Status
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Gene information
General information
TC000508 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: 10480776..10482848
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
    		TC000508
    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
    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
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_03034

    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: 25.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 2 (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, 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
    • >TC000508 RA
      MSKVILGGG LGGLSAAYY LKKFSPNQA VTLIESSSR 
TGGWIKSSV QENGAIFEQ GPRTIRPRG DAGANTLQL 
IEELNLSDQ IVPITSGHP AAKNRLIYA NGSLHLLPS 
SLTGLFRKQ EPFSKPLIL HLLNDLKAR RKEVKDESI 
YDFIGRRFG SEVADYLIS PLICGICAG NAKEISVKF 
LMKQLFEYE QKHGSVSKG LLTSLFAKS KRPTVLCET 
ALRARSEKW NIYSFKNGC ETLPIALRN NIVSNGVNI 
KFNTECTEI ITDKGQVIL NLFNNETIK CDHLVGAIP 
ANVLGRLLQ KQHPELAQC LKKLTKNVS VAVVNLLFK 
ENFIKNPAF GLLVVPKEQ LPVLGVIYD SCCFPVENC 
GTVLTVMMG GYWFEEHFG TNPQENVLL DVAVKHVKR 
ILNCDHDPF NYKVNILKQ CLPQYVVGH DENLDLING 
YIRTHKLPI SLCGASYYG VGINDVILS AKNAVKDL
    CDS sequence
    • >TC000508 RA
      atgagcaaa gtgatcctc ggcgggggc ttgggtggc 
ctgtctgct gcctactac ttgaagaag ttttcgcct 
aaccaagct gttacttta attgagtct tcgtcacgt 
accgggggc tggatcaag tcaagtgtg caagaaaat 
ggggctatt tttgaacaa gggcctcgt accatacgt 
ccccggggg gatgcaggc gctaatact ttacaactg 
attgaagaa ctaaattta agcgatcaa atcgtccct 
ataacttcg ggacaccct gctgctaaa aatcggctc 
atttacgcc aacggttct ttgcatttg ttgccgtcg 
tctttgact ggtttgttt aggaaacaa gagccgttt 
tcaaagcct ttgattctt cacttgttg aatgatttg 
aaagcgagg aggaaggaa gtgaaggat gagtcaatt 
tatgatttt atcggtcgc agatttggt agtgaagtg 
gctgattat ttgatcagt ccgttgatt tgtggcatt 
tgtgccgga aacgccaag gaaattagt gtgaagttt 
ttaatgaaa cagttgttt gaatacgaa caaaaacat 
ggaagtgta tcaaagggg ctccttaca agtttgttt 
gcaaagtca aaacgacca actgttctg tgtgaaact 
gccctcaga gctagaagt gagaaatgg aatatttat 
tcctttaaa aatgggtgt gaaacgtta cccatagcc 
ttaagaaat aatattgtt tcaaatggg gttaatatt 
aaatttaat accgaatgt acggaaatt ataacggac 
aagggccaa gtaatacta aatttattt aataacgaa 
acaattaag tgtgatcac ttagtaggt gcaatacct 
gcaaacgtt ttaggacgt cttttacaa aaacagcac 
ccggaactt gcccagtgt ttgaaaaaa ctgacaaaa 
aacgtgtca gtggctgtt gttaattta ctttttaag 
gagaatttt attaaaaat ccagccttt ggtttattg 
gttgttcct aaagaacaa cttcctgtg ctaggtgtt 
atttacgat agttgttgt ttccctgtc gaaaactgt 
ggaacggtt ttaaccgta atgatgggt ggttactgg 
tttgaggaa cattttggc acaaatccg caagaaaat 
gtgttgctg gatgttgcc gtaaaacac gtgaaacgt 
atcttaaat tgtgatcac gatccgttt aattataaa 
gtgaatatt ttaaagcag tgtttgcct caatatgtt 
gtgggtcat gacgaaaat ttggacctg attaatggt 
tacataagg acgcataaa ttaccaatt tctttgtgc 
ggtgcctct tattacggt gtggggatt aatgatgta 
attttgtcg gcgaaaaat gccgtaaag gatttgtaa
    mRNA sequence
    • >TC000508 RA
      ctatttggg tacagctgc cggttcaca tgatctcaa 
catgacaag aagggaaga cgtcattta tcatgagca 
aagtgatcc tcggcgggg gcttgggtg gcctgtctg 
ctgcctact acttgaaga agttttcgc ctaaccaag 
ctgttactt taattgagt cttcgtcac gtaccgggg 
gctggatca agtcaagtg tgcaagaaa atggggcta 
tttttgaac aagggcctc gtaccatac gtccccggg 
gggatgcag gcgctaata ctttacaac tgattgaag 
aactaaatt taagcgatc aaatcgtcc ctataactt 
cgggacacc ctgctgcta aaaatcggc tcatttacg 
ccaacggtt ctttgcatt tgttgccgt cgtctttga 
ctggtttgt ttaggaaac aagagccgt tttcaaagc 
ctttgattc ttcacttgt tgaatgatt tgaaagcga 
ggaggaagg aagtgaagg atgagtcaa tttatgatt 
ttatcggtc gcagatttg gtagtgaag tggctgatt 
atttgatca gtccgttga tttgtggca tttgtgccg 
gaaacgcca aggaaatta gtgtgaagt ttttaatga 
aacagttgt ttgaatacg aacaaaaac atggaagtg 
tatcaaagg ggctcctta caagtttgt ttgcaaagt 
caaaacgac caactgttc tgtgtgaaa ctgccctca 
gagctagaa gtgagaaat ggaatattt attccttta 
aaaatgggt gtgaaacgt tacccatag ccttaagaa 
ataatattg tttcaaatg gggttaata ttaaattta 
ataccgaat gtacggaaa ttataacgg acaagggcc 
aagtaatac taaatttat ttaataacg aaacaatta 
agtgtgatc acttagtag gtgcaatac ctgcaaacg 
ttttaggac gtcttttac aaaaacagc acccggaac 
ttgcccagt gtttgaaaa aactgacaa aaaacgtgt 
cagtggctg ttgttaatt tacttttta aggagaatt 
ttattaaaa atccagcct ttggtttat tggttgttc 
ctaaagaac aacttcctg tgctaggtg ttatttacg 
atagttgtt gtttccctg tcgaaaact gtggaacgg 
ttttaaccg taatgatgg gtggttact ggtttgagg 
aacattttg gcacaaatc cgcaagaaa atgtgttgc 
tggatgttg ccgtaaaac acgtgaaac gtatcttaa 
attgtgatc acgatccgt ttaattata aagtgaata 
ttttaaagc agtgtttgc ctcaatatg ttgtgggtc 
atgacgaaa atttggacc tgattaatg gttacataa 
ggacgcata aattaccaa tttctttgt gcggtgcct 
cttattacg gtgtgggga ttaatgatg taattttgt 
cggcgaaaa atgccgtaa aggatttgt aacagaaac 
gcgaatgtt tttataaat gatttattg ttgtcttgt 
acaaaagaa ataaattgt tacaat

    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