Status
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Gene information
General information
TC003429 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: 4956953..4997825
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
    		TC003429
    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_03555

    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)

    Fertility
    vitellarium not present - Number of animals showing the phenotype: 4
    tropharium shortened - Number of animals showing the phenotype: 4
    tropharium rounded - Number of animals showing the phenotype: 4
    egg chamber not present - Number of animals showing the phenotype: 4
    tropharium structure irregular - Number of animals showing the phenotype: 4

    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: 100.0% (includes death as larva, prepupa, pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 2 (16 dpi)
    Days post injection

    Comment: died with pupal and adult features

    adult lethality - Number of animals showing the phenotype: 6 (19 dpi)
    Days post injection

    Pupal morphology
    eyes size decreased - Number of animals showing the phenotype: 8

    antenna size shortened - Number of animals showing the phenotype: 8

    head bristle mostlynot present - Number of animals showing the phenotype: 8
    labrum size decreased - Number of animals showing the phenotype: 8
    labial palp broader - Number of animals showing the phenotype: 8

    Comment: labial palps distance broader
    longitudinal dorsal thoracic muscles fluorescence decreased - Number of animals showing the phenotype: 8
    oblique dorsal thoracic muscles thinner - Number of animals showing the phenotype: 8

    oblique dorsal thoracic muscles size shortened - Number of animals showing the phenotype: 8

    abdomen gin-traps not present - Number of animals showing the phenotype: 8

    abdomen gin-trap setae not present - Number of animals showing the phenotype: 8
    female genital lobes size decreased - Number of animals showing the phenotype: 8

    Adult morphology
    funicle number decreased - Number of animals showing the phenotype: 8


    club fused - Number of animals showing the phenotype: 8
    Comment: the 3 segments of the club seems to be fused

