Status
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Gene information
General information
TC015676 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_007421.3: 5127059..5145561
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
    		TC015676
    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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    Publish name
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_05867

    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 larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 50
    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: 40.0% (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
    • >TC015676 RA
      MGQRRLRHI STRLHWRYP QVQLFSTYC AYLPVIINP 
VTTMTEKLN PKVQEFQFH SIPKTTKWE SFQKVIYDP 
STHEIFGRT KKSWYQLLV FYSIFYICL AALFAICMK 
GLTATLSDK EPKWKLEES LIGTSPGLG FRPISNNTQ 
EGSLIWYNL KDVQTTQKW VRLVDQFLQ PYKVQQIGK 
NYQQCDYEI AVKEGHVCA VEVDKFGPC TAENNYGFN 
STSPCVFLK LNRIFGWVP DYVTQPESE MPDDLKEII 
TYATSNNKS QVWISCAGE NPFDREHVI GFDYFPSRG 
FPGYYFPYT NNDNYLSPL IAVQINVKT NVIVNIECR 
AWARNIAYD GGNNHREGS VHFEILVDS KN
    CDS sequence
    • >TC015676 RA
      atgggtcaa cgtcggctt cgtcacatc agcacgcgc 
ctccactgg cgttaccca caagttcag cttttcagc 
acatattgt gcttatctc cctgttatc ataaaccca 
gtcacaacc atgaccgaa aagttaaac ccaaaagtc 
caggaattt cagttccat tcgatcccg aaaaccacc 
aaatgggag agtttccag aaagtaatt tacgaccct 
tcaacacac gaaattttc ggaagaacg aagaaaagt 
tggtaccaa ttgctagtt ttctactcg attttctac 
atatgcctt gccgccctt ttcgcaatt tgcatgaaa 
ggcttgact gcgacctta agcgacaaa gaaccgaaa 
tggaagctt gaggaaagc ctaattggg acgagtcca 
ggactgggt tttcggcca atttccaac aacacgcaa 
gaaggttcc ctcatttgg tacaactta aaagacgtg 
caaacaaca caaaagtgg gtacgactt gtggaccag 
ttcttacaa ccctacaaa gtgcaacaa atcggcaaa 
aactaccaa caatgcgac tacgaaatt gcggtcaaa 
gaggggcac gtgtgtgcg gtagaagtg gacaaattc 
ggaccatgc actgctgaa aacaactac gggttcaat 
tcaacttcg ccttgtgtt tttctaaaa ttgaaccgg 
atttttgga tgggttccc gattacgta acgcagcca 
gaaagtgaa atgcctgat gatttaaaa gagattatt 
acgtacgcc acttcgaat aataagagc caagtgtgg 
ataagttgt gcgggagaa aatccgttt gatcgagaa 
catgtaatt gggttcgat tactttcca agtaggggg 
tttcccgga tactatttc ccttacact aataacgat 
aattatctc agtccactt atcgctgta caaataaat 
gttaaaacg aatgtgatt gtcaatatc gaatgtagg 
gcttgggct agaaacatc gcctatgat ggcgggaac 
aaccatcga gagggatcc gttcatttt gagattttg 
gtggactcc aaaaattga
    mRNA sequence
    • >TC015676 RA
      agggatgaa aacgcgaaa ccctttcag tggcagcga 
ccgttcgaa cgggggtac gcgttttgc gctacaaaa 
atcgaacgc gatgagaca tcaataaaa atcacaact 
aattttttc caaaaattc acactcggg ggtggctgt 
gagtgaaac gtgtgccaa taaatggat atttctcac 
ccccaaggc aactcgggt gggcgggcc aacgtcgag 
aggcggttt ctgccgcca ccagcgagc tagtgggag 
cattgtgtg agcaaagta tgaagctaa gcgtttcgg 
cgtatagag cccacgctt ccgcccata agaagatat 
tggacactg cttatcagc ttaattatg ggtcaacgt 
cggcttcgt cacatcagc acgcgcctc cactggcgt 
tacccacaa gttcagctt ttcagcaca tattgtgct 
tatctccct gttatcata aacccagtc acaaccatg 
accgaaaag ttaaaccca aaagtccag gaatttcag 
ttccattcg atcccgaaa accaccaaa tgggagagt 
ttccagaaa gtaatttac gacccttca acacacgaa 
attttcgga agaacgaag aaaagttgg taccaattg 
ctagttttc tactcgatt ttctacata tgccttgcc 
gcccttttc gcaatttgc atgaaaggc ttgactgcg 
accttaagc gacaaagaa ccgaaatgg aagcttgag 
gaaagccta attgggacg agtccagga ctgggtttt 
cggccaatt tccaacaac acgcaagaa ggttccctc 
atttggtac aacttaaaa gacgtgcaa acaacacaa 
aagtgggta cgacttgtg gaccagttc ttacaaccc 
tacaaagtg caacaaatc ggcaaaaac taccaacaa 
tgcgactac gaaattgcg gtcaaagag gggcacgtg 
tgtgcggta gaagtggac aaattcgga ccatgcact 
gctgaaaac aactacggg ttcaattca acttcgcct 
tgtgttttt ctaaaattg aaccggatt tttggatgg 
gttcccgat tacgtaacg cagccagaa agtgaaatg 
cctgatgat ttaaaagag attattacg tacgccact 
tcgaataat aagagccaa gtgtggata agttgtgcg 
ggagaaaat ccgtttgat cgagaacat gtaattggg 
ttcgattac tttccaagt agggggttt cccggatac 
tatttccct tacactaat aacgataat tatctcagt 
ccacttatc gctgtacaa ataaatgtt aaaacgaat 
gtgattgtc aatatcgaa tgtagggct tgggctaga 
aacatcgcc tatgatggc gggaacaac catcgagag 
ggatccgtt cattttgag attttggtg gactccaaa 
aattgatag aaacgtgta atttatttg ttatttttt 
gcacaaaat aaagagaca gtaatttg

    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