Status
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Gene information
General information
TC006555 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: 11387919..11391143
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
    		TC006555
    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_01062

    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)

    pupa 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: 1 (3 dpi)
    Days post injection

    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): less than 30%
    larva cuticle thinner - Penetrance (percentage of animals/eggs on slide): less than 30%

    abdomen segment partially 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): 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: 30.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality early (L5/6) - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (16 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC006555 RA
      MGKTGLLVL LVIWARVGA ENGKQLNVL LILADDGGF 
EMGAYRNKI CQTPNLDAL AKNSLIFNN AYTSVSSCS 
PSRSALLTG MPAHQNGMY GLHQAENHF DSFTNVKSL 
PNILRENGI RTGIIGKKH VGPKSTYRF DYEQTEENN 
SILQVGRNI TLIKLLARE FLNNSTDKP FFLYVAFHD 
PHRCGHTHP EYGQFCQRF GNGDVGMGL IPDWRPIYY 
QWDELELPY YIPDTEAAR REVANQYTT ISRLDQGVG 
LILEELEKS GHADDTLVI YSSDNGTPF PNGRTNLYD 
SGIAEPMFI SSPLHKERH NQVTYSLTS LLDIVPTVL 
DWFNITEES NEINSKKLT GKSLLPLLV KEPENTTNE 
AIFASHNLH EVTMYYPMR MIRTHRYKL IHNLNYQAP 
FPIDQDFYL SPTFQDILN RTRNKENLY WFKTLRQYY 
NRPEWELYD LKHDPVELN NLAGKSDYK DIMQELEKR 
LSEWQNATS DPWICSPHS VLENKGDYA HNPQCMPLY 
NT
    CDS sequence
    • >TC006555 RA
      atggggaaa accggtttg cttgttcta ctagtgatt 
tgggcacga gttggggct gaaaatggc aaacaatta 
aatgtgctg ctgattttg gccgacgat ggcggcttc 
gaaatgggg gcttacagg aacaaaatc tgtcaaacg 
cccaatttg gacgccttg gccaaaaac agcctaatt 
ttcaataat gcctacacc tcggtcagt agttgttcg 
cccagccgt tcggcccta cttaccggc atgccggcc 
catcagaat ggcatgtac ggcctccac caggccgaa 
aaccacttc gattccttc acgaacgtg aaaagtttg 
ccgaacatt ttgcgcgaa aacggcatt cgcaccgga 
attatcggt aaaaaacac gtgggcccc aaaagtacg 
tatcgtttc gactacgag cagactgag gagaataat 
tcaatcctg caagtcggg cgcaatatc actttgatt 
aaattgctg gccagagag ttcctcaac aattccacg 
gacaagcca tttttcctc tatgttgcg ttccatgac 
ccccatcgt tgcggccac acgcacccg gaatacggc 
cagttctgc caacggttc ggcaacggg gacgtgggc 
atgggtctg atcccggac tggcgccca atttattac 
caatgggac gaacttgag ctaccttat tatattccc 
gatacggag gcggcgagg cgtgaagtg gccaatcaa 
tacacgaca atctcgaga ttggatcaa ggcgttggt 
ttaattttg gaagaattg gaaaaatca ggtcacgct 
gatgatact cttgtgatt tacagttcg gataatggg 
accccattt ccgaacgga cgcacgaat ttatacgat 
tcggggatt gccgaaccc atgtttatt tcctcgcct 
ttgcacaag gaaaggcac aatcaggtc acctactcc 
ttgaccagc ctcctagat attgtacca actgtcctt 
gattggttc aatatcaca gaggagagc aacgaaatc 
aatagtaaa aaactgacc gggaaaagc ttattgcca 
cttctagtt aaagagccg gaaaataca acaaacgag 
gcgattttc gcgagtcat aatctccat gaagtaacg 
atgtattac ccaatgagg atgatcaga acccaccgc 
tataaattg attcataat ttgaattac caagcgccg 
ttcccgatc gatcaggac ttttactta tcgccaaca 
ttccaagat attttgaac cgcaccaga aacaaggaa 
aatctgtac tggtttaag accctgaga cagtactac 
aaccggccc gagtgggaa ctgtacgac ttgaaacac 
