Status
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Gene information
General information
TC011953 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_007424.3: 11006973..11010193
Sequence information
Transcripts / Proteins (2) 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
    		TC011953
    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
    {{ blurEvidenceResult }}
    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 *
    {{ blurReferenceResult }}
    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
    If you have entered your name and agree by marking the checkbox. we might show your name on this page to honor your contribution.
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_01908

    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: 10.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 1 (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): 50% - 80%

    larval musculature fluorescence decreased - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): more than 80%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     egg without cuticle embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): less than 30%
    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): less than 30%
    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: 10.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 100.0% (includes death as larva, prepupa, pupa, adult)

    adult lethality immediately after eclosion - Number of animals showing the phenotype: 1 (16 dpi)
    Days post injection

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 5 (16 dpi)
    Days post injection


    Pupal morphology
    elytra blistered - Number of animals showing the phenotype: 6

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC011953 RA
      MADLKSLEH PTLKVPYEI LNKKFRTAQ KSLDREASH 
VQQAARELE STISGGNVR ARDITSLLG GMVEKLQVL 
KRKAEESIS EELAASNVC KRRLEHLKE RETLTSAGT 
VSQGAVNQW KRKRLDRMM VEYFLRNGY YNAAITLAE 
KSDIKDLTN IEIFLTSRE IEKSLANHE TSKCLIWCH 
DNKSKLRKL KSNMEFNLR IQEFVELIR SERRMDAIK 
HARKHFPSF EDEHLDTIQ RVMALLAFP IGTEIKPYK 
ALFDETRWD TLIEQFRQE NYRLFQLAS QSVFTVALQ 
AGLSALKTP YPLMHFTCV FLY
    • >TC011953 RB
      MADLKSLEH PTLKVPYEI LNKKFRTAQ KSLDREASH 
VQQAARELE STISGGNVR ARDITSLLG GMVEKLQVL 
KRKAEESIS EELAASNVC KRRLEHLKE RETLTSAGT 
VSQGAVNQW KRKRLDRMM VEYFLRNGY YNAAITLAE 
KSDIKDLTN IEIFLTSRE IEKSLANHE TSKCLIWCH 
DNKSKLRKL KSNMEFNLR IQEFVELIR SERRMDAIK 
HARKHFPSF EDEHLDTIQ RVMALLAFP IGTEIKPYK 
ALFDETRWD TLIEQFRQE NYRLFQLAS QSVFTVALQ 
AGLSALKTP YPLMHFTCC YSDNGENRN PACPVCQPC 
LNQLAESLP FAHCSQSRL YCHISGLPL NENNLPMML 
PNGYIYGEQ ALEQMAKEN NGQIICPKT KEIFPFKKV 
EKVYVM
    CDS sequence
    • >TC011953 RA
      atggcagac ttgaaatct ctggagcat cccacgttg 
aaggtgccg tacgagatc ctcaacaag aagttccgg 
actgcgcaa aaatcgctc gacagggag gcctcccac 
gtgcagcag gcggcccgc gagctcgag agcaccatc 
tctgggggt aatgtgagg gcgcgcgac atcacctcg 
ctgcttgga ggcatggtg gagaagctg caggtgctg 
