Status
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Gene information
General information
TC000693 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_007417.3: 7439259..7441468
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
    		TC000693
    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_00156

    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)

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

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

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    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: 30.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 42.86% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 3 (11 dpi)
    Days post injection

    Pupal morphology
    abdomen gin-traps partially orientation irregular - Number of animals showing the phenotype: 6

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC000693 RA
      MVVLEGGGM LSTSGNQYL QPDYLSPLP TTLDAKKSP 
LALLAQTCS QIGADTPSS KPLISPLEK PKKSQENST 
RSPPVKNDK SAQRNTPTE NKLAFKPYE NNVVTKKSE 
DNRPNSKSG STHQNSTPS DEKKSETQS PERKSVSPA 
TSTAATPAP ETGKTSPGS SENKSSTPS ARGASPIIR 
SGLEILQGH PKDTPLGAY KHGALSSGL SSGLNGPLG 
SLCCPPGLE HTNPAFRPP FPGAPFSHH HAAMLAAGY 
PGATPGPYL SYARVKTPS GGEALVPVC KDPYCTSCQ 
FSMHNQQLL MSGASGPCP SGCTQCDHQ KYNLAMAMS 
LVPPGPVPS SLAYPQLGR PYVCNWIAG DTYCGKRFV 
TSEELLQHL RTHTSGSDG SAAVTSSAS PLLNPHSLF 
SSAASLHRP GYPNPPLSP LSAARYHPY GKPTLPTSL 
GASPYSAFN PTALGAYYS PYSVYGQRL GAAAVHP
    CDS sequence
    • >TC000693 RA
      atggttgtg ttggagggt ggaggcatg ctgtcaacg 
tccggaaat caatatttg cagccggat tacctatca 
ccgttaccc actacgttg gatgctaag aaaagtccg 
ttggcactc ctcgcccaa acatgcagt caaatagga 
gcagacact ccatcgtcc aagcctttg atttctcca 
ttggagaaa ccaaagaag tcgcaagag aattcgacg 
cgttcgcct ccggtaaaa aacgataag agtgctcaa 
agaaacaca ccgactgaa aataagctc gcttttaaa 
ccatatgaa aataatgtt gttacgaaa aaaagcgaa 
gacaaccgg cctaactct aaatcagga tccactcat 
caaaattcg acaccaagt gacgagaag aaatcagaa 
acgcaaagt cctgaacgg aagtcagtg tcaccagca 
accagcacc gctgcgaca ccggccccc gaaaccggg 
aagacttcc ccaggttcg agtgaaaac aaatcgtca 
actccgtcg gctcgtggt gcaagcccc atcatcaga 
tccggtctg gaaattctg caaggacat ccgaaagat 
acacctttg ggggcgtac aaacacggt gctttatcg 
tccgggtta tcgtcagga ctgaacggc cctttggga 
tcgctgtgt tgtcctccc ggactcgaa cacacgaat 
ccagctttc aggcccccg tttcccgga gctccgttt 
tcgcaccac catgccgcc atgctcgct gccggctat 
ccgggagcc actccggga ccgtacttg agttacgcg 
cgtgtcaaa actccatca ggtggtgaa gctttagtt 
ccagtgtgt aaagaccct tattgcacc agttgccaa 
ttcagcatg cacaatcag cagttgttg atgagtgga 
gcatctggc ccttgtccc agtggctgc acgcaatgc 
gaccaccag aagtataat ttggccatg gcgatgtcg 
ttagtgccc ccgggtccc gtgccgtcg tcacttgct 
taccctcag ctgggacgg ccatatgtg tgtaattgg 
atagcgggg gacacctac tgcgggaag aggttcgtc 
acatctgaa gaactgttg caacatttg agaacacac 
