Status
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Gene information
General information
TC012565 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: 11521439..11525265
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
    		TC012565
    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.
    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_07656

    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: 0.0% (includes death as pupa, adult)

    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 20
    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
    • >TC012565 RA
      MDASYVPNN PQFGLQLEC NWSSGPNAT LQSSACTDD 
LSSCWSEDM GSFSLPLDL EPLPSLFPF SPCNNTANY 
KSEAQNQPS PYKQPSSDM ADVLLSLKH AVVHPGQSP 
AEKYDQQHL YHPQVLLSP GGYSGSLCD QGFAQQPMF 
PSMSVNVSM NMTMHGYHP SSSYPANEI SCPQVQWSA 
TPQAGSTPT YQTQGLLSP SYGGTTYSF TADFRPPQE 
TPVLASYKS VPMSFSSPR RRHSINLLE EDNQKPNVC 
RICGKSYAR PSTLKTHLR THSGEKPYR CIDCNKSFS 
QAANLTAHV RTHSGEKPF RCPVCDRRF SQSSSVTTH 
MRTHSGERP YRCRLCKKA FSDSSTLTK HLRIHSGEK 
PYECKLCLL RFSQSGNLN RHMRVHGAA SMMPP
    CDS sequence
    • >TC012565 RA
      atggacgcc agttacgtc cctaacaac ccccagttc 
ggtctccaa ctcgaatgc aactggagc tctggcccc 
aacgccact ctccagtcc tcagcgtgc accgacgac 
ctctcctcc tgctggagc gaagacatg ggctctttc 
tccctgcct ctagacctg gagccgctg ccgagcctc 
ttccccttc tcgccttgc aacaacacc gccaactac 
aaaagcgaa gctcaaaac cagccctcc ccctacaag 
cagccctcg tccgacatg gccgacgtc ctcctctcc 
ctcaagcac gcggtggtg catcccggc cagagcccg 
gccgagaaa tacgaccag cagcacctc taccacccc 
caggtgctg ctctcgccg gggggctac tcggggagt 
ctctgcgac caggggttt gcccagcag cccatgttc 
cccagcatg tcggtcaac gtgtccatg aacatgacc 
atgcatggg taccatccg tctagttcc tacccagcg 
aatgaaatc tcgtgtccc caggtgcag tggagtgcg 
actccgcaa gctgggtcc acacccacg taccagact 
caaggactt ttgagtcct tcgtatgga gggacgact 
tattcgttc actgctgac tttaggcct ccgcaggaa 
acgcctgtt ctggcctcg tataagtca gtgcctatg 
tcgttctcc tcgccgagg aggaggcac agtattaat 
ctgctcgag gaggataat caaaagccg aatgtttgt 
aggatatgt ggcaaaagc tacgcccgg cccagcacc 
ctgaaaacc cacttgcgc acgcactca ggtgagaag 
ccctaccgc tgcatcgac tgcaacaaa tctttctct 
caggctgcc aacctgaca gcgcacgtc cggacccac 
tccggggaa aagcccttc cggtgtccc gtctgcgac 
cgccgcttc tcccagagc tcctcggtg acgacccac 
atgcgcacc cactccggg gagcggccc taccgctgc 
cgcctgtgc aagaaggcc ttctccgac agcagcacc 
ctcaccaag catctcagg atacacagc ggcgagaag 
ccctacgag tgcaaactg tgtcttttg cgcttcagc 
caaagcggc aacctcaac agacacatg cgggtgcac 
ggggctgcc agcatgatg cccccatga
    mRNA sequence
    • >TC012565 RA
      catttccca aatctcgta cggcttctg ttttgcaac 
aggtgcgca agttcgccg tttgatttg gtccagatc 
cagcctcac gatggacgc cagttacgt ccctaacaa 
cccccagtt cggtctcca actcgaatg caactggag 
ctctggccc caacgccac tctccagtc ctcagcgtg 
caccgacga cctctcctc ctgctggag cgaagacat 
gggctcttt ctccctgcc tctagacct ggagccgct 
gccgagcct cttcccctt ctcgccttg caacaacac 
cgccaacta caaaagcga agctcaaaa ccagccctc 
cccctacaa gcagccctc gtccgacat ggccgacgt 
cctcctctc cctcaagca cgcggtggt gcatcccgg 
ccagagccc ggccgagaa atacgacca gcagcacct 
ctaccaccc ccaggtgct gctctcgcc ggggggcta 
ctcggggag tctctgcga ccaggggtt tgcccagca 
gcccatgtt ccccagcat gtcggtcaa cgtgtccat 
gaacatgac catgcatgg gtaccatcc gtctagttc 
ctacccagc gaatgaaat ctcgtgtcc ccaggtgca 
gtggagtgc gactccgca agctgggtc cacacccac 
gtaccagac tcaaggact tttgagtcc ttcgtatgg 
agggacgac ttattcgtt cactgctga ctttaggcc 
tccgcagga aacgcctgt tctggcctc gtataagtc 
agtgcctat gtcgttctc ctcgccgag gaggaggca 
cagtattaa tctgctcga ggaggataa tcaaaagcc 
gaatgtttg taggatatg tggcaaaag ctacgcccg 
gcccagcac cctgaaaac ccacttgcg cacgcactc 
aggtgagaa gccctaccg ctgcatcga ctgcaacaa 
atctttctc tcaggctgc caacctgac agcgcacgt 
ccggaccca ctccgggga aaagccctt ccggtgtcc 
cgtctgcga ccgccgctt ctcccagag ctcctcggt 
gacgaccca catgcgcac ccactccgg ggagcggcc 
ctaccgctg ccgcctgtg caagaaggc cttctccga 
cagcagcac cctcaccaa gcatctcag gatacacag 
cggcgagaa gccctacga gtgcaaact gtgtctttt 
gcgcttcag ccaaagcgg caacctcaa cagacacat 
gcgggtgca cggggctgc cagcatgat gcccccatg 
acaggggct gctcatctg aaacggctg ggcgttttg 
accacgctt gtgggatta gctagagct cggggaatt 
gcacaacaa ttaacaatg gtcggagag caaataact 
ggctttgcc aaaaatata agatttatt taagttaat 
gtgagggat ttgcgggca aatatttga ggtttcgtg 
aatgacggc tcaaaggcg actcaaaat tgcaactcg 
ggttcggtg caaattttc cgtgaaaga ggacgcaaa 
gtcgccaaa atttacgga gatgacaaa cagttttta 
ccgcttcta ttatgaaac ttatctcag aatatctcg 
cggataaaa aatccgacg aaaacaaat cataaaatg 
gaagaaaat aacatcaat ttacaaaat ttgtaggct 
acggttaat taattaatt gctaattga aatgtgaaa 
taaatttat tttagaaaa

    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