aagcgcaaa gccgaggag agcatctcc gaggagctg 
gccgcctcg aatgtgtgc aagcggcgg ctggagcac 
ctgaaggag cgcgagacg ctcacgtcg gccgggacg 
gtctcgcag ggggccgtc aaccagtgg aagaggaag 
cggctggat aggatgatg gtggagtac ttcctcagg 
aatgggtat tacaacgct gcgattact ctggcggag 
aagagcgat atcaaggac ttgaccaat attgagatt 
tttttgacg tcgcgcgag atcgagaag agtctcgcg 
aatcatgag acgtccaag tgcttgatt tggtgccat 
gacaataag tccaaactt cgtaagctt aagtcaaat 
atggagttt aatttgagg atccaggag tttgttgaa 
ctgatcagg tctgagcgc agaatggac gctattaag 
cacgcgaga aagcatttt ccgagcttc gaagacgag 
catttagat acgattcag agggttatg gcgcttttg 
gcgtttccg ataggtaca gaaataaaa ccctacaag 
gccctcttt gacgagacc agatgggac accctcatc 
gagcaattt agacaagaa aactaccga ctgttccaa 
ttagcttca caatcagtg tttacagtg gctcttcaa 
gctggactt tcagcgctt aaaacacca tatcctttg 
atgcatttt acgtgtgtg tttttgtac tga
    • >TC011953 RB
      atggcagac ttgaaatct ctggagcat cccacgttg 
aaggtgccg tacgagatc ctcaacaag aagttccgg 
actgcgcaa aaatcgctc gacagggag gcctcccac 
gtgcagcag gcggcccgc gagctcgag agcaccatc 
tctgggggt aatgtgagg gcgcgcgac atcacctcg 
ctgcttgga ggcatggtg gagaagctg caggtgctg 
aagcgcaaa gccgaggag agcatctcc gaggagctg 
gccgcctcg aatgtgtgc aagcggcgg ctggagcac 
ctgaaggag cgcgagacg ctcacgtcg gccgggacg 
gtctcgcag ggggccgtc aaccagtgg aagaggaag 
cggctggat aggatgatg gtggagtac ttcctcagg 
aatgggtat tacaacgct gcgattact ctggcggag 
aagagcgat atcaaggac ttgaccaat attgagatt 
tttttgacg tcgcgcgag atcgagaag agtctcgcg 
aatcatgag acgtccaag tgcttgatt tggtgccat 
gacaataag tccaaactt cgtaagctt aagtcaaat 
atggagttt aatttgagg atccaggag tttgttgaa 
ctgatcagg tctgagcgc agaatggac gctattaag 
cacgcgaga aagcatttt ccgagcttc gaagacgag 
catttagat acgattcag agggttatg gcgcttttg 
gcgtttccg ataggtaca gaaataaaa ccctacaag 
gccctcttt gacgagacc agatgggac accctcatc 
gagcaattt agacaagaa aactaccga ctgttccaa 
ttagcttca caatcagtg tttacagtg gctcttcaa 
gctggactt tcagcgctt aaaacacca tatcctttg 
atgcatttt acgtgttgt tattctgat aacggggaa 
aacaggaat cccgcctgt ccagtttgc caaccttgc 
ctcaaccaa ttagcagag tctttgcct ttcgcccat 
tgctcacag tcacgtctt tattgccat attagcgga 
ttaccacta aacgaaaac aatttaccc atgatgttg 
cccaatgga tatatttac ggagaacaa gcgctagaa 
caaatggcg aaggagaat aacgggcaa ataatatgt 
cccaaaacg aaagagata ttcccgttt aagaaagtc 
gaaaaagtt tacgttatg taa
    mRNA sequence
    • >TC011953 RA
      actccttct ttaaaaata ccaaacttg ctaattgta 
tgtgctttt gccgtgtac tcgcaaatt tcgcgtttc 
ccgaacttc cctgccatt tctattgac aaaatcagc 
tgtttgcga agccagcag ctgagtgag tgacgtttt 
atttatgtt tttatttgt gcaccaaaa tggcagact 
tgaaatctc tggagcatc ccacgttga aggtgccgt 
acgagatcc tcaacaaga agttccgga ctgcgcaaa 
aatcgctcg acagggagg cctcccacg tgcagcagg 
cggcccgcg agctcgaga gcaccatct ctgggggta 
atgtgaggg cgcgcgaca tcacctcgc tgcttggag 
gcatggtgg agaagctgc aggtgctga agcgcaaag 
ccgaggaga gcatctccg aggagctgg ccgcctcga 
atgtgtgca agcggcggc tggagcacc tgaaggagc 
gcgagacgc tcacgtcgg ccgggacgg tctcgcagg 
gggccgtca accagtgga agaggaagc ggctggata 
ggatgatgg tggagtact tcctcagga atgggtatt 
