Status
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Gene information
General information
TC004429 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: 5253889..5255268
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
      		TC004429
      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
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      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
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      Name
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      Email
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      * : mandatory fields
      For help on how to submit larger datasets or non experimental data please contact us.
      iBeetle screen iB_00694

      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)

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

      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: 10.0% (includes death as larva, prepupa, pupa)
      Lethalities 22 days after larval injection: 10.0% (includes death as larva, prepupa, pupa, adult)

      larva lethality early (L5/6) - Number of animals showing the phenotype: 1 (11 dpi)
      Days post injection

      RNAi sequence
      Primers
      Left: Right:
      Protein sequence
      • >TC004429 RA
        MNSRHKNES LEASLKESL VVNPLGTKV RQATSSQLQ 
QKPKTAKLV KASQSLHRG RPGQAQFPV KRVMFGVEQ 
NFAVKTRKK PSTLDFIEK LKKIETKTE KSDFLEQAN 
DEIDIASKQ LEALRKLLT QKLQTQAEL KAQQEKNEL 
RNKQKTLMD NCNRQFEKM QKQYLNKTK IRFKSLKDV 
ENMTLPRPK DAKQDKNVK TLYQGVVAA TSSENFDFS 
AFDKNQDLD KAGPLLKTQ VVSVASQHE ILAKPAKKA 
SPKAPQKVR FDDSILNSV HYSPAGSNL QSPERSDGP 
DVANIKRLL SVPAEDLGV SRFRKKIDE SCLTTENFS 
TKYKEGRRK LNLLLHGKE KLDNVQFDD AKLEESVLK 
SAFLSKEFC SGENEASRR NRQLVESVM LKLHENKTG 
RRQDRKLSA VLKTVLQNS LFSELAK
      CDS sequence
      • >TC004429 RA
        atgaacagc agacacaaa aacgagtcc ttggaagca 
tccttgaaa gaaagctta gtcgtaaac ccactcggt 
acaaaagta cgacaagca acaagttcg caactacaa 
caaaaacca aaaactgca aaattagtc aaagcttcg 
caaagttta cacagagga agaccaggt caagcccag 
ttccctgta aaacgagtc atgttcggc gtggagcag 
aatttcgca gtgaagaca cgtaagaaa ccctcaact 
ttggatttc atcgaaaaa ttgaaaaaa atcgaaaca 
aaaactgaa aaatccgac tttttggaa caagcaaat 
gacgaaatt gacatcgcg tccaaacaa ttagaagca 
ctgcgtaaa ttactaacg cagaagctc caaactcaa 
gctgaactt aaagcccaa caagagaaa aatgagctt 
cgcaacaaa cagaaaacc ttgatggat aactgcaat 
cggcagttt gaaaaaatg caaaaacag tacttgaac 
aagacaaaa atacgcttc aagtcgtta aaagacgtt 
gaaaatatg acactaccg cggccaaaa gacgccaaa 
caagacaaa aacgttaaa acgctttat caaggtgtg 
gtggcggct acgagtagc gaaaatttc gattttagt 
gcttttgat aaaaaccaa gatttggac aaggccggg 
cctttgctc aagacacag gtggtttct gtggcttcg 
caacacgag attttggca aaacctgcc aaaaaagcc 
tcgccaaaa gcgccacag aaagtgaga tttgacgac 
tcaatcctc aattccgtt cactactct ccagctgga 
tcaaatttg caaagtcct gaacgaagt gatggtcca 
gacgttgca aatatcaag cgacttttg tcagtacct 
gctgaagat ttgggtgtt tcccgtttt cgaaaaaaa 
atcgacgag tcttgtcta acaactgaa aacttttcg 
acaaagtac aaagaaggg cgtcgtaaa ctcaatttg 
ctcctccac ggtaaggaa aaattagac aacgtgcag 
ttcgacgac gctaaactc gaagagtct gttttaaaa 
tcggcgttc ctaagcaag gaattttgc agcggggaa 
aatgaagcg tctcgaagg aatcggcag ttggtggag 
agtgtgatg ttgaagttg cacgaaaac aagaccggg 
aggcggcaa gaccggaaa ttgtccgca gtgttgaag 
accgtcttg caaaatagc ttattcagt gaactggca 
aagtaa
      mRNA sequence
      • >TC004429 RA
        caagcctgg acccacctt aatttctgc aaaacaaaa 
ttgtgtcat tttggcaat tcattgaca atcacattt 
caaaaatca tgaacagca gacacaaaa acgagtcct 
tggaagcat ccttgaaag aaagcttag tcgtaaacc 
cactcggta caaaagtac gacaagcaa caagttcgc 
aactacaac aaaaaccaa aaactgcaa aattagtca 
aagcttcgc aaagtttac acagaggaa gaccaggtc 
aagcccagt tccctgtaa aacgagtca tgttcggcg 
tggagcaga atttcgcag tgaagacac gtaagaaac 
cctcaactt tggatttca tcgaaaaat tgaaaaaaa 
tcgaaacaa aaactgaaa aatccgact ttttggaac 
aagcaaatg acgaaattg acatcgcgt ccaaacaat 
tagaagcac tgcgtaaat tactaacgc agaagctcc 
aaactcaag ctgaactta aagcccaac aagagaaaa 
atgagcttc gcaacaaac agaaaacct tgatggata 
actgcaatc ggcagtttg aaaaaatgc aaaaacagt 
acttgaaca agacaaaaa tacgcttca agtcgttaa 
aagacgttg aaaatatga cactaccgc ggccaaaag 
acgccaaac aagacaaaa acgttaaaa cgctttatc 
aaggtgtgg tggcggcta cgagtagcg aaaatttcg 
attttagtg cttttgata aaaaccaag atttggaca 
aggccgggc ctttgctca agacacagg tggtttctg 
tggcttcgc aacacgaga ttttggcaa aacctgcca 
aaaaagcct cgccaaaag cgccacaga aagtgagat 
ttgacgact caatcctca attccgttc actactctc 
cagctggat caaatttgc aaagtcctg aacgaagtg 
atggtccag acgttgcaa atatcaagc gacttttgt 
cagtacctg ctgaagatt tgggtgttt cccgttttc 
gaaaaaaaa tcgacgagt cttgtctaa caactgaaa 
acttttcga caaagtaca aagaagggc gtcgtaaac 
tcaatttgc tcctccacg gtaaggaaa aattagaca 
acgtgcagt tcgacgacg ctaaactcg aagagtctg 
ttttaaaat cggcgttcc taagcaagg aattttgca 
gcggggaaa atgaagcgt ctcgaagga atcggcagt 
tggtggaga gtgtgatgt tgaagttgc acgaaaaca 
agaccggga ggcggcaag accggaaat tgtccgcag 
tgttgaaga ccgtcttgc aaaatagct tattcagtg 
aactggcaa agtaaaatt ttgtgtcac aattaaaaa 
atatcgacc cga

      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