acgagtgga tctgacggg tcggcggcg gtgacgtcc 
tcggcatcg cctttactt aacccccat tcgttgttc 
tcgtcggcg gcgtcgctc cataggcct gggtatccc 
aatcctccg cttagcccg ttatcggca gcgaggtat 
cacccgtat gggaaaccc actctacct acctctttg 
ggagcttcg ccatacagt gcttttaat ccgacggct 
cttggagct tattactct ccgtattcc gtttacgga 
caacggctt ggcgctgct gctgtgcat ccatag
    mRNA sequence
    • >TC000693 RA
      ataaaataa ataaagctc aaccgtatt ttacgaccg 
acaggttgt aataacttc gcagtgaac tgcgccacc 
atccatccg tcatcattg tgcttttgg gcggctaac 
atcaaagca tccagaagg tctgtcgtc gtcacttca 
tgggtggta gaaaccgac aggccagaa acgtggctg 
tattagcgc tttgtcatg ctaggactt tcagcaggg 
ctgcaaagc ctggagggg ctgccaaac ctgcgcaat 
agcctctcg tttagagag cggagctct gttgccttc 
agactttca tactggagt tgtccgtcg tgtgaaagc 
tagtttgcg ctcgtgttc cgtcagttt attaatcgt 
gtaattgtt tttatccgc cgtaaacgt gcatttatt 
ccaaatggt tgtgttgga gggtggagg catgctgtc 
aacgtccgg aaatcaata tttgcagcc ggattacct 
atcaccgtt acccactac gttggatgc taagaaaag 
tccgttggc actcctcgc ccaaacatg cagtcaaat 
aggagcaga cactccatc gtccaagcc tttgatttc 
tccattgga gaaaccaaa gaagtcgca agagaattc 
gacgcgttc gcctccggt aaaaaacga taagagtgc 
tcaaagaaa cacaccgac tgaaaataa gctcgcttt 
taaaccata tgaaaataa tgttgttac gaaaaaaag 
cgaagacaa ccggcctaa ctctaaatc aggatccac 
tcatcaaaa ttcgacacc aagtgacga gaagaaatc 
agaaacgca aagtcctga acggaagtc agtgtcacc 
agcaaccag caccgctgc gacaccggc ccccgaaac 
cgggaagac ttccccagg ttcgagtga aaacaaatc 
gtcaactcc gtcggctcg tggtgcaag ccccatcat 
cagatccgg tctggaaat tctgcaagg acatccgaa 
agatacacc tttgggggc gtacaaaca cggtgcttt 
atcgtccgg gttatcgtc aggactgaa cggcccttt 
gggatcgct gtgttgtcc tcccggact cgaacacac 
gaatccagc tttcaggcc cccgtttcc cggagctcc 
gttttcgca ccaccatgc cgccatgct cgctgccgg 
ctatccggg agccactcc gggaccgta cttgagtta 
cgcgcgtgt caaaactcc atcaggtgg tgaagcttt 
agttccagt gtgtaaaga cccttattg caccagttg 
ccaattcag catgcacaa tcagcagtt gttgatgag 
tggagcatc tggcccttg tcccagtgg ctgcacgca 
atgcgacca ccagaagta taatttggc catggcgat 
gtcgttagt gcccccggg tcccgtgcc gtcgtcact 
tgcttaccc tcagctggg acggccata tgtgtgtaa 
ttggatagc gggggacac ctactgcgg gaagaggtt 
cgtcacatc tgaagaact gttgcaaca tttgagaac 
acacacgag tggatctga cgggtcggc ggcggtgac 
gtcctcggc atcgccttt acttaaccc ccattcgtt 
gttctcgtc ggcggcgtc gctccatag gcctgggta 
tcccaatcc tccgcttag cccgttatc ggcagcgag 
gtatcaccc gtatgggaa acccactct acctacctc 
tttgggagc ttcgccata cagtgcttt taatccgac 
ggctcttgg agcttatta ctctccgta ttccgttta 
cggacaacg gcttggcgc tgctgctgt gcatccata 
gtgatactt gtagtaatt tctctcatg ttttgactc 
atacagaat ggcgtctgt atcggtctg tttgctcca 
ctgtgataa cgtgtaaat aatttgtcg aagctaaag 
ctgattaaa attaagtgc aatctgaag cggacttaa 
tcatagggc aataagtta taaaacagt ccattttct 
ttctaagtt gttctcccg tttcaacga tactttaat 
ctttaaata attcaataa aaatatttg tatagactt 
gtaagtatt taatgttga gtttcgata ttgctttaa 
taaaatgtt tgtagaacg

    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