Status
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Gene information
General information
TC013872 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_007420.3: 2625157..2628167
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
    		TC013872
    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_05515

    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)

    pupa eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 1 (3 dpi)
    Days post injection

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 2 (3 dpi)
    Days post injection

    Fertility
    ovary size decreased - Number of animals showing the phenotype: 3

    previtellogenic egg chamber not present - Number of animals showing the phenotype: 3

    vitellogenic egg chamber late not present - Number of animals showing the phenotype: 3

    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: 33.33% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 100.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality early (L5/6) - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC013872 RA
      MLPKIYRSD PDIRKHQIN TLKIFNDNV VEICEGHEY 
QISFKSDRH ELCLHISLS NEFPNEKPL LTISPPIVH 
PWVNADSEV TSAPGLLNF SIHSDLGRV VQAIIREFE 
RNPPPLKND SNNITPGPG STITSPTVP IRECERSSP 
SYCAVNNFS SPTHQKRLV FPELKKLSM DELEFLNNN 
SDRQLEFLN DLPPIKEQN KLLDDLIVQ VEELAESNL 
SKQEQLSEL RSEIEQKIG EVTKLAFEN ERLHMKYQD 
MSDKYSPFN IKEQLRLAA EKAESECES IADGFLKGE 
VDVDKFVNL YTKARSLCQ ARKTKEEKL SHQLESLSK 
AGF
    CDS sequence
    • >TC013872 RA
      atgcttccg aaaatatac agaagtgac cccgacatt 
agaaaacat caaataaat actttaaaa atctttaac 
gataacgtt gtcgaaatt tgcgagggt cacgaatac 
caaatttcc ttcaagtcg gacagacac gagctttgc 
ttacacatt tcactcagt aacgaattt cccaatgaa 
aaacctttg ttaactatc tctccaccc atagtccac 
ccttgggtg aacgccgac agtgaagtt acttcagcc 
cctgggctt ttaaatttt tctattcat tccgacctg 
ggacgtgtc gttcaggca ataattcgg gaatttgag 
cgcaatcct cccccttta aaaaatgac tcaaataat 
attacacct ggacctggg agtaccatt acgtcgcca 
actgtacca atcagagaa tgtgaaagg tcgagtccc 
agttattgt gcagtgaac aatttttcc tcgccaact 
caccagaag agattggtt tttccagaa ctcaaaaaa 
ctatcaatg gatgaatta gaattttta aataataat 
tcagacagg cagctagaa tttttaaat gatttaccg 
ccgattaaa gaacaaaac aagttgctt gatgatttg 
attgtgcaa gtggaggag ttggctgaa tcaaattta 
tcaaaacag gaacagtta agtgaattg aggtcggaa 
attgagcag aaaataggc gaagtcacg aaattggcc 
tttgagaac gagaggctt cacatgaaa tatcaggac 
atgtctgat aaatattcc ccattcaat ataaaagaa 
cagttgagg ctagcggct gaaaaagcc gagtcagag 
tgtgaaagt attgctgat ggtttcctg aaaggtgaa 
gtagatgtt gataagttc gtaaatctg tacaccaaa 
gccagaagc ttatgccag gccaggaaa actaaagaa 
gagaagctc tcccaccaa cttgagagt ttatcaaaa 
gcgggtttt tag
    mRNA sequence
    • >TC013872 RA
      ttctttcaa ataacgcat ggctagcgc cattcgttt 
tttgaaaat aaattcttg cttcaaaac tggtcttat 
gcagatgga acttaatcc aaacaaaga gttattttt 
attaatgta tgtgttacc tttaatatt tacatgtgc 
gtattaaca aacttgcca actaagaac agaaatgtg 
ggcaatcct agttataat aattcactg tgttattgt 
atgcaatca acgatttta ttttattta aagaaaagc 
attaaagtt tgctatttt tacacattc ccatacgaa 
attagattt gtcttcaga ggcttactc taaattatt 
tattttaat ttatttggt caaagaata atcattaat 
cagtttata tttttattg tgtgatgtc ggactcaca 
gtcctctga aggcgatag taatagttt gtaatttaa 
ttacgacat cggttgtga tttccgcaa aaaataatt 
ttcttttcc ttcactaaa ccatgtcca taagtgtgt 
aagcattac catgttaat aacatttta aactttaag 
tgctagtag gtttaaacc gatgtaaca acataatgt 
aagttttta actttattc aaatacatt tttttatat 
acatttgtc tacattact ttatttaca cacaattaa 
aaatccgtt actcttcct ttcctctcc caatcccca 
tatctggta ggttctggc ccgcgaggg ccccctact 
tctccagtc gtagggttt gtgttgtca ggccaggct 
tctaaaggt tctttttcc tggtgggga tgtttcccg 
gatatttca tcaagtttt tcaagaggg gttgtttct 
ctcaatttt ttcctaaac tcctggaga cggcgacta 
gggggcttt tcctgtttt gaggtcgac gacagtctc 
ataaaaact gcacaagtc tgtctcaag gggttgagg 
tgacaaagt ccacttaat cttaaagtc atgatcagg 
aatttgcga aagtagcca aattcgaca taaaattgt 
tgcaaatct gtgacctgt cttaattga cactattta 
aaactgatt tattatttt ttcgatttt gaaaatcgc 
ttgacctaa cctcaactg tcaacgtga caattcaac 
tgtcagaag aggttaggt tattgtcaa gatttctca 
atttcgaga aaatttaat aatttaacg ctctgattg 
cattgaaac ttttgagtg cagtaaagt gacaatcaa 
tacgaaaaa aatattgaa gaaatgctt ccgaaaata 
tacagaagt gaccccgac attagaaaa catcaaata 
aatacttta aaaatcttt aacgataac gttgtcgaa 
atttgcgag ggtcacgaa taccaaatt tccttcaag 
tcggacaga cacgagctt tgcttacac atttcactc 
agtaacgaa tttcccaat gaaaaacct ttgttaact 
atctctcca cccatagtc cacccttgg gtgaacgcc 
gacagtgaa gttacttca gcccctggg cttttaaat 
ttttctatt cattccgac ctgggacgt gtcgttcag 
gcaataatt cgggaattt gagcgcaat cctccccct 
ttaaaaaat gactcaaat aatattaca cctggacct 
gggagtacc attacgtcg ccaactgta ccaatcaga 
gaatgtgaa aggtcgagt cccagttat tgtgcagtg 
aacaatttt tcctcgcca actcaccag aagagattg 
gtttttcca gaactcaaa aaactatca atggatgaa 
ttagaattt ttaaataat aattcagac aggcagcta 
gaattttta aatgattta ccgccgatt aaagaacaa 
aacaagttg cttgatgat ttgattgtg caagtggag 
gagttggct gaatcaaat ttatcaaaa caggaacag 
ttaagtgaa ttgaggtcg gaaattgag cagaaaata 
ggcgaagtc acgaaattg gcctttgag aacgagagg 
cttcacatg aaatatcag gacatgtct gataaatat 
tccccattc aatataaaa gaacagttg aggctagcg 
gctgaaaaa gccgagtca gagtgtgaa agtattgct 
gatggtttc ctgaaaggt gaagtagat gttgataag 
ttcgtaaat ctgtacacc aaagccaga agcttatgc 
caggccagg aaaactaaa gaagagaag ctctcccac 
caacttgag agtttatca aaagcgggt ttttagttg 
tgataattt atttataat tttaactct gaatacata 
tatttgtac taa

    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