Status
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Gene information
General information
TC030580 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_007424.3: 11552428..11556420
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
    		TC030580
    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 *
    {{ blurReferenceResult }}
    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
    If you have entered your name and agree by marking the checkbox. we might show your name on this page to honor your contribution.
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_06031

    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: 30.0% (includes death as pupa, adult)

    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: 2 (9 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg not developed/not fertilized - Penetrance (percentage of animals/eggs on slide): less than 30%
    larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    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
     embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    mandible not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    antenna sometimes decreased - Penetrance (percentage of animals/eggs on slide): less than 30%

    legs tibiotarsus sometimes bent - 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: -1.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: -1.0% (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC030580 RA
      MDIEEFRTR GKEMVDYIC QYLENIESQ RVHPDVETG 
YLRKLLPSE APEQPEEWD NIMYDVDKN IMPGITHWQ 
HPRFHAYFP SGNSFPSIL GDMLSDAIG CIGFSWAAS 
PACTELETI VMDWFGKAI GLPSDFITS SEGSTGGGV 
IQTSASECV LVSMLAARN QAIKYLKTE NPQMEDSAF 
LPKLVGYCS KEAHSCVEK AAKILLVKL RILDPDENG 
SLRGDKLRE EMEKDKEKG LFPFFVSAI LGSTASCSF 
DNLEEIGPV CKEQKRCWL HVDAAYAGN GFICPELKY 
LLNGIDYAD SFNTNPNKW LLVNFDCSC LWVRDRIRL 
THALVVDPL YLQHANADE SIDYRHWGI PLSRRFRSL 
KLWFVIRKY GLSGLRAYI RNHIKLAKH FEQLVLQDT 
RFEVVNDVR LGLVCFRLM ACDAANQKL LAMINASGK 
IHMTPSVVR NKYIIRFCV DAEHAKEED VDYAWEVIK 
EFAVETLAT GAKERPPLT RQKSKRFSF TRSISKEMY 
QRTLSRSNL CDGATPILV ADSDEEDTL VEDTTMLPD 
EPDEVFIDK QEFVNGFRI NDKEIKYNG VS
    CDS sequence
    • >TC030580 RA
      atggacatc gaagagttt cgaacacgc ggcaaggaa 
atggtcgat tacatttgc cagtatctg gagaatatc 
gagtcccag agggttcac ccggacgtg gaaacgggc 
tacttgagg aagcttttg cccagcgag gcgcccgaa 
cagcccgaa gaatgggac aatatcatg tacgacgtc 
gacaagaac atcatgcct gggataacg cactggcag 
catccccga tttcacgcg tactttccc tcaggaaac 
tccttcccg tccatcctg ggggacatg ctgtcggac 
gccatcggc tgcatcggc ttttcatgg gccgctagt 
cccgcctgc acggagctg gagaccatc gtcatggac 
tggttcggc aaagccatc ggcctcccc tccgacttc 
atcacctcc tcggagggc agcaccggc ggcggcgtc 
atccagacc tccgccagc gagtgcgtc ctagtctcc 
atgctggca gcccgcaac caggccatc aaatacctc 
aaaacggaa aacccccaa atggaggac agcgccttc 
ctcccgaaa ctagtcggc tattgctcc aaagaggcc 
cactcctgc gtggaaaaa gctgcgaaa atcctccta 
gtcaagctg cgaatcctg gatcctgac gaaaacggg 
agcttacgg ggcgataaa ctccgggag gagatggag 
aaggacaag gagaagggt ttgttcccg tttttcgtt 
tcggcgatt ttgggctcg actgcctcc tgctccttc 
gacaatctg gaggagatc gggccggtt tgcaaggaa 
cagaagcgg tgttggttg cacgtggac gcggcctac 
gccggaaac gggtttatt tgtcccgaa ttgaagtat 
ttactcaat gggatcgac tacgctgat agttttaac 
acgaatccg aacaagtgg cttttggtt aatttcgac 
tgttcctgc ttgtgggtc agggaccgg attcgacta 
acgcacgcc ctcgtggtg gaccccctg tacctgcag 
cacgccaac gctgacgag tccatcgac tacaggcac 
tgggggatt cccctaagc cggcggttc cgctccttg 
aaactgtgg ttcgtcatc cggaagtac ggcttaagc 
