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Gene information
General information
TC004492 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_007417.3: 3795766..3797538
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
      		TC004492
      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
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      Email
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      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_00708

      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: 3 (3 dpi)
      Days post injection

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

      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, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): 50% - 80%

      embryo/egg with muscle fluorescence/pattern, but not hatched (pot. late embryonic lethality) - 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): more than 80%
      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): more than 80%

      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: 20.0% (includes death as larva, prepupa, pupa, adult)

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

      RNAi sequence
      Primers
      Left: Right:
      Protein sequence
      • >TC004492 RA
        MSCNFKKCV FVPRSSFTS ALFKVLVTL KLLHGSRTG 
AKGSTLEDI AMYMIKHFC LDGDIKSQV LASLKYGVK 
MHFIQKKKE KFSLILPAS SIHLAPCRF KNEEMERIH 
CLFPAKWQS NACNDVCAN EASCCGKRR RQVPRPCCQ 
DSDEEDAEG GTCFTCPMK KRPKSMCAQ NTCSKPPAP 
SNSCATCHT TPQKNKSMA PCPKALPPA CRRRGRPTR 
SKSLYDDYC QMCGDSESD DACDTCSPA YSYKAYKNC 
SCFCSIMAP YPSYKKHVK FAKSRSPVA RKKVPNTAD 
SYANIVLYY LSKLKGLFH SPVNHEKTS YYARDAYDS 
SKPILRKDS RKMGYGDSD IDAKEKACE IVNAAIQYG 
CANNIIEKV GNYFLLKKS EQPKQRMAV RRPTPGPDY 
VRCASCKNL TKFSRKYSV VNVRENRHK SKRHRGYYD 
DYGHTSPVR RKRSASNTS TINYCSKCY ARMRSSRR
      CDS sequence
      • >TC004492 RA
        atgtcatgt aactttaaa aaatgcgtg tttgtgccc 
cgttcgagt tttacgagt gcgttgttt aaagtcttg 
gtaacgcta aagctactc catggaagt cgtaccgga 
gccaaaggg tccactctg gaggacatc gccatgtac 
atgatcaag cacttttgc ttagacggc gacatcaaa 
agtcaagtc ttggcgtct ttaaaatat ggggtcaaa 
atgcatttt attcagaaa aaaaaggag aaattcagt 
ctaatattg ccagcgtcg tccatccac ctagcacct 
tgtcgcttc aaaaacgag gaaatggag cgcattcac 
tgtcttttc ccggccaag tggcagagc aacgcctgc 
aacgacgtg tgtgcgaac gaggctagc tgttgcggc 
aaaaggaga aggcaggtc cccaggcct tgctgccag 
gacagcgac gaggaagac gccgaagga gggacctgt 
ttcacgtgt cccatgaag aagcgcccc aagtccatg 
tgcgcccaa aacacctgc tccaaaccc ccagccccc 
tcgaacagc tgtgccacg tgccacacc accccgcag 
aaaaacaaa tcgatggcg ccgtgcccc aaagccctt 
cccccagct tgccgaagg cgcggccgg cccaccagg 
tccaagtcc ctctacgac gactactgc caaatgtgt 
ggtgactcg gaatccgac gatgcatgc gatacatgc 
agtcctgcg tacagttac aaggcttac aaaaattgt 
