Status
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Gene information
General information
TC005389 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: 13824616..13827317
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
    		TC005389
    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
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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_09413

    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: 1 (3 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 2 (9 dpi)
    Days post injection

    Adult morphology
    odoriferous glands colour darker - Number of animals showing the phenotype: 4 (13 dpi)
    Days post injection


    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): 50% - 80%

    larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 80%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     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: % (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
    • >TC005389 RA
      MEVKTESPG DPNDRNGNV HKNTDLTLP HDFINNFAS 
NNTTRKKIK KILIKRIPI LSWLPEYNC DCAVGDLVA 
GITVGLTVI PQALAYSSV AGLPPQYGL YTSFLGCFV 
YIFLGSCKD VAMGPTAIL ALLVHQVTE GKGPEYAIL 
LCLLSGIVQ LLMGVLGLG FLIDFISGP VSSGFTSAA 
ALIIVSSQI KDLLGIRAS GANFLDIWE GVVKDIGNT 
KVWDCVLGI ACLVVLLLL RIISTVGTP ETGVPKWRT 
ALRLIGISR NAILVIVCG AIGYYFTTL GETPFKVIG 
YVPEGFPAI QPPRFTYTY NNTHENFLD MVTNLRSGI 
IIVPLLGLL EDIAVCKAF ANGRPVDAT QELLAIGLC 
NVANSFVQG FPGSGALAR SAVNNSSGV KTTLGGLYT 
GVIVITALF FFTPYFQYI PKATLAAII IAAAIFMVE 
IRVIQPMWR AKKSDLALA LITFVTCLV TRLEYGIST 
GVVLNIIFI LYQAARPKI TIETMKSTQ GADYLLVTP 
DRCLIFPSA DYVRNLVIK QSMRQKIPV VIDCSHIYG 
ADYTAATVI ESLTKDFKT RQQPLFFYN LKSSVSSVF 
VGLNLDYFL VYYNEDELD DMLKKWTEI CDKI
    CDS sequence
    • >TC005389 RA
      atggaggta aaaaccgag tctccggga gacccaaac 
gaccgcaac ggcaacgtc cacaaaaac actgaccta 
actctacca cacgatttt attaacaat ttcgcttca 
aacaacaca accaggaaa aaaatcaaa aaaatccta 
atcaagcga atcccaatt ttgagctgg ttgcctgaa 
tataattgt gattgcgcc gttggggat ctggtggct 
gggatcaca gtgggatta actgtaatc ccgcaagct 
ttggcctat tccagcgtt gcaggactc ccaccccag 
tatgggtta tacacctcg tttttgggc tgtttcgtt 
tatattttt ctcgggagt tgtaaggac gtggccatg 
ggccctacg gccattttg gcccttttg gtgcaccag 
gtgaccgaa ggcaaaggg ccagagtat gcaattttg 
ctgtgtttg ctcagtggg attgtgcaa cttttgatg 
ggagttctg ggattagga ttcttgatt gatttcatt 
tcgggacct gtgtcatca ggattcacc tcagctgct 
gcccttatc attgtttcg tcacaaatc aaagacttg 
ctagggatt agggcaagt ggggccaat tttttggac 
atttgggaa ggtgttgtt aaagacata ggaaatacg 
aaagtatgg gattgtgtt ttagggatt gcgtgtttg 
gtagtcttg ctcttatta cggattata tcaactgtg 
ggaaccccc gaaaccggc gttccaaaa tggcggacc 
gccctccgc ctcatcgga atctcacgt aacgccatc 
ttggtcatt gtttgcggc gctattggt tattatttc 
accacatta ggggaaacc ccattcaag gtgattggt 
tacgtcccg gagggattc cccgcaata caaccacca 
cggttcacg tacacttac aacaacaca cacgagaat 
ttcctcgac atggtcacc aacctacga tcggggatc 
ataatcgtg cctttgttg ggcctcctt gaagacatt 
gccgtttgc aaagccttc gcaaacgga cgaccggtt 
gatgccaca caagaacta ctagcgatt ggtttatgc 
aatgttgcc aactcattc gttcaggga ttccccgga 
agtggggct ttggcgcgc agtgccgtt aataattca 
