Status
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Gene information
General information
TC005634 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_007423.3: 10431644..10433148
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
      		TC005634
      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
      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
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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_00901

      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: 30.0% (includes death as pupa, adult)

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

      Analysis of larval stage 1 cuticle
      number of eggs/embryos/larvae on slide: < 20
      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: 40.0% (includes death as larva, prepupa, pupa)
      Lethalities 22 days after larval injection: 40.0% (includes death as larva, prepupa, pupa, adult)

      larva lethality - Number of animals showing the phenotype: 4 (11 dpi)
      Days post injection

      RNAi sequence
      Primers
      Left: Right:
      Protein sequence
      • >TC005634 RA
        MNHIWVICA VLYFSSMSY GLKCPTCKG ANCDKKSEI 
LLQECSFRH PFPLYRSQA TFLTAESNY GCLQFKYVK 
DNNVEEIKQ CIVVDSQRD VCKDLKSTF DVKSCSVRV 
PLQEGFERE GEDNGESVS STSNPESTP SSTESTPSS 
TESTPSSTE STPSSTEST PSTTESTPS STESTPSST 
ESTPSSTES TPSSTESTP SSTESTPSS TQSTSSSTE 
STPSSTEST PSSTESTPS STESTPSST KSTPSSTES 
TPSSTQSTP SSTESTPSS SESTPSSTQ STPSSTEST 
PSSTESTSS GTDSTTTSA DSTTASSSS TSSSTDSTG 
SSTDRTTSS TDSTSSSTG STGSSTNGT PSSTDNPPS 
TTPSSATSI QTSFGVLLA AAFYIRWM
      CDS sequence
      • >TC005634 RA
        atgaatcac atttgggtg atttgtgca gttttgtat 
tttagttcc atgtcatat ggactgaaa tgtccgacc 
tgtaagggt gcaaactgt gataaaaaa tcagagatt 
cttctgcaa gaatgtagt tttcgtcat ccttttcct 
ctataccga agtcaagca acttttcta actgccgaa 
tctaattat ggatgtttg cagtttaaa tatgttaaa 
gacaataat gttgaagaa ataaagcaa tgcattgtt 
gtggattcg caaagagat gtttgtaaa gatttgaag 
tcaactttt gatgtgaaa agttgtagt gttagagta 
ccattacaa gaaggtttt gaacgtgaa ggtgaagat 
aacggtgaa tcagtgagc tccacatct aatcctgaa 
agtacccca tctagtaca gaaagcaca ccatctagt 
acagaaagt accccatct agtacagaa agtacccca 
tctagtaca gaaagcaca ccatctact acagaaagt 
acaccatct agtacagaa agtactcca tctagtaca 
gaaagtacc ccatctagc acagaaagc acaccatca 
agtacagaa agtaccccg tctagtaca gaaagcaca 
ccatctagt acacaaagc acatcatca agtacagaa 
agtacccca tctagtaca gaaagcaca ccatctagt 
acagaaagc acaccatct agtacagaa agtacccca 
tctagtaca aaaagtacc ccgtctagt acagaaagc 
acaccatct agtacacaa agcacacca tcaagtaca 
gaaagtacc ccgtctagt tcagaaagc acaccatct 
agtacacaa agcacacca tcaagtaca gaaagtacc 
ccatctagt acagaaagt acttcatct ggtactgac 
agcactacg actagcgcc gacagcaca acagctagt 
tcaagcagc acctcatct agtaccgac agcacggga 
tctagtaca gacagaacc acatctagt acagacagt 
acttcgtct agtacaggc agcaccggt tctagtaca 
aacggtact ccgtctagt actgataat cccccttca 
acaacgcca tcttctgct acatctatt caaacatca 
tttggcgtt ttactagca gctgctttc tacatcagg 
tggatgtaa
      mRNA sequence
      • >TC005634 RA
        cgtatttaa gctcctgct aatccaggt tgtacatta 
cttcgttct ggtagtcag actaaacca cctccacga 
tgaatcaca tttgggtga tttgtgcag ttttgtatt 
ttagttcca tgtcatatg gactgaaat gtccgacct 
gtaagggtg caaactgtg ataaaaaat cagagattc 
ttctgcaag aatgtagtt ttcgtcatc cttttcctc 
tataccgaa gtcaagcaa cttttctaa ctgccgaat 
ctaattatg gatgtttgc agtttaaat atgttaaag 
acaataatg ttgaagaaa taaagcaat gcattgttg 
tggattcgc aaagagatg tttgtaaag atttgaagt 
caacttttg atgtgaaaa gttgtagtg ttagagtac 
cattacaag aaggttttg aacgtgaag gtgaagata 
acggtgaat cagtgagct ccacatcta atcctgaaa 
gtaccccat ctagtacag aaagcacac catctagta 
cagaaagta ccccatcta gtacagaaa gtaccccat 
ctagtacag aaagcacac catctacta cagaaagta 
caccatcta gtacagaaa gtactccat ctagtacag 
aaagtaccc catctagca cagaaagca caccatcaa 
gtacagaaa gtaccccgt ctagtacag aaagcacac 
catctagta cacaaagca catcatcaa gtacagaaa 
gtaccccat ctagtacag aaagcacac catctagta 
cagaaagca caccatcta gtacagaaa gtaccccat 
ctagtacaa aaagtaccc cgtctagta cagaaagca 
caccatcta gtacacaaa gcacaccat caagtacag 
aaagtaccc cgtctagtt cagaaagca caccatcta 
gtacacaaa gcacaccat caagtacag aaagtaccc 
catctagta cagaaagta cttcatctg gtactgaca 
gcactacga ctagcgccg acagcacaa cagctagtt 
caagcagca cctcatcta gtaccgaca gcacgggat 
ctagtacag acagaacca catctagta cagacagta 
cttcgtcta gtacaggca gcaccggtt ctagtacaa 
acggtactc cgtctagta ctgataatc ccccttcaa 
caacgccat cttctgcta catctattc aaacatcat 
ttggcgttt tactagcag ctgctttct acatcaggt 
ggatgtaat taatttttt cgcaaatat ttatacgta 
ataacttat ttattgtaa tcagatttt gtataaacg 
gataatatt ttcatggtt atgttaatt tataacaga 
actgcagtt gttactaac agacgaaat aaacctaca 
tttgtttt

      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