Status
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Gene information
General information
TC000444 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: 11195922..11198090
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
    		TC000444
    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_00095

    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: 20.0% (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

    adult lethality - Number of animals showing the phenotype: 1 (9 dpi)
    Days post injection

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

    thorax everted (inside-out) - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen everted (inside-out) - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    abdomen dorsal irregular - Penetrance (percentage of animals/eggs on slide): more than 80%
    abdomen everted (inside-out) - 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): 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: 10.0% (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC000444 RA
      MDVQIILEG PPFPPNYHM KQSLGQFFF DSASKFKDR 
ICQIDAKTE KSETFLTVK QKSVRVALE MQKRGITSK 
DVIVTCSAL TLETPVPIL ASFYLGAKV ANSDPTLSV 
AQTAHMLSL VSPTMIFVQ ESSLTLIEE SLQQAKLQA 
QIVVFGTCD KYPTFSDFN QAKENEEMF YPASVDIHD 
TGLMFFSSG TTGLPKAIC HSHFSFLNL AYCFCESGL 
KVDTTLSYT TFYWISGLM MLTSSFLKG GQRIVCTKV 
PEAKDVFEI IQKYKVTCL FLAPVLTYP LTDYANSGN 
FDTSSLHSI LTGGTPISE QQMTKLYAT FKHTCIVFA 
YGMTEVGMV GMFNPVTDK VLMTKKLTS SGKVAMGVS 
LKLVDVETN KTLGPNQKG EFLVKSPCM MKGYYKADC 
SDIFDEDGF LKTGDVGYY DQDGCLYIV ERRKEMFKY 
LSWHIVPSA IENVLLEHP EIKEAAVFG MPINEEMGD 
APAACVVLQ NGSKVTVQE IADFVASKV SDREKLRGG 
VFIVQELPR TPSGKLKRR DVKNYVLSL NRGTNKQ
    CDS sequence
    • >TC000444 RA
      atggatgta caaataata ttagaaggt cccccattt 
ccacccaat tatcacatg aaacaaagt ttgggtcaa 
tttttcttt gattccgcc tcaaaattc aaagaccga 
atatgccag atcgacgcc aaaaccgaa aaaagtgaa 
acgttctta acagttaaa caaaaaagt gttcgagtc 
gctttggag atgcagaaa cgaggaata acatcaaag 
gatgtgatt gttacttgc tctgcgcta actttagag 
accccagtc cccatcctt gcttctttt tacctcggt 
gctaaagtg gcaaactca gacccgact ttatcagtc 
gcacaaacg gctcacatg ctatcactt gtatcccca 
acaatgatt ttcgtccaa gaaagctca ctcactctg 
attgaagaa agcttgcaa caagccaag cttcaagca 
cagattgtg gtttttggg acgtgtgac aagtatcca 
acattttcc gatttcaac caagcgaag gaaaacgaa 
gagatgttt tatccagcc tctgtcgat attcacgac 
actggtctg atgttcttc agcagcggc acaacaggg 
cttcccaaa gcgatctgt cacagtcat ttcagtttc 
ttaaacctt gcttactgt ttttgtgaa tcggggctt 
aaggttgac acgactctt tcttacact actttttac 
tggatatcg gggcttatg atgttgact tcttcgttt 
ttaaaaggc ggacagcga attgtttgc accaaggtg 
cccgaagcc aaagacgtt tttgaaatt attcaaaaa 
tataaagta acttgtctg tttttggct ccggtttta 
acataccca ctcacagat tacgcaaac agcggcaat 
tttgatact tcttcgctg cattctatt cttaccggt 
ggtacccca ataagcgaa caacaaatg accaaactt 
tacgccact tttaagcac acttgcatt gtatttgcg 
tacggtatg acggaagtt ggcatggtt ggaatgttt 
aatccagta actgataaa gttctaatg actaagaaa 
ttaacttct tctggaaaa gtggcaatg ggggtctca 
