Status
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Gene information
General information
TC002539 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_007418.3: 24032922..24038133
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
    		TC002539
    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_03397

    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: 0.0% (includes death as pupa, adult)

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg with embryonic tissue, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    larval musculature 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): more than 80%
    remarks: muscle pattern potentially obscured by segmentation defect,
    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): more than 80%

    cuticle remnants strongly fragmented (cuticle crumbs) - Penetrance (percentage of animals/eggs on slide): less than 30%

    head capsule partially not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    head appendages random not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    head bristle irregular - Penetrance (percentage of animals/eggs on slide): less than 30%
    head not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    legs segment shortened - Penetrance (percentage of animals/eggs on slide): less than 30%
    legs segment potentiallyfused - Penetrance (percentage of animals/eggs on slide): less than 30%
    thorax not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen segment number decreased - Penetrance (percentage of animals/eggs on slide): less than 30%

    abdomen 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): 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: 0.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 0.0% (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC002539 RA
      MLFYFDQLD GEVQELRQV NETQKGKLQ SLEEQEKKW 
RQENNDLNT QLTKTREDY SELQKRTEA LQENLESLE 
KEKKLWKSE KENILSENT KLTHELSVT RTDYANLKL 
EHESLEKQC TENIERLQQ IQQILQKTE TQVKELQQK 
IEDLETNNW HLKHDLEDQ YDLRRQLHN TIQDLKGNI 
RVFCRVRPP INNELDDKE LCAISFPNE TSLDIRKSR 
ESVCAISGR VGDVKQEFS FDKVFSPEA SQVEIFEEL 
AQLVQSALD GYHVCVFAY GQTGSGKTH TMQGTPNDR 
GMIPRTIDL IFEKIEKLK ITEWSYTVT ASFLEIYNE 
NIRDLLEPN SNYDYELRY NEGRGVTVT NLKSVPIDS 
ARMLKALME EANNNRAVA TTDFNKHSS RSHAVTKIH 
LEGHNNLSR ASYSGSINL VDLAGSESA KTSAAERLN 
ETKHINKSL STLGNVMLA LHNKDSHVP YRNSKLTFL 
LQSCLGGNS KTLMIVNIA PFEDCFGES ISSLRFAAK 
VKEIKTCAK KNKTYGHQA LLPSNGSQK K
    CDS sequence
    • >TC002539 RA
      atgcttttt tattttgat caactggac ggtgaggta 
caggaacta cgacaagtg aacgaaaca cagaagggc 
aaattacaa agtttagaa gagcaggag aagaagtgg 
agacaagaa aacaatgat ttaaacact caattaacg 
aaaacaaga gaagattac agcgagttg caaaaacga 
accgaagct ttacaagaa aatttagaa tcacttgag 
aaggaaaaa aagctttgg aaatccgaa aaagaaaat 
attctgtcg gaaaatacc aaattaaca cacgaatta 
agtgtaacg agaacggat tacgctaac ttgaaactt 
gaacacgag tctttggaa aaacaatgt actgagaat 
atagagcgt cttcaacag atacaacag atcctccaa 
aaaactgaa actcaagta aaagagtta caacaaaaa 
attgaggat ttagaaacg aacaattgg cacttgaaa 
cacgatctt gaggatcaa tatgacctc agaagacag 
ttacacaac accattcag gacctgaaa ggaaatatt 
cgcgttttt tgcagagtc cgaccacca atcaacaac 
gaactggat gacaaagaa ttatgtgca atttccttc 
