Status
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Gene information
General information
TC011621 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_007424.3: 15590683..15596083
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
    		TC011621
    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 *
    {{ blurReferenceResult }}
    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
    If you have entered your name and agree by marking the checkbox. we might show your name on this page to honor your contribution.
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_06535

    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: 40.0% (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

    adult lethality - Number of animals showing the phenotype: 1 (9 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg not developed/not fertilized - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    embryo/egg with embryonic tissue potentially present, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): less than 30%

    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): more than 80%
    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
    • >TC011621 RA
      MTTQLLGKN CDGGHYTCS PPKDCCKQG CCFLLTPAV 
HRPPAIPPA NFFNPLFLG HWYFWVAVT ATVAGILCA 
CSLWRRHNQ GSFCCRDSG RDERASEPD SNGSCYAPP 
QYSRCNSFH QPPPPYSEV TSKPDLYPL VISYNGDPV 
IKNNNSSTG YLMVQYFRN FIVRPVGSL SATSTIDSL 
SSSFICNAA NEANTIIPP PYSCMGSLE EVTTENNQS 
VQSPEPPQI PQSASGDFL PTPSTHTNP PTPISISIR 
DNPCFGQNA TNIVNNLNE TLPNLEPSK CQTNCDASP 
YKKIKKPIL QRLPKDRSQ DSDEDHNFS DLLNLSVCV 
PSSVVNLGA SIQSSHLQE LQYSVTNSM TGSDISSLA 
NLGSPDSPP RATSPTLEM RELLDKIQQ LPQQKSPQP 
PKTSRVKAK TLYMPLYEG PKKGLKGWL SRSAPNTPC 
SNFAPSFPK KGSSQRSSR VVVGDGSPL LREYEEDAN 
RDECL
    CDS sequence
    • >TC011621 RA
      atgactact caactttta ggtaaaaac tgcgatgga 
ggccactat acgtgttcc ccgcctaaa gattgttgc 
aaacaaggt tgttgcttc cttttaact cctgcagta 
caccgtcct cctgccatc cctcctgcg aattttttc 
aacccttta tttctgggt cactggtat ttttgggtc 
gctgtgacg gcaactgtt gcaggaatt ctgtgtgct 
tgctcgctg tggcggcga cataaccag gggagcttc 
tgttgtagg gattcggga agggatgaa agggcttca 
gagccggat tcgaatggc tcctgctat gcgccacct 
cagtactcg aggtgtaat agctttcac cagccgcca 
ccgccttat tcagaggtg acttcaaag ccagatttg 
taccctttg gtaatcagt tacaatgga gatccggtg 
atcaaaaat aataatagt tcaactggt tatttaatg 
gtgcaatac tttagaaac tttatagta cgacctgtt 
ggatcttta tcggccaca agcaccatc gattcacta 
agttccagt tttatttgc aacgctgcg aatgaggcc 
aacacaata atccctcct ccgtactct tgcatggga 
agtctggag gaagtaact accgaaaat aatcaaagt 
gttcagtcc cccgagcct ccccaaatc ccccaatca 
gcctccggc gacttcctc ccaaccccc agcacccac 
acgaacccc ccaaccccc atctcgata tcgataaga 
gacaaccct tgcttcgga cagaacgca acgaacatt 
gtaaataat ttaaacgaa acgttgcca aatctagaa 
cctagcaaa tgccaaact aactgtgat gcttcgccc 
tacaagaag ataaaaaaa ccgatactt caaagactc 
ccgaaagac cgaagccag gactcggac gaagaccac 
aacttctcc gacttgcta aacctctcc gtttgcgtt 
cccagcagt gttgtcaac ctgggggct tcaatccaa 
tccagccac ctccaggag ctccagtac agtgtcacc 
aacagcatg accgggtcg gacatcagc agcttggcc 
aatctgggg tccccagac tcgcccccg cgggccacc 
agtcccacc ctggagatg agggaatta ctcgataaa 
atccagcag cttccgcag cagaagagc ccccagccg 
cctaagaca agccgcgtg aaggccaag acgctgtac 
atgccgctg tacgaaggg cctaagaag ggcctaaaa 
gggtggctg tcgcgctcc gcccccaac acgccctgc 
