Status
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Gene information
General information
TC007560 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_007419.2: 3021282..3024515
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
    		TC007560
    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_01218

    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: 20.0% (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

    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): more than 80%
    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 80%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     egg without cuticle 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: 20.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 20.0% (includes death as larva, prepupa, pupa, adult)

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

    Fertility
    fertility after larval injection decreased (no living offspring) -
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC007560 RA
      MSVIFLSKQ TKEEFKKFF SSFDTVLFD CDGVLWLDN 
EPISGSVPV VNRLRELGK RIFFVTNNS TKMRNEFAV 
KAKRMNFNI ETDEIISTA YLAAAYLKN MDFKQSVYV 
VGSRGITQE LDAVGIKHY GVGPDVLQN ALVHVIENF 
QMESDVGAV IVGYDEHFS YVKMMKAAS YLNNPNCLF 
IATNTDERF PMSTDLVIP GTGAIVSAV ETCAQRSPI 
VVGKPNPYI VDDLIKKYG IVPKRTLMI GDRVNTDIL 
LGTRCGFQT LLVLSGVTT LKEAVALKN SHKKEDKEM 
VADFYLEKL GDILPLLD
    CDS sequence
    • >TC007560 RA
      atgtctgtg atttttctt tcaaagcaa accaaagag 
gagtttaag aagtttttc agttctttc gacactgtt 
cttttcgac tgtgatggg gttttatgg cttgacaat 
gaaccgatt tctggttca gtcccggtt gtgaacaga 
ctccgcgaa ttgggtaaa agaatattc ttcgttaca 
aacaactcg acaaaaatg cgaaatgaa tttgccgtt 
aaggcgaaa cgtatgaat tttaacatt gaaacggac 
gaaattata tcaacggca tacttggca gcggcctat 
ttgaaaaac atggatttt aaacaatcc gtttacgtg 
gtgggctct cggggaatc acccaagag ctggacgct 
gtcggtatc aagcattac ggagttggg ccagacgtt 
ttgcaaaac gctctggtc catgtcatc gagaatttc 
caaatggaa agtgacgta ggcgccgtt atcgtcggc 
tatgacgag cacttctca tacgtgaaa atgatgaaa 
gcggcctct tatctaaac aatcctaac tgccttttt 
attgccact aacacagac gagcgattt ccgatgagt 
acggactta gtaatccca ggaactggg gccattgtc 
tcagctgtg gagacctgc gcccagcgc agccccatt 
gtcgtgggc aagcccaac ccatacatt gtggatgac 
ctcataaaa aaatacgga attgtgccc aaaagaaca 
ctcatgata ggcgatcgc gtcaacacc gatattttg 
ctgggaacg cggtgcggc tttcaaacc ttgttggtg 
ctatctgga gttacgacg ctcaaagaa gcagtcgct 
ttgaaaaat tcgcacaaa aaggaggac aaggaaatg 
gtcgctgat ttttacctg gagaagctg ggagatata 
ctgccactt ttagattga
    mRNA sequence
    • >TC007560 RA
      aagcaaaga tgacaaaat ctgaaaatt ttattttat 
tcaaattga attgatgtt tgtgattcc cagggcatg 
agcagctgt ctttttgac aggtcacct aacctaaaa 
gtatttcaa aaatcctaa ccaaaaaaa gacaacgtg 
tgatctttc tttaatttt ttattaggc gtttttata 
ctaaaaata cagttgtga aaacagaat tatgttcca 
ctggattta ttgtacgtt tggatatgt atttatttt 
cgtcacatt aacatctaa ctaaaccac ttatttttc 
tcaaaattg ataaaaatc aaataaaat ccgagattc 
cgaatagca ataacatgt tctagtggt aattattta 
cttttagca aattattcc tcctcaagt tacaatctt 
