Status
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Gene information
General information
TC008417 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_007419.2: 10007151..10030270
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
    		TC008417
    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_04483

    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: 40.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 3 (3 dpi)
    Days post injection

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

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 abdomen musculature partially randomnot present - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    abdomen musculature partially rounded - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    thorax musculature irregular - Penetrance (percentage of animals/eggs on slide): more than 80%

    Comment: because nearly all embryos are lying lateral, it is not possible to say what exactly is wrong with the thoracic muscles, only that there is soething wrong. leg muscles seem to be not affected (at least they are not rounded or missing)
    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
    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: 30.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 100.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 3 (11 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 7 (19 dpi)
    Days post injection

    Adult morphology
    elytra not closed - Number of animals showing the phenotype: 6


    elytra surface irregular - Number of animals showing the phenotype: 6


    elytra colour irregular - Number of animals showing the phenotype: 3


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC008417 RA
      MWIADLRIV LGFCICTAL AYQGSKQDY IKWRERFLP 
KRPTTTESA VTSANDIHY ENLKLRHHS RFPNLDRVL 
VKIDNLQKK NDVQPVHNR IRHQNVYKT TTTTTTTTD 
EGLFGDDYS DPEYEDDNN DELNDYDEW DDENFDDYD 
DETFDSDDP FADEWQNEE ATEPPAPVS SFTKYKWDN 
YGTRSRVEE SRRQQLHLK PHNEGRAIN AALEHYAKV 
RQEGQCRKP LPKVISVQS EHPDPSKTY TPHCTILHR 
CADDTGCCA NHTTRCGPK TQVLVHLYF YAKTLGVPG 
TKVEKLTFY NHTECACIE KSKGPTTLP DENINLTHG 
LSLKQGSEP ENMRNCKCP EEFTPKFRY DSRCSCDCE 
EYNQDCIRM KKGKEYFSL TDRRCIIEN QCGIPVCEY 
GVYMRHMGR CQRKQEKFD SFSKMTVK
    CDS sequence
    • >TC008417 RA
      atgtggatc gccgatttg agaatagtg ctgggcttc 
tgcatctgt acggctttg gcctaccaa ggatccaag 
caggattac atcaaatgg cgggagcgg ttccttccg 
aagaggccg acgacgacg gagagtgca gtgactagt 
gcaaacgat atccactac gaaaatctg aaattgagg 
caccattcg cgcttcccg aatttggac agagttctg 
gtcaagata gacaatttg cagaagaag aacgacgtg 
cagccggtt cataatagg attaggcac cagaacgtg 
tacaagacc accaccacg accaccacc acgactgac 
gaaggcctt ttcggcgac gattattcc gatccggag 
tacgaagat gacaacaac gatgagctc aatgactac 
gacgagtgg gacgacgag aatttcgat gattacgac 
gacgaaacc ttcgacagt gacgaccct ttcgccgac 
gaatggcaa aacgaagaa gccaccgag cccccagct 
cctgtctct tctttcacc aaatacaag tgggacaat 
tacggcact cgctcaagg gttgaagaa agcagacgg 
cagcagctt catctcaag ccccataac gaaggaaga 
gcaataaac gccgcattg gagcactac gcgaaggtc 
cgccaagaa ggccaatgt cgcaaacca ttaccaaaa 
gtgatctca gtccaaagc gaacatccc gatcctagc 
