Status
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Gene information
General information
TC001175 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: 12259459..12261648
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
    		TC001175
    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 *
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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_03151

    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: 20.0% (includes death as pupa, adult)

    adult lethality - Number of animals showing the phenotype: 2 (9 dpi)
    Days post injection

    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 20
    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
    • >TC001175 RA
      MSIPTVIRQ INWVRPRVL NVLRPRNFC SGEPAASSS 
GEEKKGIIL GVYESENEL VLTKAAQKF NDHVGGKLL 
DLVKKAGKT VKRGSTRIF NNVDREFWA VAVVGLGPE 
KAGYNEMEA IDEGMENVR VAAGIGAQV LRKQGVDRI 
MVEGMGFPE QAAEGSALA LWRYQENKM RENQKKTPT 
LELFDDPDG ESFQRGLFK AESQNLARR LSDTPANQM 
TPLHFAQET VNELCPCGI KVQVHDKDW IEQKKFSAF 
LTVARGSCE PPVVLEISY CGGPNDQKP ILFCGKGIT 
FDSGGLCLK KCKGMDVYK ADMCGAAAI ISAIRAASA 
LSLPLNIEA VIPLCENMP SGMAMKCGD IVMGMNGKS 
IMITDTDNE GRLILADAL VYGQGIYKP RLIIDVASL 
TPGVRSALG SSASGVFSN SQTMWSQVR KAGVITGDR 
VWRLPLWKF FSKKVTRFK SHDVNNKGQ GQGSSCLGA 
AFLNEFISC VDWIHFDIT GVGFKSNHK VTPYYTKGR 
MTGRPTRTL IQLLYQLSC PSEGQREL
    CDS sequence
    • >TC001175 RA
      atgtcgatt ccaacagtt ataagacaa ataaattgg 
gtaaggcct cgagtactg aacgtttta agacctcgg 
aatttctgt tccggtgag ccagcggcg tcttcatca 
ggcgaagaa aagaaaggc ataatttta ggcgtatac 
gagtctgaa aatgaattg gtattgacg aaggctgca 
caaaaattc aacgaccat gtaggagga aaattactg 
gatttggta aaaaaagcc ggaaagact gtaaaacgg 
ggtagtaca aggatcttc aacaacgtc gaccgggaa 
ttctgggcc gtggccgtg gtgggcttg ggccccgag 
aaggcgggc tacaacgag atggaagct atcgacgag 
ggtatggag aacgtccgc gtggccgcc ggaattggg 
gcgcaagtc ctccggaag cagggcgtg gaccggatc 
atggtcgaa ggcatggga ttcccggag caagcggcc 
gaagggagc gccctcgcc ctttggagg taccaggag 
aacaaaatg cgcgagaac cagaagaag acccccacg 
ctggagctg ttcgacgat cccgacgga gagagcttc 
cagcgcggg ctcttcaag gcggagtcg cagaacttg 
gcccggcgc ttgtccgac acccccgcc aaccaaatg 
acccctctg catttcgcc caggaaact gtcaacgag 
ctgtgcccg tgcggcatc aaggtgcaa gtccacgac 
aaggactgg attgagcag aagaagttc agcgcgttc 
ctgacggtg gcacgaggc tcgtgcgag ccgccggtc 
gtgttggag atctcgtac tgcggcggt cccaacgac 
cagaagccg atcctgttc tgcgggaag ggcatcacg 
tttgacagc ggtggtctc tgtttgaag aaatgcaag 
gggatggat gtgtacaag gcggatatg tgcggagcg 
gcggcgatt atttcggcc attcgcgcc gcctccgcg 
ttgagtctc ccgctgaat atcgaggcg gtgattccc 
ctgtgtgag aatatgccg agtggcatg gccatgaag 
tgtggcgac atcgtgatg ggcatgaac ggcaagagc 
atcatgatt acggacact gacaacgaa ggacggctg 
attctggcc gacgcgctg gtctacggc caagggatt 
tacaagccg aggctcatc attgacgtt gcgagtcta 
actccgggg gtgcggtcg gccttgggg tcctccgcg 
