Status
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Gene information
General information
TC004849 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_007417.3: 3049299..3054086
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
    		TC004849
    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
    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
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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_07795

    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: 40.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 4 (3 dpi)
    Days post injection

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

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 80%
    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): more than 80%
    affected eggs/embryos/larvae - 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: % (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: % (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004849 RA
      MESSEAPSS GKDSSQCKV LIVGAGMAG LSAAYHLSK 
NGFNDYKLL EARNRVGGR IVQIKMGSE PVELGANWI 
HGVLGNPVY ELAMQHGLV DIMQTPKPH KVIAATENG 
KQVPFATLH EIYEAYLCF LRRCEEYFL SQYLPPEGI 
DSVGDHIKL EISLYLDKV QDPRDRHLR ELLFECLLK 
RETCISGCD DMSEIDLLE LGTYTELQG GNITLPGGY 
SSILGPVTQ AIPAENLLV GHPVSQIRW NLNKRNSID 
NGNDSDDSD RTVIEETTK ESNSPNVEV HCDNGKVFK 
ADQLICTIP LGVLKYNKD TLFQPPLPE YKREAIDRL 
LFGTVDKIL LEYERPFLH PSITEVLLL WESDTEHPE 
GQNDLSKNW YKKIYSFSK ITETIILGW ISGKEAEYM 
ETLSKDEIK DTCTTVLRK FLNDPFIPK PKNVVCTSW 
HSQPYTRGS YTAIAVGAS QIDIECLAQ PLFLDEEET 
KPVVLFAGE HTHCNFYST VHGAYLTGR TAAQAVLHA 
DAPQEMVLD CEDDADLSS WVQGICLE
    CDS sequence
    • >TC004849 RA
      atggaaagc tccgaagcc ccctcaagc ggaaaagac 
tcgtcgcaa tgtaaagtg ttgatcgtg ggggcgggc 
atggcgggg ctctccgcc gcctaccac ctctccaag 
aacggtttc aacgactac aagctcctg gaggcccgc 
aaccgggtc gggggccgt atcgtgcaa attaaaatg 
gggagcgaa ccggtggaa ctgggggcc aactggatc 
cacggagtg ctgggcaac cccgtgtac gaactggca 
atgcagcac ggtctcgtc gacattatg caaacgccc 
aaaccccat aaagtaatc gcggcgacc gaaaacggg 
aagcaagtc ccttttgca accttgcac gaaatctac 
gaagcatat ctgtgtttt ctgcggcgc tgcgaggag 
tatttttta tcgcagtat ttgccccct gaaggcatc 
gacagtgtg ggtgatcac attaagtta gagattagt 
ttgtatctg gacaaggtc caggacccg cgtgataga 
cacttgagg gaactgttg tttgagtgt ttgttgaaa 
cgggagact tgtatcagt gggtgcgac gatatgagc 
gaaattgac ttgctcgag ttggggacg tacacggag 
ctgcaaggg gggaatatc acgcttcca ggggggtac 
agctccatt ttggggccc gtgacgcaa gccattccc 
gcggaaaac ctgctagtg gggcacccg gtgtcccaa 
atccggtgg aatctcaac aagaggaac agtatcgac 
aacgggaac gactcggat gattccgac cggactgtg 
attgaggaa accacgaaa gaatcaaat tcgcccaac 
gttgaagta cattgtgat aacgggaaa gtattcaaa 
gccgaccaa ctcatctgc accattccg ttaggggtc 
ctaaagtac aataaagac actcttttc caaccacct 
ttacccgaa tataaacgc gaggcgatt gaccggttg 
ctattcggg accgtagat aagatttta ctagagtac 