ctgaagcta gtggatgtt gaaaccaat aaaaccttg 
ggcccgaac cagaaaggc gaatttctg gttaaatcc 
ccttgcatg atgaagggc tattacaaa gccgattgt 
tccgacatt ttcgacgaa gacggtttc ctaaagacg 
ggagatgtt ggttattac gaccaagac gggtgtctt 
tacattgta gaaagacgc aaagaaatg tttaaatat 
ctgtcctgg cacattgtt ccatcggct atcgaaaat 
gttttgctt gaacatccc gaaataaaa gaggctgca 
gttttcgga atgccgata aatgaagaa atgggggac 
gcacctgcg gcttgtgtg gtcttgcaa aatgggagt 
aaagtcact gtgcaagaa attgcagat tttgtcgct 
agcaaggtt tcagacagg gagaaatta agaggaggt 
gtcttcata gtgcaagaa ctgcccagg acaccgagt 
ggcaaattg aaaaggcga gacgttaaa aattacgtt 
ttaagttta aatagggga acaaataaa caataa
    mRNA sequence
    • >TC000444 RA
      aaactacat caaacatgg atgtacaaa taatattag 
aaggtcccc catttccac ccaattatc acatgaaac 
aaagtttgg gtcaatttt tctttgatt ccgcctcaa 
aattcaaag accgaatat gccagatcg acgccaaaa 
ccgaaaaaa gtgaaacgt tcttaacag ttaaacaaa 
aaagtgttc gagtcgctt tggagatgc agaaacgag 
gaataacat caaaggatg tgattgtta cttgctctg 
cgctaactt tagagaccc cagtcccca tccttgctt 
ctttttacc tcggtgcta aagtggcaa actcagacc 
cgactttat cagtcgcac aaacggctc acatgctat 
cacttgtat ccccaacaa tgattttcg tccaagaaa 
gctcactca ctctgattg aagaaagct tgcaacaag 
ccaagcttc aagcacaga ttgtggttt ttgggacgt 
gtgacaagt atccaacat tttccgatt tcaaccaag 
cgaaggaaa acgaagaga tgttttatc cagcctctg 
tcgatattc acgacactg gtctgatgt tcttcagca 
gcggcacaa cagggcttc ccaaagcga tctgtcaca 
gtcatttca gtttcttaa accttgctt actgttttt 
gtgaatcgg ggcttaagg ttgacacga ctctttctt 
acactactt tttactgga tatcggggc ttatgatgt 
tgacttctt cgtttttaa aaggcggac agcgaattg 
tttgcacca aggtgcccg aagccaaag acgtttttg 
aaattattc aaaaatata aagtaactt gtctgtttt 
tggctccgg ttttaacat acccactca cagattacg 
caaacagcg gcaattttg atacttctt cgctgcatt 
ctattctta ccggtggta ccccaataa gcgaacaac 
aaatgacca aactttacg ccactttta agcacactt 
gcattgtat ttgcgtacg gtatgacgg aagttggca 
tggttggaa tgtttaatc cagtaactg ataaagttc 
taatgacta agaaattaa cttcttctg gaaaagtgg 
caatggggg tctcactga agctagtgg atgttgaaa 
ccaataaaa ccttgggcc cgaaccaga aaggcgaat 
ttctggtta aatcccctt gcatgatga agggctatt 
acaaagccg attgttccg acattttcg acgaagacg 
gtttcctaa agacgggag atgttggtt attacgacc 
aagacgggt gtctttaca ttgtagaaa gacgcaaag 
aaatgttta aatatctgt cctggcaca ttgttccat 
cggctatcg aaaatgttt tgcttgaac atcccgaaa 
taaaagagg ctgcagttt tcggaatgc cgataaatg 
aagaaatgg gggacgcac ctgcggctt gtgtggtct 
tgcaaaatg ggagtaaag tcactgtgc aagaaattg 
cagattttg tcgctagca aggtttcag acagggaga 
aattaagag gaggtgtct tcatagtgc aagaactgc 
ccaggacac cgagtggca aattgaaaa ggcgagacg 
ttaaaaatt acgttttaa gtttaaata ggggaacaa 
ataaacaat aatacttca gaagtttgt gtttcttta 
tcataaaaa ctaacatgt tttgccagg taattgaat 
actgatgtt ttatgaaaa aataagtga tcttgtcgc 
tgattattg attctcgtt caatatttt tatcactgt 
caacacgtt tatcggagt atgagacaa gcaattaaa 
tttataaaa tatgtctta ttaattttt attaaaatt 
tgatgaagc acaacagcc gttcataaa ttttcctca 
attaaatcc agaatggtt ggaattatt aattttttc 
ctaattcaa ttagcaaca cccgccgta ctatttgtg 
gaatcatgt caattggta ataaatatc ttattgtta 
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