cccaacgaa accagtcta gatatacga aagtcgcgt 
gaaagtgtc tgtgcaata agtggaaga gttggggac 
gttaaacag gaattttcc tttgataaa gttttttca 
cctgaagca agccaggtg gaaattttt gaggaactt 
gcacaattg gttcagtcg gctttggac ggatatcat 
gtgtgtgtt tttgcttat ggacagact gggtcagga 
aaaacacac acgatgcaa ggaacacca aatgatcgt 
ggcatgatc cctcggacg atagacttg atcttcgaa 
aaaatcgag aaactgaaa attactgaa tggagttac 
actgtgaca gccagcttc ttggaaatc tacaacgaa 
aacatcaga gacttgctg gaacctaac agtaactac 
gactacgaa ttgcgttac aacgagggt cgaggtgta 
accgtaacc aacttaaaa agtgttcca attgattca 
gctcgcatg ctcaaagca cttatggag gaagctaac 
aacaacaga gcggttgcc acaaccgat ttcaacaaa 
cacagttct cgatcgcac gcagtcacc aaaattcat 
ctcgaagga cacaataat ttaagtaga gcgagttat 
tccggatca atcaatctc gtggacttg gccggctct 
gaaagcgcc aaaacctcg gcagccgaa cgtttaaac 
gagacgaaa catattaat aagagtctg tctactttg 
ggaaatgta atgctggca ctacataat aaagactcc 
catgtgcca tatcgcaat tcgaaactt actttccta 
ttgcaatca tgtcttggc ggtaattcg aagactttg 
atgatcgtg aatattgcg ccgtttgag gactgtttt 
ggggaaagc atcagttcg ctaagattt gcagccaaa 
gttaaggaa atcaaaact tgtgccaaa aaaaacaag 
acttatggt catcaggct ttattgcca tcgaatggc 
tcccaaaag aagtaa
    mRNA sequence
    • >TC002539 RA
      aaaacaaaa tttttagcg ttttttcca aagcacgct 
tggtaaaaa tgctttttt attttgatc aactggacg 
gtgaggtac aggaactac gacaagtga acgaaacac 
agaagggca aattacaaa gtttagaag agcaggaga 
agaagtgga gacaagaaa acaatgatt taaacactc 
aattaacga aaacaagag aagattaca gcgagttgc 
aaaaacgaa ccgaagctt tacaagaaa atttagaat 
cacttgaga aggaaaaaa agctttgga aatccgaaa 
aagaaaata ttctgtcgg aaaatacca aattaacac 
acgaattaa gtgtaacga gaacggatt acgctaact 
tgaaacttg aacacgagt ctttggaaa aacaatgta 
ctgagaata tagagcgtc ttcaacaga tacaacaga 
tcctccaaa aaactgaaa ctcaagtaa aagagttac 
aacaaaaaa ttgaggatt tagaaacga acaattggc 
acttgaaac acgatcttg aggatcaat atgacctca 
gaagacagt tacacaaca ccattcagg acctgaaag 
gaaatattc gcgtttttt gcagagtcc gaccaccaa 
tcaacaacg aactggatg acaaagaat tatgtgcaa 
tttccttcc ccaacgaaa ccagtctag atatacgaa 
agtcgcgtg aaagtgtct gtgcaataa gtggaagag 
ttggggacg ttaaacagg aattttcct ttgataaag 
ttttttcac ctgaagcaa gccaggtgg aaatttttg 
aggaacttg cacaattgg ttcagtcgg ctttggacg 
gatatcatg tgtgtgttt ttgcttatg gacagactg 
ggtcaggaa aaacacaca cgatgcaag gaacaccaa 
atgatcgtg gcatgatcc ctcggacga tagacttga 
tcttcgaaa aaatcgaga aactgaaaa ttactgaat 
ggagttaca ctgtgacag ccagcttct tggaaatct 
acaacgaaa acatcagag acttgctgg aacctaaca 
gtaactacg actacgaat tgcgttaca acgagggtc 
gaggtgtaa ccgtaacca acttaaaaa gtgttccaa 
ttgattcag ctcgcatgc tcaaagcac ttatggagg 
aagctaaca acaacagag cggttgcca caaccgatt 
tcaacaaac acagttctc gatcgcacg cagtcacca 
aaattcatc tcgaaggac acaataatt taagtagag 
cgagttatt ccggatcaa tcaatctcg tggacttgg 
ccggctctg aaagcgcca aaacctcgg cagccgaac 
gtttaaacg agacgaaac atattaata agagtctgt 
ctactttgg gaaatgtaa tgctggcac tacataata 
aagactccc atgtgccat atcgcaatt cgaaactta 
ctttcctat tgcaatcat gtcttggcg gtaattcga 
agactttga tgatcgtga atattgcgc cgtttgagg 
actgttttg gggaaagca tcagttcgc taagatttg 
cagccaaag ttaaggaaa tcaaaactt gtgccaaaa 
aaaacaaga cttatggtc atcaggctt tattgccat 
cgaatggct cccaaaaga agtaaaaat agtgtttta 
atttgtgaa tatgcgaat tttttagtg tttttgttt 
taatcattt taacatgta tgcgttgac ttagctgta 
tatatcatt ttataaaat aaagttaat taagtctg

    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