Status
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Gene information
General information
TC000963 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_007417.3: 8976150..8980403
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
    		TC000963
    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_00198

    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: 40.0% (includes death as pupa, adult)

    pupa eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 1 (3 dpi)
    Days post injection

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

    adult lethality - Number of animals showing the phenotype: 2 (9 dpi)
    Days post injection

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

    larval musculature differentiation incomplete - 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%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     labrum size decreased - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    labrum not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    gena bristle number increased - 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: 20.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 20.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 3 (41 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC000963 RA
      MSGSAHKHR YKNAALDSV ELRRRREEE GLQLRKQKR 
EQQLNKRRN VNVNQLAED NDHLQVDSE ILSPVSPMI 
TPEMVQALY SPDVEQQIS ATQKFRQLL SYEPNPPID 
EVVQTGIIP RFVEFLQNS NNCSLQFEA AWALTNVAS 
GTSQQTRMV IEAGAVPIF IRLLSSQYE DVQEQAVWA 
LGNIAGDSP ECRDHVLDS GILVPLLQL LSKSTRLSM 
TRNAVWALS NLCRGKNPP PDFAKVSPA LPVLARLLF 
HSDPDVLSD TCWALSYLS DGPNEKIQA VIDAGVCRK 
LVELLMHQQ PNVVSAALR AVGNIVTGD DVQTQVILN 
CSALHCLHH LLSSSKESV RKEACWTIS NITAGNRQQ 
IQAVIDANI FPVLIEILS KAEFKTRKE AAWAITNAT 
SGGTPDQIR YLVNQACIG PLCDLLTVM DAKIVQVAL 
NGLENILRL GEQDAKNHS GTNPYAVLI EQCYGLDKI 
EFLQSHVNM EIYQKAFDI IEHFFGTEE EDTTVAPSV 
NPDQQQYHF SSDQSVPMG GFHF
    CDS sequence
    • >TC000963 RA
      atgtcgggc tccgctcac aaacaccgc tacaaaaac 
gcggcgctg gacagcgtc gagttgcga cggcggcga 
gaggaagaa ggcctccag ttaaggaaa cagaaacgg 
gaacagcag ctgaacaag cggcggaat gttaacgtc 
aaccaattg gccgaggac aatgaccat ctgcaagtg 
gacagcgag atcctctcg cctgtctcg cccatgatc 
acccccgaa atggtccag gcgttgtac agccccgac 
gtggagcag caaatcagc gccacgcaa aaattcaga 
caactgctg agctacgaa cccaaccca cccattgat 
gaggtggtc cagaccggg atcatccca cgatttgta 
gagtttttg cagaattca aacaattgt agccttcag 
tttgaagca gcatgggct ttgaccaac gttgcctct 
ggtacctct cagcaaacc aggatggtc attgaagct 
ggtgctgtt cctattttt atacgtttg ttgagcagt 
caatatgag gatgttcag gagcaagct gtttgggca 
ttagggaat atagcaggg gattcaccc gaatgtaga 
gatcacgtc ctggattcg ggtattttg gttccactc 
ttacaactc cttagtaaa tcgacgcgt ttatcgatg 
actcgcaat gccgtgtgg gcgctttcg aacctctgc 
aggggcaag aaccctcct ccagacttt gcgaaagtc 
tccccagct ctgcccgta ctcgctcgt ctcttgttt 
cactccgac cctgacgtg ctctctgac acttgctgg 
gccttgagc tacctatcc gacggtcct aacgaaaaa 
atccaggcg gtcatagac gccggcgtt tgtcggaaa 
ctggtcgaa ttgctaatg caccaacag cccaacgta 
gtctcggca gctctgcgc gctgtcggc aacatagtg 
actggtgac gacgtccaa actcaggtc atactaaac 
tgctccgct ctacattgc ttgcaccac ttgttgtca 
tcctcgaag gagtccgtg aggaaggag gcgtgttgg 
