Status
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Gene information
General information
TC005870 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: 6145848..6150322
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
      		TC005870
      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
      If you have entered your name and agree by marking the checkbox. we might show your name on this page to honor your contribution.
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      * : mandatory fields
      For help on how to submit larger datasets or non experimental data please contact us.
      iBeetle screen iB_04025

      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: 20.0% (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

      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: 20.0% (includes death as larva, prepupa, pupa)
      Lethalities 22 days after larval injection: 20.0% (includes death as larva, prepupa, pupa, adult)

      larva lethality - Number of animals showing the phenotype: 3 (11 dpi)
      Days post injection

      RNAi sequence
      Primers
      Left: Right:
      Protein sequence
      • >TC005870 RA
        MSKLTVRLV NVIKLFSFH HDNLRTLGD RVIKLQFLT 
LFKAITNFG LPPNGEDKV TKYWTGKSV DEIIAEADL 
LFDQGKYLQ VYELLNRLK FCNNIEVQW RIGRALFKL 
SHEHEITED IRREMIDEA YEIIQSSLT VAENSPIIH 
KWAAIIIDR KNGMKGLEH RVKNSEVVK HHLIRTCEL 
DPDDVTAQY LLGRWCYEM SNITWFQRI IAKLLYGEA 
PRSSFEEAN KYLSRAEDL HPRFYLQNT YLLGKTCLK 
LGQYYRAKH YFGVVGNLP VHNEYERHC ANDAKKLLK 
RLDKYSLEK NALFYEYPF GTNE
      CDS sequence
      • >TC005870 RA
        atgtcaaaa ttaactgta cgtctcgtg aacgtaata 
aaactcttc tctttccac cacgataat ttgcgaact 
ttgggcgac cgtgtgata aaattgcaa tttttgact 
ctattcaaa gccataacg aatttcggt ttgccccca 
aatggcgaa gacaaagtg acgaaatac tggactggt 
aaatcagtc gacgaaatc atcgccgaa gccgatctc 
ctcttcgac caaggcaaa tacttgcaa gtttacgaa 
ttactaaac cgtttgaaa ttctgcaac aacatcgaa 
gttcaatgg cgaatcggt cgagccctc tttaaacta 
tcacacgaa catgaaatc accgaagat atccggcgc 
gaaatgatt gacgaagcc tacgagatc atccaaagc 
agtcttaca gttgcggaa aattccccg ataatccac 
aaatgggcc gcaatcatt atcgatcgg aaaaacggg 
atgaaagga ctcgaacat cgagtcaaa aattcggaa 
gttgtcaaa caccacctc atcagaacg tgcgaactg 
gaccccgac gacgtcacc gcgcagtat cttctaggt 
cggtggtgc tacgaaatg agcaacatc acgtggttt 
caacgcatc attgcgaaa ctgttgtac ggggaagcc 
ccgagatcg agcttcgaa gaagccaac aagtattta 
tcacgtgct gaagacttg cacccccga ttttaccta 
caaaatacg tatttattg ggcaaaact tgcctaaaa 
ttagggcaa tactaccgg gccaaacac tatttcgga 
gtcgtgggt aatttaccc gtccataac gagtacgag 
aggcattgt gcgaacgac gcgaaaaaa ttactcaaa 
cgtttagac aagtacagt ttggagaaa aacgccctt 
ttttacgaa taccccttc ggaaccaac gagtaa
      mRNA sequence
      • >TC005870 RA
        aaaacttcc gcagtgtta tcagtgcaa aaaatatgg 
gtcaaggtc ccattttgc atagttatg gcaaccaaa 
aaccattga caaatatga gaaatgtca aaattaact 
gtacgtctc gtgaacgta ataaaactc ttctctttc 
