Status
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Gene information
General information
TC012889 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: 18783931..18808393
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
      		TC012889
      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_05349

      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: 2 (3 dpi)
      Days post injection

      adult lethality - Number of animals showing the phenotype: 1 (9 dpi)
      Days post injection

      Fertility
      ovary without detectable defects - Number of animals showing the phenotype: 2
      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 potentially present, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): less than 30%

      larval musculature pattern irregular - 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%
      remarks: muscle pattern potentially obscured by segmentation defect,
      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 cuticle remnants without visible segmentation, differentiation or axis - Penetrance (percentage of animals/eggs on slide): less than 30%

      cuticle remnants cuticle remnants with unidentifyable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

      appendages partially remaining - Penetrance (percentage of animals/eggs on slide): less than 30%
      head not present - Penetrance (percentage of animals/eggs on slide): less than 30%

      Comment: abdomen is stronger affected than thorax and head
      thorax not present - Penetrance (percentage of animals/eggs on slide): less than 30%
      Comment: abdomen is stronger affected than thorax and head
      abdomen partially not present - Penetrance (percentage of animals/eggs on slide): less than 30%

      abdomen not present - Penetrance (percentage of animals/eggs on slide): less than 30%
      Comment: abdomen is stronger affected than thorax and head
      affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): more than 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: 30.0% (includes death as larva, prepupa, pupa, adult)

      larva lethality early (L5/6) - Number of animals showing the phenotype: 2 (11 dpi)
      Days post injection

      eclosion not fulfilled (not completely eclosed) - Number of animals showing the phenotype: 1 (16 dpi)
      Days post injection

