Status
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Gene information
General information
TC004664 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: 25266..27722
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
    		TC004664
    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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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_03808

    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

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    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): 30% - 50%
    cuticle remnants with unidentifyable segments - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    head not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    thorax present - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    thorax not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen present - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    abdomen 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: 0.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 0.0% (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004664 RA
      MNELEKAES DCAKKAELV KSLEKQLAD AKAAYAKAS 
STLEELKRL KSLEENRKR IALTEDTLS DWLEEKFPW 
SAQLKSLLK EKFKFDHFR AKQLAAINA TLSKKDVLL 
VMPTGGGKS LVFQLPALI DPGFTLVVT PLVSLIQDQ 
LVALEKFKI EAATIHAST SKSEIKEIY DSMTSKKSA 
LKLLYVTPE WIARSKKFM SVLKKCYEA KRVARVAID 
EVHCCSTWG HDFRPDYPY LGLVRSLLE KVPFLGLTA 
TATMSVLND VQTMLNLEN CLIITAPFN RPNLFYQVL 
PKPATKDGV LNYLEKLMT EKYAGQSGI IYTNTINEC 
ISLATALKG SNLRVAPFH AQLEPEQKK KIHRKWLDN 
TYQAVVATV AFGMGIDKP DVRFVIHHV IPRSMESLY 
QESGRAGRD GKRADCIVL FSLNDYLKI SAMSTSLVE 
EKKAQQVLE YCVERLRCR RSIIATYFE QVWETSDCN 
KMCDICKRD VKIPAYYDL TQICKDLHS LIDQAKGFD 
EKLTLIKLI DAWYQAGLK KFRLSNVEK PKMSKEHAE 
LVIAFLLLE KYLAIDKGY TMYSTVSYI VKGRAVGDE 
KVEMLASDG MKIPKRLKE EGDGSPAKK KPRTD
    CDS sequence
    • >TC004664 RA
      atgaacgaa ttagaaaaa gctgaaagt gattgtgcc 
aaaaaggct gagttggta aagtcttta gaaaagcaa 
ctagcggac gctaaagcg gcatacgcg aaggccagt 
agcacctta gaagagtta aaacggtta aaatcgctt 
gaagaaaat cgcaagaga atagcctta actgaagac 
accttgagc gactggctt gaggagaag tttccctgg 
tcggcccaa ctcaaatca ctgctgaag gaaaaattt 
aaatttgac catttccgg gccaaacaa ctcgccgcc 
atcaatgcc accctctcc aaaaaggac gtccttctt 
gtcatgcca acggggggt ggaaaatca ctagtcttc 
caacttccc gccctcata gaccccggt tttaccctg 
gtggtcacc cccttagtg tcgctaatc caggaccag 
ttagtcgcc ttagaaaaa ttcaaaatt gaagccgcc 
accatccac gcaagtacc tcaaaaagt gaaattaag 
gagatttac gattcaatg actagtaaa aaatcggca 
ttgaaattg ctctacgta acccctgag tggatcgct 
cgcagtaaa aaatttatg tcggttttg aaaaagtgc 
tacgaggcg aagcgagtg gctcgcgtt gcgattgac 
gaggtgcat tgttgctca acctggggg cacgatttc 
cgccctgat tacccctac ttggggcta gttcgctcc 
ctgctggag aaagtgcct tttttgggg ctgacggcg 
accgccaca atgtcggtt ttaaacgat gtgcaaaca 
atgctgaat cttgagaat tgtctcatt attacagcg 
ccttttaat cgaccgaat ttgttttac caagttttg 
ccgaaaccg gctactaaa gacggggtt ttaaattat 
ttagagaaa ctaatgact gagaaatac gccggtcag 
agtggcatt atttatact aataccata aatgaatgt 
attagttta gcaacagct ttaaaaggc tcgaattta 
cgcgtggcc ccatttcat gcgcaattg gagcccgaa 
caaaagaaa aaaatacac agaaagtgg ttagataac 
acgtatcaa gctgtggtc gcaactgta gcattcgga 