acgatcagc aacatcacg gctggaaac cggcagcaa 
atccaggcg gtcatagac gcgaacatt ttcccggtt 
ttgatagag attttgagc aaggcggag tttaagacg 
cggaaggag gcggcctgg gctatcacg aatgccacc 
agcgggggc acacccgac cagatcagg tatctagtg 
aaccaggct tgcattggg ccgctttgt gaccttttg 
accgtcatg gacgcgaaa atcgtgcaa gtggccctc 
aacggcctg gagaatatt ctgagatta ggggagcaa 
gacgccaag aatcactcg gggaccaac ccgtatgct 
gtgctaatc gagcagtgc tatgggttg gataaaatc 
gaatttttg caatcgcat gtcaatatg gagatttat 
cagaaggcc ttcgacatt attgaacac ttcttcggg 
acggaggag gaggacacg actgtggcg ccctcggtg 
aatcccgac caacagcag taccatttc agctcggat 
cagtcggtg ccgatggga ggattccat ttttaa
    mRNA sequence
    • >TC000963 RA
      ttgcaaata gttccgaat gccagaatt ttcattttc 
acgattcca tttccaatt atcgctgaa ttcctgatt 
cgtccaaaa gtatcaaat gtgtgtttc catctgagt 
gtgagaaaa accgtcgga cattacgga agatgtcgg 
gctccgctc acaaacacc gctacaaaa acgcggcgc 
tggacagcg tcgagttgc gacggcggc gagaggaag 
aaggcctcc agttaagga aacagaaac gggaacagc 
agctgaaca agcggcgga atgttaacg tcaaccaat 
tggccgagg acaatgacc atctgcaag tggacagcg 
agatcctct cgcctgtct cgcccatga tcacccccg 
aaatggtcc aggcgttgt acagccccg acgtggagc 
agcaaatca gcgccacgc aaaaattca gacaactgc 
tgagctacg aacccaacc cacccattg atgaggtgg 
tccagaccg ggatcatcc cacgatttg tagagtttt 
tgcagaatt caaacaatt gtagccttc agtttgaag 
cagcatggg ctttgacca acgttgcct ctggtacct 
ctcagcaaa ccaggatgg tcattgaag ctggtgctg 
ttcctattt ttatacgtt tgttgagca gtcaatatg 
aggatgttc aggagcaag ctgtttggg cattaggga 
atatagcag gggattcac ccgaatgta gagatcacg 
tcctggatt cgggtattt tggttccac tcttacaac 
tccttagta aatcgacgc gtttatcga tgactcgca 
atgccgtgt gggcgcttt cgaacctct gcaggggca 
agaaccctc ctccagact ttgcgaaag tctccccag 
ctctgcccg tactcgctc gtctcttgt ttcactccg 
accctgacg tgctctctg acacttgct gggccttga 
gctacctat ccgacggtc ctaacgaaa aaatccagg 
cggtcatag acgccggcg tttgtcgga aactggtcg 
aattgctaa tgcaccaac agcccaacg tagtctcgg 
cagctctgc gcgctgtcg gcaacatag tgactggtg 
acgacgtcc aaactcagg tcatactaa actgctccg 
ctctacatt gcttgcacc acttgttgt catcctcga 
aggagtccg tgaggaagg aggcgtgtt ggacgatca 
gcaacatca cggctggaa accggcagc aaatccagg 
cggtcatag acgcgaaca ttttcccgg ttttgatag 
agattttga gcaaggcgg agtttaaga cgcggaagg 
aggcggcct gggctatca cgaatgcca ccagcgggg 
gcacacccg accagatca ggtatctag tgaaccagg 
cttgcattg ggccgcttt gtgaccttt tgaccgtca 
tggacgcga aaatcgtgc aagtggccc tcaacggcc 
tggagaata ttctgagat taggggagc aagacgcca 
agaatcact cggggacca acccgtatg ctgtgctaa 
tcgagcagt gctatgggt tggataaaa tcgaatttt 
tgcaatcgc atgtcaata tggagattt atcagaagg 
ccttcgaca ttattgaac acttcttcg ggacggagg 
aggaggaca cgactgtgg cgccctcgg tgaatcccg 
accaacagc agtaccatt tcagctcgg atcagtcgg 
tgccgatgg gaggattcc atttttaaa tcgagtttt 
agattattt taaggactt ggtcacgcc aaaggataa 
ccttcacga tatccggta tttagtttg aatcaagtg 
atagtgtta cttcattgt aacagaatt ttatgcatg 
tatggcgga aatacaaag tcgacagca aaaattatt 
cttttcgga gataagtgt cttgattct cgaaattcg 
gttttgtaa aattgcttc gatttttca gaaatgatt 
gttgtgtaa gtgagctta acatacgct atttatttt 
atacagagg ccagctttt gtcttcact gatctaggt 
tttgtaaca gctatgtac atattttac gtaaagtgt 
gaaacatac atgtataaa tattcctaa cagcatatt 
tgtttatag tttttattg taaaataaa ctaacattt 
aagta

    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