Status
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Gene information
General information
TC014209 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_007416.3: 3205668..3207529
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
    		TC014209
    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
    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
    We will use your email address only for possible questions regarding this annotation. We will never show your address or give it away.
    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_05585

    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 larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): less than 30%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 50
    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: 20.0% (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC014209 RA
      MLLSREFYT FLKSATSPA KLITLKNFH SCASYAAQV 
SFKLSDIGE GIREVTVKE WFVKVGDKV SQFDEICEV 
QSDKASVTI TSRYDGVIK KLHYKIDEI ASVGKPLVD 
IETEGDEPS AAPTPEEES KPPVEEIKI SEPTDPQPT 
AEILCIPSV RRLAKEHKV NLWEVTGTG KSGRILKED 
VLKYLQAGP APAKAPARQ ARTEPIKGF QKAMVKTMS 
DALKIPHFV YSDEIAVTQ LSQLRQTLK KLPETQDLK 
LSFMPFFIK AASNALQRF PVLNASLDE NCENVTYKS 
EHNIGVAMD TKVGLAVPV IKNVETLSI IEISNELNR 
LIKSGRSGS FSPQDLAGG TFTISNIGA IGGTYMKPV 
IMPPHVAIV ALGASQVVP RFDDAGNVV PVEVLNLSG 
AADHRIIDG ATMARFVQT LKRQIENPY LLFLNL
    CDS sequence
    • >TC014209 RA
      atgttgctg tcaagggag ttttacact tttttaaaa 
agtgcgacc agtccggca aaactaatc actttgaaa 
aactttcac tcgtgtgcg agctatgcg gcccaagtg 
tctttcaaa ctgtctgac attggtgaa ggcataagg 
gaggtaaca gtcaaagag tggttcgtc aaagtcggc 
gacaaagtc tcccaattt gacgaaatt tgcgaagta 
cagagtgac aaagcctcg gtcacaatc acaagcaga 
tacgatgga gttattaag aaactacat tacaaaatc 
gacgagatt gcgtcagtt ggcaaaccc ctggtggac 
attgaaacc gaaggggat gaaccaagc gcagcacca 
acccccgaa gaagaatca aaaccccca gtcgaagaa 
attaaaata agcgaaccc actgacccc caaccaacc 
gctgaaatt ttatgcatc ccctctgtc cgaagactc 
gccaaagaa cacaaggtg aacttatgg gaggtcaca 
ggaaccgga aaatccggc cgcattctc aaagaagac 
gttctgaaa tacctgcaa gccggccct gcgccggcc 
aaggccccc gcccgccag gcccgcacc gagcccatc 
aagggcttc cagaaggcc atggtcaag acaatgagc 
gacgctctg aaaatccct cacttcgtc tacagcgac 
gaaatcgca gtaacgcaa ctgtcgcaa ctgcgacaa 
acccttaaa aaactgcca gaaacgcag gacttgaag 
ctgtcgttc atgcccttc ttcatcaaa gcggcctcc 
aacgccctg cagcgcttc ccggttttg aacgccagc 
ttggacgag aactgcgag aatgtgacc tacaagagc 
gagcacaac atcggggtt gcgatggac acgaaagtc 
gggctggcc gtcccggtg ataaaaaac gtggagaca 
cttagtatt attgaaatt agcaacgaa ctgaaccga 
cttatcaag tcggggcgc agcggctcc ttctcgccc 
caggacttg gccgggggc acgttcacg atttcgaac 
attggggct atcggcggc acgtacatg aagccggtc 
attatgccg ccgcacgtg gccattgtt gcgctcggg 
gcgtcccag gtggttccc cggtttgac gacgccggg 
aatgtcgtc cctgtcgaa gtgcttaat ctgagcggg 
gccgccgac caccggatc atagacggg gccacgatg 
gcccgcttt gtgcagact ttgaaacgg caaatcgaa 
aacccctat ctcttgttc ctgaacttg tga
    mRNA sequence
    • >TC014209 RA
      aatttgaat aaatgtatt tgtgttttt gtggcaagt 
cttaatctt tttgcaata atttactta accggttga 
cctcaaaac gagttgatt cacctttgc ctctttctc 
ttatcacgg agagataaa attcggata agttccacc 
aaacgtagt gctctgtgt gtttttcga aaatgtgtt 
aatcaacgt agcgggaaa tttaaaaat tgataatta 
gtgattgag aaaaaacaa cgtcaatta tttaaatga 
ctggacact ccgttactc aatacgacc atcacttgc 
gttgataag cggccccaa gttgtattg ttatcagtc 
gaaatttaa aataattaa aaacatgtt gctgtcaag 
ggagtttta cactttttt aaaaagtgc gaccagtcc 
ggcaaaact aatcacttt gaaaaactt tcactcgtg 
tgcgagcta tgcggccca agtgtcttt caaactgtc 
tgacattgg tgaaggcat aagggaggt aacagtcaa 
agagtggtt cgtcaaagt cggcgacaa agtctccca 
atttgacga aatttgcga agtacagag tgacaaagc 
ctcggtcac aatcacaag cagatacga tggagttat 
taagaaact acattacaa aatcgacga gattgcgtc 
agttggcaa acccctggt ggacattga aaccgaagg 
ggatgaacc aagcgcagc accaacccc cgaagaaga 
atcaaaacc cccagtcga agaaattaa aataagcga 
acccactga cccccaacc aaccgctga aattttatg 
catcccctc tgtccgaag actcgccaa agaacacaa 
ggtgaactt atgggaggt cacaggaac cggaaaatc 
cggccgcat tctcaaaga agacgttct gaaatacct 
gcaagccgg ccctgcgcc ggccaaggc ccccgcccg 
ccaggcccg caccgagcc catcaaggg cttccagaa 
ggccatggt caagacaat gagcgacgc tctgaaaat 
ccctcactt cgtctacag cgacgaaat cgcagtaac 
gcaactgtc gcaactgcg acaaaccct taaaaaact 
gccagaaac gcaggactt gaagctgtc gttcatgcc 
cttcttcat caaagcggc ctccaacgc cctgcagcg 
cttcccggt tttgaacgc cagcttgga cgagaactg 
cgagaatgt gacctacaa gagcgagca caacatcgg 
ggttgcgat ggacacgaa agtcgggct ggccgtccc 
ggtgataaa aaacgtgga gacacttag tattattga 
aattagcaa cgaactgaa ccgacttat caagtcggg 
gcgcagcgg ctccttctc gccccagga cttggccgg 
gggcacgtt cacgatttc gaacattgg ggctatcgg 
cggcacgta catgaagcc ggtcattat gccgccgca 
cgtggccat tgttgcgct cggggcgtc ccaggtggt 
tccccggtt tgacgacgc cgggaatgt cgtccctgt 
cgaagtgct taatctgag cggggccgc cgaccaccg 
gatcataga cggggccac gatggcccg ctttgtgca 
gactttgaa acggcaaat cgaaaaccc ctatctctt 
gttcctgaa cttgtgatg tgataaata aaacacgct 
ttgcatc

    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