ccgctttct attacctac ttttctcca gttgttcag 
tgactgtac aactgcaac aacatgcac ctacttttc 
aacataaat ctctgcaaa ctgtttttt gtgataata 
acatcgtct ttggtgata ctcggtgtt ttgataaat 
ttttttgag ccacacttg ccggctttt atcaaaaaa 
accttcaga tatggaaaa tttgcatct gatgaaaaa 
tcacttcta gtgcaaagt gtggaagtc ccaaaatcg 
tatttcagg catttttat gttgctgca gcattcatt 
ttttgccca atttttctg aaagaggtt gtggctgtt 
tatgtgttt aataaggga gttgatgat tggattgag 
actttgctc aatttttct tgtggatat ggcagacta 
tcaacagtt ccagcccat cgtgtccta attgcgtcc 
atattattg agcctacaa atatttcgc cgattttac 
gacacacat tttgtgtcg gtttttagc gaaaatgcg 
atgattaat ttaagccat tacctcatc ggaatggct 
ttttaccca gctgtgatg ttgattatc ctaagtgaa 
gccccgaag tttgcccaa aacggtata atagctccc 
ttcacgcga cacagtttt tatacctct aaattagta 
gaaaccaac actactact ttcaattta agcgagatt 
atgtttaat ttctttata attgttgtc tttttgtgg 
gcttggtat caccagcat gttgccact gtgatacta 
gccaatctg aggaaaaac aaaaaaggt gatttgaga 
acaaaacaa aaaatattt aatagttat gatgggttc 
taggtgacg ttgttgatc agggttaca gactccctg 
agggtgact ggttcaatt acttatctt cacctcact 
caacagcag aaataataa tgtatacag ccctgactt 
tgttattgg caaaaaata caagttggt tgtacgtct 
atgcttgga ttttaagca atcaagtaa ttataattt 
gttttatga ctgaaacta attcccaat ttgcagatt 
gaaacaatt cttttaagc cattggtgg tatttggat 
cgtttcaaa aattttccc ccacaaagg aaggccctc 
attccattt atttattaa ttattagtc aaggtgtat 
ttcatttgt tgcaaataa attattttt tatttaccc 
gtgtttgca tttaccgat acataaaaa tttaaaacg 
aggtcaata attacgtct tttgaaata atctcctaa 
tggcgggag aacagtggc attggattg gtcaaacaa 
cttatgttg ccatagaaa catttttcc atttttttg 
attgacgtt tacgttttc aggttaggt taaaagtca 
ccttcacgc aataatttg gtacaaatt cctagataa 
cagtgaatt ttttgcccc acattattt aaaaaaatt 
gtcggcttg aaagcccgt tcagtgaaa ctaatttca 
aacacacct gccaaaatg tctgtgatt tttctttca 
aagcaaacc aaagaggag tttaagaag tttttcagt 
tctttcgac actgttctt ttcgactgt gatggggtt 
ttatggctt gacaatgaa ccgatttct ggttcagtc 
ccggttgtg aacagactc cgcgaattg ggtaaaaga 
atattcttc gttacaaac aactcgaca aaaatgcga 
aatgaattt gccgttaag gcgaaacgt atgaatttt 
aacattgaa acggacgaa attatatca acggcatac 
ttggcagcg gcctatttg aaaaacatg gattttaaa 
caatccgtt tacgtggtg ggctctcgg ggaatcacc 
caagagctg gacgctgtc ggtatcaag cattacgga 
gttgggcca gacgttttg caaaacgct ctggtccat 
gtcatcgag aatttccaa atggaaagt gacgtaggc 
gccgttatc gtcggctat gacgagcac ttctcatac 
gtgaaaatg atgaaagcg gcctcttat ctaaacaat 
cctaactgc ctttttatt gccactaac acagacgag 
cgatttccg atgagtacg gacttagta atcccagga 
actggggcc attgtctca gctgtggag acctgcgcc 
cagcgcagc cccattgtc gtgggcaag cccaaccca 
tacattgtg gatgacctc ataaaaaaa tacggaatt 
gtgcccaaa agaacactc atgataggc gatcgcgtc 
aacaccgat attttgctg ggaacgcgg tgcggcttt 
caaaccttg ttggtgcta tctggagtt acgacgctc 
aaagaagca gtcgctttg aaaaattcg cacaaaaag 
gaggacaag gaaatggtc gctgatttt tacctggag 
aagctggga gatatactg ccactttta gattgaaat 
tttaggaca ttagaccaa ttcttaaat tatttattg 
ttagtaggt accgcatat ctacctcca tgcaacagt 
agataagaa aatgtctgt taactcaga ataaaaagt 
gtcttatgc c

    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