Status
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Gene information
General information
TC002838 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: 8695186..8698503
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
      		TC002838
      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_07981

      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: 0.0% (includes death as pupa, adult)

      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): more than 80%

      affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 80%
      Analysis of larval stage 1 cuticle
      number of eggs/embryos/larvae on slide: > 50
       embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): more than 80%
      affected eggs/embryos/larvae - 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: % (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
      • >TC002838 RA
        MADAFAFNA RQYFDFTQE HDELNSDSF FDENVEENG 
PLGQNLEEN FQCNGEVFE REVSDPESD YFFSPMEDT 
KTNSSTIYL KSRMRKSLS MNDLRLKKV PNQNGLDRA 
MDELCLNNH QPAEPRPSS ACSLNSRKT ISKEHINRL 
AQPKRYTSH DNLARQSSM TLAEAVNKF QAGTPKRFR 
SKPLNNKAP LGPTIPKTP KFLTNARVR PVTALSKEE 
QEERELEEA RKFKIKANP VNKKVLRGP MKPPVDKKC 
PTVAEPFHL TEVRKKPEP DEPDKAPSF KAQPVPKSL 
HNPFRVIPK GQPPTQPES PNFSKKIAR TTPNKVTKQ 
EEAPKPCKP TNTHVKPFS FEERDKKLM KKKEELINR 
YLEEEKKAR EFHARPVPK SILRSRNNS QENISDPGS 
SKSFKRSTE ELDFGTFKA RPAKVLTMK PFEPKKCED 
HGIVIKEFQ FATNQRLEK RHEFDEAVR AKEARLEAQ 
KREIEERLR RQEEEEKLK LRKQAELKA QPIKKYKEV 
TIKPANKIT NPVSPKFSS RVRNKENIE E
      CDS sequence
      • >TC002838 RA
        atggccgat gcatttgct tttaacgcc cgacagtat 
ttcgatttc actcaagaa cacgacgaa ctaaacagt 
gattctttc tttgatgaa aatgtagaa gagaacggc 
cctttaggc cagaacctg gaagaaaat ttccaatgc 
aatggagag gttttcgaa agggaggtg tctgatccc 
gaaagtgac tatttcttc tcccctatg gaggataca 
aagacgaat agctcgact atttatctc aaaagtcgg 
atgcggaag tctttgagt atgaatgat ttacgtctt 
aagaaagtg ccaaatcaa aacggactc gatcgagcc 
atggatgag ttatgtcta aataaccac caacctgca 
gagcccagg ccgagttct gcttgttcc ttgaacagc 
agaaaaaca atctcaaag gaacacatc aatcgatta 
gctcaacct aaacgttac acctcgcac gataacttg 
gcccgacaa tcgtccatg actttagca gaggctgtc 
aataaattc caagctggg acacccaaa cgcttccgc 
tccaaaccc ctaaacaat aaagcccca ctgggtcca 
actatacca aaaacgccc aaatttctc acaaacgct 
cgtgtgcgt ccagtgaca gcactctca aaggaagag 
caagaagaa agggagctt gaagaagcc agaaagttc 
aagatcaag gcaaatccg gtgaacaag aaagtccta 
aggggcccc atgaagccc ccagtcgat aaaaagtgc 
cccactgtt gcggaaccc ttccatttg actgaagtg 
aggaagaag cccgagccc gatgagcct gataaagcc 
ccctcattc aaggcacaa cctgtgcct aaaagtttg 
cacaatcca ttcagagtc atacccaag ggacagccc 
ccgacccag cctgagtcc cccaatttt tcgaaaaaa 
attgccaga accacacca aataaagta acgaagcag 
gaagaagcg ccaaaacca tgcaaacct acaaacaca 
catgtcaaa ccgtttagt ttcgaagaa cgcgacaag 