atggggatt gataaacct gacgtcagg tttgtaatt 
caccatgtg attcccaga agcatggaa agcctgtat 
caggagagt ggtagagct ggacgcgac ggcaaacgc 
gccgattgc atagtccta tttagctta aacgattat 
ttaaaaatt tcagccatg tccacttcg ctagtagaa 
gaaaaaaag gcacaacaa gtactagaa tattgcgtt 
gagcgccta cgatgtcga cgctcaatt atagctaca 
tattttgag caagtttgg gaaactagc gattgtaac 
aaaatgtgc gatatttgc aaacgcgac gtaaaaatt 
cccgcctat tatgaccta acgcagata tgtaaagac 
ctacactca ttgatagac caagctaaa gggttcgac 
gagaaatta actctaatt aaactgata gatgcgtgg 
tatcaagcc ggtctgaaa aaattccga ctgtcgaac 
gtggaaaaa ccgaaaatg tcgaaagag catgccgag 
ctcgttatc gccttcctt ttgctagaa aaataccta 
gcaattgat aaggggtac accatgtat tccacggtt 
tcctacatc gtcaaaggg agggcagtc ggtgatgaa 
aaagtcgaa atgttggct tcggacggc atgaaaata 
ccgaaaaga ctgaaggag gaaggcgat ggatctccc 
gcaaagaaa aaaccaaga actgactaa
    mRNA sequence
    • >TC004664 RA
      gtaacgcag tttccggca actatatga aaaaataac 
ctaattttt tcgcacttt ttccaaaaa acagtatta 
tcaattgtg ataatttaa ccggctttc cgataagtt 
tttacattt cctagtgtt ggtttttag atattgtag 
cacaataaa aaaatgaac gaattagaa aaagctgaa 
agtgattgt gccaaaaag gctgagttg gtaaagtct 
ttagaaaag caactagcg gacgctaaa gcggcatac 
gcgaaggcc agtagcacc ttagaagag ttaaaacgg 
ttaaaatcg cttgaagaa aatcgcaag agaatagcc 
ttaactgaa gacaccttg agcgactgg cttgaggag 
aagtttccc tggtcggcc caactcaaa tcactgctg 
aaggaaaaa tttaaattt gaccatttc cgggccaaa 
caactcgcc gccatcaat gccaccctc tccaaaaag 
gacgtcctt cttgtcatg ccaacgggg ggtggaaaa 
tcactagtc ttccaactt cccgccctc atagacccc 
ggttttacc ctggtggtc accccctta gtgtcgcta 
atccaggac cagttagtc gccttagaa aaattcaaa 
attgaagcc gccaccatc cacgcaagt acctcaaaa 
agtgaaatt aaggagatt tacgattca atgactagt 
aaaaaatcg gcattgaaa ttgctctac gtaacccct 
gagtggatc gctcgcagt aaaaaattt atgtcggtt 
ttgaaaaag tgctacgag gcgaagcga gtggctcgc 
gttgcgatt gacgaggtg cattgttgc tcaacctgg 
gggcacgat ttccgccct gattacccc tacttgggg 
ctagttcgc tccctgctg gagaaagtg ccttttttg 
gggctgacg gcgaccgcc acaatgtcg gttttaaac 
gatgtgcaa acaatgctg aatcttgag aattgtctc 
attattaca gcgcctttt aatcgaccg aatttgttt 
taccaagtt ttgccgaaa ccggctact aaagacggg 
gttttaaat tatttagag aaactaatg actgagaaa 
tacgccggt cagagtggc attatttat actaatacc 
ataaatgaa tgtattagt ttagcaaca gctttaaaa 
ggctcgaat ttacgcgtg gccccattt catgcgcaa 
ttggagccc gaacaaaag aaaaaaata cacagaaag 
tggttagat aacacgtat caagctgtg gtcgcaact 
gtagcattc ggaatgggg attgataaa cctgacgtc 
aggtttgta attcaccat gtgattccc agaagcatg 
gaaagcctg tatcaggag agtggtaga gctggacgc 
gacggcaaa cgcgccgat tgcatagtc ctatttagc 
ttaaacgat tatttaaaa atttcagcc atgtccact 
tcgctagta gaagaaaaa aaggcacaa caagtacta 
gaatattgc gttgagcgc ctacgatgt cgacgctca 
attatagct acatatttt gagcaagtt tgggaaact 
agcgattgt aacaaaatg tgcgatatt tgcaaacgc 
gacgtaaaa attcccgcc tattatgac ctaacgcag 
atatgtaaa gacctacac tcattgata gaccaagct 
aaagggttc gacgagaaa ttaactcta attaaactg 
atagatgcg tggtatcaa gccggtctg aaaaaattc 
cgactgtcg aacgtggaa aaaccgaaa atgtcgaaa 
gagcatgcc gagctcgtt atcgccttc cttttgcta 
gaaaaatac ctagcaatt gataagggg tacaccatg 
tattccacg gtttcctac atcgtcaaa gggagggca 
gtcggtgat gaaaaagtc gaaatgttg gcttcggac 
ggcatgaaa ataccgaaa agactgaag gaggaaggc 
gatggatct cccgcaaag aaaaaacca agaactgac 
taactgtat ttattattt tcaatatag agttttata 
aagt

    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