      RNAi sequence
      Primers
      Left: Right:
      Protein sequence
      • >TC012889 RA
        MIGANLRFG SSVANASLN ATKVFQCHP GGTAEAALI 
FALGTMGMA ANIALMGVI LANRQLRRW SQGLLFHQG 
AVDCARAAL LLPLGISIL HCQPVQKCS LVETAFLLL 
VTVATVNML TTVLNDSPV FPEDDDSDS LSDVPLLMD 
SPQCVLFGT FMIWFASIT INLGPTFLS GALAAQGEA 
GHKAPSCPL IHGPLRHYI LNALWIAVN LVCVFLTLF 
HLRKLHRDL TKANVEAVR VAGLVTTLV NVTGGGGAA 
ANGERASGA LEEHRRMRE YLRRMERDG VQRVKMFLV 
ITAAYVLFW GPLFFVTLV NHPIVGNPL GHEITLHIS 
YVHAIVNPT LFLVLHRGL RRATLDLCC GWIPLWLGN 
PNVPPPPDP PRTDISLLK PPLPVPAHP DSSMGDSDL 
SPWTPEPVN GGIQIPQYI SPEPSSPPE SD
      CDS sequence
      • >TC012889 RA
        atgataggt gccaacctg cgtttcggc agttcggtg 
gcgaatgca agtctcaat gccaccaag gtcttccaa 
tgtcatcct ggagggacc gctgaagcc gcgctgata 
ttcgcctta ggaacgatg ggaatggcc gccaatata 
gcgctcatg ggagttata ctggccaac agacagctc 
cgaaggtgg tctcagggc cttctcttc caccaagga 
gccgtcgac tgcgcccgt gcggctctc ctcctccct 
ctgggtatc tcaatcctc cactgccag ccggtgcag 
aaatgctcc cttgtggaa actgccttc ctcctcctg 
gtgacggtc gccaccgtc aacatgctg accacagtc 
ctcaacgac tcgcccgtc ttccccgag gacgacgac 
tccgactcc ctctccgac gtgcccctc ctcatggac 
tcgccccaa tgcgtgctc ttcggcacg ttcatgatc 
tggttcgcg tcgattacc atcaacttg ggccccacg 
ttcctctcg ggggcgctg gcggcccaa ggcgaggcg 
ggccacaag gccccctcg tgccccctc atccacggc 
ccgctgcgc cactacatc ctcaacgcg ctctggatc 
gccgtcaac ctggtgtgc gtctttctg acgctcttc 
cacttgcgg aagctgcac cgcgacctc accaaggcc 
aacgtggag gcggtgcgg gtggcgggc ctcgtcacc 
acactggtg aacgtgaca ggaggcggc ggcgctgcc 
gccaacggg gagcgggcc tccggcgcc ctcgaagag 
caccgcaga atgcgagaa tacctccgt cgaatggag 
cgcgacggc gtccagcgc gtaaagatg ttcctcgtc 
ataaccgcc gcctacgtc cttttctgg ggtccactt 
ttcttcgtc accctcgtc aaccacccc atcgtaggc 
aaccctctc ggacacgag ataacgctg cacatatca 
tacgttcat gccattgtc aatcctaca ctttttttg 
gtactgcac agagggctc cgaagagcc acccttgat 
ctctgttgc ggatggata ccgctgtgg ttgggcaac 
cccaacgta cccccgccc ccagacccc cccagaact 
gacatatcg ctgctcaaa ccacccctg cccgtacca 
gcccaccct gatagctct atgggagac tccgatttg 
agtccgtgg actccggag ccggtaaac ggaggaatc 
caaatccca caatacatc agcccggag ccgagttca 
ccacccgag agtgactag
      mRNA sequence
      • >TC012889 RA
        aatgcagtc tttcgcccc atattcaaa ttctttttt 
agcagttgt aggaaacac acattcatt tttcgtcat 
aacaaaggt tccgtttta aaattcaca ttccactgt 
cgcatctcg cttctgttc ttgaaacgt gaagtgatt 
catgaggtt tgttactga actgggtta accgaaatt 
ccgtgacag gctctgcgg tggcgatga taggtgcca 
acctgcgtt tcggcagtt cggtggcga atgcaagtc 
tcaatgcca ccaaggtct tccaatgtc atcctggag 
ggaccgctg aagccgcgc tgatattcg ccttaggaa 
cgatgggaa tggccgcca atatagcgc tcatgggag 
ttatactgg ccaacagac agctccgaa ggtggtctc 
agggccttc tcttccacc aaggagccg tcgactgcg 
cccgtgcgg ctctcctcc tccctctgg gtatctcaa 
tcctccact gccagccgg tgcagaaat gctcccttg 
tggaaactg ccttcctcc tcctggtga cggtcgcca 
ccgtcaaca tgctgacca cagtcctca acgactcgc 
ccgtcttcc ccgaggacg acgactccg actccctct 
ccgacgtgc ccctcctca tggactcgc cccaatgcg 
tgctcttcg gcacgttca tgatctggt tcgcgtcga 
ttaccatca acttgggcc ccacgttcc tctcggggg 
cgctggcgg cccaaggcg aggcgggcc acaaggccc 
cctcgtgcc ccctcatcc acggcccgc tgcgccact 
acatcctca acgcgctct ggatcgccg tcaacctgg 
tgtgcgtct ttctgacgc tcttccact tgcggaagc 
tgcaccgcg acctcacca aggccaacg tggaggcgg 
tgcgggtgg cgggcctcg tcaccacac tggtgaacg 
tgacaggag gcggcggcg ctgccgcca acggggagc 
gggcctccg gcgccctcg aagagcacc gcagaatgc 
gagaatacc tccgtcgaa tggagcgcg acggcgtcc 
agcgcgtaa agatgttcc tcgtcataa ccgccgcct 
acgtccttt tctggggtc cacttttct tcgtcaccc 
tcgtcaacc accccatcg taggcaacc ctctcggac 
acgagataa cgctgcaca tatcatacg ttcatgcca 
ttgtcaatc ctacacttt ttttggtac tgcacagag 
ggctccgaa gagccaccc ttgatctct gttgcggat 
ggataccgc tgtggttgg gcaacccca acgtacccc 
cgcccccag accccccca gaactgaca tatcgctgc 
tcaaaccac ccctgcccg taccagccc accctgata 
gctctatgg gagactccg atttgagtc cgtggactc 
cggagccgg taaacggag gaatccaaa tcccacaat 
acatcagcc cggagccga gttcaccac ccgagagtg 
actagcatc cggattggg acagatcca cccggatct 
aagttcgtc gtcagttaa agactgcaa tcggactct 
tgtagtaga atcaaccga actgaactg ttttatttg 
taaaaatta aattatgta tactgacaa gaaggtgaa 
gagcgaaag ttttgtgca actccaacc aaaatccgc 
ctattttag gaattgata attttaaga gactatgcg 
agacgatta gataggaaa taaatgttg gtgactaga

      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