agtggggtt aaaacaaca ctagggggg ctatacacg 
ggcgttata gtcataaca gccctattt ttcttcact 
ccttatttt caatacatt ccaaaagcg acactagcc 
gccattatt atcgccgcc gccattttc atggtcgaa 
attagggtc attcaaccc atgtggagg gccaaaaaa 
agcgaccta gccctagcc cttatcact ttcgtcacc 
tgtctggtg acaagacta gaatatggc atttcaaca 
ggggttgta cttaacata attttcatt ttgtatcaa 
gcggcaagg ccaaaaatt acaatcgaa accatgaaa 
agcacgcaa ggagcagat tatttgctt gtgacgcct 
gaccgatgc ttgattttt ccctcagct gattatgtc 
cgaaatttg gtgattaag caatcgatg aggcaaaaa 
attccggtt gttatcgac tgttcacac atttatggt 
gctgattat acggcagct acagtcatt gagagttta 
accaaagat ttcaaaacg cgacaacaa ccgctgttt 
ttttacaat ctcaagtca agtgtgagc tcggttttt 
gtcggccta aacctggac tattttcta gtctattac 
aacgaagat gagttggat gatatgctc aagaagtgg 
accgaaatc tgtgataaa atctag
    mRNA sequence
    • >TC005389 RA
      cgtcgaata acagacacc ttatcaaaa acccgccaa 
ttatcatac aaaaacgac cacttttag taacaaaaa 
cgcataatt atggaggta aaaaccgag tctccggga 
gacccaaac gaccgcaac ggcaacgtc cacaaaaac 
actgaccta actctacca cacgatttt attaacaat 
ttcgcttca aacaacaca accaggaaa aaaatcaaa 
aaaatccta atcaagcga atcccaatt ttgagctgg 
ttgcctgaa tataattgt gattgcgcc gttggggat 
ctggtggct gggatcaca gtgggatta actgtaatc 
ccgcaagct ttggcctat tccagcgtt gcaggactc 
ccaccccag tatgggtta tacacctcg tttttgggc 
tgtttcgtt tatattttt ctcgggagt tgtaaggac 
gtggccatg ggccctacg gccattttg gcccttttg 
gtgcaccag gtgaccgaa ggcaaaggg ccagagtat 
gcaattttg ctgtgtttg ctcagtggg attgtgcaa 
cttttgatg ggagttctg ggattagga ttcttgatt 
gatttcatt tcgggacct gtgtcatca ggattcacc 
tcagctgct gcccttatc attgtttcg tcacaaatc 
aaagacttg ctagggatt agggcaagt ggggccaat 
tttttggac atttgggaa ggtgttgtt aaagacata 
ggaaatacg aaagtatgg gattgtgtt ttagggatt 
gcgtgtttg gtagtcttg ctcttatta cggattata 
tcaactgtg ggaaccccc gaaaccggc gttccaaaa 
tggcggacc gccctccgc ctcatcgga atctcacgt 
aacgccatc ttggtcatt gtttgcggc gctattggt 
tattatttc accacatta ggggaaacc ccattcaag 
gtgattggt tacgtcccg gagggattc cccgcaata 
caaccacca cggttcacg tacacttac aacaacaca 
cacgagaat ttcctcgac atggtcacc aacctacga 
tcggggatc ataatcgtg cctttgttg ggcctcctt 
gaagacatt gccgtttgc aaagccttc gcaaacgga 
cgaccggtt gatgccaca caagaacta ctagcgatt 
ggtttatgc aatgttgcc aactcattc gttcaggga 
ttccccgga agtggggct ttggcgcgc agtgccgtt 
aataattca agtggggtt aaaacaaca ctagggggg 
ctatacacg ggcgttata gtcataaca gccctattt 
ttcttcact ccttatttt caatacatt ccaaaagcg 
acactagcc gccattatt atcgccgcc gccattttc 
atggtcgaa attagggtc attcaaccc atgtggagg 
gccaaaaaa agcgaccta gccctagcc cttatcact 
ttcgtcacc tgtctggtg acaagacta gaatatggc 
atttcaaca ggggttgta cttaacata attttcatt 
ttgtatcaa gcggcaagg ccaaaaatt acaatcgaa 
accatgaaa agcacgcaa ggagcagat tatttgctt 
gtgacgcct gaccgatgc ttgattttt ccctcagct 
gattatgtc cgaaatttg gtgattaag caatcgatg 
aggcaaaaa attccggtt gttatcgac tgttcacac 
atttatggt gctgattat acggcagct acagtcatt 
gagagttta accaaagat ttcaaaacg cgacaacaa 
ccgctgttt ttttacaat ctcaagtca agtgtgagc 
tcggttttt gtcggccta aacctggac tattttcta 
gtctattac aacgaagat gagttggat gatatgctc 
aagaagtgg accgaaatc tgtgataaa atctaggtg 
taaaagcaa cacgtctgt gttttatag tacttttat 
ttaattctg tataatgaa taaattatg gaaaataaa

    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