Status
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Gene information
General information
TC002552 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_007418.3: 23558040..23573980
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
    		TC002552
    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_03403

    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 larval musculature fluorescence decreased - Penetrance (percentage of animals/eggs on slide): more than 80%

    larval musculature partially not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    larval musculature thinner - Penetrance (percentage of animals/eggs on slide): more than 80%
    larval musculature mostly fluorescence not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    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
     larva shape irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): 30% - 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: 20.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 87.5% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection

    eclosion not fulfilled (not completely eclosed) - Number of animals showing the phenotype: 1 (16 dpi)
    Days post injection

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 5 (16 dpi)
    Days post injection


    adult lethality - Number of animals showing the phenotype: 1 (41 dpi)
    Days post injection

    Pupal morphology
    wings not closed - Number of animals showing the phenotype: 8

    metathoracic leg orientation irregular - Number of animals showing the phenotype: 8

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC002552 RA
      MWLAVLLFF VFVVTYVIQ QVKKPPNFP PGPYWLPFV 
GNLPQLKKL SKKLGGQHL ALSHLAKEY NTNVLGLKL 
GKDYVVTVF TYPLIRDVL ISEEFEGRP DNFFLRLRC 
MGQKRGITC TEGEEWNTL RNFVNRHLR NLGFGKKPM 
EKMIQDEIC DILTILKKD GSDIQVDKF LAPCVLSVI 
WTLITGEKI SRENNQLDE LLDLFNLRS KAFDMTGGT 
LTQYPWLRY FLPEWSGFN LIKSVNTSL KNLFMKYIR 
EHKDGWFEG RNEDLIYRY ISEMKTNTE ASKYFTDDH 
LVMVCVDLF IGGAQTTSR TLGFAFLMM IMYPEVQKK 
VQEQIDKHY DKNSSIEYS DRYKLPYVE AVLLETIRY 
RYVVPIGGP RRVTKNTTL DGYYLPKNT TVLISFYSI 
NNDPENWQN PEIFNPERF LDEKGSLLP DEKLIPFAL 
GRRRCVGEI LAKNCIFLL FVEILRRYN VSLAPGSKP 
PTGKPIAGI TLSPESYRV KFTERSL
    CDS sequence
    • >TC002552 RA
      atgtggctt gcagttttg ttgtttttc gtttttgtg 
gtgacttat gtgatacaa caagtgaaa aaaccacct 
aattttcct ccaggtcct tactggtta ccattcgtt 
ggtaacctc ccccagctc aagaaactc tcaaaaaaa 
ctaggcgga caacacctc gcgttatca catctagcc 
aaagaatac aacaccaac gtcttaggc ctcaaatta 
ggaaaggac tatgttgta acagttttt acatatccc 
ctcatacgg gacgtccta attagcgaa gaattcgaa 
ggaagaccc gacaacttc tttctacgt cttcggtgc 
atgggccaa aaaagaggc atcacttgc accgaaggc 
gaagaatgg aacacgtta cgaaacttt gtaaatcgc 
cacttgcga aacttaggt ttcgggaaa aaaccaatg 
gaaaaaatg atccaagac gagatttgc gacattcta 
acaattctg aaaaaggac gggtccgac attcaagtc 
gataaattt ttggctcct tgtgtccta agtgttatt 
tggacgtta attacggga gaaaaaatt tcaagggaa 
aataaccaa ttggacgaa ttgttggat ttgtttaat 
ttgaggtcg aaagcgttt gatatgact ggaggtact 
ctaacacag tatccctgg ttaaggtat tttttgccc 
gaatggagt ggcttcaat ttgataaag tcggtaaac 
acgagcttg aaaaatttg tttatgaaa tatattcgc 
gagcataaa gatgggtgg tttgagggg agaaacgaa 
gacttgata tatcgctac atttccgaa atgaagacc 
aatacagaa gcctccaaa tatttcaca gatgatcat 