aaaacctac actcctcat tgcaccatc ctgcatcgt 
tgcgccgat gacacagga tgttgcgct aaccacacc 
accagatgt gggcccaaa acccaagtc ctcgttcac 
ctttacttt tacgcgaaa accttaggc gtgcccgga 
accaaagta gaaaagttg actttttac aatcacacg 
gaatgtgct tgtatcgaa aaatcgaaa gggccgaca 
acactaccc gatgaaaat attaacttg actcacgga 
ctatccctc aagcagggc tccgaaccg gaaaacatg 
cgaaactgc aaatgcccg gaggagttc accccgaaa 
ttccggtac gattccaga tgcagttgc gattgcgag 
gagtataat caggactgc atcaggatg aagaagggg 
aaggagtac ttcagtctc actgacaga aggtgcatc 
atcgagaac caatgcgga attccggtt tgcgagtat 
ggggtttac atgcgccat atgggtcgt tgccaacga 
aaacaggag aaattcgat agttttagc aaaatgacc 
gtgaaatga
    mRNA sequence
    • >TC008417 RA
      taatgataa taaaacgaa atgacctga ggtgcttat 
tttacaaga agcgtattc caggaacag tgtccgccg 
acttttagt gcaaattgg gtaaattgc aagcgcaca 
taatcgtaa aatattgtc caaagtctc gataagagc 
gacgtttaa taaattcgc gtatttaat ggccccggt 
gcaaatccg tcccgattt tatgggacc ggataataa 
caccgcaat gccgtggtg gtaaaaatc cttcgacaa 
attacaatg cttccatac gtgtttatg cttcctcct 
gaaatacga gatcagaca gttcgggag atgaatgga 
ccacaatga atgcgcttt aacaaataa agagacacc 
acaggctca gtcgatccg ttggcgcga cttcgaaag 
cactacgcg tacgggaat ctcgcacaa acacgcgat 
tatttttta aaatgcaga aaatgcaac ggttgtgtg 
agtgtgtat ccggtctga ctcgaaatt aagcaattt 
tcgccggaa aaatggcat gaatttgtc gtaaatcgt 
cggcgcgtc ctttccaaa ctaacgata atgtgtaag 
aaataaaca caaaatgtg gatcgccga tttgagaat 
agtgctggg cttctgcat ctgtacggc tttggccta 
ccaaggatc caagcagga ttacatcaa atggcggga 
gcggttcct tccgaagag gccgacgac gacggagag 
tgcagtgac tagtgcaaa cgatatcca ctacgaaaa 
tctgaaatt gaggcacca ttcgcgctt cccgaattt 
ggacagagt tctggtcaa gatagacaa tttgcagaa 
gaagaacga cgtgcagcc ggttcataa taggattag 
gcaccagaa cgtgtacaa gaccaccac cacgaccac 
caccacgac tgacgaagg ccttttcgg cgacgatta 
ttccgatcc ggagtacga agatgacaa caacgatga 
gctcaatga ctacgacga gtgggacga cgagaattt 
cgatgatta cgacgacga aaccttcga cagtgacga 
ccctttcgc cgacgaatg gcaaaacga agaagccac 
cgagccccc agctcctgt ctcttcttt caccaaata 
caagtggga caattacgg cactcgctc aagggttga 
agaaagcag acggcagca gcttcatct caagcccca 
taacgaagg aagagcaat aaacgccgc attggagca 
ctacgcgaa ggtccgcca agaaggcca atgtcgcaa 
accattacc aaaagtgat ctcagtcca aagcgaaca 
tcccgatcc tagcaaaac ctacactcc tcattgcac 
catcctgca tcgttgcgc cgatgacac aggatgttg 
cgctaacca caccaccag atgtgggcc caaaaccca 
agtcctcgt tcaccttta cttttacgc gaaaacctt 
aggcgtgcc cggaaccaa agtagaaaa gttgacttt 
ttacaatca cacggaatg tgcttgtat cgaaaaatc 
gaaagggcc gacaacact acccgatga aaatattaa 
cttgactca cggactatc cctcaagca gggctccga 
accggaaaa catgcgaaa ctgcaaatg cccggagga 
gttcacccc gaaattccg gtacgattc cagatgcag 
ttgcgattg cgaggagta taatcagga ctgcatcag 
gatgaagaa ggggaagga gtacttcag tctcactga 
cagaaggtg catcatcga gaaccaatg cggaattcc 
ggtttgcga gtatggggt ttacatgcg ccatatggg 
tcgttgcca acgaaaaca ggagaaatt cgatagttt 
tagcaaaat gaccgtgaa atgaatcgt attattaaa 
tttagtgta attaaagca attttgcca gtgatatat 
tagtgaatt tatttgacg gtgacttta atttgtgtg 
aaatgtggg tttccgcaa ttcggagcg cactgaatt 
ggcggaaat ttacaagaa ttcgtgtac ggtgcatgt 
gtttattgt ataagtgtc tttttttta ttgtacccg 
aaacctagt ctttaggtc aaattaggt gctgtattt 
aaaagcttc gatgattaa tataactgt ctcaaggaa

    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