caccacgat aatttgcga actttgggc gaccgtgtg 
ataaaattg caatttttg actctattc aaagccata 
acgaatttc ggtttgccc ccaaatggc gaagacaaa 
gtgacgaaa tactggact ggtaaatca gtcgacgaa 
atcatcgcc gaagccgat ctcctcttc gaccaaggc 
aaatacttg caagtttac gaattacta aaccgtttg 
aaattctgc aacaacatc gaagttcaa tggcgaatc 
ggtcgagcc ctctttaaa ctatcacac gaacatgaa 
atcaccgaa gatatccgg cgcgaaatg attgacgaa 
gcctacgag atcatccaa agcagtctt acagttgcg 
gaaaattcc ccgataatc cacaaatgg gccgcaatc 
attatcgat cggaaaaac gggatgaaa ggactcgaa 
catcgagtc aaaaattcg gaagttgtc aaacaccac 
ctcatcaga acgtgcgaa ctggacccc gacgacgtc 
accgcgcag tatcttcta ggtcggtgg tgctacgaa 
atgagcaac atcacgtgg tttcaacgc atcattgcg 
aaactgttg tacggggaa gccccgaga tcgagcttc 
gaagaagcc aacaagtat ttatcacgt gctgaagac 
ttgcacccc cgattttac ctacaaaat acgtattta 
ttgggcaaa acttgccta aaattaggg caatactac 
cgggccaaa cactatttc ggagtcgtg ggtaattta 
cccgtccat aacgagtac gagaggcat tgtgcgaac 
gacgcgaaa aaattactc aaacgttta gacaagtac 
agtttggag aaaaacgcc cttttttac gaatacccc 
ttcggaacc aacgagtaa attttgtgt tctttttgg 
actcaccta gcatcagag gaacggcct gaaaatcgg 
gatcgtcct cgtcgaaga ggatgtctt cctcaaact 
cggtgaatc cctcaagtt tcgtgttac tttcaactc 
gcaacatct gaaatttga ggaaataaa ggtcatcat 
cttgaactt gaacgctca ttccattat tttgggcta 
gcgactgtt gccatggat cttgcccca aacacaaac 
acttttaac cccaaaaaa acaataaca aaatggcga 
aacttcgtg gcatatgtc gctaactaa aatagcttt 
ctttttcca gttattagt cgcattccg gacaagcct 
cgacctaac ctcaaaacc taacggtac tcgtgtcgt 
tttttgcgt gattgatgt ttttcccat tgatttatt 
gcggaaaat taccttttt tggggtcga agtgtgcga 
attttggcg ttttctttg tgttgcact cacacacag 
acacgcgac cagtcgact agatgcacc agcgactgg 
aatgaaatg ccattcagg tcgaagact tttaaaatc 
gaacggtgg tattatcga aagtcgcgg gattacgag 
ataacgtag actgaggac ggacgggaa gaaaatcgc 
cgattttta aactaggtt gaaaaagta aaacggttt 
ttgtttttg cgaaacaac tgctgcagc tgcaacttg 
atgaaatgg tcaacaact ggcgtttcg acatattat 
atttgtttt gtcattgcg attaataaa cggatcggg 
tgtttttat tattacaca tagtggggc tatttttgg 
acgttgtga ttggaaaaa attgacttt ttgagataa 
ggaggccaa attttgatt acaatttcg atttcttaa 
cgtagcaaa atttagcga aatgctggc aaaacggcg 
attttgtgg aacatccgt aggtcaagg ttgaaatat 
accttgtca gtgactgtt tttgacaat tttattgtt 
ttatgactt tcaattttt ttttgtttg tcgccgtta 
aattttacc atttccttg ttcattaaa gtataaacg 
taatgaatg tggggtaaa aaaatagtt atacgttgc 
cagaaacta taaataccc actgtaatt aatgttaat 
gataaagaa ggcgctgct ttctaattt ttgccaaat 
acgagtaca tatactttg gaaatggct gtatttctc 
actacatct tttttaatt gtgaattgt tggttgttt 
gatacattt cttaacttt aaacacttt ttgatagct 
aatctttca aggtcattg tcagaaaca tgacaaagt 
gcggtcaag tttaattat ttatttctg tcaaattct 
gattttata aaatgatat tattcaaga ccacttctg 
acgtttgta tttagtctt ttttaggaa aaatagttg 
ccaaaataa tgattagaa aatcgtctg cttttgttt 
atttttaaa ttatttcgt tttaatttt cccttaatt 
tttttacgc cgttacaaa atcgtagat cataattgt 
caaaaattg ccgcagtct ttgattttt tactaaata 
atttttgac ttt

      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