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Gene information
General information
TC000590 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: 9341226..9344386
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
    		TC000590
    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
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    Email
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    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_00132

    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)

    pupa eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 1 (3 dpi)
    Days post injection

    potentially confused/crosscontaminated with : iB # (comma separated) iB 147
    Pupal morphology
    potentially confused/crosscontaminated with : iB # (comma separated) iB 147
    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg with embryonic tissue, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): more than 80%
    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - 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: 0.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 0.0% (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC000590 RA
      MVKETKFYD ILGVKPGCT QDDLKKAYR KLALKYHPD 
KNPNEGEKF KQISQAYEV LSDPEKKRI YDQGGEQAL 
KEGGVSGGF SSPMDLFDM FFGGGGFGG GRGRRRERK 
GKDVIHQLN VSLEELYKG TVRKLALQK NVICDKCEG 
RGGKKGAVE TCPTCRGSG MQVQIQQLG PGMIQQIQS 
MCSDCRGQG QRINPKDRC KQCQGKKVT RERKILEVH 
VDKGMVDGQ KIVFNGEGD QEPELEPGD IIIVLEEKE 
HPVFRRSGL DLIIRLELQ LVESLCGFQ KVIRTLDDR 
DLVITSLPG EVTKHGDVK CIMNEGMPQ YKNPFEKGR 
LIVQFLVQF PDKLPPEVI PALENALPP RPEIMIPDQ 
AEECILLPF DVDKQDSRR RQNRNVYDE DDEMHGPGQ 
RVQCAAN
    CDS sequence
    • >TC000590 RA
      atggtaaaa gagacgaaa ttctacgac atcctgggc 
gttaagccc ggctgcacc caggacgac ctgaagaaa 
gcctaccga aaactcgcc cttaaatac caccccgac 
aagaacccc aatgaaggg gagaagttc aagcaaatc 
tcgcaagcg tacgaggtg ctgtccgac ccggaaaag 
aagcgcatt tacgaccaa ggcggcgaa caggccctc 
aaagagggc ggcgtctcg ggcggcttc tccagccct 
atggacttg ttcgatatg ttcttcggc ggaggcggc 
tttggtggc ggcagaggc cgacgtcgc gaacgtaaa 
ggcaaagat gtcattcat caacttaat gtttctctg 
gaagagttg tacaaagga accgtccgg aaattggct 
ctacagaaa aacgtcatc tgtgataag tgcgaaggc 
aggggtggg aagaagggg gctgtggag acgtgtccc 
acgtgtcgg ggctccggc atgcaggtg caaatccag 
cagttgggg ccaggcatg atccaacaa atccagagc 
atgtgttcg gattgccga ggccaaggt caacgcatc 
aatcccaaa gaccgttgc aagcaatgc caaggcaag 
aaagtgact cgcgaacgc aaaattctc gaagtccac 
gtggacaag ggcatggtt gacggtcaa aaaatcgtt 
tttaacgga gaaggggac caagaacca gaactggaa 
cctggcgat attataatt gtgcttgag gagaaagaa 
catcccgtt tttcgaaga tccggcttg gatctcata 
atccgcctt gagttgcag ttagtagag tcgctttgc 
ggattccag aaagtaatc aggactttg gacgaccgc 
gatttggtt atcacgtcg cttccgggc gaggtcacg 
aaacacggg gatgttaag tgtattatg aacgaggga 
atgccgcag tataagaat ccgttcgag aaaggacgg 
cttatcgta caatttttg gtacagttt ccggataag 
ttgccacct gaggtgatt ccggcgctg gagaatgcg 
ctaccgcct cggcctgaa attatgatc ccggatcag 
gcggaagaa tgcattttg ttgccgttt gatgtggat 
aagcaggac tcgaggagg aggcagaat aggaatgtt 
tatgacgaa gatgatgag atgcatggt ccgggacag 
cgggtccaa tgtgcggct aactaa
    mRNA sequence
    • >TC000590 RA
      aacctttta agtggaata cgtgactta aaatcaaaa 
attctatta aaaggcgcc gcttttcga ataagtaag 
ctgagtagg cctgcagag ggcgtcctg tcaatttct 
agaattcgt cattcgtta cgtcttcga cctttctct 
tcgtcgaat tttccagaa cctcgtggc tgggagttt 
tatccctga acacgcgct ctagaacca gtctttgct 
ttgtgctgc gtcagtgtg caaacttaa aaaatccac 
gagttgtaa tccccgttc cagaaatat tgattattt 
ctgaggact acaaccatg gtaaaagag acgaaattc 
tacgacatc ctgggcgtt aagcccggc tgcacccag 
gacgacctg aagaaagcc taccgaaaa ctcgccctt 
aaataccac cccgacaag aaccccaat gaaggggag 
aagttcaag caaatctcg caagcgtac gaggtgctg 
tccgacccg gaaaagaag cgcatttac gaccaaggc 
ggcgaacag gccctcaaa gagggcggc gtctcgggc 
ggcttctcc agccctatg gacttgttc gatatgttc 
ttcggcgga ggcggcttt ggtggcggc agaggccga 
cgtcgcgaa cgtaaaggc aaagatgtc attcatcaa 
cttaatgtt tctctggaa gagttgtac aaaggaacc 
gtccggaaa ttggctcta cagaaaaac gtcatctgt 
gataagtgc gaaggcagg ggtgggaag aagggggct 
gtggagacg tgtcccacg tgtcggggc tccggcatg 
caggtgcaa atccagcag ttggggcca ggcatgatc 
caacaaatc cagagcatg tgttcggat tgccgaggc 
caaggtcaa cgcatcaat cccaaagac cgttgcaag 
caatgccaa ggcaagaaa gtgactcgc gaacgcaaa 
attctcgaa gtccacgtg gacaagggc atggttgac 
ggtcaaaaa atcgttttt aacggagaa ggggaccaa 
gaaccagaa ctggaacct ggcgatatt ataattgtg 
cttgaggag aaagaacat cccgttttt cgaagatcc 
ggcttggat ctcataatc cgccttgag ttgcagtta 
gtagagtcg ctttgcgga ttccagaaa gtaatcagg 
actttggac gaccgcgat ttggttatc acgtcgctt 
ccgggcgag gtcacgaaa cacggggat gttaagtgt 
attatgaac gagggaatg ccgcagtat aagaatccg 
ttcgagaaa ggacggctt atcgtacaa tttttggta 
cagtttccg gataagttg ccacctgag gtgattccg 
gcgctggag aatgcgcta ccgcctcgg cctgaaatt 
atgatcccg gatcaggcg gaagaatgc attttgttg 
ccgtttgat gtggataag caggactcg aggaggagg 
cagaatagg aatgtttat gacgaagat gatgagatg 
catggtccg ggacagcgg gtccaatgt gcggctaac 
taattttcg agtattatt aagggactt tgatataga 
catcttgat agcatagac gaaattgtt ttagtaggc 
aattttatt aagtaattg taattattt aaacataaa 
atagggaca gcagaaggt tccgttcat gctgaatgt 
atgtggctt tttgttgga attatttac ggtcttcta 
attgtgaaa attgatcag tttcgtggt atttatttt 
tttatttga agcgtctta ccgagatat tttgaataa 
atgtttctt tatgtt
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY