Status
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Gene information
General information
TC009964 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: 11281609..11283313
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
    		TC009964
    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_04733

    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: 20.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 2 (3 dpi)
    Days post injection

    adult nutritional state potentially bad (cachectic) - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection

    Fertility
    mature egg deposition blocked number 1st lateral oviduct: 4 number 2nd lateral oviduct: 2 - Number of animals showing the phenotype: 2
    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: 0.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 0.0% (includes death as larva, prepupa, pupa, adult)

    Fertility
    egg production: number no/almost no eggs -
    ovary without detectable defects - Number of animals showing the phenotype: 4
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC009964 RA
      MDITGSLTT QNIQGTELA SILKELDVE YTLRLPELS 
IRDILQLLN VYMSVAQNQ ITEYKFYNK ALNALNDSL 
PTLDKKELL QFIFYLGVR KKCLESQTM LRQCQKTMT 
NEFIDSLTS EELCIICIS TFKTSTKII NKALLEKVK 
KYIDGNLSV LHDFPLFVT LVKTLRHNR CQDDNLLNT 
ISYTIIFNK TYPLYTFPT ICHIMALFA DYFYYDKNL 
FKIITQQGL EQLNDCKFV SRNVYLAHQ LRAKDIKRF 
LWVLSMFSD LKLVNRSVL KTLFIPKII ERIDGGEIN 
RDVASLVDI TLYLWMLNC HPHELVPYV FTKENVQVL 
RRDSKNHLR LNLLLYAIL IEDPALAKT LPIKPSMVR 
ENDYSSVFQ LRKRPLFER LLKNLDKIK KDLNISKFE 
LSYEIPHIN IVGITGYRS GGTKAVYIE VLDGYTQIR 
NVEFDVPVG LMALKLRLL DQFEEGVLV VSQRETDDM 
TDSELINFL LDEIKLIC
    CDS sequence
    • >TC009964 RA
      atggatatt acgggcagc ttaacgact cagaatatc 
caaggaact gagctcgct tcaatactg aaagaactc 
gatgtcgaa tatacctta agactgcca gagttatca 
attagagat attttacag ttgctaaac gtgtacatg 
tctgtggcc caaaatcaa atcaccgaa tacaagttt 
tacaataaa gcattgaac gccttaaat gattcactt 
cctacttta gataagaaa gagttgcta cagttcatt 
ttctacttg ggtgttagg aagaaatgt ctcgagtcg 
caaacaatg ctgcgccag tgccagaaa actatgacc 
aacgaattt atcgatagt ctaacaagc gaggaatta 
tgcatcatt tgcatctca acattcaaa actagcact 
aaaatcatc aacaaagca ctactcgag aaagtgaag 
aaatacatt gatggcaac ttatctgtg ttacacgac 
tttccatta tttgtaact ttagttaaa actttgcgg 
cataatcgc tgccaagac gataatttg ctcaacacg 
atttcctac accattatt tttaataaa acatatccc 
ttgtacacc ttcccaacg atatgccac attatggcc 
ctctttgcc gattatttc tactacgac aaaaatttg 
tttaaaata atcacgcag cagggtttg gagcagctc 
aatgattgt aaatttgtc tcgagaaat gtttactta 
gcgcaccaa ttgcgggct aaggatatt aagcgcttc 
ctgtgggtg ctgagcatg tttagtgat ttgaaactc 
gtaaatcgg agcgttttg aaaactctg tttattccg 
aaaattatc gaacgaatc gatggggga gaaataaac 
agggatgtc gcctctttg gtcgacatc acgctgtat 
ttgtggatg ctcaactgc catccgcat gaactagtg 
ccttatgta ttcactaaa gaaaatgtc caggtgttg 
cgaagggat tccaaaaat catttaaga ctgaattta 
ttattgtat gcaatttta atcgaggat cctgcgtta 
gctaagacg ttaccgatc aagccgtca atggtacga 
gaaaatgat tattcgagt gtttttcaa ttacgcaaa 
agaccgttg tttgaaagg ctgttgaaa aacttggat 
aagattaaa aaggatcta aacatcagt aaattcgaa 
ttgtcgtat gaaattcca cacattaat attgtgggg 
atcacggga tacaggagt ggaggaacc aaggctgtg 
tatatcgaa gttttagat gggtacact caaataaga 
aacgtcgaa tttgatgtt cctgtaggt ttaatggcc 
ctgaagcta agactgttg gaccagttt gaggagggt 
gttttagtg gtttcgcag agagaaacg gacgacatg 
acggattcc gaattaata aatttttta ttggatgag 
attaaattg atctgttga
    mRNA sequence
    • >TC009964 RA
      cttttatta tatttaaat attgataaa gaacaaagt 
acaaatccg ataattcct gcaacaaaa accttcaaa 
aacatacgt cagaatgta aatcatttg tacaagtta 
agcacgcaa gaaatcatg gatattacg ggcagctta 
acgactcag aatatccaa ggaactgag ctcgcttca 
atactgaaa gaactcgat gtcgaatat accttaaga 
ctgccagag ttatcaatt agagatatt ttacagttg 
ctaaacgtg tacatgtct gtggcccaa aatcaaatc 
accgaatac aagttttac aataaagca ttgaacgcc 
ttaaatgat tcacttcct actttagat aagaaagag 
ttgctacag ttcattttc tacttgggt gttaggaag 
aaatgtctc gagtcgcaa acaatgctg cgccagtgc 
cagaaaact atgaccaac gaatttatc gatagtcta 
acaagcgag gaattatgc atcatttgc atctcaaca 
ttcaaaact agcactaaa atcatcaac aaagcacta 
ctcgagaaa gtgaagaaa tacattgat ggcaactta 
tctgtgtta cacgacttt ccattattt gtaacttta 
gttaaaact ttgcggcat aatcgctgc caagacgat 
aatttgctc aacacgatt tcctacacc attattttt 
aataaaaca tatcccttg tacaccttc ccaacgata 
tgccacatt atggccctc tttgccgat tatttctac 
tacgacaaa aatttgttt aaaataatc acgcagcag 
ggtttggag cagctcaat gattgtaaa tttgtctcg 
agaaatgtt tacttagcg caccaattg cgggctaag 
gatattaag cgcttcctg tgggtgctg agcatgttt 
agtgatttg aaactcgta aatcggagc gttttgaaa 
actctgttt attccgaaa attatcgaa cgaatcgat 
gggggagaa ataaacagg gatgtcgcc tctttggtc 
gacatcacg ctgtatttg tggatgctc aactgccat 
ccgcatgaa ctagtgcct tatgtattc actaaagaa 
aatgtccag gtgttgcga agggattcc aaaaatcat 
ttaagactg aatttatta ttgtatgca attttaatc 
gaggatcct gcgttagct aagacgtta ccgatcaag 
ccgtcaatg gtacgagaa aatgattat tcgagtgtt 
tttcaatta cgcaaaaga ccgttgttt gaaaggctg 
ttgaaaaac ttggataag attaaaaag gatctaaac 
atcagtaaa ttcgaattg tcgtatgaa attccacac 
attaatatt gtggggatc acgggatac aggagtgga 
ggaaccaag gctgtgtat atcgaagtt ttagatggg 
tacactcaa ataagaaac gtcgaattt gatgttcct 
gtaggttta atggccctg aagctaaga ctgttggac 
cagtttgag gagggtgtt ttagtggtt tcgcagaga 
gaaacggac gacatgacg gattccgaa ttaataaat 
tttttattg gatgagatt aaattgatc tgttgacgt 
ttagttaac aatttatt

    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