Status
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Gene information
General information
TC004088 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.

NW_015450468.1: 17..6259
Sequence information
Transcripts / Proteins (2) 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
    		TC004088
    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
    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_00661

    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 larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     thorax everted (inside-out) - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    abdomen everted (inside-out) - 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%
    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: 70.0% (includes death as larva, prepupa, pupa, adult)

    pupal molt delayed (still larva) - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection

    larva lethality late (L7) - Number of animals showing the phenotype: 1 (16 dpi)
    Days post injection

    pupal molt not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 3 (16 dpi)
    Days post injection

    eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 1 (16 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (19 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (22 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004088 RA
      MKDEEDRAV ENWKGEVKM STSTEIEKQ IFTAIESGD 
AVLLRTALA SKPDVNILD ENAMTPLQH AAYKGNKDM 
VQMLLDYGA DPNLCKHQH NYTALHFAG LSGNSDVCL 
ALLVAGAFP EVTNAVNRT ASQMAAFVG HHKCVAIIN 
NYIPKSEVD YYSRLQGAQ TEPYLPPFL SESFHKLII 
QVNVHPVKI ALNINSFIG LSQHLAKIK KVLELMYDK 
EMQRGAGNN EVMAFKLYY LAFIVGEVM TIQNKHQSP 
DATLQTFCK KVLKPATDG ALEILDGLL RECIKHFPF 
RECTLFRQM VTTLTGKDT PTALSVINS AINGQRGFV 
DNVPICYTC GEEKPSKKC SQCKVAQYC DKTCQKLHW 
CWHKKACPQ LAQEPLKCN NDTQIDPQE LSSEIQNLL 
VTN
    • >TC004088 RB
      MSTSTEIEK QIFTAIESG DAVLLRTAL ASKPDVNIL 
DENAMTPLQ HAAYKGNKD MVQMLLDYG ADPNLCKHQ 
HNYTALHFA GLSGNSDVC LALLVAGAF PEVTNAVNR 
TASQMAAFV GHHKCVAII NNYIPKSEV DYYSRLQGA 
QTEPYLPPF LSESFHKLI IQVNVHPVK IALNINSFI 
GLSQHLAKI KKVLELMYD KEMQRGAGN NEVMAFKLY 
YLAFIVGEV MTIQNKHQS PDATLQTFC KKVLKPATD 
GALEILDGL LRECIKHFP FRECTLFRQ MVTTLTGKD 
TPTALSVIN SAINGQRGF VDNVPICYT CGEEKPSKK 
CSQCKVAQY CDKTCQKLH WCWHKKACP QLAQEPLKC 
NNDTQIDPQ ELSSEIQNL LVTN
    CDS sequence
    • >TC004088 RA
      atgaaagat gaagaagat agagcagtt gaaaactgg 
aaaggggaa gtaaaaatg tccacaagc accgaaatt 
gagaagcaa atcttcact gcgatcgaa tccggagac 
gctgtttta ctccgaacc gcattagca tccaaacct 
gacgtaaac atcctagat gaaaatgca atgacacca 
ctgcagcat gctgcttat aagggcaac aaggacatg 
gtccaaatg ctcctcgac tatggggca gacccaaac 
ctttgcaaa caccaacac aattacaca gcgctacat 
ttcgcgggc ctttcgggc aattccgac gtgtgtctg 
gcactgctc gtggctggg gccttcccc gaagtcacg 
