Status
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Gene information
General information
TC007562 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: 2983954..2986172
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
    		TC007562
    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_01220

    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

    Fertility
    ovary without detectable defects - Number of animals showing the phenotype: 4
    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: < 50 embryo/egg with embryonic tissue, no cuticle, but muscle fluorescence - Penetrance (percentage of animals/eggs on slide): more than 80%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 80%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     cuticle remnants without visible segmentation but polarity - Penetrance (percentage of animals/eggs on slide): less than 30%

    cuticle remnants with some identifiable segments - Penetrance (percentage of animals/eggs on slide): less than 30%
    cuticle everted (inside-out) - Penetrance (percentage of animals/eggs on slide): less than 30%

    larva cuticle dorsaldecreased - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    larva appendages sometimesshape irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    Comment: Head appendages sometimes un-identifiable.
    head mostly decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    mandible not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    labrum not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    antenna not present - 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): more than 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: 85.71% (includes death as larva, prepupa, pupa, adult)

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


    Pupal morphology
    antenna shortened - Number of animals showing the phenotype: 8

    antenna distal broader - Number of animals showing the phenotype: 8
    maxillary palp size increased - Number of animals showing the phenotype: 8

    wings shape irregular - Number of animals showing the phenotype: 8

    legs orientation irregular - Number of animals showing the phenotype: 8

    Adult morphology
    flagellomeres number decreased - Number of animals showing the phenotype: 5


    flagellomeres partially fused - Number of animals showing the phenotype: 5

    prothoracic leg shortened - Number of animals showing the phenotype: 3


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC007562 RA
      MPNEARYAL LYSDYETST VLRLPFEKF SIITVGLPL 
FAFLFCIIY SVIFHFETA TYTHCQVFN VLPSISAAI 
GNFSPQRQV WQTAIVLHA VPRFSIAFV YLQHHQNVL 
YQNDQWMGA VACVLNVVE NISLIILSF WTSSQHYPV 
HEKAFITFI LMSEFYMIL IYILQRRCK KRHKESLKW 
KKRLLITNI SSILVATYC FLRHNSYCE PYVYSGFAL 
AEYTVVLTN MAFHMTAYL DFKNKDLVV YRYGVALTE 
R
    CDS sequence
    • >TC007562 RA
      atgcctaat gaagctcgg tatgcgtta ctatacagt 
gattacgaa acttccaca gttttgcgt ttgcctttt 
gaaaaattt tcgattata accgtgggt ttgccgttg 
tttgctttc ctgttttgc attatttat tcggtgatt 
tttcatttc gaaaccgcc acttacacc cattgtcaa 
gtgtttaat gttttaccg tccatttct gcggctatc 
ggaaatttt tcaccacaa cgacaagtc tggcaaacg 
gctatagtt ttacatgct gtgccaaga ttctcgatt 
gcctttgtt tacctccaa caccaccaa aacgtttta 
taccaaaat gaccaatgg atgggggcc gtcgcatgt 
gttcttaat gttgttgaa aacatttcg ttgattata 
ctgtctttt tggacctca tctcagcac tatcctgtt 
catgaaaaa gccttcatc acctttata ttgatgtcg 
gagttttat atgatttta atttacatt ctccaaaga 
cgttgtaaa aagcgccac aaagaaagt ctgaaatgg 
aagaaaaga ctactcatc acaaacata tcatctatt 
ttagtagca acgtattgc tttttaagg cacaactca 
tattgtgag ccttatgta tattctggt tttgccttg 
gcagaatat acagtagta ttaacaaat atggcgttc 
cacatgact gcttattta gattttaaa aataaagat 
ttggtggtc tataggtac ggtgttgct ttaacagaa 
agataa
    mRNA sequence
    • >TC007562 RA
      aatcaaaca gctgatcta acctaaaat gaattaagt 
taagtgagt ttttaaatc taatctagc gaagtgtgt 
ttcgaataa tgcctaatg aagctcggt atgcgttac 
tatacagtg attacgaaa cttccacag ttttgcgtt 
tgccttttg aaaaatttt cgattataa ccgtgggtt 
tgccgttgt ttgctttcc tgttttgca ttatttatt 
cggtgattt ttcatttcg aaaccgcca cttacaccc 
attgtcaag tgtttaatg ttttaccgt ccatttctg 
cggctatcg gaaattttt caccacaac gacaagtct 
ggcaaacgg ctatagttt tacatgctg tgccaagat 
tctcgattg cctttgttt acctccaac accaccaaa 
acgttttat accaaaatg accaatgga tgggggccg 
tcgcatgtg ttcttaatg ttgttgaaa acatttcgt 
tgattatac tgtcttttt ggacctcat ctcagcact 
atcctgttc atgaaaaag ccttcatca cctttatat 
tgatgtcgg agttttata tgattttaa tttacattc 
tccaaagac gttgtaaaa agcgccaca aagaaagtc 
tgaaatgga agaaaagac tactcatca caaacatat 
catctattt tagtagcaa cgtattgct ttttaaggc 
acaactcat attgtgagc cttatgtat attctggtt 
ttgccttgg cagaatata cagtagtat taacaaata 
tggcgttcc acatgactg cttatttag attttaaaa 
ataaagatt tggtggtct ataggtacg gtgttgctt 
taacagaaa gataatatt tagttgtat agctagtta 
tacaataaa tttttcgtt gtgtaggaa agtatcaaa 
tggacatac agattgtat atttgtaat tattgccca 
cacaccaaa acgatatgt attcgaaaa ttttacttt 
ctggatctt caaaacgta taactttcc caaaaatgg 
cacttacag attttagat tgtaaattg taagttcgt 
gatctacga gttgattaa atgaaatgt cttctacgt 
tttgaacgt ttttaactt gtaataaga taatatatt 
ctgcatgta cactgccta aaaatcaag tgcacacag 
tttatttca acagccaag tggtggctg gctgtgcac 
ttgatttag attacaagc tgaagatat ttttgacga 
aatgtaagg tcgtaatat cttcgaatt gttccagta 
atgtagcta ttcctgcat ttcaagtaa tgagtgtgg 
tttaaatgt tactctttt gtccattgt atctacttt 
ttgatgtta caatgaaga gcacatttt atacttcgg 
gcacagtag agatttact acttaattc acaagggtt 
gcagtttaa tgttgtcgc gaaaaaacg accaaattt 
tttcgtttc gaacttttt caaattttt agtgacaaa 
aagacgtct aaaaataga atgttttag gcacttggt 
atgaaagta cttatctgt gtgaatgta atcttgtaa 
tataaacgt gctcagttg tgatatgta tttttgaga 
agcgaaaga tttattata aatagacga aattggtat 
tgaaaacat atcttgtat ttttcaaat aattattat 
gattgaaaa aaaaatcgg gacggaaaa cacgaaacg 
gtgttaata tttttagta attatgcga tggacgcat 
ttagtgtca aattttgaa gaacaaaaa aattgatgt 
cttcaccac ccaactttg ttttaagac gatgtgata 
tgagtttgt gcttccgaa ggagcaatt tttttaatg 
tcggtacat gtttatatc agtatatga ataattgtg 
ataaaaaat tggttattt atgcatttc atttaagtt 
ttacggatg gtaatggtt gtaaacaat gatataact 
taaggaaat gtctcatta ttgtgcagt atttttgtc 
ttaaaaaac tgttttttt ttcaaatgt ttattattt 
cacatttaa gtgatgtgt tactgttaa tacgttgtt 
aaactcgac tctttctaa ttgtactat tcttgtacg 
tagctacct tttattaaa aaagttatt cttca

    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