Status
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Gene information
General information
TC005889 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_007423.3: 5985607..5988143
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
    		TC005889
    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_00953

    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)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 2 (3 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection

    Fertility
    vitellogenic egg chamber late number increased - Number of animals showing the phenotype: 2

    vitellogenic egg chamber late potentiallydegenerated - Number of animals showing the phenotype: 2
    yolk late potentiallydegenerated - Number of animals showing the phenotype: 2

    mature egg not present - Number of animals showing the phenotype: 2
    ovary without detectable defects - Number of animals showing the phenotype: 2
    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
    • >TC005889 RA
      MENTGYVLN NFDHTSQEG PIRCIFFCE FHPTAGPII 
SCQEPEQYI SKELFDSIS VYIITKAEL QKSTITVTL 
SDYKILGFP VRIDDKKYP RNAYHFNLC LVCDSNVRT 
VHYEPVVIK LSDYLMAME IESSFLSDG KAATKLAPI 
LKQVIEELN TKGECALTE GPTATHLKV VHVRSDPAP 
VADHQVPVF IKPLPDQQW DLTTQQVAP YIDGFNHVA 
RIAALSDVE NNLVKACVQ NLVYYGVVA LVPLFQYGN 
VYCTTPQLN ILAHDVNLQ NKCLKYVAV SQRQLPNFR 
DVFRMFAAM TRGTTMRDL CLRFNPANL RINERKLVQ 
IGVLEGLIR RVHKYPILL SDTSELQKS LSGAANLDE 
ICCATGVAT QQLEDQLER DHNIVLLWK
    CDS sequence
    • >TC005889 RA
      atggaaaat acaggttat gtcctgaac aactttgat 
cacacaagt caggagggc cccattcgg tgcattttt 
ttctgtgaa tttcatcca acagccggg cctatcatt 
tcgtgtcaa gaaccagag cagtacatt tcaaaggaa 
ctattcgac agtattagc gtttacata atcacgaaa 
gcggagtta cagaagagt acaatcact gttactcta 
tcggattat aaaatattg gggttcccg gtccgcatt 
gacgacaaa aaatatccc cggaacgcc taccacttc 
aatctatgc ctagtgtgt gacagtaac gtccgaacc 
gttcattac gaacccgtc gttataaaa ctatcagac 
tacctaatg gcaatggaa attgaaagc agtttttta 
tcggacggt aaagcagca acgaaactc gccccaatt 
ttgaagcaa gttatcgag gaattgaac acgaagggg 
gagtgcgcc ctcacggag ggccccacc gccacccat 
ctcaaggtc gtgcacgtt cgcagcgac ccggccccc 
gtggccgac caccaggtc cctgtcttc atcaagccc 
ctcccggac cagcagtgg gacttgacc acgcaacaa 
gtggccccc tacattgac ggcttcaat cacgtggcc 
cgaatcgcg gccctctcc gatgtcgaa aataatttg 
gtcaaggct tgtgtccaa aacctcgtc tattacgga 
gtcgttgct ttagtgcct ttgttccaa tacgggaat 
gtttattgc acgacgccg cagttaaat attctggct 
cacgatgtc aatttacaa aacaaatgt ttgaagtat 
gtggcggtg tcccaaaga cagttaccc aattttcgc 
gacgttttt cgcatgttt gccgccatg acaaggggc 
acgaccatg cgggacttg tgcctgaga tttaatcca 
gctaatttg cgaataaac gaaaggaaa ttggtacag 
attggagtg ttggaaggt ctgattcga cgggttcat 
aagtatccg attttgttg agtgatact tctgaatta 
caaaaatcg ctctcgggg gcggctaat ttggatgag 
atttgctgc gccactggc gttgccacg caacaactc 
gaggaccag ctggagaga gaccacaat atcgtcctg 
ttgtggaaa tga
    mRNA sequence
    • >TC005889 RA
      ttcagtagt ggcgccgta cagaaacct gtaattgga 
ttcttgttc aatatctat ggaattata tttcacgtc 
aaatgttac gaaacgtac aaaacatgg aaaatacag 
gttatgtcc tgaacaact ttgatcaca caagtcagg 
agggcccca ttcggtgca tttttttct gtgaatttc 
atccaacag ccgggccta tcatttcgt gtcaagaac 
cagagcagt acatttcaa aggaactat tcgacagta 
ttagcgttt acataatca cgaaagcgg agttacaga 
agagtacaa tcactgtta ctctatcgg attataaaa 
tattggggt tcccggtcc gcattgacg acaaaaaat 
atccccgga acgcctacc acttcaatc tatgcctag 
tgtgtgaca gtaacgtcc gaaccgttc attacgaac 
ccgtcgtta taaaactat cagactacc taatggcaa 
tggaaattg aaagcagtt ttttatcgg acggtaaag 
cagcaacga aactcgccc caattttga agcaagtta 
tcgaggaat tgaacacga agggggagt gcgccctca 
cggagggcc ccaccgcca cccatctca aggtcgtgc 
acgttcgca gcgacccgg cccccgtgg ccgaccacc 
aggtccctg tcttcatca agcccctcc cggaccagc 
agtgggact tgaccacgc aacaagtgg ccccctaca 
ttgacggct tcaatcacg tggcccgaa tcgcggccc 
tctccgatg tcgaaaata atttggtca aggcttgtg 
tccaaaacc tcgtctatt acggagtcg ttgctttag 
tgcctttgt tccaatacg ggaatgttt attgcacga 
cgccgcagt taaatattc tggctcacg atgtcaatt 
tacaaaaca aatgtttga agtatgtgg cggtgtccc 
aaagacagt tacccaatt ttcgcgacg tttttcgca 
tgtttgccg ccatgacaa ggggcacga ccatgcggg 
acttgtgcc tgagattta atccagcta atttgcgaa 
taaacgaaa ggaaattgg tacagattg gagtgttgg 
aaggtctga ttcgacggg ttcataagt atccgattt 
tgttgagtg atacttctg aattacaaa aatcgctct 
cgggggcgg ctaatttgg atgagattt gctgcgcca 
ctggcgttg ccacgcaac aactcgagg accagctgg 
agagagacc acaatatcg tcctgttgt ggaaatgac 
tgtgataat aaagatttg cttaaaaa
    The data is licensed under a Creative Commons Attribution 3.0 Unported License. (CC-BY) CC-BY