Status
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Gene information
General information
TC002078 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_007425.3: 6146683..6148536
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
    		TC002078
    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
    {{ goGene }}
    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_07716

    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 embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg not developed/not fertilized - Penetrance (percentage of animals/eggs on slide): more than 80%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 80%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 20
     embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): more than 80%
    Comment: Few empty eggs while remaining shows empty hatched eggs shells.
    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: % (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
    • >TC002078 RA
      MSCVTHLNF EVKNMSSTY LKVTFFEAG GEFEVCDEW 
KYRVVSFAV SEIYHKGVK SARKLAEGS KTVYKLGLD 
LEGVGVDFM PGDTIGVLP RNDESLVEK IFIRLGVEA 
QADQPCELG VSPNSGKKN AVVPKHLPV RSTLRTIFL 
NHVDLHTPP KKLFLKSLL GFATGSDAS RLTSLSSPQ 
SPDYSDFIA SNPSLLNVL ETFPSLTPP ISLLLEHLP 
PLQPRPYSI CSSPLSHTL EITFDVTGL CTKFMEKQI 
SSKNQIAFY FRKPGLFRL PNLANPVIM IATGTGIAP 
FRGFLQHWK LANEFGDVW LFYGCRFRD RDFLFKDEI 
NELMCEGIV NRLNVAFSR ESDSKKYIQ SEIDKRGAD 
FVDWVNRGA RIYVCGDFR TVVKDVRTC VAKNLVKYG 
GLDEEKAED FVKGDRFIV DTWN
    CDS sequence
    • >TC002078 RA
      atgtcatgt gttacacat ttgaatttt gaggttaaa 
aacatgtct tcaacttat ttgaaagtc acatttttt 
gaggctggg ggcgagttt gaggtttgt gatgagtgg 
aaatatcgg gtggtctca tttgcggtt agtgaaatt 
taccacaaa ggggtgaaa agtgcaagg aaattggca 
gaagggtcg aaaacggtt tataaatta gggctggat 
ttggagggt gtgggggtt gattttatg ccgggggac 
accattggg gtgctccca cgtaacgat gagtcccta 
gttgagaaa attttcata cggttgggg gtcgaagcc 
caggctgac caaccgtgc gaattgggg gtttcaccc 
aacagtggg aaaaaaaac gcagtggtg ccaaaacac 
ctcccggtg cggagcacc ctaaggacg attttccta 
aatcatgtg gatttgcac acgccgccc aaaaaattg 
tttctcaag tcgttactc ggcttcgcc acgggctcg 
gacgcttct agactcacc tccctctcc tccccccaa 
tcccccgac tactctgat tttatcgca tcaaatccc 
tcgttactt aacgtcctt gagacgttc ccctccctc 
accccgccc atttcgctc ctccttgaa cacctccca 
ccgctccag ccccgcccc tactccata tgctcctcc 
cccttgtca cacacgctc gaaatcacg ttcgacgtc 
actggtctg tgtacgaaa ttcatggaa aagcaaatt 
tcgtccaaa aatcaaatc gccttctat ttccgcaaa 
ccgggatta ttccggctc ccgaatttg gcgaatccg 
gtgattatg atcgccacg ggcaccgga atcgcccca 
ttccgggga ttcctccaa cactggaaa ttggcaaac 
gaattcggc gatgtttgg ttgttttac ggttgccgt 
ttcagagat cgtgatttt ttattcaaa gacgaaatc 
aacgaactg atgtgtgaa gggattgtg aatcgttta 
aatgtcgcg ttttcacgc gagagtgac tcgaaaaaa 
tatatacag agtgagatt gataagcga ggggcggat 
ttcgtcgat tgggtcaat cggggggct cgtatttac 
gtttgtggg gattttagg actgtggtc aaggatgta 
cggacttgt gtggcaaaa aatttggtt aaatacggc 
ggacttgac gaggaaaaa gccgaggat tttgtcaaa 
ggggataga tttattgtc gacacttgg aattaa
    mRNA sequence
    • >TC002078 RA
      ttctccaac ccccaaaaa cgaaaaatt ttaatgagg 
tacaaatcg gcaaaaaac actaaaaca cgaaaaaac 
aaccccccg aacggccca aacgccact aacacgtcc 
agccgcccc cctacaacc cactcggac gtttcgccc 
ccctttttg cacaatttt ctcgaaatt tttggaaat 
ttttacgca ataatagga cgtgttcac gaataaggg 
ggcccgtaa cgcgattat tgtcacaat tttcgctta 
attgtgcta ttttgtggc attttgaca gcacttgac 
aaggaccca accaacatg tcatgtgtt acacatttg 
aattttgag gttaaaaac atgtcttca acttatttg 
aaagtcaca ttttttgag gctgggggc gagtttgag 
gtttgtgat gagtggaaa tatcgggtg gtctcattt 
gcggttagt gaaatttac cacaaaggg gtgaaaagt 
gcaaggaaa ttggcagaa gggtcgaaa acggtttat 
aaattaggg ctggatttg gagggtgtg ggggttgat 
tttatgccg ggggacacc attggggtg ctcccacgt 
aacgatgag tccctagtt gagaaaatt ttcatacgg 
ttgggggtc gaagcccag gctgaccaa ccgtgcgaa 
ttgggggtt tcacccaac agtgggaaa aaaaacgca 
gtggtgcca aaacacctc ccggtgcgg agcacccta 
aggacgatt ttcctaaat catgtggat ttgcacacg 
ccgcccaaa aaattgttt ctcaagtcg ttactcggc 
ttcgccacg ggctcggac gcttctaga ctcacctcc 
ctctcctcc ccccaatcc cccgactac tctgatttt 
atcgcatca aatccctcg ttacttaac gtccttgag 
acgttcccc tccctcacc ccgcccatt tcgctcctc 
cttgaacac ctcccaccg ctccagccc cgcccctac 
tccatatgc tcctccccc ttgtcacac acgctcgaa 
atcacgttc gacgtcact ggtctgtgt acgaaattc 
atggaaaag caaatttcg tccaaaaat caaatcgcc 
ttctatttc cgcaaaccg ggattattc cggctcccg 
aatttggcg aatccggtg attatgatc gccacgggc 
accggaatc gccccattc cggggattc ctccaacac 
tggaaattg gcaaacgaa ttcggcgat gtttggttg 
ttttacggt tgccgtttc agagatcgt gatttttta 
ttcaaagac gaaatcaac gaactgatg tgtgaaggg 
attgtgaat cgtttaaat gtcgcgttt tcacgcgag 
agtgactcg aaaaaatat atacagagt gagattgat 
aagcgaggg gcggatttc gtcgattgg gtcaatcgg 
ggggctcgt atttacgtt tgtggggat tttaggact 
gtggtcaag gatgtacgg acttgtgtg gcaaaaaat 
ttggttaaa tacggcgga cttgacgag gaaaaagcc 
gaggatttt gtcaaaggg gatagattt attgtcgac 
acttggaat taatttatt tatacatca tagaaaaac 
attacaata aaattatcg ccgtttttg gacctctgt 
gtaaatatc ccgttaagg aactataaa aatatcgta 
atttacaaa atatatagg gtggagcga cgaaattgt 
gggaataaa tgttcagtc atgtg

    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