aacgcagtg aatcggacg gcgtcacaa atggcggcc 
tttgtcggc catcataag tgcgtcgcc attatcaat 
aattacatc ccaaagtca gaagtagat tattatagt 
aggctacaa ggcgctcaa acggagcca tatttgccg 
ccatttttg tccgaaagc ttccacaaa ttaataata 
caagtaaac gtacacccg gtcaaaatc gcgctaaac 
atcaacagt tttatcggg ttatcgcaa cacttggcg 
aaaatcaaa aaagtgcta gaattgatg tacgacaaa 
gaaatgcaa agaggggcc ggtaataac gaagtgatg 
gcgttcaaa ctatactac ctggcgttt atagtaggc 
gaggttatg acgattcaa aacaaacac caatcgcct 
gacgccacg ttgcaaacg ttttgcaaa aaagtgcta 
aaaccggct acagatggc gctttagaa atactcgat 
gggttgttg cgggagtgc attaaacat ttcccattt 
cgggagtgt acacttttt cgccaaatg gttacaaca 
ctaacgggg aaagacacc ccaacagct ctaagtgtt 
atcaattcg gccataaat ggtcagaga gggttcgtt 
gataacgtc ccgatttgt tacacttgt ggggaagag 
aaacctagt aagaagtgc tcgcaatgt aaagtggcg 
cagtattgt gataagacg tgccaaaag ttgcactgg 
tgttggcac aaaaaggcg tgcccacag ttggctcaa 
gagcccctc aaatgtaat aatgacaca caaattgat 
cctcaggaa ctgtcttca gaaatacag aatctttta 
gttactaat taa
    • >TC004088 RB
      atgtccaca agcaccgaa attgagaag caaatcttc 
actgcgatc gaatccgga gacgctgtt ttactccga 
accgcatta gcatccaaa cctgacgta aacatccta 
gatgaaaat gcaatgaca ccactgcag catgctgct 
tataagggc aacaaggac atggtccaa atgctcctc 
gactatggg gcagaccca aacctttgc aaacaccaa 
cacaattac acagcgcta catttcgcg ggcctttcg 
ggcaattcc gacgtgtgt ctggcactg ctcgtggct 
ggggccttc cccgaagtc acgaacgca gtgaatcgg 
acggcgtca caaatggcg gcctttgtc ggccatcat 
aagtgcgtc gccattatc aataattac atcccaaag 
tcagaagta gattattat agtaggcta caaggcgct 
caaacggag ccatatttg ccgccattt ttgtccgaa 
agcttccac aaattaata atacaagta aacgtacac 
ccggtcaaa atcgcgcta aacatcaac agttttatc 
gggttatcg caacacttg gcgaaaatc aaaaaagtg 
ctagaattg atgtacgac aaagaaatg caaagaggg 
gccggtaat aacgaagtg atggcgttc aaactatac 
tacctggcg tttatagta ggcgaggtt atgacgatt 
caaaacaaa caccaatcg cctgacgcc acgttgcaa 
acgttttgc aaaaaagtg ctaaaaccg gctacagat 
ggcgcttta gaaatactc gatgggttg ttgcgggag 
tgcattaaa catttccca tttcgggag tgtacactt 
tttcgccaa atggttaca acactaacg gggaaagac 
accccaaca gctctaagt gttatcaat tcggccata 
aatggtcag agagggttc gttgataac gtcccgatt 
tgttacact tgtggggaa gagaaacct agtaagaag 
tgctcgcaa tgtaaagtg gcgcagtat tgtgataag 
acgtgccaa aagttgcac tggtgttgg cacaaaaag 
gcgtgccca cagttggct caagagccc ctcaaatgt 
aataatgac acacaaatt gatcctcag gaactgtct 
tcagaaata cagaatctt ttagttact aattaa
    mRNA sequence
    • >TC004088 RA
      gaccttctt tctttgtca gagaaaaca catccaaat 
tccaaagaa gtggaaaca acaaacgat tacaacgac 
gagacaatg aaagatgaa gaagataga gcagttgaa 
aactggaaa ggggaagta aaaatgtcc acaagcacc 
gaaattgag aagcaaatc ttcactgcg atcgaatcc 
ggagacgct gttttactc cgaaccgca ttagcatcc 
aaacctgac gtaaacatc ctagatgaa aatgcaatg 
acaccactg cagcatgct gcttataag ggcaacaag 
gacatggtc caaatgctc ctcgactat ggggcagac 
ccaaacctt tgcaaacac caacacaat tacacagcg 
ctacatttc gcgggcctt tcgggcaat tccgacgtg 
