Status
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Gene information
General information
TC004579 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: 7400504..7405454
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
    		TC004579
    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
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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_00725

    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: 60.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 2 (3 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 4 (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): 50% - 80%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): 50% - 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): 50% - 80%

    labium not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    head not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    thorax partially not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    thorax not present - 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): 50% - 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: 40.0% (includes death as larva, prepupa, pupa, adult)

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

    remarks: animals lost, adult lethality immediately after eclosion - Number of animals showing the phenotype: 2 (19 dpi)
    Days post injection

    Pupal morphology
    remarks: animals lost,
    Adult morphology
    remarks: animals lost,
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004579 RA
      MSLATETTR LLSDQTQPQ YAFDTSLVR ERKKRIKQF 
QCCLCVIFV CCLVVAFLI AAVWGINRA ENSFTNVTN 
TSSPSDTLT TLLAISWPR PDKPMNTSY CNNQSEWSQ 
ALAAGLKAL NTKHQIEKN VTEMTTDSP SYKHQKVFL 
DSNKTQALA NLGYLRESA RRFFPNNGS TICNKAEPC 
PVPQKCTEF AKFRTFDGT CNNLERPNL GAAFQPFRR 
ALPPDYADG VSSPRGAKT GALPSARTV SLEVHRPFY 
KNDDKFSVM LAVWGQFLD HDMTATAPS RGPNGSTIA 
CCGQKVTHP ECFPVKLDR FDPLSEFNV TCMEFVRSA 
NAATCCLGP REQMNQVTA FIDGSVIYG VEEKTVGAL 
RTMSGGELE MFVTSDNRT LLPVSKDLT DGCNRLEES 
RKGRYCFLT GDGRANENL HLTSMHLIW ARQHNSIAK 
QLAKLNPDW ADERLFQES RKIIGAQMQ HICYREFLP 
ILLGRGLME KSGLYPRTS GYFTEYNSA VDPSIANNF 
ATAAFRFAH SIIPGLMKF LAKDSSSPE FVQLHKMLF 
DPFRLYQAG GLDRALRGA MDTPIQAND PYFSSELKD 
KLFEDAANE TIRAYGLDL VSLNIQRGR DHGLVGYNS 
WREHCGLRR VSTFQQLQG DFDDDSLRN IQAIYRDVD 
DVDLYTGAL SEKPLNGSI LGPTLTCLI HDQFVRVKY 
GDRFWYENP HWFTLDQLA EIRKTSLAR IICDNSDEV 
DEVQPLVME KIRSDNKVV PCSALPAPQ WGPWKEALH 
RVRTSADTL SVESITN
    CDS sequence
    • >TC004579 RA
      atgtctctc gcgactgaa acgacaaga ttactttcg 
gaccaaacg caaccgcaa tatgcgttt gataccagc 
ctcgtacgg gagcgtaaa aaacgaatt aaacaattc 
caatgttgc ttatgcgtg atttttgtt tgttgtctc 