ggcctccgg gcctacatc cggaaccac atcaaactg 
gccaaacac ttcgaacag ttggtcctg caggacacc 
cggttcgag gtcgtgaat gacgtgagg ctgggcctt 
gtgtgtttc cggttgatg gcgtgcgat gccgccaac 
cagaagctg ctagcgatg atcaacgcc tctgggaag 
attcacatg acaccgtcg gtggtccgg aacaagtac 
attatccgg ttctgtgtg gacgcggag catgccaaa 
gaggaggac gttgattat gcgtgggag gtgatcaag 
gagttcgct gttgaaacg ctggcgacg ggggccaag 
gagcggccg ccgctcacg agacagaag tcgaagcgg 
ttctcgttc accaggagc atttcgaag gagatgtac 
cagaggact ttgagtcgg tcgaatttg tgcgacggg 
gcgacgccc attcttgtg gcggattcg gatgaggag 
gacacgctg gttgaggac acgacgatg ctgccagat 
gagcccgat gaggttttt attgacaaa caagagttt 
gttaatggg tttaggata aatgacaaa gagattaag 
tacaatggg gttagttaa
    mRNA sequence
    • >TC030580 RA
      aggaagtac ttttattac gtcgatttt atgggaaat 
cagccttga aatgggctt ttatgaagt cctgttgga 
agtccatga aattccgga aaacctccc cgttttctg 
tctattatt agcctgcag gtagttgtc ttcgtcaat 
taataaatt ggattatgc cacaaccct atacgtagc 
cacacagaa catgaatgc gtttgacta gaggttccg 
acttcagag tggggcaac cttaaatat aaaagtata 
ccttggcag tatgcagtg attttgtgg tacgctccc 
agtgctaag ttagtgtga caatggaca tcgaagagt 
ttcgaacac gcggcaagg aaatggtcg attacattt 
gccagtatc tggagaata tcgagtccc agagggttc 
acccggacg tggaaacgg gctacttga ggaagcttt 
tgcccagcg aggcgcccg aacagcccg aagaatggg 
acaatatca tgtacgacg tcgacaaga acatcatgc 
ctgggataa cgcactggc agcatcccc gatttcacg 
cgtactttc cctcaggaa actccttcc cgtccatcc 
tgggggaca tgctgtcgg acgccatcg gctgcatcg 
gcttttcat gggccgcta gtcccgcct gcacggagc 
tggagacca tcgtcatgg actggttcg gcaaagcca 
tcggcctcc cctccgact tcatcacct cctcggagg 
gcagcaccg gcggcggcg tcatccaga cctccgcca 
gcgagtgcg tcctagtct ccatgctgg cagcccgca 
accaggcca tcaaatacc tcaaaacgg aaaaccccc 
aaatggagg acagcgcct tcctcccga aactagtcg 
gctattgct ccaaagagg cccactcct gcgtggaaa 
aagctgcga aaatcctcc tagtcaagc tgcgaatcc 
tggatcctg acgaaaacg ggagcttac ggggcgata 
aactccggg aggagatgg agaaggaca aggagaagg 
gtttgttcc cgtttttcg tttcggcga ttttgggct 
cgactgcct cctgctcct tcgacaatc tggaggaga 
tcgggccgg tttgcaagg aacagaagc ggtgttggt 
tgcacgtgg acgcggcct acgccggaa acgggttta 
tttgtcccg aattgaagt atttactca atgggatcg 
actacgctg atagtttta acacgaatc cgaacaagt 
ggcttttgg ttaatttcg actgttcct gcttgtggg 
tcagggacc ggattcgac taacgcacg ccctcgtgg 
tggaccccc tgtacctgc agcacgcca acgctgacg 
agtccatcg actacaggc actggggga ttcccctaa 
gccggcggt tccgctcct tgaaactgt ggttcgtca 
tccggaagt acggcttaa gcggcctcc gggcctaca 
tccggaacc acatcaaac tggccaaac acttcgaac 
agttggtcc tgcaggaca cccggttcg aggtcgtga 
atgacgtga ggctgggcc ttgtgtgtt tccggttga 
tggcgtgcg atgccgcca accagaagc tgctagcga 
tgatcaacg cctctggga agattcaca tgacaccgt 
cggtggtcc ggaacaagt acattatcc ggttctgtg 
tggacgcgg agcatgcca aagaggagg acgttgatt 
atgcgtggg aggtgatca aggagttcg ctgttgaaa 
cgctggcga cgggggcca aggagcggc cgccgctca 
cgagacaga agtcgaagc ggttctcgt tcaccagga 
gcatttcga aggagatgt accagagga ctttgagtc 
ggtcgaatt tgtgcgacg gggcgacgc ccattcttg 
tggcggatt cggatgagg aggacacgc tggttgagg 
acacgacga tgctgccag atgagcccg atgaggttt 
ttattgaca aacaagagt ttgttaatg ggtttagga 
taaatgaca aagagatta agtacaatg gggttagtt 
aagagtgtg attgggtgt gtagatgtg tagacacaa 
cagtattat tttaagtaa taatcttaa gttatttgt 
tcattcaca tatcattag acgtaagga cggttgtgt 
accaagtga tcatttgaa ttcattaca attagagta 
cctactgaa actgatatt gaaagaatg gttaagact 
tgagtctac caactattc ggaggaaac tctcctact 
ctaattaca aatgacgac atataatac tcgctcatt 
agtattaag tagcgtcct tgttgttgt taaagagtt 
tttttactc atttataaa atgtagacg taataaatt 
atgatatta att

    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