aaactgatg aagaagaaa gaagaattg attaataga 
tatctggaa gaagagaag aaagctcgt gagttccac 
gctaggcca gttccgaaa tctatactg aggtcgagg 
aacaacagc caggaaaat atcagtgat cctggatcg 
tcaaaatca tttaaacgc agcactgaa gaattggat 
tttggcact ttcaaagca cggcccgcc aaagtctta 
actatgaaa ccttttgag ccgaaaaag tgcgaggat 
catggaatc gtgatcaaa gagtttcaa tttgcgacc 
aatcaaaga cttgaaaag cgacacgag tttgacgag 
gcagtgaga gctaaggaa gcgagactt gaagctcaa 
aaacgggaa attgaggag agactgagg cgacaggaa 
gaagaggag aagttgaag ttgagaaaa caggcggag 
ttaaaagcg caaccaatt aaaaagtac aaggaagta 
accatcaag ccggcgaat aaaattaca aacccggtc 
agtccgaag ttcagttcc agggtcagg aacaaggag 
aatattgag gaataa
      mRNA sequence
      • >TC002838 RA
        agactaaaa tatatattt tagtttctg tctataggg 
actaactaa cggttgcac agatcagtt catctcaaa 
ctttgtttt tgtggcctg aaagccggt aattatttt 
gctaaaatc atggccgat gcatttgct tttaacgcc 
cgacagtat ttcgatttc actcaagaa cacgacgaa 
ctaaacagt gattctttc tttgatgaa aatgtagaa 
gagaacggc cctttaggc cagaacctg gaagaaaat 
ttccaatgc aatggagag gttttcgaa agggaggtg 
tctgatccc gaaagtgac tatttcttc tcccctatg 
gaggataca aagacgaat agctcgact atttatctc 
aaaagtcgg atgcggaag tctttgagt atgaatgat 
ttacgtctt aagaaagtg ccaaatcaa aacggactc 
gatcgagcc atggatgag ttatgtcta aataaccac 
caacctgca gagcccagg ccgagttct gcttgttcc 
ttgaacagc agaaaaaca atctcaaag gaacacatc 
aatcgatta gctcaacct aaacgttac acctcgcac 
gataacttg gcccgacaa tcgtccatg actttagca 
gaggctgtc aataaattc caagctggg acacccaaa 
cgcttccgc tccaaaccc ctaaacaat aaagcccca 
ctgggtcca actatacca aaaacgccc aaatttctc 
acaaacgct cgtgtgcgt ccagtgaca gcactctca 
aaggaagag caagaagaa agggagctt gaagaagcc 
agaaagttc aagatcaag gcaaatccg gtgaacaag 
aaagtccta aggggcccc atgaagccc ccagtcgat 
aaaaagtgc cccactgtt gcggaaccc ttccatttg 
actgaagtg aggaagaag cccgagccc gatgagcct 
gataaagcc ccctcattc aaggcacaa cctgtgcct 
aaaagtttg cacaatcca ttcagagtc atacccaag 
ggacagccc ccgacccag cctgagtcc cccaatttt 
tcgaaaaaa attgccaga accacacca aataaagta 
acgaagcag gaagaagcg ccaaaacca tgcaaacct 
acaaacaca catgtcaaa ccgtttagt ttcgaagaa 
cgcgacaag aaactgatg aagaagaaa gaagaattg 
attaataga tatctggaa gaagagaag aaagctcgt 
gagttccac gctaggcca gttccgaaa tctatactg 
aggtcgagg aacaacagc caggaaaat atcagtgat 
cctggatcg tcaaaatca tttaaacgc agcactgaa 
gaattggat tttggcact ttcaaagca cggcccgcc 
aaagtctta actatgaaa ccttttgag ccgaaaaag 
tgcgaggat catggaatc gtgatcaaa gagtttcaa 
tttgcgacc aatcaaaga cttgaaaag cgacacgag 
tttgacgag gcagtgaga gctaaggaa gcgagactt 
gaagctcaa aaacgggaa attgaggag agactgagg 
cgacaggaa gaagaggag aagttgaag ttgagaaaa 
caggcggag ttaaaagcg caaccaatt aaaaagtac 
aaggaagta accatcaag ccggcgaat aaaattaca 
aacccggtc agtccgaag ttcagttcc agggtcagg 
aacaaggag aatattgag gaataattt gtaattgtt 
taaggtgat attattttt acgtt

      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