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Gene information
General information
TC002113 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_007418.3: 20390483..20391666
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
      		TC002113
      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_03306

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

      RNAi sequence
      Primers
      Left: Right:
      Protein sequence
      • >TC002113 RA
        MALLKSKVK GCRDPKMMA VNSRMLFTL LFLLQNRAN 
GCKSLVDSN SNIESKELS HLDSSQISQ NKLDFSVTK 
NGAGTIRKQ GTDLDLKSI KRPNFSNIE QIKDIFEDS 
HYESSHRYK RKAPERSLS NLFKRLNEE LKKDDLMAA 
DANPRLEPN YTGTPKKMN DDSRFGGIN TEQLYNKKN 
DKIRQLHLQ HNEEKLKIV EPALDTDCE FETECTWTW 
RKDIANGFF VTSGDKLAM NETGPKVDA SSNALGKSY 
CF
      CDS sequence
      • >TC002113 RA
        atggctttg ttgaaaagc aaggtaaaa ggatgtaga 
gacccaaaa atgatggct gttaatagt agaatgctc 
tttacgtta ctattttta ctccaaaac agagcaaat 
ggttgcaag agtttagta gactcgaac tcgaacatc 
gaatctaaa gaattgtca cacttagat tcaagccag 
atttcacaa aacaaatta gattttagc gtaactaaa 
aatggtgct ggaacaata agaaagcaa ggcactgac 
ttagattta aaatcaatc aaacgtcca aactttagc 
aatatagaa caaataaaa gacatattt gaagattct 
cattacgaa tccagccat cgctacaag agaaaagct 
ccagagcgg agtctttcc aaccttttc aaacgactc 
aatgaggaa ctgaagaag gatgacctt atggccgct 
gacgccaat cctaggtta gaacccaac tacactgga 
acaccaaag aagatgaac gatgattcg cgctttggt 
ggcattaac accgagcag ctgtacaac aagaagaac 
gacaaaatt cgccagttg catctgcag cacaacgag 
gaaaagctc aaaatcgtg gaaccggct ctggacacc 
gactgcgag tttgagacg gaatgcact tggacctgg 
aggaaggac atcgccaat gggtttttt gtgacttcg 
ggggacaaa ctggccatg aacgagaca ggacctaag 
gtggacgcg agctcaaac gcccttggt aagtcttac 
tgtttttag
      mRNA sequence
      • >TC002113 RA
        gacagtgaa agaataaca tacaattaa agcggaaac 
acaatattt ttaaaatgt ggtgtattc gtatggcgt 
aatgttcac ccaaggtgt ttgaacggc tcaacccgg 
aatggcttt gttgaaaag caaggtaaa aggatgtag 
agacccaaa aatgatggc tgttaatag tagaatgct 
ctttacgtt actattttt actccaaaa cagagcaaa 
tggttgcaa gagtttagt agactcgaa ctcgaacat 
cgaatctaa agaattgtc acacttaga ttcaagcca 
gatttcaca aaacaaatt agattttag cgtaactaa 
aaatggtgc tggaacaat aagaaagca aggcactga 
cttagattt aaaatcaat caaacgtcc aaactttag 
caatataga acaaataaa agacatatt tgaagattc 
tcattacga atccagcca tcgctacaa gagaaaagc 
tccagagcg gagtctttc caacctttt caaacgact 
caatgagga actgaagaa ggatgacct tatggccgc 
tgacgccaa tcctaggtt agaacccaa ctacactgg 
aacaccaaa gaagatgaa cgatgattc gcgctttgg 
tggcattaa caccgagca gctgtacaa caagaagaa 
cgacaaaat tcgccagtt gcatctgca gcacaacga 
ggaaaagct caaaatcgt ggaaccggc tctggacac 
cgactgcga gtttgagac ggaatgcac ttggacctg 
gaggaagga catcgccaa tgggttttt tgtgacttc 
gggggacaa actggccat gaacgagac aggacctaa 
ggtggacgc gagctcaaa cgcccttgg taagtctta 
ctgttttta gcaggatat cctgcaaat atttaaatc 
gtttaaaat aatctcgct tgaatttaa actgtttac 
atcggaatg attgatcat ttattcaac tccaataat 
aatgtaaaa taactaaaa tatactgaa acgt

      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