tgtctggca ctgctcgtg gctggggcc ttccccgaa 
gtcacgaac gcagtgaat cggacggcg tcacaaatg 
gcggccttt gtcggccat cataagtgc gtcgccatt 
atcaataat tacatccca aagtcagaa gtagattat 
tatagtagg ctacaaggc gctcaaacg gagccatat 
ttgccgcca tttttgtcc gaaagcttc cacaaatta 
ataatacaa gtaaacgta cacccggtc aaaatcgcg 
ctaaacatc aacagtttt atcgggtta tcgcaacac 
ttggcgaaa atcaaaaaa gtgctagaa ttgatgtac 
gacaaagaa atgcaaaga ggggccggt aataacgaa 
gtgatggcg ttcaaacta tactacctg gcgtttata 
gtaggcgag gttatgacg attcaaaac aaacaccaa 
tcgcctgac gccacgttg caaacgttt tgcaaaaaa 
gtgctaaaa ccggctaca gatggcgct ttagaaata 
ctcgatggg ttgttgcgg gagtgcatt aaacatttc 
ccatttcgg gagtgtaca ctttttcgc caaatggtt 
acaacacta acggggaaa gacacccca acagctcta 
agtgttatc aattcggcc ataaatggt cagagaggg 
ttcgttgat aacgtcccg atttgttac acttgtggg 
gaagagaaa cctagtaag aagtgctcg caatgtaaa 
gtggcgcag tattgtgat aagacgtgc caaaagttg 
cactggtgt tggcacaaa aaggcgtgc ccacagttg 
gctcaagag cccctcaaa tgtaataat gacacacaa 
attgatcct caggaactg tcttcagaa atacagaat 
cttttagtt actaattaa attgtaatt tattagtgt 
gttagtaaa taaagtgag cttaacaaa
    • >TC004088 RB
      gaccttctt tctttgtca gagaaaaca catccaaat 
tccaaagaa gtggaaaca acaaacgat tacaacgac 
gagacaatg aaagatgaa gaagataga gcagttgaa 
aactggaaa ggggaagtg acatttcat ctttccccg 
attttgcca accgtcatt cctgtcaaa atttttgtt 
ccatgttta tcacccgca aaaatctca acacaaagt 
aaaaatgtc cacaagcac cgaaattga gaagcaaat 
cttcactgc gatcgaatc cggagacgc tgttttact 
ccgaaccgc attagcatc caaacctga cgtaaacat 
cctagatga aaatgcaat gacaccact gcagcatgc 
tgcttataa gggcaacaa ggacatggt ccaaatgct 
cctcgacta tggggcaga cccaaacct ttgcaaaca 
ccaacacaa ttacacagc gctacattt cgcgggcct 
ttcgggcaa ttccgacgt gtgtctggc actgctcgt 
ggctggggc cttccccga agtcacgaa cgcagtgaa 
tcggacggc gtcacaaat ggcggcctt tgtcggcca 
tcataagtg cgtcgccat tatcaataa ttacatccc 
aaagtcaga agtagatta ttatagtag gctacaagg 
cgctcaaac ggagccata tttgccgcc atttttgtc 
cgaaagctt ccacaaatt aataataca agtaaacgt 
acacccggt caaaatcgc gctaaacat caacagttt 
tatcgggtt atcgcaaca cttggcgaa aatcaaaaa 
agtgctaga attgatgta cgacaaaga aatgcaaag 
aggggccgg taataacga agtgatggc gttcaaact 
atactacct ggcgtttat agtaggcga ggttatgac 
gattcaaaa caaacacca atcgcctga cgccacgtt 
gcaaacgtt ttgcaaaaa agtgctaaa accggctac 
agatggcgc tttagaaat actcgatgg gttgttgcg 
ggagtgcat taaacattt cccatttcg ggagtgtac 
actttttcg ccaaatggt tacaacact aacggggaa 
agacacccc aacagctct aagtgttat caattcggc 
cataaatgg tcagagagg gttcgttga taacgtccc 
gatttgtta cacttgtgg ggaagagaa acctagtaa 
gaagtgctc gcaatgtaa agtggcgca gtattgtga 
taagacgtg ccaaaagtt gcactggtg ttggcacaa 
aaaggcgtg cccacagtt ggctcaaga gcccctcaa 
atgtaataa tgacacaca aattgatcc tcaggaact 
gtcttcaga aatacagaa tcttttagt tactaatta 
aattgtaat ttattagtg tgttagtaa ataaagtga 
gcttaacaa a

    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