Status
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Gene information
General information
TC004714 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_007416.3: 4540121..4542063
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
    		TC004714
    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
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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_03822

    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: 10.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 1 (3 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 larval musculature irregular - 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%
    remarks: muscle pattern potentially obscured by segmentation defect,
    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): less than 30%
    cuticle remnants without visible segmentation, differentiation or axis - Penetrance (percentage of animals/eggs on slide): 50% - 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: 10.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 60.0% (includes death as larva, prepupa, pupa, adult)

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

    adult lethality - Number of animals showing the phenotype: 3 (19 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 2 (22 dpi)
    Days post injection

    Pupal morphology
    maxillary palp elongated - Number of animals showing the phenotype: 8
    maxillary palp thinner - Number of animals showing the phenotype: 8

    labial palp elongated - Number of animals showing the phenotype: 8

    wings bent - Number of animals showing the phenotype: 6

    female genital lobes shortened - Number of animals showing the phenotype: 8
    female genital lobes rounded - Number of animals showing the phenotype: 8

    Adult morphology
    club cuticularisation not present - Number of animals showing the phenotype: 9


    maxillary palp elongated - Number of animals showing the phenotype: 8

    labial palp elongated - Number of animals showing the phenotype: 8


    maxillary palp thinner - Number of animals showing the phenotype: 8


    elytra not closed - Number of animals showing the phenotype: 9


    legs sometimes not present - Number of animals showing the phenotype: 4


    Fertility
    egg production: number no/almost no eggs -
    mature egg deposition >5 number 2nd lateral oviduct: number 1st lateral oviduct: blocked - Number of animals showing the phenotype: 3
    mature egg deposition 3 number 2nd lateral oviduct: 2 number 1st lateral oviduct: blocked - Number of animals showing the phenotype: 1
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004714 RA
      MSIIPEDGD LEEYFREYS DMYYEETAL DIWNNCVVL 
SILSVVPSV LSLVVPNLV FGCLVSTGF IPLSVLHFS 
TGCIGIYLV STLESHFGK IVLLFCWII SYVLLYTGF 
QLKKYSKSS ISLKLTFII LLVLCEYYL IEAEVWLQI 
RGIVMVLVM KVLSLADDI NKLDAMPGF IQYFGYTLC 
GANVMFGPW ISFSDYLNF YKKPTKKNL IWICAIVKV 
LTTSLFFLT LSNCWSGYI ISDDANRWL IAYKEAFAF 
RTSHYFISY LAEVGMIAA GFTNSSKRD SLNQYRFVI 
TEPLEIEFP SSLSIVVKK WNQPMHDFL KKYVYYSWL 
GFGKFYAIL ATFLISSLL HGLELKVSM VLVSIGVFS 
YLQVVPRDR IAEIFDYCV RVRPCKDCK HKYKRDNIR 
VRIILLIYS LATVFHLAY LGVLMDPST NEIGIYEKW 
QNLYFISHI VMFFNVMVI L
    CDS sequence
    • >TC004714 RA
      atgtccata atcccggaa gatggagat ctggaagaa 
tactttcgt gaatactct gatatgtac tatgaagaa 
accgcctta gatatttgg aacaattgt gttgtactc 
tctatttta agtgtagtc ccttccgtc ctctcttta 
