Status
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Gene information
General information
TC004410 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: 19811219..19815278
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
    		TC004410
    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
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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_03748

    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: 10.0% (includes death as pupa, adult)

    adult lethality - Number of animals showing the phenotype: 1 (9 dpi)
    Days post injection

    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 50
     egg without cuticle embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    head not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    thorax not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen 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): 50% - 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: 10.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 10.0% (includes death as larva, prepupa, pupa, adult)

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

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004410 RA
      MILKIFLEC LVAHLAYSL SQSPILIVV SYDAFRYDF 
FDTKSVPHM NRLRKLGTY SDYLINVFP TKTFPNHHS 
IATGLYPDI HGVVGNSYF NKSTNSVVH INYEMFHFD 
EKVVPIWRQ NEDAGKGRH SGVVMWPGG CYPYQGKQV 
TYCKDYDHN FDWFKRVDL VIGWIKDPK KPANLIMLY 
FDEPDTDGH IYGINSDVV NKLINKLDN ITLYLQQQL 
EKNNLTGKV TVVHLSDHG MLDVKPPNF INVTQYLTP 
GTYTYAGST PVLQFHPKK GFETEVYQK LKNASSQDH 
FTVYKKEEF LPRWHYKDN PRSPPILVL AEVGYGLDD 
LIISAKQNA EKNHYKLTN QSTFGVHGY DYTVKEMRP 
FFMARGPKI KVNHKVPPF NTVDLFNFF CAILEIAPT 
KNNGSLANV EDIFVGTSG YSLTTILTI TAGGIVVSL 
ILISCAAVL TLMMIKRQQ SITTTAALN KRFPQTFQT 
SIEAQHLLE PEDA
    CDS sequence
    • >TC004410 RA
      atgatttta aaaatattt ttagaatgt ctcgtggca 
cacttggca tattccctc tcccagagc ccgattcta 
atcgttgtg tcgtatgac gccttcagg tatgacttt 
ttcgacaca aaatctgtg ccccatatg aacagattg 
cgaaaattg gggacctac tctgactat ttgattaac 
gtattcccg accaaaacg ttcccaaat caccattca 
atcgccacg ggcttgtac cccgacatc cacggggtg 
gtgggtaac agttacttc aataaatca acaaatagt 
gtggttcat attaattat gaaatgttc cactttgat 
gagaaagtt gtcccgatt tggcggcaa aacgaggat 
gcgggcaag gggaggcac tcgggggtt gtgatgtgg 
ccaggtggt tgctacccc tatcaaggg aaacaagtg 
acgtattgt aaagattac gaccacaat tttgattgg 
tttaagcgc gttgatttg gtgattggg tggatcaaa 
gacccgaaa aagccggct aatttaata atgctctat 
tttgatgag ccagacact gatggacac atttacggc 
attaactcg gatgtagtc aataagttg ataaataaa 
ttggacaat attacgctt tatttgcaa caacaactt 
gaaaaaaat aatttgacg ggtaaagtc acagtggtg 
catctaagt gaccatggg atgttagat gtgaaacca 
cctaatttt atcaacgtg acgcaatat ttaacacct 
ggcacgtac acatacgct ggatcaacg ccagttttg 
cagtttcat ccgaaaaaa ggatttgag actgaagtt 
tatcaaaag ctgaaaaat gcgtcctca caagatcat 
tttacagtt tataaaaaa gaggaattt ttaccacga 
tggcactac aaggacaat cctagaagc cccccgatt 
ttagtttta gcagaggtt ggatacgga ttagatgat 
ttaataatt tccgcaaaa caaaatgcg gaaaagaat 
cattacaaa ttaacaaat cagtcgacc tttggggtt 
cacggctac gactacact gtcaaagaa atgcgcccc 
tttttcatg gcaaggggc ccgaaaata aaagtcaat 
cacaaggtg ccccctttt aacactgtc gatttgttt 
aacttcttt tgtgcgatt ctggaaatt gcgccaact 
aaaaataac ggttcgctt gcaaatgtt gaagatatt 
tttgttgga acaagtggg tattcactg acgactatt 
ctcacaatc actgcggga ggtatagtc gtttcgttg 
attttgatt agttgcgcg gctgtttta acgttaatg 
atgatcaaa agacagcag agtattacc acaactgct 
