Status
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Gene information
General information
TC016363 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_007422.5: 7054157..7092107
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
    		TC016363
    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
    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_06007

    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)

    adult lethality - Number of animals showing the phenotype: 1 (9 dpi)
    Days post injection

    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): 30% - 50%
    head irregular - 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): 30% - 50%
    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: -1.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: -1.0% (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC016363 RA
      MYTPKLSQM DISENSTYL FDKHEDRNN TDRDENLAR 
VEVATLAII FLVTVIGNS TVLLALWTR RRYAGRKKL 
SRMYFFILH LSIADLITA FLSVLPQLA WDITYRFYG 
GFLLCKVVK YGQTLGPYL SSYVLMATA IDRHQAICY 
PLTYCSWTS RRSKVMVYL AWVASLAFC IPQLTIFTY 
TSVGEDEYD CWATFQEPW GKRAYVTWY SISVFMVPL 
VVLIFTYTS ICIEIWQSS ESSLRPRSS QKSAPGKRT 
PLISRAKIN TVKQTIAVI VMYIACSTP FILAQLWAT 
WDPQSPFID GPVFVILTL LYSLNSCVN PWIYLAFNR 
ELPRLLLRH YTASSKNYR SATGGNSAS NSSGDAQST 
SLRPFSRWS LCNSARSNK YPTRVPHRP YVAQYNARR 
WIVTTTT
    CDS sequence
    • >TC016363 RA
      atgtacacc ccgaaactt tcccaaatg gacatctct 
gagaactct acgtatctc ttcgacaaa cacgaagac 
agaaacaac accgatcgg gacgaaaac ctcgcccgc 
gtggaggtt gccaccctt gccatcata tttcttgtc 
accgtcatc gggaacagc acagtatta ctggcttta 
tggacccgc cgaagatac gccggtcgc aagaaactc 
tcccgaatg tacttcttt atcttacat ctgagcatc 
gccgatttg atcacggct tttctcagc gtactgccg 
cagctggcc tgggacata acttataga ttctacgga 
ggtttcctt ctctgtaaa gtcgttaaa tatggacag 
actttaggt ccgtatctg agctcgtac gtgctgatg 
gcgacggcc attgatcgc catcaggcc atttgttac 
cctttgacc tactgctcg tggacttcc aggaggtcg 
aaagttatg gtgtatctg gcgtgggtg gccagcctc 
gccttctgt attccacag ctgacgatc ttcacatac 
acgagcgtc ggagaagac gaatacgac tgctgggcc 
actttccaa gaaccatgg ggtaaaaga gcttacgtc 
acatggtac agcatttct gtgttcatg gtgccgttg 
gtggttcta attttcacg tatacgtcg atttgtatc 
gagatttgg caaagctcg gaatcgagt ctgcgacca 
cgaagctct cagaaatca gcacctggg aaacgtacc 
cctttgatc tctcgagcg aagattaat actgtcaag 
cagactatt gccgtcatt gtaatgtat atagcgtgc 
tcgactccg ttcattcta gcacaacta tgggccact 
tgggacccc caaagcccc ttcatcgac ggcccggtg 
tttgtaatc ttaacgctc ctctactcg ctaaacagc 
tgtgtaaat ccttggatt tatctggca ttcaaccgg 
gagttgccg cgcctcctg ctccgtcac tacacggct 
tccagcaag aactaccgt tctgcgacc ggaggtaac 
agtgcaagt aactcctca ggtgacgcg cagagcacg 
tcattgcgg ccgttctcg cgctggtcg ctctgcaac 
agcgccagg tccaacaag taccccacg agggtgccg 
cacaggccc tacgtcgcc cagtacaac gcccgccgg 
tggatcgtc acgacgacc acctga
    mRNA sequence
    • >TC016363 RA
      cgcaagcac cgaagagaa gttgaatgg acttgcgat 
gcgacgcgc cagtgaaga aacagtgcg aatttttac 
taacttttg aattaaaca agaacaaga cagtaaaat 
cgcagttta aggacttag aaatccgag tgttggtgg 
atttttata tcgaaaagt ttcaacaac tggaaactt 
cgctgaaag accgaaata atttcaaaa tagtctcat 
gtacacccc gaaactttc ccaaatgga catctctga 
gaactctac gtatctctt cgacaaaca cgaagacag 
aaacaacac cgatcggga cgaaaacct cgcccgcgt 
ggaggttgc cacccttgc catcatatt tcttgtcac 
cgtcatcgg gaacagcac agtattact ggctttatg 
gacccgccg aagatacgc cggtcgcaa gaaactctc 
ccgaatgta cttctttat cttacatct gagcatcgc 
cgatttgat cacggcttt tctcagcgt actgccgca 
gctggcctg ggacataac ttatagatt ctacggagg 
tttccttct ctgtaaagt cgttaaata tggacagac 
tttaggtcc gtatctgag ctcgtacgt gctgatggc 
gacggccat tgatcgcca tcaggccat ttgttaccc 
tttgaccta ctgctcgtg gacttccag gaggtcgaa 
agttatggt gtatctggc gtgggtggc cagcctcgc 
cttctgtat tccacagct gacgatctt cacatacac 
gagcgtcgg agaagacga atacgactg ctgggccac 
tttccaaga accatgggg taaaagagc ttacgtcac 
atggtacag catttctgt gttcatggt gccgttggt 
ggttctaat tttcacgta tacgtcgat ttgtatcga 
gatttggca aagctcgga atcgagtct gcgaccacg 
aagctctca gaaatcagc acctgggaa acgtacccc 
tttgatctc tcgagcgaa gattaatac tgtcaagca 
gactattgc cgtcattgt aatgtatat agcgtgctc 
gactccgtt cattctagc acaactatg ggccacttg 
ggaccccca aagcccctt catcgacgg cccggtgtt 
tgtaatctt aacgctcct ctactcgct aaacagctg 
tgtaaatcc ttggattta tctggcatt caaccggga 
gttgccgcg cctcctgct ccgtcacta cacggcttc 
cagcaagaa ctaccgttc tgcgaccgg aggtaacag 
tgcaagtaa ctcctcagg tgacgcgca gagcacgtc 
attgcggcc gttctcgcg ctggtcgct ctgcaacag 
cgccaggtc caacaagta ccccacgag ggtgccgca 
caggcccta cgtcgccca gtacaacgc ccgccggtg 
gatcgtcac gacgaccac ctgaaatac ggagaccgg 
tggtctgcc agaccacga catcgacga tatttccgg 
ctcctcgct gctggaaat cagcgagct gacgaccga 
attgacaga aatggaatc tgtgatgtg acagcacga 
cgatgctac ttgtacctg acctcaagg aactattta 
tttgtaatt ttgcgtgtt ttcgagttt taaatagta 
cgaaagtcc acttctgtc cactcccat acgtgtaat 
tttgtactt ttgatgtga tacttgtta actccgaag 
atacattat tcttgtttc tgggttact caaatgttg 
tgagatttc atattttat aaggaaata ttatataat 
ttgctgtaa tatttttct aaataaatt caacttgca 
tac

    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