Status
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Gene information
General information
TC013905 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: 488124..499872
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
    		TC013905
    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_02224

    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 not developed/not fertilized - Penetrance (percentage of animals/eggs on slide): less than 30%
    embryo/egg with embryonic tissue, no cuticle, no fluorescence - 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%
    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): 50% - 80%
    cuticle remnants with some identifiable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

    larva complete circumference irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae - 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: 20.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 20.0% (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC013905 RA
      MFAYQDDDM DSDPFINIT GGRAPGGAF 
RSQSFNFQG SPQRGKDKQ DPAIEHDLY 
VSLEDIAKG CTKKMKISR KVLQADGST 
RSEDKVLTI NVKPGWKAG TKITFPREG 
DQGPNKIPA DIVFIIRDK SHPLFKREG 
SDIKYVAKI TLKQALCGC SIEVPTLTG 
QKIPIHFTN EVVKPTTVR RLQGYGLPL 
PKEPSRRGD LIVNVDIKF PERLSQSAK 
DILYDTLPN
    CDS sequence
    • >TC013905 RA
      atgtttgcg taccaagac gacgacatg gactccgat 
ccgtttatt aacatcacg ggtgggagg gctcctggg 
ggcgccttc cgcagccag tccttcaac ttccagggc 
agcccccag cgcgggaaa gacaagcag gaccccgct 
atcgagcac gacctctac gtctcgctg gaggacatc 
gccaaaggc tgcacgaag aagatgaag attagcagg 
aaggtgttg caagcggac ggctctacg aggagcgaa 
gacaaggtt ttgactatt aatgtgaag ccggggtgg 
aaagcggga actaagatc accttcccc agggaaggg 
gaccaaggg ccaaataaa atcccggcg gatattgtg 
tttatcatc agggataag tcgcatcct ttgttcaaa 
cgtgaggga agtgatatt aaatatgtg gctaagatt 
acgctcaag caggctttg tgcgggtgt tcgattgaa 
gtgccaacc ctaaccggc cagaaaatc cctatccat 
ttcaccaac gaggttgtt aaacccaca acagtgagg 
aggttgcaa ggttacggc ttgccccta cccaaggaa 
ccttccaga agaggagat ctcattgtc aatgttgac 
atcaagttt ccagagagg ctttcacaa tctgctaag 
gacattttg tacgataca ttgcctaac taa
    mRNA sequence
    • >TC013905 RA
      ttaagagtg tattctcat tttctgcag cccaagtcg 
atgaatttt tcttcgctc aatttttat tttaaattc 
tttcagaaa acgtcttta tccattttc cgtcttgcc 
agaggttct ttataatag tttgcactg tattaatgt 
ataatacca agagtcccg attagatta tgcttttct 
tttgatttc tttggttca gcagtaaag ctcttaaac 
ggtctttac agaattttc cactgcttg ttcgaatgt 
gtcgtttca ccttgtacg attgtagaa aatgttccg 
ttaatttta agttgagaa tgttccgtt atcggaaac 
tgttgtttc tcaatcaac cttctacat tatttacgg 
ccatttcga gaaaaggtg aatgtaaga aacattggt 
tttcgtatt tattgtata tcggatttt tcataaggt 
tctcatggt ctcatttct tgcttggct ttttcttaa 
catcgtcaa agtacccta tacaatttg tctggtatt 
tgtgctcgc aatttggtt gttataata tatcaccct 
acattaatt ttttttcct aagttacct cgttttttc 
tgtcaaaat acagtttag gaaaaaatt ctaccctat 
ttctccatt tgcctctcg tcaacttga tttttctca 
acatattgt ctctttttg tagttaaac ccgataaga 
aattgctca attttccaa cctgttaag gatttgtgc 
ccccataaa taatgttga aacttcttc actctatag 
tatacattg tttccctcc aatccgtcg agtaatttt 
tctctgttg ctgtcttgt atatgattt aaaactgtt 
gacattctg tcttttgta gaatcattt tgtcattaa 
gatggatag ttttatgag gttaaaatg ggctaaaca 
gaaatgtga agtcaacag tttttttat tttcttaaa 
tatttcgtc acattagct attcttaat tatttttgc 
atgtttttt cagtaagtg agtgatggg tttgagtaa 
taaagccga tgagtgtta gctcaattt cagtttagt 
ttagtgtta gttgcagtt cagtttcaa ttcaatttt 
aattaagtt cagctaaca acactgtgg tgacgtgaa 
caacaggaa ataagtgtt tactgatag aaatagtgt 
ctctagaaa gtgctttgg gcctcgaaa aagtgtgtg 
cacattacg aaattgctc agcttggat gccagctag 
atagtacgt caactgtcg tcgcacatt tggactaca 
gactcacca tacagaaat tcaccaagc aatgcttca 
ggaaagaga tgttcgtta taatgaaga ggaggctga 
tcaacgttg cctcttggt ttttctatg attttattt 
gcggaaaaa tgctgcttc agcttttcc tgaaatttc 
cagccgcgt cctccagcg gggtgcgac aattccaga 
atcttctag aaattccta acctatata aagcatcga 
cgcgagcgc tcgcgcact caatacgaa acgaacaat 
cactacgtg tacactaat ttattctcg aagaagctt 
gtgatttta agtttgtgt ggacttttc gtgacatta 
gtgcagtga aaatgggaa aagactatt accgaatcc 
tcggcatat caaaaggag ccagtgacg acgagatca 
agaaagcct accgcaaac tcgccctca aataccacc 
cggacaaga acaagtcca aagaggctg aagagcgct 
tcaaggaag tggccgagg cttacgaag ttctttccg 
acaagaaaa aacgcgaca tctacgacg cctacggcg 
aggagggcc tcaaggggg ggcatcccc ggcgactct 
ggcacctca gcccccggg ggcttcacc tacacctac 
cacggagac ccgcgcgcc accttcgcc cagttcttc 
ggcaatgcg agccccttc gaagccttc ttcagaggc 
aatcagacc atgtttgcg taccaagac gacgacatg 
gactccgat ccgtttatt aacatcacg ggtgggagg 
gctcctggg ggcgccttc cgcagccag tccttcaac 
ttccagggc agcccccag cgcgggaaa gacaagcag 
gaccccgct atcgagcac gacctctac gtctcgctg 
gaggacatc gccaaaggc tgcacgaag aagatgaag 
attagcagg aaggtgttg caagcggac ggctctacg 
aggagcgaa gacaaggtt ttgactatt aatgtgaag 
ccggggtgg aaagcggga actaagatc accttcccc 
agggaaggg gaccaaggg ccaaataaa atcccggcg 
gatattgtg tttatcatc agggataag tcgcatcct 
ttgttcaaa cgtgaggga agtgatatt aaatatgtg 
gctaagatt acgctcaag caggctttg tgcgggtgt 
tcgattgaa gtgccaacc ctaaccggc cagaaaatc 
cctatccat ttcaccaac gaggttgtt aaacccaca 
acagtgagg aggttgcaa ggttacggc ttgccccta 
cccaaggaa ccttccaga agaggagat ctcattgtc 
aatgttgac atcaagttt ccagagagg ctttcacaa 
tctgctaag gacattttg tacgataca ttgcctaac 
taaacagtt tgtttatgt aattgaata agtcaggct 
gtacgtttt agtacaaat tagttaaat ttaagcttt 
gttaattta atcgacttg tatgatgtt tattgtatt 
ataaagtag cgtcgtgtg tgatatttt atctgttat 
gaattagta ataaactct tttattatt t

    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