt 
aagtggggc agtcacaac acgaaattt cttaatttg 
tggtttaat ttggggcta tgtgtgagt ttagttttg 
ctgcctgct tcgatctac ctattgtta gtggctttc 
ttccaaaac tttttgtct tcggcaagt ggcgaggaa 
agcataatt cagccggta gtcccggga ataaacctt 
ccagcatcc gaaatgggt tactacagt ttaactttg 
ctaatcagt tcggttttg cacgagcta ggccatgcg 
ttaggggct gtgcaagaa gacgtaaat gtgatcaat 
gtgggcgcc aacgtaatt tttattttg ccagtggct 
tacgttaac ttaaattcc gacaaatta ttttctcta 
aatccttgg aaaagactc aagattttg tgcgccgga 
gtttggcac aacttgcta attgcactc gtagcttac 
ttactctac acttctcta ccgtccgtt ttttcaccg 
tttttcaac tttggtaaa ggagttgtg gtaacggaa 
tttgaggca aaatcgcca attttcgga aataggggt 
ttaaatgtt ggcgattta attttgaaa attaatgat 
tgtgaggtg gacgatgaa aatgcgtgg tacaaatgt 
ttagtggct ttacgcaca aaaaagccc gcgttttgt 
attgagggc gacgttgtg cgcgatctg gatgagagc 
gttcatttg aaacactcc gaaagtggg attgtaagc 
tgctgccat tcagagaat aaaggcaaa ttgtgtttt 
gagtacttg gatagtaaa gacagcatt ttggagctg 
cccccttac gcctgtttg cctggaaga cctgcgatc 
gaagcctcg acaaatttc tgcatatct gacccccat 
gtttgcccc aaagatact tattgtttc agaccgatt 
ttaacgaat aacacgaat ttgtttaaa atcaagcga 
gtcaacaaa aacgacgtt atctacatt gggcccgtg 
tctgatctt gtgaggaca gtgacggtg tcctcatac 
gtcccaaaa tattcgttt ttagggacg cgaattccc 
gatgttact accaaattt ctagggtat ttagctatg 
ttttcaatg gggctggct ctagttaat atcttgccc 
tgtctgttt atggacggc cagcacata acgaacact 
ttgttccac ataatattc gcgagtcat ttgaggacc 
actcatatc aagattatt tcaggcgtt gtgaccgct 
tctttcaca ctcttgtta gtgattcac tgcgttatt 
gtcatatgg actagactt aattaa
    mRNA sequence
    • >TC000469 RA
      cttaaaaat ggacttgat ttttggctt aatgacaat 
agcggcgat ttacttatg ggttctctt catggacag 
gttttttaa atcatgttc tcattacgg atacatcca 
atttcttaa aggaacggg cctggagat caaattgtt 
ccagttttc gtggaccac gacagcctt taataaatt 
gctgcttaa gtggggcag tcacaacac gaaatttct 
taatttgtg gtttaattt ggggctatg tgtgagttt 
agttttgct gcctgcttc gatctacct attgttagt 
ggctttctt ccaaaactt tttgtcttc ggcaagtgg 
cgaggaaag cataattca gccggtagt cccgggaat 
aaaccttcc agcatccga aatgggtta ctacagttt 
aactttgct aatcagttc ggttttgca cgagctagg 
ccatgcgtt aggggctgt gcaagaaga cgtaaatgt 
gatcaatgt gggcgccaa cgtaatttt tattttgcc 
agtggctta cgttaactt aaattccga caaattatt 
ttctctaaa tccttggaa aagactcaa gattttgtg 
cgccggagt ttggcacaa cttgctaat tgcactcgt 
agcttactt actctacac ttctctacc gtccgtttt 
ttcaccgtt tttcaactt tggtaaagg agttgtggt 
aacggaatt tgaggcaaa atcgccaat tttcggaaa 
taggggttt aaatgttgg cgatttaat tttgaaaat 
taatgattg tgaggtgga cgatgaaaa tgcgtggta 
caaatgttt agtggcttt acgcacaaa aaagcccgc 
gttttgtat tgagggcga cgttgtgcg cgatctgga 
tgagagcgt tcatttgaa acactccga aagtgggat 
tgtaagctg ctgccattc agagaataa aggcaaatt 
gtgttttga gtacttgga tagtaaaga cagcatttt 
ggagctgcc cccttacgc ctgtttgcc tggaagacc 
tgcgatcga agcctcgac aaatttctg catatctga 
cccccatgt ttgccccaa agatactta ttgtttcag 
accgatttt aacgaataa cacgaattt gtttaaaat 
caagcgagt caacaaaaa cgacgttat ctacattgg 
gcccgtgtc tgatcttgt gaggacagt gacggtgtc 
ctcatacgt cccaaaata ttcgttttt agggacgcg 
aattcccga tgttactac caaatttct agggtattt 
agctatgtt ttcaatggg gctggctct agttaatat 
cttgccctg tctgtttat ggacggcca gcacataac 
gaacacttt gttccacat aatattcgc gagtcattt 
gaggaccac tcatatcaa gattatttc aggcgttgt 
gaccgcttc tttcacact cttgttagt gattcactg 
cgttattgt catatggac tagacttaa ttaaattgt 
tgaataaaa ccgtttttt atctaacaa gtgtattca 
tttcaatca caacctatt ttgccaaag aaatggtat 
tttccagtt cctttaaac acctttccc cgtacttga 
tgtacattt taatagtta tctcatccg tgtgatgag 
cgttgctcc tgaaatcac gtcttgccc attccttca 
gctcctgct ggtgcccct gatcgggca cttgccgta 
tagccctga agattttcc tgtaaagat tcttaactt 
cttgtttca agataaa

    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