    antenna shortened - Number of animals showing the phenotype: 8


    eyes size decreased - Number of animals showing the phenotype: 6


    legs tibia thinner - Number of animals showing the phenotype: 6


    legs pretarsus decreased - Number of animals showing the phenotype: 6

    Comment: no pretarsal claws

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC003429 RA
      MWPAWGHPA EAAAAASPL PLVLRCLAQ ALATGFHRF 
LARFSGRRR SLYRYNPKY PPPWAFLVL VLASSLFSI 
VDACSSRTT PKPRPPAPT ARPNITFHT YECPPAYAA 
WYCLNGATC FTVKIGDSL LYNCECAEG YMGPRCEYK 
DLDGSYLPS QRRFMLETA SIAGGATIA VFLVVIVCV 
VVYLQYKRY NKMSRASTD CVDGHSTPL NTPTFGTRW 
RTSPPADIP VAVQEAGDS KEVSWNVIR SQRYTLPIN 
RDVCSA
    CDS sequence
    • >TC003429 RA
      atgtggccg gcatggggc catcccgcc gaggcggcg 
gcggcggcg agccccctg cctctcgtc ctccggtgc 
ctggcgcaa gcactcgcc accggcttc caccgcttc 
ctagcaaga ttttcaggt cgaagacga tcactatat 
cgatacaat ccgaaatat ccgccacct tgggccttc 
ctagtttta gtgttagcg tcttcttta tttagtata 
gtcgatgcg tgttcgtca cgcaccacg ccgaaaccg 
aggcctcca gcacctact gcacggcct aacatcaca 
ttccacacg tacgaatgt ccgccggcg tacgcggcc 
tggtactgc cttaacgga gcaacgtgc tttaccgtc 
aaaattggc gattccctc ctatacaat tgcgagtgt 
gcagaaggt tacatgggt cctagatgt gaatataaa 
gatttagac ggttcatat ttaccgtca caacgaagg 
ttcatgttg gaaacggcg agtatagcc ggtggggcg 
acgatagcc gttttttta gtggtgata gtgtgcgtc 
gttgtgtat ctgcagtat aaacgctat aataaaatg 
agtcgtgcg agcacggac tgcgtggac ggacacagc 
acccctttg aacacgccg accttcggc acccgatgg 
cggacgagt ccgccggcg gatatcccg gtggcggtg 
caagaagcg ggcgactcg aaggaggtc agttggaac 
gtgatcagg tcgcagcga tacacgctt ccaatcaat 
cgcgacgtg tgcagtgca tag
    mRNA sequence
    • >TC003429 RA
      tgggttttc gcaaatcga atattaatt atttgctcc 
gtttttaat tggctgacc gcgaatttt accgattcg 
accccacgc aacctgtga acccgctcc gatatatcg 
tcgaccgat ttcattttt tttcgttgc agtgttgtg 
ttttgtgtg gtaattttt tatttcgtt atggttttt 
tttgcggcc gcgatggct tgtgatgtc tgaaaactt 
gtggaaaca ctgcgagcc ggattttcc gctgtgtga 
tgtttttcg caaacagac cgagtgcta tggaatttt 
tatttaatg tgagcttta ttggaccac cttcatgtt 
gctgagatc ttttcaatt ggcgcacgt gatgtggcc 
ggcatgggg ccatcccgc cgaggcggc ggcggcggc 
gagccccct gcctctcgt cctccggtg cctggcgca 
agcactcgc caccggctt ccaccgctt cctagcaag 
attttcagg tcgaagacg atcactata tcgatacaa 
tccgaaata tccgccacc ttgggcctt cctagtttt 
agtgttagc gtcttcttt atttagtat agtcgatgc 
gtgttcgtc acgcaccac gccgaaacc gaggcctcc 
agcacctac tgcacggcc taacatcac attccacac 
gtacgaatg tccgccggc gtacgcggc ctggtactg 
ccttaacgg agcaacgtg ctttaccgt caaaattgg 
cgattccct cctatacaa ttgcgagtg tgcagaagg 
ttacatggg tcctagatg tgaatataa agatttaga 
cggttcata tttaccgtc acaacgaag gttcatgtt 
ggaaacggc gagtatagc cggtggggc gacgatagc 
cgttttttt agtggtgat agtgtgcgt cgttgtgta 
tctgcagta taaacgcta taataaaat gagtcgtgc 
gagcacgga ctgcgtgga cggacacag caccccttt 
gaacacgcc gaccttcgg cacccgatg gcggacgag 
tccgccggc ggatatccc ggtggcggt gcaagaagc 
gggcgactc gaaggaggt cagttggaa cgtgatcag 
gtcgcagcg atacacgct tccaatcaa tcgcgacgt 
gtgcagtgc atagctagc aaactgcta ttcaaatta 
acagtgatg tcggcttta atgtgttat agaatcaaa 
ctatgcctt tgtaaacca acaaataca gaagtgagt 
agcacttgt tatacgcag ctttcgttc acaccgtgc 
agcttattg tcaatcctt tggcagaac ctacagttt 
ggagtaatg ttgtcaaac attttgcga aattcctac 
gtccgaatg cgacttttt ggattgttc cgattttgc 
tagctatga cttggcgtt ctcagtgag cagaactgt 
gtcacaaca gtgtatttg tacagcaag tctgatata 
tgtaagtct gaactttaa gttattaag ttatttaaa 
tgaattata tgtaaatag gtacctcgc cgaggtatt 
ttaattaaa ttgtataat acgcagtta cgtatgttt 
tcgaactat tcgtgcaga ttgagtggt tttaaatta 
ttatccttt ttagtttgt tgaaatatt acattcccg 
gatgtatcg tttattcaa acctcgcta acaaacgtt 
gttattgtt aaattgttg atttaataa gtgattttt 
atagctgat ttattgata ggcgtgcaa gtatgttga 
tgggattga gcagtgatt agtcgaatg tagcatagc 
aataagtac ctacaccaa acgtacatc aaatggata 
tttttcgta aatttttac gtacacgct atcaataac 
tacaacacc gatgaacga acgaacttg ttgtataaa 
tgtagatat acagtaact tattccaat aacggatgc 
tcgcattcg caattattg gcaataata tgagatgta 
atttagtaa tttaaatat ttattgtaa gcacttggt 
tcctaactt attgaagta aacttttgt attatttta 
gagacgcgt tcccatacc aaaactaca aatatcctt 
aacccaatg tattgtttt aaattatcc aagtattct 
aacatgatg tgtacctac ttagcaagc tccgccgat 
atttgtgat tttggtatc aggccaaat acgtttgcc 
agttgttta gccgtaaat gattattta cgcccccaa 
accaaagcc caagtgtat cttttgtgc agcccaaac 
gacacaatc gcattacca tttcactcc atgatatta 
tttatgctt tctgatacg ttttgtttg ggctccaca 
aaatatatc gaacaagta ttaatatca ttaatatat 
taatagtta tatt

    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