gtggtggca tttttgatt gccgctgtt tggggcata 
aacagggcg gaaaacagc ttcacaaac gtgactaat 
actagttcc ccctcggac acactcacg actctactt 
gcaatttcg tggccccgt cccgacaaa cccatgaat 
acgtcctat tgtaacaac cagagtgaa tggtcacag 
gcccttgcc gcgggccta aaggcccta aacaccaaa 
caccaaatc gagaaaaat gtcacagaa atgaccacc 
gacagcccc agctacaaa caccagaag gtgttccta 
gactcgaat aaaactcaa gctttggcc aacttgggc 
tacttgcga gaatcagca aggcggttt ttccccaac 
aacgggagc acaatttgc aataaggct gaaccgtgt 
cctgtgccc caaaaatgc accgaattt gcgaaattt 
cgcacgttt gatggcact tgtaacaat ctggagcgc 
cccaatttg ggggctgcg ttccagcct tttcgccgc 
gcgctcccg ccggactac gccgacggg gttagcagc 
ccccggggg gccaaaacc ggggcgctt ccatcggct 
cgcaccgtc agcttggag gtccatcgg ccgttttac 
aaaaacgac gataagttt agcgtaatg ttggccgtt 
tgggggcag tttctggat cacgatatg acggcgaca 
gcccccagt cggggcccc aacggctcc acgatcgcc 
tgttgtggc caaaaagtc acacatccg gagtgcttt 
cccgtcaag ttggaccgc tttgaccct ttatccgaa 
tttaatgtc acttgtatg gaatttgtg cggtcggca 
aatgccgcc acttgttgt ctggggccc agggaacag 
atgaaccaa gtgacggcg tttatagac gggtcggtt 
atttacggg gtggaggaa aagacagtt ggggcgctc 
cggacgatg tcagggggt gaactcgaa atgtttgta 
acttcggat aatcggacg ttgttaccg gtttcgaaa 
gacttaacc gatggttgt aaccggttg gaggagagt 
cggaaaggg aggtattgt ttcctaaca ggtgatgga 
agggccaac gaaaatttg cacttgact agtatgcac 
ttaatttgg gcaagacaa cacaactca atcgccaaa 
caattggca aaattgaac cctgattgg gctgacgag 
cgcttgttt caagaaagt cgcaagata atcggggcg 
cagatgcag cacatttgc tacagagag ttcctcccg 
attctttta ggccggggt ttgatggaa aaatcgggc 
ttgtaccca cgaacttcc ggttatttc actgaatac 
aactcagcc gtcgaccca tctatagcc aacaatttt 
gcaacagca gcattccgc ttcgcccac tccataatc 
ccgggttta atgaaattt ttggcaaag gactcgtct 
agtcccgag ttcgttcaa ttgcataaa atgctgttc 
gatccgttc aggttgtac caggccggg gggctcgac 
cgggccttg aggggcgcc atggacacc cccatccaa 
gccaacgac ccctacttc agcagcgaa ctgaaagac 
aagctcttt gaggacgct gcgaacgag acaattcgc 
gcgtatggt ttagatttg gtctctttg aatatacaa 
cgaggccgc gaccatgga ttagttggc tataacagc 
tggcgagag cattgcgga ttaaggaga gtctctacg 
tttcagcaa cttcagggg gactttgac gatgattca 
ctcagaaac attcaggct atctataga gacgtggac 
gacgtggac ttgtacacg ggggctctg agcgagaag 
cccctcaac gggagcatt ctgggcccg actctgacg 
tgtttgatc cacgaccag ttcgtgcga gtgaaatat 
ggggaccgt ttttggtac gagaacccc cattggttc 
actcttgac caacttgcc gaaattcga aaaacgagt 
cttgcccgg attatttgt gacaattcg gatgaagtt 
gacgaagtg cagcctcta gtgatggag aaaatccga 
agcgataat aaagtcgtc ccttgtagc gcccttccc 
gctcctcag tggggcccc tggaaggaa gccctccac 
cgcgtccgc acgtccgct gatacactt tcagtggaa 
tcaatcacg aattag
    mRNA sequence
    • >TC004579 RA
      ctgattttc tattccaat agttagtgt gtttacaac 
tgcgtcagt gttggtcgg tcaaaaatt cttttcagg 
attttggga acatgtctc tcgcgactg aaacgacaa 
gattacttt cggaccaaa cgcaaccgc aatatgcgt 
