Status
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Gene information
General information
TC011376 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.

NW_015450233.1: 406701..408758
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
    		TC011376
    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
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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_09609

    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: 30.0% (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

    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): 50% - 80%

    larval musculature fluorescence decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     cuticle remnants with some identifiable segments - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    cuticle remnants with unidentifyable segments - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    head capsule size decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    head appendages number decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    thorax segment number decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    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
    • >TC011376 RA
      MAPTWLLLV FFIAHCMGE RPMVSTPLG QIQGYHRKS 
AKGNVFAAF EGIPYAKPP IGGLRFEPP EPIDPWKGV 
WNASTTFEC AQTTLMRPE LIEGDEDCL YLNVYVPRD 
HPDPSATHD VVVHIHGGL FMYGSGHSY AHPDYFMDA 
NLIFVTFNY RVGVFGFLS TGDDVISGN NGLKDQVMA 
LKWVQDNIA SFGGNPSSV TLHGLSTGG SCVHLHYLS 
PMSHGLFHR GFSQSGVAL NSFALQEEA LVKAKRVGA 
GVGCPIGST RELVTCLKT RPAGHILGQ VSRFFGYKF 
LPVAPFGPV LEKGDKAFV TKNFYYLLA MGQVMNVPW 
MVSSVTHEG LFPTAFLTK ELELVSKNW TDLARFILD 
YNDTLATPL WKTTAQEIR NFYFEENEE ISEEKLVRL 
VSDRFLVDV DSAIKLQAK SNKSPVFYY QFGFPSESS 
TQKTVAHSE DAQYLFHNM FQKQPTTDE LKMKDVMME 
MFLSFVKKG KPEIFDLEW PSVQAPDIS FVKIAGVKP 
EDVTVETLK ELAPRDFWK SLGFLENQN LVLLKDEL
    CDS sequence
    • >TC011376 RA
      atggcccct acgtggctt cttctagtc ttttttatt 
gcccattgc atgggtgaa agacccatg gtgagtacc 
ccattgggt cagattcaa gggtaccat cgaaagtca 
gccaaaggc aacgttttc gcagctttt gaaggcatt 
ccatatgcg aaaccaccc attggtggg cttagattc 
gaaccaccg gaacccatc gacccatgg aagggtgtc 
tggaacgcc agtaccacc tttgagtgt gcccagacc 
actctgatg cgacccgaa ttaatagaa ggggatgag 
gactgtctt tatttaaac gtctacgtg ccacgtgac 
cacccagac ccatcggcc acccatgac gtggtggtc 
cacatccat ggtgggtta tttatgtat ggtagtggc 
cactcctac gcccatcct gactatttc atggacgca 
aacctaatt ttcgtcact tttaactat cgagttggc 
gtttttggc tttttgagt accggcgat gacgtcatt 
tcgggcaac aatgggtta aaagaccaa gtcatggcc 
ttgaaatgg gtccaagac aatattgct agtttcggg 
ggaaaccca tcaagtgtg accttgcat gggttatca 
acgggtggt tcttgcgtc catttgcac tacctgtca 
cccatgagt catgggctg ttccatcgt gggttctcg 
caaagtggc gtggccttg aactcgttt gccttgcaa 
gaggaggcg cttgtcaag gccaaaaga gtgggggca 
ggagtgggg tgtccaata gggagtacg agagagttg 
gtcacgtgt ttgaagaca cgcccagcg gggcatatt 
ttgggacaa gtgtctagg ttttttggg tacaagttt 