tcgtgtttt tgtagcatt atggcgcct tatccctct 
tacaaaaag cacgtgaag tttgcaaag tcgcgatcg 
cctgtcgcg cgtaaaaaa gtcccgaat acggccgat 
agttatgca aatattgtg ctctactac ctgtccaag 
ttgaaaggt ctgtttcac tcgccggta aaccacgaa 
aaaacgagt tactacgcc cgggatgcg tacgattcg 
tccaaaccc atcttgagg aaagattcc cgaaaaatg 
ggctatgga gatagtgac attgatgca aaggaaaaa 
gcttgtgaa attgttaac gcagcgatt cagtacgga 
tgtgccaat aatatcata gaaaaagtc gggaattat 
ttccttctg aagaagtct gagcagccg aagcaaaga 
atggcggtc cggagaccc actccaggg cctgactac 
gtccggtgt gctagttgt aaaaacttg accaaattt 
tccagaaaa tatagtgta gtgaatgta agagaaaat 
agacacaaa tcgaaaaga cataggggg tattatgat 
gattatgga cacacttct ccagttaga aggaaaaga 
agcgcttcg aacacatcc accataaac tactgctca 
aagtgttac gcacgcatg aggtccagt aggaggtag
      mRNA sequence
      • >TC004492 RA
        caatttcta atgtttaac ttggagaac aattaaata 
aatcatgtt tgtgaaaat taataatca atctatcga 
actttacaa aaaattgtc cagccgcta tggcgacgt 
ggaattatt tgccgactt ccgaaaaga tgaatttct 
catgtcatt caaatttct gtcacattt ctcgacgcg 
atttaatta acccgatta aattaccag ttgtcgata 
tgataaaat atgtcatgt aactttaaa aaatgcgtg 
tttgtgccc cgttcgagt tttacgagt gcgttgttt 
aaagtcttg gtaacgcta aagctactc catggaagt 
cgtaccgga gccaaaggg tccactctg gaggacatc 
gccatgtac atgatcaag cacttttgc ttagacggc 
gacatcaaa agtcaagtc ttggcgtct ttaaaatat 
ggggtcaaa atgcatttt attcagaaa aaaaaggag 
aaattcagt ctaatattg ccagcgtcg tccatccac 
ctagcacct tgtcgcttc aaaaacgag gaaatggag 
cgcattcac tgtcttttc ccggccaag tggcagagc 
aacgcctgc aacgacgtg tgtgcgaac gaggctagc 
tgttgcggc aaaaggaga aggcaggtc cccaggcct 
tgctgccag gacagcgac gaggaagac gccgaagga 
gggacctgt ttcacgtgt cccatgaag aagcgcccc 
aagtccatg tgcgcccaa aacacctgc tccaaaccc 
ccagccccc tcgaacagc tgtgccacg tgccacacc 
accccgcag aaaaacaaa tcgatggcg ccgtgcccc 
aaagccctt cccccagct tgccgaagg cgcggccgg 
cccaccagg tccaagtcc ctctacgac gactactgc 
caaatgtgt ggtgactcg gaatccgac gatgcatgc 
gatacatgc agtcctgcg tacagttac aaggcttac 
aaaaattgt tcgtgtttt tgtagcatt atggcgcct 
tatccctct tacaaaaag cacgtgaag tttgcaaag 
tcgcgatcg cctgtcgcg cgtaaaaaa gtcccgaat 
acggccgat agttatgca aatattgtg ctctactac 
ctgtccaag ttgaaaggt ctgtttcac tcgccggta 
aaccacgaa aaaacgagt tactacgcc cgggatgcg 
tacgattcg tccaaaccc atcttgagg aaagattcc 
cgaaaaatg ggctatgga gatagtgac attgatgca 
aaggaaaaa gcttgtgaa attgttaac gcagcgatt 
cagtacgga tgtgccaat aatatcata gaaaaagtc 
gggaattat ttccttctg aagaagtct gagcagccg 
aagcaaaga atggcggtc cggagaccc actccaggg 
cctgactac gtccggtgt gctagttgt aaaaacttg 
accaaattt tccagaaaa tatagtgta gtgaatgta 
agagaaaat agacacaaa tcgaaaaga cataggggg 
tattatgat gattatgga cacacttct ccagttaga 
aggaaaaga agcgcttcg aacacatcc accataaac 
tactgctca aagtgttac gcacgcatg aggtccagt 
aggaggtag ccgtaatgt tgttttgtt taattgtcc 
gagaataaa cccgttttg tcctt

      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