Status
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Gene information
General information
TC005723 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: 8495726..8498688
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
    		TC005723
    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
    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_00913

    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)

    adult lethality - Number of animals showing the phenotype: 3 (9 dpi)
    Days post injection

    Fertility
    vitellogenic egg chamber not present - Number of animals showing the phenotype: 4
    previtellogenic egg chamber mostly not present - Number of animals showing the phenotype: 4

    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: 30.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 100.0% (includes death as larva, prepupa, pupa, adult)

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

    pupal molt delayed (still larva) - Number of animals showing the phenotype: 7 (11 dpi)
    Days post injection

    larva lethality late (L7) - Number of animals showing the phenotype: 7 (16 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC005723 RA
      MSEKSAAIR TQLSNIIAS GGSHKDQAE KYRGILENI 
LAGSGPELT EGLQIFIEA IVNENVSLV ISRQILTEI 
SSHLMKLPD DVSKTVSHF MLEKVQPRV ISFEEQVAS 
IRQHLADIY ERNHMWREA AAVLVGIPL ETGQKQYTV 
DYKLETYLK IARLYLEDD DPVQAEAFI NRASLLQAE 
SRNEQLQIY YKVCYARVL DYRRKFIEA AQRYNELSY 
RTIVHEDER MTALRNALV CTVLASAGQ QRSRMLATL 
FKDERCQQL PAVAILEKM YLERIIRRS ELRDFEALL 
QPHQKASTI DGSTILDRA VIEHNLLSA SKLYNNISF 
EELGALLEI HPSKAEKIA SQMITEGRM NGYIDQIDS 
IVHFETRET LPQWDKQIQ SLCYQVNSI IESIAKSEP 
EWISKVMEE QMDLK
    CDS sequence
    • >TC005723 RA
      atgtcggag aaaagcgcg gctatccgc acccaactc 
tccaacata atcgcgtcc gggggctcc cacaaagac 
caggccgaa aaatatcgc ggtattctt gagaacatc 
ctcgccggt tcgggcccc gagctgacc gaaggcttg 
cagatattc atcgaagca attgtcaat gagaacgtt 
agtttggtc atctcgcgc caaatcctg accgaaata 
agctcgcat ttgatgaaa ctacccgac gatgtttcc 
aaaactgtc tcacacttt atgcttgag aaggtgcaa 
ccccgggtt atttcgttt gaggagcag gtggcaagt 
attcgccaa catttggcc gatatctac gaacgtaac 
cacatgtgg cgcgaggct gcagctgtc ctggtggga 
atcccgctc gaaaccggc cagaaacaa tacaccgtg 
gattacaaa cttgaaacg tatttgaaa atcgcgagg 
ttgtatctt gaggatgac gatccggtc caggctgag 
gctttcatc aaccgggcg tcgctgctt caggccgag 
tcacggaat gagcagctt caaatttat tacaaagtt 
tgttatgct cgagttttg gattatcgg cggaagttt 
attgaggcg gctcagaga tacaatgaa ttgtcctat 
aggacgatt gttcatgaa gatgaacgc atgacagcc 
cttcggaat gctttagtt tgcactgtt ttggcttca 
gcggggcaa caaagatcg cgcatgttg gccacactg 
ttcaaggac gagaggtgc caacagttg ccagcagtg 
gcgattttg gaaaaaatg tacctcgaa agaatcatc 
aggaggtcc gaattgagg gattttgag gccttgttg 
cagccccac caaaaggcg agcaccatt gatgggtca 
acaattctg gaccgcgcc gttatcgaa cacaatctc 
ctgtctgct agtaaactt tataataat attagtttc 
gaagagttg ggagctttg ctcgaaata cacccttcc 
aaggctgaa aaaatcgca agtcagatg ataaccgaa 
gggcgaatg aacggttac attgaccaa atcgattca 
atcgtccac tttgaaact cgtgaaact ttgccccag 
tgggacaaa caaatccag tctctctgc taccaggtg 
aattcaatc attgaatca atcgcaaaa agcgagccc 
gaatggatc agtaaggtg atggaggag cagatggat 
cttaagtga
    mRNA sequence
    • >TC005723 RA
      ttgctgttt tgtcagtca tttgtcaaa aactacttt 
tagttaaat taaaataat ttattatta tttgtggcc 
aaaatagta gcggagcac catgtcgga gaaaagcgc 
ggctatccg cacccaact ctccaacat aatcgcgtc 
cgggggctc ccacaaaga ccaggccga aaaatatcg 
cggtattct tgagaacat cctcgccgg ttcgggccc 
cgagctgac cgaaggctt gcagatatt catcgaagc 
aattgtcaa tgagaacgt tagtttggt catctcgcg 
ccaaatcct gaccgaaat aagctcgca tttgatgaa 
actacccga cgatgtttc caaaactgt ctcacactt 
tatgcttga gaaggtgca accccgggt tatttcgtt 
tgaggagca ggtggcaag tattcgcca acatttggc 
cgatatcta cgaacgtaa ccacatgtg gcgcgaggc 
tgcagctgt cctggtggg aatcccgct cgaaaccgg 
ccagaaaca atacaccgt ggattacaa acttgaaac 
gtatttgaa aatcgcgag gttgtatct tgaggatga 
cgatccggt ccaggctga ggctttcat caaccgggc 
gtcgctgct tcaggccga gtcacggaa tgagcagct 
tcaaattta ttacaaagt ttgttatgc tcgagtttt 
ggattatcg gcggaagtt tattgaggc ggctcagag 
atacaatga attgtccta taggacgat tgttcatga 
agatgaacg catgacagc ccttcggaa tgctttagt 
ttgcactgt tttggcttc agcggggca acaaagatc 
gcgcatgtt ggccacact gttcaagga cgagaggtg 
ccaacagtt gccagcagt ggcgatttt ggaaaaaat 
gtacctcga aagaatcat caggaggtc cgaattgag 
ggattttga ggccttgtt gcagcccca ccaaaaggc 
gagcaccat tgatgggtc aacaattct ggaccgcgc 
cgttatcga acacaatct cctgtctgc tagtaaact 
ttataataa tattagttt cgaagagtt gggagcttt 
gctcgaaat acacccttc caaggctga aaaaatcgc 
aagtcagat gataaccga agggcgaat gaacggtta 
cattgacca aatcgattc aatcgtcca ctttgaaac 
tcgtgaaac tttgcccca gtgggacaa acaaatcca 
gtctctctg ctaccaggt gaattcaat cattgaatc 
aatcgcaaa aagcgagcc cgaatggat cagtaaggt 
gatggagga gcagatgga tcttaagtg aaacgtgtc 
ttttgtaaa ttacatttt atttgtttt acaatactt 
gtcataatc ataaaacaa ttgaattaa aagcttgca 
caagta

    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