gcgttaaat aagcgattt cctcagact tttcaaacg 
agtattgag gcacaacac ttgctagaa ccagaagat 
gcgtaa
    mRNA sequence
    • >TC004410 RA
      gctgacttg tgtcacaat tgtcaagtg tcatgtgtg 
gcccaaatt ctaaaaaac ttttggaat gattttaaa 
aatattttt agaatgtct cgtggcaca cttggcata 
ttccctctc ccagagccc gattctaat cgttgtgtc 
gtatgacgc cttcaggta tgacttttt cgacacaaa 
atctgtgcc ccatatgaa cagattgcg aaaattggg 
gacctactc tgactattt gattaacgt attcccgac 
caaaacgtt cccaaatca ccattcaat cgccacggg 
cttgtaccc cgacatcca cggggtggt gggtaacag 
ttacttcaa taaatcaac aaatagtgt ggttcatat 
taattatga aatgttcca ctttgatga gaaagttgt 
cccgatttg gcggcaaaa cgaggatgc gggcaaggg 
gaggcactc gggggttgt gatgtggcc aggtggttg 
ctaccccta tcaagggaa acaagtgac gtattgtaa 
agattacga ccacaattt tgattggtt taagcgcgt 
tgatttggt gattgggtg gatcaaaga cccgaaaaa 
gccggctaa tttaataat gctctattt tgatgagcc 
agacactga tggacacat ttacggcat taactcgga 
tgtagtcaa taagttgat aaataaatt ggacaatat 
tacgcttta tttgcaaca acaacttga aaaaaataa 
tttgacggg taaagtcac agtggtgca tctaagtga 
ccatgggat gttagatgt gaaaccacc taattttat 
caacgtgac gcaatattt aacacctgg cacgtacac 
atacgctgg atcaacgcc agttttgca gtttcatcc 
gaaaaaagg atttgagac tgaagttta tcaaaagct 
gaaaaatgc gtcctcaca agatcattt tacagttta 
taaaaaaga ggaattttt accacgatg gcactacaa 
ggacaatcc tagaagccc cccgatttt agttttagc 
agaggttgg atacggatt agatgattt aataatttc 
cgcaaaaca aaatgcgga aaagaatca ttacaaatt 
aacaaatca gtcgacctt tggggttca cggctacga 
ctacactgt caaagaaat gcgcccctt tttcatggc 
aaggggccc gaaaataaa agtcaatca caaggtgcc 
cccttttaa cactgtcga tttgtttaa cttcttttg 
tgcgattct ggaaattgc gccaactaa aaataacgg 
ttcgcttgc aaatgttga agatatttt tgttggaac 
aagtgggta ttcactgac gactattct cacaatcac 
tgcgggagg tatagtcgt ttcgttgat tttgattag 
ttgcgcggc tgttttaac gttaatgat gatcaaaag 
acagcagag tattaccac aactgctgc gttaaataa 
gcgatttcc tcagacttt tcaaacgag tattgaggc 
acaacactt gctagaacc agaagatgc gtaattgat 
ttgtgtagt aaatgacca aagattcct agttacgga 
ggactaaaa ctaagaggc gaaacgata aacaaaatc 
acttaattt tccctagat aaaaaagga tgttttaaa 
ttaattttt attcagacg gtcttaagt tcctaataa 
actactaaa attttcacg aaaaacggg aaaaaacac 
gtgggtaca agtgaaagt aagcaaaaa attttcaaa 
ggaatgtca gaagggact acactttta tcaactgta 
tttcagtta agagttatt tacaactac aattcattt 
tttctcaaa taatctgat actttctga accacaatt 
ggaaaaagt gtagtcttt tgttgactg caccctttc 
tttagtttc tatacaaag tttcacgaa ttactttga 
ataatttgc actccgtac taaaatttt taaagacac 
aaaaaagtg taagtttaa aattaaaat gtgctcatt 
tttactggg aagtttaac tttaaaccg ctgaagttc 
aattttcta gaactttgt accttataa tagttatct 
acttgtttg tttgatttg tttgccgtt tacctcgta 
atattttta gtcctcctt ggtcctatc taattttta 
taacccatt gtgatttac tgtgtgatg tgtcgaggc 
gggaccttg acagttttt cgtggtcat aatttaatt 
tactacagt ttaaaagaa ttgtatatt gtatgattt 
ataaaaata agataggat aggattcag tttatgctc 
aattaatta agtttttta accgcccat tagttttta 
aaaatcaaa atatttctt ttattgtat ttagcatta 
cttaataac tttaccgac ttaaaaatt tcaaaaaga 
ggttgaaca tttcaagga gaattaata taatcatta 
atcagagag tttttgtgg tcacaattt ttatttagt 
ttttaaaca ttagattgt tacgagtta ttagaatat 
tgttggttt ctagtcatt taataaaat gatatggaa 
gaaatgtta aaaagacat tattttaga cagaaaaat 
aatcaaaaa attgaggct ctttcttgg ttatttttc 
tcttatttt aatacataa cacattaaa ttaaattag 
tatgttgcg ttgattttg cggatgaat cattttttc 
gcttataaa aatgtaaat atctgtatt aaccaaaaa 
tcaagaaac aaataattc cattattag attattaca 
tctaataat atggggatg tatacaaga caatatttt 
ttggatcac ttcgtacat tatattaaa taaaaagga 
aagaataaa aatttaaaa ctagt

    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