Status
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Gene information
General information
TC013861 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: 2769534..2771098
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
    		TC013861
    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
    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.
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_02212

    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: 50.0% (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

    adult lethality - Number of animals showing the phenotype: 2 (9 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection

    Fertility
    ovary without detectable defects - Number of animals showing the phenotype: 4
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
    About 55
    egg without cuticle embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    cuticle remnants with some identifiable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

    cuticle remnants without visible segmentation, differentiation or axis - Penetrance (percentage of animals/eggs on slide): less than 30%

    legs sometimes remaining - Penetrance (percentage of animals/eggs on slide): less than 30%
    head not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    legs shape irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    legs shortened - Penetrance (percentage of animals/eggs on slide): less than 30%
    legs podomer partially fused - Penetrance (percentage of animals/eggs on slide): less than 30%
    thorax not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 30% - 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: 10.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 10.0% (includes death as larva, prepupa, pupa, adult)

    Fertility
    egg production: number <50% of expected -
    mature egg deposition blocked number 1st lateral oviduct: 2 number 2nd lateral oviduct: - Number of animals showing the phenotype: 1
    ovary without detectable defects - Number of animals showing the phenotype: 3
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC013861 RA
      MKEYHQVTS PNYSYVFNF ESDFIHQET RTWMKDNWT 
LGFYYVGIY MVLIFGGQH LMQNRPRFE LRGVLSLWN 
TLLATFSII GACRTVPEF LHTLTHHGL YHSVCVPSF 
IEQDKVSGF WTWMFVLSK LPELGDTIF VVLRKQPLI 
FLHWYHHIT VLLYSWFSY TEYTASARW FIVMNYCVH 
SVMYTYYAL RAMGYSPPR QIAMVITSL QLLQMVIGC 
AVNIWAHQL LQNQAECHI TPFNIKLSI AMYLSYFVL 
FARFFHKAY LSGDKRGKT KSKVH
    CDS sequence
    • >TC013861 RA
      atgaaggag taccaccag gtcacgtcc ccgaactac 
tcgtacgtg ttcaacttc gagtcggac ttcatccac 
caggagacc cggacgtgg atgaaggac aactggacg 
ttggggttc tactacgtg ggcatctac atggtgctc 
atcttcggc gggcagcac ctgatgcag aaccggccg 
cgcttcgag ctccgcggc gtcctcagc ctctggaac 
accctcctc gccacgttc agcatcatc ggcgcctgc 
aggacggtg ccggagttc ctgcacacg ctcacccac 
cacggcctc taccactcg gtgtgcgtg cccagcttc 
atcgagcag gacaaggtg tcgggcttc tggacgtgg 
atgttcgtc ctgagcaag ctgcccgag ctgggcgac 
accatcttc gtggtgctg cggaagcag ccgctgatc 
ttcctccac tggtaccac cacatcacc gtgctgctc 
tactcctgg ttcagctac acggagtac acggccagc 
gcgcgctgg ttcattgtg atgaactac tgtgtccac 
tctgtgatg tacacctac tacgcgctc agggccatg 
ggctacagc cccccgagg cagatcgcg atggtcatc 
acctcgctg cagctgctc cagatggtg atcggctgc 
gccgtcaac atctgggcg caccagctc ctccagaac 
caggccgaa tgccacata acccccttt aacattaaa 
ttgtcaatt gccatgtat ctgagctac tttgttctt 
ttcgcgcgg ttcttccac aaggcctat ctgtcaggg 
gacaagagg ggcaaaact aaatcaaaa gttcactag
    mRNA sequence
    • >TC013861 RA
      ataaaattt gaaatcagc tgaaacttt aatccctcg 
cgcgctcaa cactcaaac cggtttgca tgtcggatc 
tttaccgca cgattttgg caaagaaag aggcccaac 
gtgcaatcc ccacgttag aaggagacg agtgtcgag 
tttggtgac gcaggcgcg gagtatggc ggtgtggtg 
agctagggc ggtgcgata tatccggcg aaattccgt 
ctcgtttcc agattcgaa agtgcttca gtgccgcaa 
ccatgaagg agtaccacc aggtcacgt ccccgaact 
actcgtacg tgttcaact tcgagtcgg acttcatcc 
accaggaga cccggacgt ggatgaagg acaactgga 
cgttggggt tctactacg tgggcatct acatggtgc 
tcatcttcg gcgggcagc acctgatgc agaaccggc 
cgcgcttcg agctccgcg gcgtcctca gcctctgga 
acaccctcc tcgccacgt tcagcatca tcggcgcct 
gcaggacgg tgccggagt tcctgcaca cgctcaccc 
accacggcc tctaccact cggtgtgcg tgcccagct 
tcatcgagc aggacaagg tgtcgggct tctggacgt 
ggatgttcg tcctgagca agctgcccg agctgggcg 
acaccatct tcgtggtgc tgcggaagc agccgctga 
tcttcctcc actggtacc accacatca ccgtgctgc 
tctactcct ggttcagct acacggagt acacggcca 
gcgcgcgct ggttcattg tgatgaact actgtgtcc 
actctgtga tgtacacct actacgcgc tcagggcca 
tgggctaca gccccccga ggcagatcg cgatggtca 
tcacctcgc tgcagctgc tccagatgg tgatcggct 
gcgccgtca acatctggg cgcaccagc tcctccaga 
accaggccg aatgccaca taaccccct ttaacatta 
aattgtcaa ttgccatgt atctgagct actttgttc 
ttttcgcgc ggttcttcc acaaggcct atctgtcag 
gggacaaga ggggcaaaa ctaaatcaa aagttcact 
agttccggg catccaccg ttttgttcg tttttttgt 
ggttgtgat atgttcttc aataaaatg ttccaactg 
cgttcgcaa attttataa caaaaacgt tataaatta 
tatgtatat tttttataa agcatttag aaaatgtgc 
atttcatag ggcatttac ggttttgtt gttacagat 
atcacaaga cgaaggcac gaccatcgt gtacttagc 
gaactaaat ttttcattc tgtgataat cacgaactt 
aattttgtc aacaccatt gtttcacta attaattca 
atttgtttt gtggtatct ctaaaatgt tggaaaagg 
aacacgagg actagtcat tgttaggtt tataattat 
gtatggaat tacattctt atcataatc gctacttta 
tttattttc tacttttag acaattcaa agtggacag 
gcaaactgt taaattgtt ctgcaacag tcgttcaat 
aaaatattt tttaccaa

    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