Status
Please wait ...
Gene information
General information
TC013165 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_007420.3: 12855172..12874565
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
    		TC013165
    Gene ontology

    GO terms for Tribolium

    • {{ goTerm.term }}
      ({{ goTerm.evidence }}){{ goTerm.evidenceTooltip }}
      {{goTerm.showAll ? '[-]' : '[+]'}}
      Status: {{ goTerm.status }}
      Evidence: {{ goTerm.evidence }} ({{ goTerm.evidenceTooltip }})
      Reference: {{ goTerm.referenceText }}
      Quotation: {{ goTerm.quotation }}
      Submitter: {{ goTerm.name }}

    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 *
    {{ blurIdResult }}
    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.
      {{ unavailableText }}

    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_05394

    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: 50.0% (includes death as pupa, adult)

    pupa eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 3 (3 dpi)
    Days post injection

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 1 (3 dpi)
    Days post injection

    beetle stock: bad (increased lethality), adult lethality - Number of animals showing the phenotype: 1 (9 dpi)
    Days post injection

    Pupal morphology
    beetle stock: bad (increased lethality),
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 50
     larva partially constricted - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    head partially not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    labium not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    head not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    thorax not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): 50% - 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: 30.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 50.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality early (L5/6) - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection

    pupal molt delayed (still larva) - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection

