Status
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Gene information
General information
TC001643 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: 2865474..2876214
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
    		TC001643
    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
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    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
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    Name
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    Email
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_00276

    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: 0.0% (includes death as pupa, adult)

    pupa eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 1 (3 dpi)
    Days post injection

    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 50
     abdomen segment number decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    posterior terminus sometimes decreased - 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): 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: 11.11% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 11.11% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC001643 RA
      MIHNVWSVQ SPRLTFFIS FMVLHIWHN PTDSGAVQL 
TQDNLDMTL ASNELVFIN FYAEWCRFS NILMPVFDE 
ASDKIAQEF PEPGKVVMG KVDCDKEGS VATRFHITK 
YPTLKVIRN GQPAKREYR GERSIEAFT NFIKKQLED 
PVKEFKELR ELNEIESNK RIVIGYFDR RDQPEYNIF 
RRVATNVKD DCQFYAGFG EASRTMHPE NQPIIVFRP 
DRDRSNDLD ETYTGSLSN FDELHIWVS EKCVPLVRE 
ITFENAEEL TEEGLPFLI LFHAPDDKE SIKRFTEIV 
QTDLLSEKQ SINFLTADG KKFAHPLHH LGKGEKDLP 
LIAIDSFRH MYLFPNYKD MEIPGKLKQ FIQDLYSGK 
LHREFHYGP DSDELSSSQ KAPTTPPES TFKKLAPSK 
NRYTLLKDE L
    CDS sequence
    • >TC001643 RA
      atgattcat aacgtttgg tcagtgcaa agccccagg 
ctcacattc tttatcagt tttatggtc ttacacatt 
tggcataac cccacagat agtggagcc gtccagtta 
acacaagat aatctggac atgactcta gcttcaaat 
gaattagtt tttatcaat ttttacgcc gagtggtgt 
aggtttagc aatattttg atgccagtg tttgacgaa 
gcctctgat aaaatcgcc caagagttt cccgaacct 
ggcaaagtt gttatggga aaagtcgat tgtgataaa 
gaaggatca gttgccaca agatttcac ataactaag 
tatccaact cttaaagtt atacgaaat ggacagccg 
gccaaaaga gagtatcga ggcgaacgt tcgatcgaa 
gcgttcacc aatttcatc aaaaaacag cttgaagac 
cctgttaaa gaattcaag gagttgagg gagcttaac 
gagattgaa tcaaataaa aggattgtt attggttat 
tttgaccgt cgagatcaa cctgaatac aacatattc 
agacgagtt gctacaaac gttaaagac gattgccaa 
ttttacgct ggttttggc gaagcttca cgcactatg 
catccagaa aatcaacca ataatcgtt tttcgacca 
gatcgagac cgttcaaat gatttagat gaaacttac 
acaggaagt ttatcaaat ttcgatgaa ttacacatt 
tgggtttct gaaaaatgt gtgcctcta gtgcgtgaa 
ataacgttc gaaaatgct gaagagttg acagaggaa 
ggattgcca tttttaatt ctgttccat gcacctgat 
gataaagaa agtattaag cgatttact gaaattgta 
caaacagat ctcctgtca gagaaacag tctatcaac 
ttcctgact gcggacggt aaaaaattt gcgcacccg 
ttgcatcac ctcggaaag ggcgaaaaa gacttgcca 
cttattgca attgatagt tttagacat atgtatctg 
tttccgaac tataaggat atggaaatc cctgggaaa 
ctgaaacag tttattcaa gatctctat tcaggcaaa 
ttgcatcga gagtttcat tacggtcct gattcggat 
gaacttagt tcgtcgcag aaagcgcca acaacccca 
cctgaaagt actttcaaa aagttagca ccatcaaag 
aatcgatat actctactt aaagatgaa ttgtaa
    mRNA sequence
    • >TC001643 RA
      gaattgaca cttgtgcgc ttaaccctt caaacttat 
atgacgttt tgaatcatc gaactgcct ggcttttac 
gcaaattta ttgtaaaat taataccgt aaacaatta 
tttatcaaa atgattcat aacgtttgg tcagtgcaa 
agccccagg ctcacattc tttatcagt tttatggtc 
ttacacatt tggcataac cccacagat agtggagcc 
gtccagtta acacaagat aatctggac atgactcta 
gcttcaaat gaattagtt tttatcaat ttttacgcc 
gagtggtgt aggtttagc aatattttg atgccagtg 
tttgacgaa gcctctgat aaaatcgcc caagagttt 
cccgaacct ggcaaagtt gttatggga aaagtcgat 
tgtgataaa gaaggatca gttgccaca agatttcac 
ataactaag tatccaact cttaaagtt atacgaaat 
ggacagccg gccaaaaga gagtatcga ggcgaacgt 
tcgatcgaa gcgttcacc aatttcatc aaaaaacag 
cttgaagac cctgttaaa gaattcaag gagttgagg 
gagcttaac gagattgaa tcaaataaa aggattgtt 
attggttat tttgaccgt cgagatcaa cctgaatac 
aacatattc agacgagtt gctacaaac gttaaagac 
gattgccaa ttttacgct ggttttggc gaagcttca 
cgcactatg catccagaa aatcaacca ataatcgtt 
tttcgacca gatcgagac cgttcaaat gatttagat 
gaaacttac acaggaagt ttatcaaat ttcgatgaa 
ttacacatt tgggtttct gaaaaatgt gtgcctcta 
gtgcgtgaa ataacgttc gaaaatgct gaagagttg 
acagaggaa ggattgcca tttttaatt ctgttccat 
gcacctgat gataaagaa agtattaag cgatttact 
gaaattgta caaacagat ctcctgtca gagaaacag 
tctatcaac ttcctgact gcggacggt aaaaaattt 
gcgcacccg ttgcatcac ctcggaaag ggcgaaaaa 
gacttgcca cttattgca attgatagt tttagacat 
atgtatctg tttccgaac tataaggat atggaaatc 
cctgggaaa ctgaaacag tttattcaa gatctctat 
tcaggcaaa ttgcatcga gagtttcat tacggtcct 
gattcggat gaacttagt tcgtcgcag aaagcgcca 
acaacccca cctgaaagt actttcaaa aagttagca 
ccatcaaag aatcgatat actctactt aaagatgaa 
ttgtaattt attttcttc tgtaaataa acatttttg 
aaacgt

    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