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Gene information
General information
TC013645 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: 7106587..7109248
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
      		TC013645
      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_05472

      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: 40.0% (includes death as pupa, adult)

      pupa eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 2 (3 dpi)
      Days post injection

      adult lethality - Number of animals showing the phenotype: 2 (9 dpi)
      Days post injection

      Fertility
      mature egg deposition number 2nd lateral oviduct: 2 number 1st lateral oviduct: blocked - Number of animals showing the phenotype: 1
      ovary without detectable defects - Number of animals showing the phenotype: 2
      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: 60.0% (includes death as larva, prepupa, pupa)
      Lethalities 22 days after larval injection: 60.0% (includes death as larva, prepupa, pupa, adult)

      larva lethality - Number of animals showing the phenotype: 5 (11 dpi)
      Days post injection

      RNAi sequence
      Primers
      Left: Right:
      Protein sequence
      • >TC013645 RA
        MFPFEFKFK YSQNKSAKE LRLSDYKSR VFTGVQYLT 
MILVVSSSF FTGVARPDM SWKISQHCE DPKFNQPLT 
QVDKTWAIG TTVVVSLII VCLMSTKML FYGWENKDV 
LDIVNYFFG ILSLWVACY ALKSLIGYP IPSFFTKNE 
LYAFYCCKH CLPIPQTKK LTELDLDSR GSFPSFLIC 
ALSYSSTFL FVVCTYLDE NRRFAAKLL ALLLPGGVS 
FIYSWYLWQ SNEHHLQDV VGGALLGCF LGAYIARDI 
YKRDNTSAR FQDDFVTVL MAREIIAQA ERANRGGTH 
TPNEYVINL YPHENEAIG TQNSNNNNA VVAFNDDPP 
PYSSLNLAE
      CDS sequence
      • >TC013645 RA
        atgttcccg ttcgaattc aaattcaag tattcccaa 
aataaatcg gccaaagag cttcggctc tctgactac 
aaatcccga gttttcact ggggttcag tacctaact 
atgatccta gtcgtttct tcttcattt ttcacgggc 
gtcgcccgc ccggacatg tcttggaaa atctcccaa 
cactgcgag gaccctaaa ttcaaccaa cccttaact 
caagttgac aagacatgg gcaattggg acaactgtc 
gtcgttagt ctcataatc gtgtgtctg atgtcaacc 
aagatgctg ttttacggc tgggagaac aaggatgtg 
ctggacata gtgaactac ttctttggc attttgtct 
ttatgggtt gcatgttac gccctgaag agcctcatc 
ggttacccc atcccgtct ttcttcacc aaaaatgaa 
ctctacgcg ttttattgt tgcaaacat tgtcttccc 
atcccacaa acgaaaaaa ctaactgaa cttgacctc 
gactcccgt ggctctttt ccctctttc ctgatctgc 
gccctctcc tactcctct actttcctc tttgtagtt 
tgcacttat ctggacgaa aatagacgt tttgctgct 
aaactcctt gcactgttg ctgcctgga ggcgtctcg 
ttcatctac tcttggtac ctttggcaa agcaacgag 
caccatctc caggacgtc gtcgggggt gcacttctt 
gggtgtttt cttggcgca tacattgca agagatatc 
tataaacgt gacaacaca tctgccaga tttcaggac 
gacttcgtt accgtgctt atggcaagg gagatcatt 
gcacaagcg gagagggca aatcgaggc ggaacgcac 
acgcctaac gaatatgtc attaatctg tacccgcac 
gaaaatgaa gctattgga actcaaaat agcaacaat 
aacaatgcc gtagtcgcc ttcaacgac gatccacca 
ccgtattcc agtcttaat ctcgcagag taa
      mRNA sequence
      • >TC013645 RA
        tgacacggc ccccaccta atgagagga gtccacccc 
ggcaaagtt ttgttagag tttcagttg caaaaaaga 
tgttcccgt tcgaattca aattcaagt attcccaaa 
ataaatcgg ccaaagagc ttcggctct ctgactaca 
aatcccgag ttttcactg gggttcagt acctaacta 
tgatcctag tcgtttctt cttcatttt tcacgggcg 
tcgcccgcc cggacatgt cttggaaaa tctcccaac 
actgcgagg accctaaat tcaaccaac ccttaactc 
aagttgaca agacatggg caattggga caactgtcg 
tcgttagtc tcataatcg tgtgtctga tgtcaacca 
agatgctgt tttacggct gggagaaca aggatgtgc 
tggacatag tgaactact tctttggca ttttgtctt 
tatgggttg catgttacg ccctgaaga gcctcatcg 
gttacccca tcccgtctt tcttcacca aaaatgaac 
tctacgcgt tttattgtt gcaaacatt gtcttccca 
tcccacaaa cgaaaaaac taactgaac ttgacctcg 
actcccgtg gctcttttc cctctttcc tgatctgcg 
ccctctcct actcctcta ctttcctct ttgtagttt 
gcacttatc tggacgaaa atagacgtt ttgctgcta 
aactccttg cactgttgc tgcctggag gcgtctcgt 
tcatctact cttggtacc tttggcaaa gcaacgagc 
accatctcc aggacgtcg tcgggggtg cacttcttg 
ggtgttttc ttggcgcat acattgcaa gagatatct 
ataaacgtg acaacacat ctgccagat ttcaggacg 
acttcgtta ccgtgctta tggcaaggg agatcattg 
cacaagcgg agagggcaa atcgaggcg gaacgcaca 
cgcctaacg aatatgtca ttaatctgt acccgcacg 
aaaatgaag ctattggaa ctcaaaata gcaacaata 
acaatgccg tagtcgcct tcaacgacg atccaccac 
cgtattcca gtcttaatc tcgcagagt aactccact 
ttgttattt catttattt tattatata tccgtatta 
acatattat atatttata ttatattat tgttatttt 
tattactac catattatg tttgtgtgt tctattact 
gtattttaa aaatgaata ataaagtat ttttttgaa 
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      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