Status
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Gene information
General information
TC002295 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.

NW_015451937.1: 175145..176827
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
    		TC002295
    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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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_00352

    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: 1 (3 dpi)
    Days post injection

    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
    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
    • >TC002295 RA
      MFSPVTSYL FCCRSLLST VLLLGSLKS TLAQCDTPS 
PTTASGTHA PSGPYCSGD LIFEDEFDE FDLKKWSHE 
LTLGGGGNW EFEWYANSR YNSYVEDGL LYLKPTLVA 
DEMGEEFLS SGHLDINGG SPADECTNP QWYGCVRDG 
TPTNYLNPI KSARIRTVN SFSFKYGKA EIRAKLPAG 
DWLWPAIWF LPRWNLYSG WPVSGEIDL MESRGNRNL 
VNGSGVNIG TQMVGSTLH WGPASNYNM YSLTHTEKL 
DPNGFDADW HNYQLTWDE KSISFAIDN EPLATFEPP 
EGGFWEWGN FDSTGLDNP WKHSKSKLA PFDQEFYII 
LNLACGGTA YFPDDATNP GGKPWANTS PTASTDFWK 
GKDQWLPTW QLETDNAAL KIDYVKIWA L
    CDS sequence
    • >TC002295 RA
      atgtttagt cctgtgact tcttacctt ttttgctgc 
agatcacta ctcagtaca gttcttctc ctgggctct 
ctcaaatcc accttagcc caatgtgac actcctagt 
cccacaaca gcaagtggc acccacgct ccatctggt 
ccttactgc tccggggat ctcattttt gaagatgag 
tttgacgaa tttgacttg aaaaagtgg agccatgag 
ctaactcta ggaggtggc ggtaattgg gaatttgaa 
tggtatgcc aacagccga tataacagt tacgttgaa 
gatggtctt ttgtacctg aaaccaact ttggtcgct 
gatgaaatg ggggaagag tttttatcg tctggccat 
ctagacatc aacgggggt tctccggct gatgagtgc 
actaatcct cagtggtat ggatgcgtg agggatggt 
accccaacc aattacctc aaccctatt aaaagtgct 
cgtattcgc actgtcaat tccttttct ttcaaatat 
ggtaaagca gaaataaga gccaaattg ccagctggt 
gattggttg tggcctgcg atttggttc ttacctaga 
tggaatctt tactccggt tggcctgtt tctggtgaa 
attgactta atggaaagt cgaggaaat cgcaattta 
gtcaacggt tccggggtc aatatcgga acgcaaatg 
gtcggttcg acactgcat tggggccct gcttcaaat 
tacaacatg tacagtctc acacacacc gagaaactt 
gatccgaat ggttttgac gccgattgg cacaactat 
cagttaacg tgggacgaa aagagtatt tctttcgct 
atcgacaat gagcctttg gccacattt gagccacca 
gaaggtggt ttttgggaa tggggtaat tttgattcc 
actggtttg gacaatcct tggaaacat agcaaatcc 
aagttggca ccgtttgat caagaattt tacattatc 
ttgaatttg gcgtgtgga ggaacagct tatttccca 
gatgatgca actaatcct gggggtaaa ccgtgggct 
aatacgtct ccaacggct tctacggat ttctggaag 
ggaaaggat cagtggttg ccaacgtgg cagctggag 
actgataat gcagcttta aaaattgac tatgtgaaa 
atctgggcg ttgtaa
    mRNA sequence
    • >TC002295 RA
      tacctacac aatgtttag tcctgtgac ttcttacct 
tttttgctg cagatcact actcagtac agttcttct 
cctgggctc tctcaaatc caccttagc ccaatgtga 
cactcctag tcccacaac agcaagtgg cacccacgc 
tccatctgg tccttactg ctccgggga tctcatttt 
tgaagatga gtttgacga atttgactt gaaaaagtg 
gagccatga gctaactct aggaggtgg cggtaattg 
ggaatttga atggtatgc caacagccg atataacag 
ttacgttga agatggtct tttgtacct gaaaccaac 
tttggtcgc tgatgaaat gggggaaga gtttttatc 
gtctggcca tctagacat caacggggg ttctccggc 
tgatgagtg cactaatcc tcagtggta tggatgcgt 
gagggatgg taccccaac caattacct caaccctat 
taaaagtgc tcgtattcg cactgtcaa ttccttttc 
tttcaaata tggtaaagc agaaataag agccaaatt 
gccagctgg tgattggtt gtggcctgc gatttggtt 
cttacctag atggaatct ttactccgg ttggcctgt 
ttctggtga aattgactt aatggaaag tcgaggaaa 
tcgcaattt agtcaacgg ttccggggt caatatcgg 
aacgcaaat ggtcggttc gacactgca ttggggccc 
tgcttcaaa ttacaacat gtacagtct cacacacac 
cgagaaact tgatccgaa tggttttga cgccgattg 
gcacaacta tcagttaac gtgggacga aaagagtat 
ttctttcgc tatcgacaa tgagccttt ggccacatt 
tgagccacc agaaggtgg tttttggga atggggtaa 
ttttgattc cactggttt ggacaatcc ttggaaaca 
tagcaaatc caagttggc accgtttga tcaagaatt 
ttacattat cttgaattt ggcgtgtgg aggaacagc 
ttatttccc agatgatgc aactaatcc tgggggtaa 
accgtgggc taatacgtc tccaacggc ttctacgga 
tttctggaa gggaaagga tcagtggtt gccaacgtg 
gcagctgga gactgataa tgcagcttt aaaaattga 
ctatgtgaa aatctgggc gttgtaata attagtgag 
aatttgaat tgtaataaa aataaaatg cgtat

    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