agcaacttt gcgcccagt ttccccaag aagggctcc 
agccagcgg agcagccgg gtggtggtg ggcgacggc 
agccccctt ctgagggag tacgaggag gacgcaaac 
agggacgag tgtttgtga
    mRNA sequence
    • >TC011621 RA
      aaaatttgt aaataaaaa agacgtttt ttcctcaaa 
tcggtttac gatttaaaa agtaagcgg gaaaaggcc 
gattacgta ggaactgct gaacgcaac tgcgggaaa 
tttgaacat ctggtggaa acaagctcg tgttagggg 
attttgccc aaacggcca cacttgtta ggttttaac 
gggaacgcc cctcacaca agcgccaat ttcaaacac 
tgactgatt taatgaagc caatagaaa atatttttc 
acttttggc ttgtttact ggctttaat tggccacca 
gttaattac acgtaatta atcgacgcc gagatgaaa 
ccgacgcca atgcggaga gtagcgtcg cggcgctgc 
ttcagtcac ccctccaca atggcgtcg gtgaaacaa 
acgagcttc ggttgaatg acgaaattt cgcgatttc 
tttaaatca ccgaagcga aaaatacgg cgaaaattg 
tggattttc tatccaaaa tcaagcaaa ttgtcttcc 
attcttcct gctgctggc ttctaggct ggagaaacg 
tggagagaa agtgcaatg cgacactta tactatctt 
gtgcgtctg gcaacttta ctattctcc cagtactta 
tgactactc aacttttag gtaaaaact gcgatggag 
gccactata cgtgttccc cgcctaaag attgttgca 
aacaaggtt gttgcttcc ttttaactc ctgcagtac 
accgtcctc ctgccatcc ctcctgcga attttttca 
accctttat ttctgggtc actggtatt tttgggtcg 
ctgtgacgg caactgttg caggaattc tgtgtgctt 
gctcgctgt ggcggcgac ataaccagg ggagcttct 
gttgtaggg attcgggaa gggatgaaa gggcttcag 
agccggatt cgaatggct cctgctatg cgccacctc 
agtactcga ggtgtaata gctttcacc agccgccac 
cgccttatt cagaggtga cttcaaagc cagatttgt 
accctttgg taatcagtt acaatggag atccggtga 
tcaaaaata ataatagtt caactggtt atttaatgg 
tgcaatact ttagaaact ttatagtac gacctgttg 
gatctttat cggccacaa gcaccatcg attcactaa 
gttccagtt ttatttgca acgctgcga atgaggcca 
acacaataa tccctcctc cgtactctt gcatgggaa 
gtctggagg aagtaacta ccgaaaata atcaaagtg 
ttcagtccc ccgagcctc cccaaatcc cccaatcag 
cctccggcg acttcctcc caaccccca gcacccaca 
cgaaccccc caaccccca tctcgatat cgataagag 
acaaccctt gcttcggac agaacgcaa cgaacattg 
taaataatt taaacgaaa cgttgccaa atctagaac 
ctagcaaat gccaaacta actgtgatg cttcgccct 
acaagaaga taaaaaaac cgatacttc aaagactcc 
cgaaagacc gaagccagg actcggacg aagaccaca 
acttctccg acttgctaa acctctccg tttgcgttc 
ccagcagtg ttgtcaacc tgggggctt caatccaat 
ccagccacc tccaggagc tccagtaca gtgtcacca 
acagcatga ccgggtcgg acatcagca gcttggcca 
atctggggt ccccagact cgcccccgc gggccacca 
gtcccaccc tggagatga gggaattac tcgataaaa 
tccagcagc ttccgcagc agaagagcc cccagccgc 
ctaagacaa gccgcgtga aggccaaga cgctgtaca 
tgccgctgt acgaagggc ctaagaagg gcctaaaag 
ggtggctgt cgcgctccg cccccaaca cgccctgca 
gcaactttg cgcccagtt tccccaaga agggctcca 
gccagcgga gcagccggg tggtggtgg gcgacggca 
gcccccttc tgagggagt acgaggagg acgcaaaca 
gggacgagt gtttgtgat tgcgctgtc caacaccaa 
aattcgtgt tgagttgaa gaaaaccag tcaattgga 
ttgaccctg ctcaagtta tttttatac actcattgg 
gggtttcgg cacacgtat ttacaaaaa cgctaatta 
gagtttgat taggcacaa gtgcttcaa gcctaggcc 
taggtattg tttcggtac caattctct tcggttatg 
gctctaaaa ttcgatatt tttgtaaaa attcgtgtt 
caattacca ttattatta tgaatgttt gtagtgatt 
ttctcggtg ttggatgtt aaaaacgat gattcattt 
ttgcaaaag tgtacttat accgaggtt tggttcaaa 
gtgtggtgg ataatgttg cttggtttt agatgcctt 
ggcgatatt tttcatacc taccgactt acaaaaata 
aatgctttt gactagttg gctggacta aacaagggt 
gaaacaatc aaaactagg ggacagtct actagaaag 
ttggtttcg ttttttcac attttcgtt gtcctgaat 
tgcattaaa cttgaatgt ttatctaca gttttattc 
gaaacagca acttgaaat gtaataaaa tggtgacta 
ataa

    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