acaacgctg cgattactc tggcggaga agagcgata 
tcaaggact tgaccaata ttgagattt ttttgacgt 
cgcgcgaga tcgagaaga gtctcgcga atcatgaga 
cgtccaagt gcttgattt ggtgccatg acaataagt 
ccaaacttc gtaagctta agtcaaata tggagttta 
atttgagga tccaggagt ttgttgaac tgatcaggt 
ctgagcgca gaatggacg ctattaagc acgcgagaa 
agcattttc cgagcttcg aagacgagc atttagata 
cgattcaga gggttatgg cgcttttgg cgtttccga 
taggtacag aaataaaac cctacaagg ccctctttg 
acgagacca gatgggaca ccctcatcg agcaattta 
gacaagaaa actaccgac tgttccaat tagcttcac 
aatcagtgt ttacagtgg ctcttcaag ctggacttt 
cagcgctta aaacaccat atcctttga tgcatttta 
cgtgtgtgt ttttgtact gagtgttgt tccttaaca 
aaacttaat cagtgttat tctgataac ggggaaaac 
aggaatccc gcctgtcca gtttgccaa ccttgcctc 
aaccaatta gcagagtct ttgcctttc gcccattgc 
tcacagtca cgtctttat tgccatatt agcggatta 
ccactaaac gaaaacaat ttacccatg atgttgccc 
aatggatat atttacgga gaacaagta agttgattt 
tgcgattgg tcggttgtt actggacga cttgcaggc 
gctagaaca aatggcgaa ggagaataa cgggcaaat 
aatatgtcc caaaacgaa agagatatt cccgtttaa 
gaaagtcga aaaagttta cgttatgta aatgtgata 
ttttctttt ttatagtat tgtttatac ctctctaag 
ttgagttaa gttaagtac tcatagggt aacagtttt 
ttgtgaaat atactttat gcttatcg
    • >TC011953 RB
      actccttct ttaaaaata ccaaacttg ctaattgta 
tgtgctttt gccgtgtac tcgcaaatt tcgcgtttc 
ccgaacttc cctgccatt tctattgac aaaatcagc 
tgtttgcga agccagcag ctgagtgag tgacgtttt 
atttatgtt tttatttgt gcaccaaaa tggcagact 
tgaaatctc tggagcatc ccacgttga aggtgccgt 
acgagatcc tcaacaaga agttccgga ctgcgcaaa 
aatcgctcg acagggagg cctcccacg tgcagcagg 
cggcccgcg agctcgaga gcaccatct ctgggggta 
atgtgaggg cgcgcgaca tcacctcgc tgcttggag 
gcatggtgg agaagctgc aggtgctga agcgcaaag 
ccgaggaga gcatctccg aggagctgg ccgcctcga 
atgtgtgca agcggcggc tggagcacc tgaaggagc 
gcgagacgc tcacgtcgg ccgggacgg tctcgcagg 
gggccgtca accagtgga agaggaagc ggctggata 
ggatgatgg tggagtact tcctcagga atgggtatt 
acaacgctg cgattactc tggcggaga agagcgata 
tcaaggact tgaccaata ttgagattt ttttgacgt 
cgcgcgaga tcgagaaga gtctcgcga atcatgaga 
cgtccaagt gcttgattt ggtgccatg acaataagt 
ccaaacttc gtaagctta agtcaaata tggagttta 
atttgagga tccaggagt ttgttgaac tgatcaggt 
ctgagcgca gaatggacg ctattaagc acgcgagaa 
agcattttc cgagcttcg aagacgagc atttagata 
cgattcaga gggttatgg cgcttttgg cgtttccga 
taggtacag aaataaaac cctacaagg ccctctttg 
acgagacca gatgggaca ccctcatcg agcaattta 
gacaagaaa actaccgac tgttccaat tagcttcac 
aatcagtgt ttacagtgg ctcttcaag ctggacttt 
cagcgctta aaacaccat atcctttga tgcatttta 
cgtgttgtt attctgata acggggaaa acaggaatc 
ccgcctgtc cagtttgcc aaccttgcc tcaaccaat 
tagcagagt ctttgcctt tcgcccatt gctcacagt 
cacgtcttt attgccata ttagcggat taccactaa 
acgaaaaca atttaccca tgatgttgc ccaatggat 
atatttacg gagaacaag cgctagaac aaatggcga 
aggagaata acgggcaaa taatatgtc ccaaaacga 
aagagatat tcccgttta agaaagtcg aaaaagttt 
acgttatgt aaatgtgat attttcttt tttatagta 
ttgtttata cctctctaa gttgagtta agttaagta 
ctcataggg taacagttt tttgtgaaa tatacttta 
tgcttatcg

    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