gaaagaccg tttttacac cccagtatt accgaagtt 
ttgctcttg tgggagtca gatactgag catcccgaa 
ggtcagaat gacctgagc aaaaattgg tacaagaaa 
atctactcg ttttccaaa atcactgaa actattatc 
ctcggctgg atttcgggg aaagaagct gagtatatg 
gagacgttg tcaaaagac gagattaaa gacacctgc 
acgactgtt ttacggaag ttcctcaat gaccctttc 
atacccaaa ccaaaaaat gtagtttgc acaagctgg 
cacagtcag ccctatacc cgcggctcc tacactgcg 
atagccgtg ggggcctca cagatcgac atcgagtgt 
ctggcacaa cccctattc ctcgacgag gaagaaact 
aaacctgtg gtattattc gctggcgaa catacccac 
tgtaatttt tactcaaca gttcatggg gcttattta 
actgggaga acagcggca caagcagtt ttacacgca 
gatgccccc caggaaatg gtgctagat tgtgaagat 
gatgccgat ttgagttcg tgggtgcaa ggaatctgt 
cttgagtaa
    mRNA sequence
    • >TC004849 RA
      atggggctg caagtatgg aaagctccg aagccccct 
caagcggaa aagactcgt cgcaatgta aagtgttga 
tcgtggggg cgggcatgg cggggctct ccgccgcct 
accacctct ccaagaacg gtttcaacg actacaagc 
tcctggagg cccgcaacc gggtcgggg gccgtatcg 
tgcaaatta aaatgggga gcgaaccgg tggaactgg 
gggccaact ggatccacg gagtgctgg gcaaccccg 
tgtacgaac tggcaatgc agcacggtc tcgtcgaca 
ttatgcaaa cgcccaaac cccataaag taatcgcgg 
cgaccgaaa acgggaagc aagtccctt ttgcaacct 
tgcacgaaa tctacgaag catatctgt gttttctgc 
ggcgctgcg aggagtatt ttttatcgc agtatttgc 
cccctgaag gcatcgaca gtgtgggtg atcacatta 
agttagaga ttagtttgt atctggaca aggtccagg 
acccgcgtg atagacact tgagggaac tgttgtttg 
agtgtttgt tgaaacggg agacttgta tcagtgggt 
gcgacgata tgagcgaaa ttgacttgc tcgagttgg 
ggacgtaca cggagctgc aagggggga atatcacgc 
ttccagggg ggtacagct ccattttgg ggcccgtga 
cgcaagcca ttcccgcgg aaaacctgc tagtggggc 
acccggtgt cccaaatcc ggtggaatc tcaacaaga 
ggaacagta tcgacaacg ggaacgact cggatgatt 
ccgaccgga ctgtgattg aggaaacca cgaaagaat 
caaattcgc ccaacgttg aagtacatt gtgataacg 
ggaaagtat tcaaagccg accaactca tctgcacca 
ttccgttag gggtcctaa agtacaata aagacactc 
ttttccaac cacctttac ccgaatata aacgcgagg 
cgattgacc ggttgctat tcgggaccg tagataaga 
ttttactag agtacgaaa gaccgtttt tacacccca 
gtattaccg aagttttgc tcttgtggg agtcagata 
ctgagcatc ccgaaggtc agaatgacc tgagcaaaa 
attggtaca agaaaatct actcgtttt ccaaaatca 
ctgaaacta ttatcctcg gctggattt cggggaaag 
aagctgagt atatggaga cgttgtcaa aagacgaga 
ttaaagaca cctgcacga ctgttttac ggaagttcc 
tcaatgacc ctttcatac ccaaaccaa aaaatgtag 
tttgcacaa gctggcaca gtcagccct atacccgcg 
gctcctaca ctgcgatag ccgtggggg cctcacaga 
tcgacatcg agtgtctgg cacaacccc tattcctcg 
acgaggaag aaactaaac ctgtggtat tattcgctg 
gcgaacata cccactgta atttttact caacagttc 
atggggctt atttaactg ggagaacag cggcacaag 
cagttttac acgcagatg ccccccagg aaatggtgc 
tagattgtg aagatgatg ccgatttga gttcgtggg 
tgcaaggaa tctgtcttg agtaactgc cttaaatat 
tgtgttttc gttaatttg tgaacgact agtagtcaa 
ttttaggac cgcttaact ttttgttac cgtttaaac 
tatcacggc ttcattggt caacgaaag ttgagttac 
tatggttaa ctgtggtaa ttggtcaaa gaagctgtg 
aaatcagtt gttactttt ataggcttt acatgatgt 
atgctagtc attttttta aga

    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