gttgtacca aatttagta tttggatgt ctggtgtcc 
acgggtttc atccccttg tcagtatta catttcagc 
accggttgc attggtatt tatttagtg tcaacgctt 
gaatctcat tttgggaaa attgtttta ttattttgt 
tggattatt tcgtacgtt ttgctctat acgggcttc 
caattgaaa aaatactct aaaagctcc atatcccta 
aaactcacc tttataatc ctcttagtg ctatgcgaa 
tattacttg attgaggca gaagtgtgg cttcaaatt 
cgcggaatc gtcatggtt ttggtaatg aaggttttg 
tcgttagct gacgatata aacaaatta gacgcaatg 
ccgggcttt attcagtat tttgggtac acgttatgt 
ggggccaat gtcatgttt gggccctgg atttcattt 
agcgattac ttgaatttt tacaagaag cctacgaaa 
aagaatctc atttggatt tgtgcaatt gttaaagtc 
ctcaccacg tcgttgttt tttctaact ttgtcaaac 
tgttggagc ggttacatc atatcagat gacgcgaat 
cgatggctg atagcatac aaagaagca tttgcgttc 
aggacaagt cattacttt attagttat ttggcagaa 
gttggaatg atcgccgct ggtttcacg aactcctca 
aagcgcgat tctttgaat cagtacaga ttcgtcata 
accgagcct ctggagatc gaattcccg tcatctctg 
tcaatagtc gtcaagaaa tggaaccaa ccgatgcac 
gattttctc aaaaaatat gtttattat tcgtggttg 
ggtttcggg aagttttac gcaattctc gcaaccttc 
ctaatttct tcgttactc cacggcctt gaacttaaa 
gtctccatg gttttagtc tcgattggg gtattctcg 
tatttacaa gtggtgcca agggaccga attgccgaa 
atatttgat tattgcgtg agagtccgt ccttgtaaa 
gactgtaaa cataaatat aaacgtgat aatattaga 
gttaggatt attttactc atttattcg ctcgcgaca 
gtattccat ttggcttat ttaggggtc ctcatggac 
ccctcaacc aacgaaatc ggaatctac gagaaatgg 
cagaatctc tactttatt agtcacatc gtaatgttc 
ttcaatgta atggtcatt ttgtga
    mRNA sequence
    • >TC004714 RA
      accttaaac attagacaa aacgaattt ttccttaaa 
ttactgaaa taatgtgat aataatgtc cataatccc 
ggaagatgg agatctgga agaatactt tcgtgaata 
ctctgatat gtactatga agaaaccgc cttagatat 
ttggaacaa ttgtgttgt actctctat tttaagtgt 
agtcccttc cgtcctctc tttagttgt accaaattt 
agtatttgg atgtctggt gtccacggg tttcatccc 
cttgtcagt attacattt cagcaccgg ttgcattgg 
tatttattt agtgtcaac gcttgaatc tcattttgg 
gaaaattgt tttattatt ttgttggat tatttcgta 
cgttttgct ctatacggg cttccaatt gaaaaaata 
ctctaaaag ctccatatc cctaaaact cacctttat 
aatcctctt agtgctatg cgaatatta cttgattga 
ggcagaagt gtggcttca aattcgcgg aatcgtcat 
ggttttggt aatgaaggt tttgtcgtt agctgacga 
tataaacaa attagacgc aatgccggg ctttattca 
gtattttgg gtacacgtt atgtggggc caatgtcat 
gtttgggcc ctggatttc atttagcga ttacttgaa 
tttttacaa gaagcctac gaaaaagaa tctcatttg 
gatttgtgc aattgttaa agtcctcac cacgtcgtt 
gttttttct aactttgtc aaactgttg gagcggtta 
catcatatc agatgacgc gaatcgatg gctgatagc 
atacaaaga agcatttgc gttcaggac aagtcatta 
ctttattag ttatttggc agaagttgg aatgatcgc 
cgctggttt cacgaactc ctcaaagcg cgattcttt 
gaatcagta cagattcgt cataaccga gcctctgga 
gatcgaatt cccgtcatc tctgtcaat agtcgtcaa 
gaaatggaa ccaaccgat gcacgattt tctcaaaaa 
atatgttta ttattcgtg gttgggttt cgggaagtt 
ttacgcaat tctcgcaac cttcctaat ttcttcgtt 
actccacgg ccttgaact taaagtctc catggtttt 
agtctcgat tggggtatt ctcgtattt acaagtggt 
gccaaggga ccgaattgc cgaaatatt tgattattg 
cgtgagagt ccgtccttg taaagactg taaacataa 
atataaacg tgataatat tagagttag gattatttt 
actcattta ttcgctcgc gacagtatt ccatttggc 
ttatttagg ggtcctcat ggacccctc aaccaacga 
aatcggaat ctacgagaa atggcagaa tctctactt 
tattagtca catcgtaat gttcttcaa tgtaatggt 
cattttgtg aataaaaat agctaaaac cacactttc 
ttccttcat tatttaacc catgaaact aatttcccc 
aagttttct aatcaaaaa acttttata tggaaaagt 
tcccaaacc gctacgcgt ttcgacagt taagtggca 
tcatcaggt tataattta attgaatta gtttcgtta 
aaaacaaaa caataagta tatttaaaa tttaccgag 
tacgtaata ctttcttct ttaaaataa attattaaa 
gctgaa

    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