    eclosion delayed (still pupa) - Number of animals showing the phenotype: 2 (16 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC013165 RA
      MCEGGFSAA EGLSRMASL GGAALGVPQ GLQNPQATK 
KQEDHIKRP MNAFMVWSR LQRRKIAQE NPKMHNSEI 
SKRLGAEWK LLTEDEKRP FIDEAKRLR AMHMKEHPD 
YKYRPRRKP KTLRKEGYP YSIPYPSVP MDALRAGMA 
ASSMGQSMA SYYNPSAAY GSLSAASMA AAAAAAQQS 
AAAMSAGLT APAQVVSSM DAMKYSMEA DKYRSPYIP 
PSTLAMSMY SDPKYMDSS SKSYLERGY LDSTSALTK 
AYFESSKMY MDSKYNPDP SRSYPLDIG KMYSDASAP 
QQVPGNLGS PRSPDSPDV KPNPERQDG ASSSSSTTT 
SSAGASPGA LPGYYPSSG MQQGATVPG LLPMAQYAS 
QYPTQTPGG EFRRPLTVI F
    CDS sequence
    • >TC013165 RA
      atgtgcgag ggcggcttc agtgccgcg gagggactc 
tcgaggatg gcttccttg ggtggagcc gccttgggc 
gtccctcaa ggtctgcaa aacccgcaa gcaacgaag 
aagcaagaa gaccacatc aagcggccg atgaacgcc 
ttcatggtg tggtcgcgg ctgcagagg cgaaaaatt 
gctcaagaa aaccccaaa atgcacaac tcggaaatc 
tccaagcga ttaggtgcg gaatggaag ctcctgacg 
gaggacgaa aagcggcct ttcatcgac gaagcaaaa 
cggttacgt gcaatgcat atgaaggag catcccgac 
tacaaatac cggccaaga cgtaagcca aaaaccttg 
cgaaaagaa ggctatccc tactcgatt ccataccct 
tcagtgcca atggacgca ttgagagct ggcatggcc 
gccagcagc atgggtcag tccatggcc tcgtactac 
aacccatcg gccgcctac ggctcccta agtgccgcc 
tccatggcg gcggcagcg gcggcggcc cagcaatcg 
gccgctgca atgtccgca ggactcaca gcacccgct 
caggtggtg agttcgatg gacgccatg aagtactcc 
atggaagcg gacaagtac cgctcgccc tacatcccc 
ccatccacc ctggccatg tccatgtac tccgacccc 
aagtacatg gactcgtcc tcgaagagc tacctggag 
cgcggctac ctggactcg acctccgcc ctcaccaag 
gcctacttc gagtcctcc aagatgtac atggacagc 
aagtacaac ccggacccc tcacggtcg taccccctg 
gacatcggc aagatgtac tcggacgcc tccgccccc 
cagcaagtc ccggggaat ttggggtcg ccccggtcg 
ccggactcc ccggacgtg aagcccaac ccggagcgg 
caggacggg gcgtcgtcg tcgagttcg acgacgacg 
tcgtcggcc ggggcctcg ccgggggcc ctcccgggg 
tactacccc agcagcggc atgcagcaa ggagccaca 
gtgcccgga ctcctgccc atggcccag tacgccagc 
cagtacccc acacagacg cccggagga gagttccgg 
agacccctc actgtaata ttttga
    mRNA sequence
    • >TC013165 RA
      tgccacaac tgcatagag ttcagtgct tttcggtga 
gatacacgc atttacacc tatgtcgcc aatgttgcc 
attatttct gacaatagg gacattgta attaattgt 
gcgattgtg ccgtgtgtt ggactgata ggttttgtg 
ctaatcatc gggacgaaa ctgcttcaa aattgatct 
ggacctaca gaggcaggc ctccaacgg ccacttcat 
cagatctgt gggtcagat gtgcgaggg cggcttcag 
tgccgcgga gggactctc gaggatggc ttccttggg 
tggagccgc cttgggcgt ccctcaagg tctgcaaaa 
cccgcaagc aacgaagaa gcaagaaga ccacatcaa 
gcggccgat gaacgcctt catggtgtg gtcgcggct 
gcagaggcg aaaaattgc tcaagaaaa ccccaaaat 
gcacaactc ggaaatctc caagcgatt aggtgcgga 
atggaagct cctgacgga ggacgaaaa gcggccttt 
catcgacga agcaaaacg gttacgtgc aatgcatat 
gaaggagca tcccgacta caaataccg gccaagacg 
taagccaaa aaccttgcg aaaagaagg ctatcccta 
ctcgattcc atacccttc agtgccaat ggacgcatt 
gagagctgg catggccgc cagcagcat gggtcagtc 
catggcctc gtactacaa cccatcggc cgcctacgg 
ctccctaag tgccgcctc catggcggc ggcagcggc 
ggcggccca gcaatcggc cgctgcaat gtccgcagg 
actcacagc acccgctca ggtggtgag ttcgatgga 
cgccatgaa gtactccat ggaagcgga caagtaccg 
ctcgcccta catcccccc atccaccct ggccatgtc 
catgtactc cgaccccaa gtacatgga ctcgtcctc 
gaagagcta cctggagcg cggctacct ggactcgac 
ctccgccct caccaaggc ctacttcga gtcctccaa 
gatgtacat ggacagcaa gtacaaccc ggacccctc 
acggtcgta ccccctgga catcggcaa gatgtactc 
ggacgcctc cgcccccca gcaagtccc ggggaattt 
ggggtcgcc ccggtcgcc ggactcccc ggacgtgaa 
gcccaaccc ggagcggca ggacggggc gtcgtcgtc 
gagttcgac gacgacgtc gtcggccgg ggcctcgcc 
gggggccct cccggggta ctaccccag cagcggcat 
gcagcaagg agccacagt gcccggact cctgcccat 
ggcccagta cgccagcca gtaccccac acagacgcc 
cggaggaga gttccggag acccctcac tgtaatatt 
ttgaccaga tcggttgtg aatgtgatt ggtgggttt 
taggtgcgt tcgtgtgaa tatctctct aagtattct 
agccgcaaa ggcaaccat agacgtaat tgtatgtaa 
acgtataca tagttaaaa gaatttgtt tcgattgga 
aattaattt attttgttt tgttcaaat tttaaatac 
ctaacactt gtataaatg taaataatt ctctagcgt 
gtacaaata gttgttttt aattatgta ttattgcaa 
caaccacgt tgtccttat ttcgaagta ttgtacaaa 
gcgcttggt tagttcaca caaattttt gttcctatt 
tttcggtag ctataaact acgtatcca cgcatatac 
cttgttatt atgaactta tctacatat agaattaat 
gtaatggta tgttattga aaaatccaa aaaatctcg 
aacaataaa ctagtttgt gattg

    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