Status
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Gene information
General information
TC002562 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_007418.3: 23332442..23344389
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
    		TC002562
    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_09019

    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: 40.0% (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

    adult lethality - Number of animals showing the phenotype: 1 (9 dpi)
    Days post injection

    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
    • >TC002562 RA
      MFKTYLCFV IISSFSYSE CARILGAVF TPSYSHQVA 
FQPIWKELS LRGHQLTVL TTNPLNDSS LKNLTEIDL 
SMSYDTMKA YKADEILSS NNDSVAVRI KKYMEALHV 
IADKQLAHP KVQDLLHNK RNDFDLLMV EAIYPTQMA 
FSWWFNIPF IGLISLDAP SRIHAAVGN PVHPVLYPD 
YDLPFDKNL TFGERVIST LFHCAMLLY TKFRLHARE 
ERTLRKYFG EDVPPINEI QKNMSMLFI NANPIFHNI 
RPLVPATIQ IGGGIHLHE PKPLPKDIQ EYLDNSSDG 
FIYFSLGTN VKSAALPPQ IKDAILQTF AELPYNILW 
KFEDEHIPN KPKNVKIVK WLPQTAVLA HKNIKAFIM 
QCGLQSMEE AIVYNVPMI GLPFYGDQG NNAKVLESK 
GLGIRLNTE KLEKNTFSN AILTVISDT KYKDNLKEL 
AALYSDHPM SGLEKAIWW TEYVIRHKG AKHLRSHII 
DVPISSFNC DNFRYNNHT
    CDS sequence
    • >TC002562 RA
      atgtttaaa acatatctg tgttttgta ataatttca 
tcatttagt tacagtgag tgtgcaaga attcttggc 
gccgttttc accccatca tacagtcac caagtggcg 
tttcaacca atatggaaa gaactttcc ctgcgcggc 
caccaatta actgtcttg actacaaat ccgctaaac 
gactcaagc ttgaaaaac ctgaccgaa atcgacctc 
agcatgtcc tacgacaca atgaaagcg tacaaagcc 
gatgagatt ttgtcctca aacaacgac agtgtggcc 
gtacgtata aaaaaatac atggaagcg ttgcacgtt 
atcgcagat aagcaatta gcgcatcca aaagtgcaa 
gatttgctg cataataag cgaaacgat ttcgattta 
ttgatggtg gaggcgatc taccccaca cagatggcg 
ttttcctgg tggtttaat atcccgttt attggatta 
atttccctg gatgcgcct tcccggatt catgcggct 
gtgggtaat ccagtgcat ccagttttg tacccggat 
tatgatctg ccgtttgat aaaaacttg acttttggg 
gaaagagtg atcagtact ttgtttcac tgcgctatg 
ttgctctac acgaaattt cgactgcat gcaagggag 
gaaagaacg ctaaggaag tattttggt gaagatgta 
ccgccgatt aatgaaata cagaaaaat atgagcatg 
ttgtttatc aatgccaat cctattttt cacaatatc 
aggcctttg gtgccagct accatccaa attgggggt 
ggtattcac ttgcatgaa ccaaagcct ctcccaaaa 
gacattcaa gaataccta gacaactcc agcgacgga 
tttatctac tttagcctt ggcacaaac gtaaaaagc 
gcagccctt ccaccacaa atcaaagac gcaattctc 
caaaccttt gccgaactc ccctacaac atcctctgg 
aaatttgaa gacgaacac atccccaac aaacccaaa 
aacgtgaaa attgtaaag tggctgccg caaaccgct 
gttttagca cacaaaaat atcaaggcg tttattatg 
cagtgtgga ctgcaatcg atggaagag gcgattgtc 
tacaacgtt ccgatgatc ggcttacct ttttacggg 
gaccaagga aacaatgcg aaagttcta gagagcaaa 
ggtctcggt atcagactg aatacggag aagttggaa 
aaaaacacg ttttcgaat gcgatttta acagttatt 
tcggataca aagtataaa gacaatttg aaagaactt 
gccgcgctt tacagcgac catccaatg tcaggtcta 
gaaaaagca atctggtgg actgaatat gtaattaga 
cacaaaggc gccaaacac ttgagatct cacattatt 
gacgtaccg atcagcagt tttaactgc gataatttt 
cgttataac aatcacact taa
    mRNA sequence
    • >TC002562 RA
      catttaacg tttcattaa aaacatttc gctaaatct 
ctcttatta tttgacaat tggtaaatt aatgataaa 
ccttatcaa taaggtgaa aaaccactt ttacacaca 
cctgattac tctttcggc aaccatgtt taaaacata 
tctgtgttt tgtaataat ttcatcatt tagttacag 
tgagtgtgc aagaattct tggcgccgt tttcacccc 
atcatacag tcaccaagt ggcgtttca accaatatg 
gaaagaact ttccctgcg cggccacca attaactgt 
cttgactac aaatccgct aaacgactc aagcttgaa 
aaacctgac cgaaatcga cctcagcat gtcctacga 
cacaatgaa agcgtacaa agccgatga gattttgtc 
ctcaaacaa cgacagtgt ggccgtacg tataaaaaa 
atacatgga agcgttgca cgttatcgc agataagca 
attagcgca tccaaaagt gcaagattt gctgcataa 
taagcgaaa cgatttcga tttattgat ggtggaggc 
gatctaccc cacacagat ggcgttttc ctggtggtt 
taatatccc gtttattgg attaatttc cctggatgc 
gccttcccg gattcatgc ggctgtggg taatccagt 
gcatccagt tttgtaccc ggattatga tctgccgtt 
tgataaaaa cttgacttt tggggaaag agtgatcag 
tactttgtt tcactgcgc tatgttgct ctacacgaa 
atttcgact gcatgcaag ggaggaaag aacgctaag 
gaagtattt tggtgaaga tgtaccgcc gattaatga 
aatacagaa aaatatgag catgttgtt tatcaatgc 
caatcctat ttttcacaa tatcaggcc tttggtgcc 
agctaccat ccaaattgg gggtggtat tcacttgca 
tgaaccaaa gcctctccc aaaagacat tcaagaata 
cctagacaa ctccagcga cggatttat ctactttag 
ccttggcac aaacgtaaa aagcgcagc ccttccacc 
acaaatcaa agacgcaat tctccaaac ctttgccga 
actccccta caacatcct ctggaaatt tgaagacga 
acacatccc caacaaacc caaaaacgt gaaaattgt 
aaagtggct gccgcaaac cgctgtttt agcacacaa 
aaatatcaa ggcgtttat tatgcagtg tggactgca 
atcgatgga agaggcgat tgtctacaa cgttccgat 
gatcggctt accttttta cggggacca aggaaacaa 
tgcgaaagt tctagagag caaaggtct cggtatcag 
actgaatac ggagaagtt ggaaaaaaa cacgttttc 
gaatgcgat tttaacagt tatttcgga tacaaagta 
taaagacaa tttgaaaga acttgccgc gctttacag 
cgaccatcc aatgtcagg tctagaaaa agcaatctg 
gtggactga atatgtaat tagacacaa aggcgccaa 
acacttgag atctcacat tattgacgt accgatcag 
cagttttaa ctgcgataa ttttcgtta taacaatca 
cacttaaat tcattttca ggagggttt ttagaagga 
attccaaa

    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