gaccccgtg gaactaaac aatctggct ggaaagagc 
gactacaaa gacatcatg caggagctg gagaaacga 
ctttccgag tggcaaaac gccacaagt gacccgtgg 
atttgctcc ccacattca gtcttggaa aataagggt 
gactatgca cacaacccc caatgcatg cccctgtac 
aacacgtaa
    mRNA sequence
    • >TC006555 RA
      cccgaattt atactgcac gagcccatt ttccgggaa 
gacgtagtc gaatctgaa aatgacgtc ctcgccgtt 
catttgctc ggcgatttt cttgaaatc ggagccccc 
gaccaggcc gagggtgca caagggctt gattttcgt 
ttggatgaa ctcgtcgaa ttcggggtc gattgcttg 
gcggggttt tgtgagggt gccgtccat gtcgaataa 
acacaaaat tttctttgg tggcatgtt tgaatttgg 
ctccgttgt gtgaaaaga tggggaaaa ccggtttgc 
ttgttctac tagtgattt gggcacgag ttggggctg 
aaaatggca aacaattaa atgtgctgc tgattttgg 
ccgacgatg gcggcttcg aaatggggg cttacagga 
acaaaatct gtcaaacgc ccaatttgg acgccttgg 
ccaaaaaca gcctaattt tcaataatg cctacacct 
cggtcagta gttgttcgc ccagccgtt cggccctac 
ttaccggca tgccggccc atcagaatg gcatgtacg 
gcctccacc aggccgaaa accacttcg attccttca 
cgaacgtga aaagtttgc cgaacattt tgcgcgaaa 
acggcattc gcaccggaa ttatcggta aaaaacacg 
tgggcccca aaagtacgt atcgtttcg actacgagc 
agactgagg agaataatt caatcctgc aagtcgggc 
gcaatatca ctttgatta aattgctgg ccagagagt 
tcctcaaca attccacgg acaagccat ttttcctct 
atgttgcgt tccatgacc cccatcgtt gcggccaca 
cgcacccgg aatacggcc agttctgcc aacggttcg 
gcaacgggg acgtgggca tgggtctga tcccggact 
ggcgcccaa tttattacc aatgggacg aacttgagc 
taccttatt atattcccg atacggagg cggcgaggc 
gtgaagtgg ccaatcaat acacgacaa tctcgagat 
tggatcaag gcgttggtt taattttgg aagaattgg 
aaaaatcag gtcacgctg atgatactc ttgtgattt 
acagttcgg ataatggga ccccatttc cgaacggac 
gcacgaatt tatacgatt cggggattg ccgaaccca 
tgtttattt cctcgcctt tgcacaagg aaaggcaca 
atcaggtca cctactcct tgaccagcc tcctagata 
ttgtaccaa ctgtccttg attggttca atatcacag 
aggagagca acgaaatca atagtaaaa aactgaccg 
ggaaaagct tattgccac ttctagtta aagagccgg 
aaaatacaa caaacgagg cgattttcg cgagtcata 
atctccatg aagtaacga tgtattacc caatgagga 
tgatcagaa cccaccgct ataaattga ttcataatt 
tgaattacc aagcgccgt tcccgatcg atcaggact 
tttacttat cgccaacat tccaagata ttttgaacc 
gcaccagaa acaaggaaa atctgtact ggtttaaga 
ccctgagac agtactaca accggcccg agtgggaac 
tgtacgact tgaaacacg accccgtgg aactaaaca 
atctggctg gaaagagcg actacaaag acatcatgc 
aggagctgg agaaacgac tttccgagt ggcaaaacg 
ccacaagtg acccgtgga tttgctccc cacattcag 
tcttggaaa ataagggtg actatgcac acaaccccc 
aatgcatgc ccctgtaca acacgtaaa cacaaaaat 
atatttatt gtcacatat tctaaacaa atgcgtata 
taaaacatc tacgtttgc atatggcga cttattccc 
taattaact aatcacacg caacatttt aataaatta 
gtcaacaac ggctagact tctccagtg ataacacaa 
attaaaaac aaaagcgat aagtgtgaa ttgaccaag 
cgcttgcgt tagaatatt ttacggaaa ttaccatca 
cctcgtttt aattttttt taatctgcc cctaagcgt 
cctccgttt cacagtctt ttccaactt gctaactag 
aaccgaagt ggtgttcgc gaccgcttc gacactgtg 
catagtttc tgcgatttc agtcatctg caaaattgg 
gtttaattg cgtccaagg ccgctgatt gactcactc 
tctcgtgga tctcttgta tccgtaaat gcttctggt 
ggttgttat acaatacct taaattgta acataaaac 
ccgcggaca aaatcaaca cacaaaata tcagcaaat 
tatttgact gccggaaat gccacatca ctgttgtaa 
ttcatttta gcagtgttt gagctgcaa tcaagcaat 
tagcactga catcaacac aaacacctt acttaacaa 
gggatttaa ttacatcaa gagaatttg taaaca

    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