tctggagtt ttcagcaac agccagacg atgtggtcg 
caagtgcgc aaagccggg gttataacc ggggaccgc 
gtctggaga ctccctctg tggaagttc ttttcgaag 
aaggtgacc cgcttcaag tcacacgat gtgaataac 
aagggccaa gggcaaggc tcgtcctgt ctgggggcc 
gctttcctc aacgagttt atcagttgc gtggactgg 
attcatttt gatatcacc ggagttggc ttcaagagc 
aaccataag gtcacgccg tactacacc aaagggcgg 
atgaccggc cgtccgacg agaaccctg attcagtta 
ctttaccaa ctttcgtgt ccttctgaa ggacaacgg 
gaactatag
    mRNA sequence
    • >TC001175 RA
      tgtgaaaaa aattcaagt gaaggcccg taaccaata 
aataagaaa aatattatt tgtctttcc gatctaaat 
tattcttgt aaaatgtat atattttaa atgaacaat 
gtcgattcc aacagttat aagacaaat aaattgggt 
aaggcctcg agtactgaa cgttttaag acctcggaa 
tttctgttc cggtgagcc agcggcgtc ttcatcagg 
cgaagaaaa gaaaggcat aattttagg cgtatacga 
gtctgaaaa tgaattggt attgacgaa ggctgcaca 
aaaattcaa cgaccatgt aggaggaaa attactgga 
tttggtaaa aaaagccgg aaagactgt aaaacgggg 
tagtacaag gatcttcaa caacgtcga ccgggaatt 
ctgggccgt ggccgtggt gggcttggg ccccgagaa 
ggcgggcta caacgagat ggaagctat cgacgaggg 
tatggagaa cgtccgcgt ggccgccgg aattggggc 
gcaagtcct ccggaagca gggcgtgga ccggatcat 
ggtcgaagg catgggatt cccggagca agcggccga 
agggagcgc cctcgccct ttggaggta ccaggagaa 
caaaatgcg cgagaacca gaagaagac ccccacgct 
ggagctgtt cgacgatcc cgacggaga gagcttcca 
gcgcgggct cttcaaggc ggagtcgca gaacttggc 
ccggcgctt gtccgacac ccccgccaa ccaaatgac 
ccctctgca tttcgccca ggaaactgt caacgagct 
gtgcccgtg cggcatcaa ggtgcaagt ccacgacaa 
ggactggat tgagcagaa gaagttcag cgcgttcct 
gacggtggc acgaggctc gtgcgagcc gccggtcgt 
gttggagat ctcgtactg cggcggtcc caacgacca 
gaagccgat cctgttctg cgggaaggg catcacgtt 
tgacagcgg tggtctctg tttgaagaa atgcaaggg 
gatggatgt gtacaaggc ggatatgtg cggagcggc 
ggcgattat ttcggccat tcgcgccgc ctccgcgtt 
gagtctccc gctgaatat cgaggcggt gattcccct 
gtgtgagaa tatgccgag tggcatggc catgaagtg 
tggcgacat cgtgatggg catgaacgg caagagcat 
catgattac ggacactga caacgaagg acggctgat 
tctggccga cgcgctggt ctacggcca agggattta 
caagccgag gctcatcat tgacgttgc gagtctaac 
tccgggggt gcggtcggc cttggggtc ctccgcgtc 
tggagtttt cagcaacag ccagacgat gtggtcgca 
agtgcgcaa agccggggt tataaccgg ggaccgcgt 
ctggagact ccctctgtg gaagttctt ttcgaagaa 
ggtgacccg cttcaagtc acacgatgt gaataacaa 
gggccaagg gcaaggctc gtcctgtct gggggccgc 
tttcctcaa cgagtttat cagttgcgt ggactggat 
tcattttga tatcaccgg agttggctt caagagcaa 
ccataaggt cacgccgta ctacaccaa agggcggat 
gaccggccg tccgacgag aaccctgat tcagttact 
ttaccaact ttcgtgtcc ttctgaagg acaacggga 
actatagac ttttttggt ggattttag aaatgggat 
atgacccac atgaccttt aaaatttaa ttgtaataa 
atacttagg ggaatgttt tgacttgaa tcgcaatct 
ggtcagttg ctcaaatac gattttttt ggctttttt 
atcataaat cctgataat gctctccct ccctctcaa 
aaaaataaa aataacatt ccgagttat gcctaagtg 
gtctattac atttttgta gccagttta caagaattt 
tgaaatttg tcgtatacc aatttattg tttatttta 
aactcaaaa actgtccta tactgtaca ttttgtatc 
aataaaata taatgcttc ga

    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