ttggttatg gtctgtgtg gacctattt ataggcggt 
gcccaaacc actagtcgg actttaggg tttgctttc 
cttatgatg attatgtat ccagaagtg cagaaaaaa 
gtgcaagag caaattgat aagcattat gataagaat 
tcatccatt gagtattct gatcgttac aagttacct 
tatgttgaa gcagtatta ttagaaaca ataagatat 
cggtacgta gttccaatc gggggaccc cgaagagtc 
acaaaaaac accacatta gatggctac tatttacca 
aagaacacg actgtttta attagtttt tattcaatc 
aacaacgac cccgaaaac tggcaaaac cccgaaatt 
tttaacccg gaacgtttt ctagacgag aaaggttca 
ttacttccc gacgaaaaa ctaatccct tttgcttta 
gggcgtaga cgttgtgtt ggcgaaatc ttagcaaaa 
aactgcatt tttttgttg tttgttgaa attttgcga 
cggtataat gtgtcttta gcccccggt tcgaagcct 
ccgactgga aaacctata gcaggaatt actttatct 
ccagaaagc tacagagtt aagtttacg gaacggtcg 
ttataa
    mRNA sequence
    • >TC002552 RA
      cagccgttt agttcgagt acgagtctg cagatgtct 
accatgttt gcgtttgtc gaccgtttg cctggcttt 
tggagataa aaccattcg agggacgag tgcaaagca 
tacttacct ggcgtaggg gttaccgtg atcaagaag 
gcggttccc ccagggtga ggcccttcc attgcactg 
aggtcgggc tgacccctg cgattatcc ctaatgcgg 
ataactcgg gcgcacaat ttttggcga acatttata 
gtattgaag cgttttata ttgtacagc tgacacaaa 
tattaacag ttttataca gctgagcta aaagtaccg 
cctacaaat tggttcaag tgtggacta gacacacca 
agtcgttgt aaccagcaa ccttgcttt agtaatagt 
cgaggcttt accttacga tgttcgcca aatcacttt 
cgtaacttg attcatctt tatcgacaa aggaattta 
aaatgtggc ttgcagttt tgttgtttt tcgtttttg 
tggtgactt atgtgatac aacaagtga aaaaaccac 
ctaattttc ctccaggtc cttactggt taccattcg 
ttggtaacc tcccccagc tcaagaaac tctcaaaaa 
aactaggcg gacaacacc tcgcgttat cacatctag 
ccaaagaat acaacacca acgtcttag gcctcaaat 
taggaaagg actatgttg taacagttt ttacatatc 
ccctcatac gggacgtcc taattagcg aagaattcg 
aaggaagac ccgacaact tctttctac gtcttcggt 
gcatgggcc aaaaaagag gcatcactt gcaccgaag 
gcgaagaat ggaacacgt tacgaaact ttgtaaatc 
gccacttgc gaaacttag gtttcggga aaaaaccaa 
tggaaaaaa tgatccaag acgagattt gcgacattc 
taacaattc tgaaaaagg acgggtccg acattcaag 
tcgataaat ttttggctc cttgtgtcc taagtgtta 
tttggacgt taattacgg gagaaaaaa tttcaaggg 
aaaataacc aattggacg aattgttgg atttgttta 
atttgaggt cgaaagcgt ttgatatga ctggaggta 
ctctaacac agtatccct ggttaaggt attttttgc 
ccgaatgga gtggcttca atttgataa agtcggtaa 
acacgagct tgaaaaatt tgtttatga aatatattc 
gcgagcata aagatgggt ggtttgagg ggagaaacg 
aagacttga tatatcgct acatttccg aaatgaaga 
ccaatacag aagcctcca aatatttca cagatgatc 
atttggtta tggtctgtg tggacctat ttataggcg 
gtgcccaaa ccactagtc ggactttag ggtttgctt 
tccttatga tgattatgt atccagaag tgcagaaaa 
aagtgcaag agcaaattg ataagcatt atgataaga 
attcatcca ttgagtatt ctgatcgtt acaagttac 
cttatgttg aagcagtat tattagaaa caataagat 
atcggtacg tagttccaa tcgggggac cccgaagag 
tcacaaaaa acaccacat tagatggct actatttac 
caaagaaca cgactgttt taattagtt tttattcaa 
tcaacaacg accccgaaa actggcaaa accccgaaa 
tttttaacc cggaacgtt ttctagacg agaaaggtt 
cattacttc ccgacgaaa aactaatcc cttttgctt 
tagggcgta gacgttgtg ttggcgaaa tcttagcaa 
aaaactgca tttttttgt tgtttgttg aaattttgc 
gacggtata atgtgtctt tagcccccg gttcgaagc 
ctccgactg gaaaaccta tagcaggaa ttactttat 
ctccagaaa gctacagag ttaagttta cggaacggt 
cgttataaa tatgtattg aacttagca aggttaaat 
actcgaatg atagccaaa tgtaaaata gtgacgtca 
gacacgtgt tctagtcct acatgttgt acattccga 
atgcttgga gacggatcg agttatgta atagtggcc 
tgtttaaag ttcactgtc aataaaaac tgattaatt 
ag

    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