ttgatacca gcctcgtac gggagcgta aaaaacgaa 
ttaaacaat tccaatgtt gcttatgcg tgatttttg 
tttgttgtc tcgtggtgg catttttga ttgccgctg 
tttggggca taaacaggg cggaaaaca gcttcacaa 
acgtgacta atactagtt ccccctcgg acacactca 
cgactctac ttgcaattt cgtggcccc gtcccgaca 
aacccatga atacgtcct attgtaaca accagagtg 
aatggtcac aggcccttg ccgcgggcc taaaggccc 
taaacacca aacaccaaa tcgagaaaa atgtcacag 
aaatgacca ccgacagcc ccagctaca aacaccaga 
aggtgttcc tagactcga ataaaactc aagctttgg 
ccaacttgg gctacttgc gagaatcag caaggcggt 
ttttcccca acaacggga gcacaattt gcaataagg 
ctgaaccgt gtcctgtgc cccaaaaat gcaccgaat 
ttgcgaaat ttcgcacgt ttgatggca cttgtaaca 
atctggagc gccccaatt tgggggctg cgttccagc 
cttttcgcc gcgcgctcc cgccggact acgccgacg 
gggttagca gcccccggg gggccaaaa ccggggcgc 
ttccatcgg ctcgcaccg tcagcttgg aggtccatc 
ggccgtttt acaaaaacg acgataagt ttagcgtaa 
tgttggccg tttgggggc agtttctgg atcacgata 
tgacggcga cagccccca gtcggggcc ccaacggct 
ccacgatcg cctgttgtg gccaaaaag tcacacatc 
cggagtgct ttcccgtca agttggacc gctttgacc 
ctttatccg aatttaatg tcacttgta tggaatttg 
tgcggtcgg caaatgccg ccacttgtt gtctggggc 
ccagggaac agatgaacc aagtgacgg cgtttatag 
acgggtcgg ttatttacg gggtggagg aaaagacag 
ttggggcgc tccggacga tgtcagggg gtgaactcg 
aaatgtttg taacttcgg ataatcgga cgttgttac 
cggtttcga aagacttaa ccgatggtt gtaaccggt 
tggaggaga gtcggaaag ggaggtatt gtttcctaa 
caggtgatg gaagggcca acgaaaatt tgcacttga 
ctagtatgc acttaattt gggcaagac aacacaact 
caatcgcca aacaattgg caaaattga accctgatt 
gggctgacg agcgcttgt ttcaagaaa gtcgcaaga 
taatcgggg cgcagatgc agcacattt gctacagag 
agttcctcc cgattcttt taggccggg gtttgatgg 
aaaaatcgg gcttgtacc cacgaactt ccggttatt 
tcactgaat acaactcag ccgtcgacc catctatag 
ccaacaatt ttgcaacag cagcattcc gcttcgccc 
actccataa tcccgggtt taatgaaat ttttggcaa 
aggactcgt ctagtcccg agttcgttc aattgcata 
aaatgctgt tcgatccgt tcaggttgt accaggccg 
gggggctcg accgggcct tgaggggcg ccatggaca 
cccccatcc aagccaacg acccctact tcagcagcg 
aactgaaag acaagctct ttgaggacg ctgcgaacg 
agacaattc gcgcgtatg gtttagatt tggtctctt 
tgaatatac aacgaggcc gcgaccatg gattagttg 
gctataaca gctggcgag agcattgcg gattaagga 
gagtctcta cgtttcagc aacttcagg gggactttg 
acgatgatt cactcagaa acattcagg ctatctata 
gagacgtgg acgacgtgg acttgtaca cgggggctc 
tgagcgaga agcccctca acgggagca ttctgggcc 
cgactctga cgtgtttga tccacgacc agttcgtgc 
gagtgaaat atggggacc gtttttggt acgagaacc 
cccattggt tcactcttg accaacttg ccgaaattc 
gaaaaacga gtcttgccc ggattattt gtgacaatt 
cggatgaag ttgacgaag tgcagcctc tagtgatgg 
agaaaatcc gaagcgata ataaagtcg tcccttgta 
gcgcccttc ccgctcctc agtggggcc cctggaagg 
aagccctcc accgcgtcc gcacgtccg ctgatacac 
tttcagtgg aatcaatca cgaattagt ttgcacaat 
aaatgcacc aacttttg

    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