Status
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Gene information
General information
TC009608 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_007422.5: 3224156..3228409
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
    		TC009608
    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_02837

    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 (died as pupa) - Number of animals showing the phenotype: 1 (3 dpi)
    Days post injection

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 2 (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 larval musculature pattern irregular - 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): less than 30%
    remarks: muscle pattern potentially obscured by segmentation defect,
    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: 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

    eclosion delayed (still pupa) - Number of animals showing the phenotype: 1 (16 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC009608 RA
      MSDESHPKT LYVGNLDPS VSEDLLCTL FSQIGPVKG 
CKIIREPGN DPYAFVEFT NHQSASTAL AAMNKRLFL 
DKEMKVNWA TSPGNQPKQ DTSNHHHIF VGDLSPEIE 
TETLREAFA PFGEISNCR IVRDPQTLK SKGYAFVSF 
VKKAEAENA IQAMNGQWL GSRSIRTNW STRKPPPPK 
TEKAAQRAK QPTFDEVYN QSSPTNCTV YCGGFTTGL 
TEDLMQKTF SQFGVIQDI RVFKDKGYA FIKFATKES 
ATHAIETIH NTEINGQMV KCFWGKENG GMGADPGAA 
MTSGGAAVA PGAQAQPYS YGYGGYWYQ GYGGYPYPY 
QQYQYQQQY CMMPQQGQW ASAQPGGGQ QPNVPVMYK 
YPSQ
    CDS sequence
    • >TC009608 RA
      atgtcggac gagagccat ccaaaaact ttgtatgtg 
ggcaatctg gacccctcc gtcagcgag gacctgctc 
tgcaccctc ttctcccag atcggcccc gtcaagggg 
tgcaagatc atccgcgag cccggcaac gacccctac 
gccttcgtc gagttcacc aaccaccag tcggcctcc 
acggcgctg gcggcgatg aacaagcgc ctcttcctc 
gacaaggag atgaaggtg aactgggcc acctcgccg 
gggaatcag cccaagcag gacacctcc aaccaccac 
cacatcttc gttggtgac ctgtcgccg gagatcgag 
actgaaacc ctacgagag gccttcgct cccttcggg 
gagatctcc aactgccgc atcgtgcgc gacccccaa 
acgctcaaa agcaagggg tatgcgttc gtgtcgttt 
gtcaagaaa gcggaggct gagaacgcg attcaggcg 
atgaatggg caatggttg gggtccagg tccatcagg 
accaactgg tccacgagg aagccgccg ccgccgaag 
acggagaag gcggcgcaa cgcgccaaa cagcccact 
tttgacgag gtttacaac cagagttcc ccgaccaat 
tgcacggtg tactgcggc ggcttcacc accggcctc 
accgaagac ctcatgcag aagaccttc tctcagttc 
ggcgtcatc caggacatc cgagtgttc aaggacaaa 
ggctacgcc ttcatcaaa ttcgcgacc aaagaatca 
gcaacgcac gccatcgaa acaatccac aacaccgaa 
atcaacggt caaatggtc aagtgtttc tggggcaag 
gagaacggg ggcatgggc gcggacccg ggcgccgcc 
atgacgtcg ggcggggcg gcggtggcg ccgggggcg 
caggcccag ccctactcg tacggctac gggggctac 
tggtaccag ggctacggg ggctatccc tacccctac 
cagcagtac cagtaccag cagcagtac tgcatgatg 
ccccagcag ggccagtgg gcctccgcc cagccgggg 
ggcggccag cagcccaac gtgccggtg atgtacaag 
tacccgtca cagtga
    mRNA sequence
    • >TC009608 RA
      acaaaaaaa attcattaa acagtttat taaaaaact 
gatcctggt gtttcaaat tgcgcgtag taattttct 
gcaccattt gaagatcga aacgagata aattggcgt 
ggttttgcg gccgattga ccgtccgcg ctctatgta 
agtgcttca gtggtgtgg gatttgggg acatttgct 
tcttggccg ttttcgaat gacagctgt aagtgtctg 
tagaaaagt tggccatca gtttttgtc ccttgttcg 
caatcgttt cggtcgcga agccccctt atgttgtgt 
tcgagggcg tagcctccc agccccgct gtatgtgca 
atcggcttg tgtagtgtg gagtagtgc cgcccccag 
cccgtgccg gcgtcacca tgtcggacg agagccatc 
caaaaactt tgtatgtgg gcaatctgg acccctccg 
tcagcgagg acctgctct gcaccctct tctcccaga 
tcggccccg tcaaggggt gcaagatca tccgcgagc 
ccggcaacg acccctacg ccttcgtcg agttcacca 
accaccagt cggcctcca cggcgctgg cggcgatga 
acaagcgcc tcttcctcg acaaggaga tgaaggtga 
actgggcca cctcgccgg ggaatcagc ccaagcagg 
acacctcca accaccacc acatcttcg ttggtgacc 
tgtcgccgg agatcgaga ctgaaaccc tacgagagg 
ccttcgctc ccttcgggg agatctcca actgccgca 
tcgtgcgcg acccccaaa cgctcaaaa gcaaggggt 
atgcgttcg tgtcgtttg tcaagaaag cggaggctg 
agaacgcga ttcaggcga tgaatgggc aatggttgg 
ggtccaggt ccatcagga ccaactggt ccacgagga 
agccgccgc cgccgaaga cggagaagg cggcgcaac 
gcgccaaac agcccactt ttgacgagg tttacaacc 
agagttccc cgaccaatt gcacggtgt actgcggcg 
gcttcacca ccggcctca ccgaagacc tcatgcaga 
agaccttct ctcagttcg gcgtcatcc aggacatcc 
gagtgttca aggacaaag gctacgcct tcatcaaat 
tcgcgacca aagaatcag caacgcacg ccatcgaaa 
caatccaca acaccgaaa tcaacggtc aaatggtca 
agtgtttct ggggcaagg agaacgggg gcatgggcg 
cggacccgg gcgccgcca tgacgtcgg gcggggcgg 
cggtggcgc cgggggcgc aggcccagc cctactcgt 
acggctacg ggggctact ggtaccagg gctacgggg 
gctatccct acccctacc agcagtacc agtaccagc 
agcagtact gcatgatgc cccagcagg gccagtggg 
cctccgccc agccggggg gcggccagc agcccaacg 
tgccggtga tgtacaagt acccgtcac agtgatgag 
gacgaaacc gtggcggtc tgacgtgca gtgacttgg 
ttttagtta agagactcg gtgattaca tatttggat 
atgtagttg tcatcagcg cactttggt tggttcttc 
agacgtggg tgtcgcgcc gctcataga attattttt 
tcatactac atatttttg tatagttgc gtttcgatg 
cgttttgtc tcttttgta tatagtagt tgatgtcaa 
agtgcgatt ggtgcgctc gctcgctcg ctcgctctt 
aaactgatc atatgcgtg atacaattt agttgtctt 
ttttgtggc aaggagtga ctgggactg gacttcggc 
ggtcgtgac aattaaaac agttactgt agatgatta 
tgtataatt aggttagac aaacacatt gtaatcatt 
aatatatca cgtttatct gagtaaatg attttatga 
tgatacgca tgattggtc tttccaact gaataagac 
agattttat aacaaaaaa ataattatg tatatgcta 
gttgttaat aaaaacttc aggtctgg

    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