ttaccagtt gccccattt gggcccgtt ttggaaaaa 
ggagacaag gcttttgtg accaaaaat ttctactat 
ctcttggcc atgggacag gtgatgaat gtaccatgg 
atggtgtcg agtgtgaca catgaaggg ctttttcca 
acggcgttt ttgaccaaa gaacttgaa cttgttagt 
aaaaactgg accgatttg gctcgtttt attcttgat 
tataatgat acgttggcg acgcctctg tggaagacc 
acagcccaa gaaatcaga aatttctat ttcgaagaa 
aatgaagaa atttctgaa gaaaagcta gtcagactg 
gtcagtgac cggtttttg gtcgatgtt gactctgct 
attaaacta caagccaaa agcaacaaa tcgcctgtt 
ttttattac cagtttggg ttcccttct gaatctagc 
acccaaaaa accgtggct catagcgag gatgctcag 
tatttgttc cacaacatg ttccaaaaa cagccaaca 
accgacgaa ctcaaaatg aaggatgtc atgatggag 
atgttcctc agtttcgtc aaaaaaggg aaaccagaa 
atttttgat ttagaatgg ccaagtgtc caagcacct 
gatatttcc ttcgtcaaa attgccggt gttaagcct 
gaagatgtc acagtcgaa acgttgaaa gagctcgca 
ccccgtgat ttttggaag agtttgggt tttttagaa 
aaccaaaac ttagttttg ttaaaagat gagttgtaa
    mRNA sequence
    • >TC011376 RA
      atagtatta tcacttatc acaccatgg cccctacgt 
ggcttcttc tagtctttt ttattgccc attgcatgg 
gtgaaagac ccatggtga gtaccccat tgggtcaga 
ttcaagggt accatcgaa agtcagcca aaggcaacg 
ttttcgcag cttttgaag gcattccat atgcgaaac 
cacccattg gtgggctta gattcgaac caccggaac 
ccatcgacc catggaagg gtgtctgga acgccagta 
ccacctttg agtgtgccc agaccactc tgatgcgac 
ccgaattaa tagaagggg atgaggact gtctttatt 
taaacgtct acgtgccac gtgaccacc cagacccat 
cggccaccc atgacgtgg tggtccaca tccatggtg 
ggttattta tgtatggta gtggccact cctacgccc 
atcctgact atttcatgg acgcaaacc taattttcg 
tcactttta actatcgag ttggcgttt ttggctttt 
tgagtaccg gcgatgacg tcatttcgg gcaacaatg 
ggttaaaag accaagtca tggccttga aatgggtcc 
aagacaata ttgctagtt tcgggggaa acccatcaa 
gtgtgacct tgcatgggt tatcaacgg gtggttctt 
gcgtccatt tgcactacc tgtcaccca tgagtcatg 
ggctgttcc atcgtgggt tctcgcaaa gtggcgtgg 
ccttgaact cgtttgcct tgcaagagg aggcgcttg 
tcaaggcca aaagagtgg gggcaggag tggggtgtc 
caataggga gtacgagag agttggtca cgtgtttga 
agacacgcc cagcggggc atattttgg gacaagtgt 
ctaggtttt ttgggtaca agtttttac cagttgccc 
catttgggc ccgttttgg aaaaaggag acaaggctt 
ttgtgacca aaaatttct actatctct tggccatgg 
gacaggtga tgaatgtac catggatgg tgtcgagtg 
tgacacatg aagggcttt ttccaacgg cgtttttga 
ccaaagaac ttgaacttg ttagtaaaa actggaccg 
atttggctc gttttattc ttgattata atgatacgt 
tggcgacgc ctctgtgga agaccacag cccaagaaa 
tcagaaatt tctatttcg aagaaaatg aagaaattt 
ctgaagaaa agctagtca gactggtca gtgaccggt 
ttttggtcg atgttgact ctgctatta aactacaag 
ccaaaagca acaaatcgc ctgtttttt attaccagt 
ttgggttcc cttctgaat ctagcaccc aaaaaaccg 
tggctcata gcgaggatg ctcagtatt tgttccaca 
acatgttcc aaaaacagc caacaaccg acgaactca 
aaatgaagg atgtcatga tggagatgt tcctcagtt 
tcgtcaaaa aagggaaac cagaaattt ttgatttag 
aatggccaa gtgtccaag cacctgata tttccttcg 
tcaaaattg ccggtgtta agcctgaag atgtcacag 
tcgaaacgt tgaaagagc tcgcacccc gtgattttt 
ggaagagtt tgggttttt tagaaaacc aaaacttag 
ttttgttaa aagatgagt tgtaatatc gttgttaat 
aaattttta aaaaggta

    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