Status
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Gene information
General information
TC005946 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_007423.3: 5078871..5093501
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
    		TC005946
    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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    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_00965

    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)

    adult lethality - Number of animals showing the phenotype: 1 (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): more than 80%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): more than 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): more than 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: 30.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 30.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 3 (11 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC005946 RA
      MDNGVKVRM SGYLHLKTK KRMISSWKN YWFVLEDRL 
LLYYRSKAE YETISPCKG SINLGPPCM VKSLPSVTN 
SFQVETRSL TYTLKADNS DDQKKWMQA ILAVLNQNQ 
NFPSESPKR LSHFRYSLD DLFPQTEPN DPQTPPKAP 
LERQNTLPH RLKLEPKKS NEIIQRLQK LGAQSYGGS 
LGAISKIAT KKVTKEEKC KNVSQGSLP SCLFNEEDE 
FEEVVRPTT NNREENIYE RISGDSQYS GESVKYSVP 
LRRGFSVSE QRDKGATSR ETKSLLVEN DQYATTRHV 
QSDEVIYAE PKLDCNKNS LLVENTFYA SCDVVGHTN 
DNIYEDLDK YNPYSEPVL DSSQSSGKK EKIKKSKSF 
IRRVWKKKY RKQDEKKVE EEIYAEVDP TVVNKVDMS 
DDSAVQMLS ELQNILENK KAQLRAKAS NNPTAETAE 
STAKPDEEE EEEEAPKLP PKIHPPEQF RSLDEILED 
LDREKLESK GKVQLLIEK FTESEPDVI LRKHDKSGY 
RYSDDLNLL LDELAKVTS APILTPGVT TSLVNPNLT 
DEEWLKLLP VRQRRLSEP DYDIPRPLK PVQTPEKSE 
NTDVIPATR FFGPVLPPT IIDNKDESL CVSMTPDSL 
EIDSQKFQT LCSYTSHNY TDLKCFQKK DDVIYALPK 
SYLSTHIVN TCHNLCGGN LDECQIIYK NVKNIEHEE 
IFNDSLELC TETKTEF
    CDS sequence
    • >TC005946 RA
      atggacaat ggagtcaaa gtgcggatg tccggatat 
ctccacttg aagaccaaa aagcgcatg atatcatca 
tggaaaaat tactggttt gtgttggaa gatcggtta 
ttgctgtat tacaggtcg aaggccgaa tatgagaca 
atttcgccc tgcaagggc tccattaat ctggggccc 
ccttgcatg gtcaaatct ctgccttcg gtaacgaac 
tcctttcaa gtggagaca cgaagtttg acctacact 
ttgaaagcg gacaactcc gacgaccag aaaaaatgg 
atgcaagcc atcctggcc gtccttaac cagaaccaa 
aacttcccc agcgaaagt cccaaacga ctgagccac 
ttccgctac tccctcgac gacttattc cctcaaact 
gaacccaac gacccccag acaccgcca aaagcgccc 
ctcgaacgc caaaacaca ctcccccat cgactaaaa 
ttagaaccc aaaaaaagt aatgaaata atccagagg 
ttacagaaa ctaggggcg caaagctat ggcggtagt 
ttgggcgca atcagtaaa atagcgacg aaaaaagtc 
accaaggag gagaaatgc aaaaatgtg tctcagggc 
tcgttacca agctgcctt ttcaacgaa gaggacgag 
ttcgaggaa gttgttaga ccaacaacc aacaacagg 
gaggaaaat atttacgag cggatttcg ggcgattcg 
caatattcg ggggaaagt gtaaagtac agtgttccg 
ttgaggcgg ggcttcagt gtgagtgag caaagggac 
aagggggcc acatctcgc gaaacgaag agtttattg 
gtggaaaat gaccaatac gcaaccact agacatgtc 
caaagtgac gaagttatt tacgctgag cccaagttg 
gactgtaat aaaaatagt cttttggtt gagaacacg 
ttttatgct agttgcgat gttgtgggg cacacgaat 
gataatatt tacgaggat ttggataag tataaccct 
tacagtgag ccagttttg gattctagt caaagttcc 
ggcaaaaaa gagaaaatc aaaaaatcg aaaagtttc 
attcggcga gtttggaag aagaagtat cgaaaacaa 
gacgagaaa aaggttgag gaggaaatt tacgcagag 
gttgacccg actgtagtt aacaaagtc gatatgagc 
gatgacagc gctgttcaa atgttgtca gagcttcaa 
aacatttta gaaaataag aaagcacag ttgagggcc 
aaggcctcc aataaccca acggccgaa accgcggaa 
tcaacagca aaaccagac gaagaagaa gaagaagaa 
gaagccccg aaattgccc cccaaaata caccctccc 
gaacagttc cgaagtctc gacgaaatc cttgaagat 
ttagaccgg gaaaagctc gaatccaag ggcaaagtg 
cagctccta attgaaaaa tttacggag tcggaaccg 
gacgtaatt ttgcgaaaa catgacaaa tctgggtat 
cgatattcg gatgatctt aatttatta ctggatgaa 
cttgcgaaa gtcacttcg gcccccatt ttgacgcct 
ggcgtgacc acaagtctc gtcaacccc aatcttacc 
gatgaagag tggctgaaa ctcctcccc gtgcggcag 
agaaggtta tcagaaccg gactacgat attccgcgc 
ccccttaag ccggtccag accccggaa aagtcggaa 
aataccgat gtcatcccc gcgactcgg tttttcgga 
ccagtgcta ccacccaca atcattgac aacaaagac 
gagtctttg tgtgttagt atgactcca gattcgctg 
gaaatcgat tcgcaaaaa ttccagact ttgtgttcc 
tacacgtcc cataattat accgatttg aaatgtttt 
caaaaaaaa gacgacgtt atttacgca ctgcccaag 
tcatacctc tccacgcat attgtaaac acgtgtcac 
aacttgtgc ggtggaaat ttggacgag tgtcagatt 
atttacaaa aatgtgaag aatatcgaa catgaagaa 
atcttcaac gattccctc gaactttgt accgaaact 
aagacagag ttctaa
    mRNA sequence
    • >TC005946 RA
      atacgctac aattccaca acataaacg cgcaactat 
cgcaacgga agtttactt ccgcaaggg tccgactgg 
caaaagacc acgacgtag ccttgtgct gactgtgcg 
ctccgtttg aatttccga gtaacagtt ttgaaaaga 
tgcgccttt ttcaaatcg tgctgcgaa tgtgagcgg 
cgagagtgt cacagttca ggccaatca tggacaatg 
gagtcaaag tgcggatgt ccggatatc tccacttga 
agaccaaaa agcgcatga tatcatcat ggaaaaatt 
actggtttg tgttggaag atcggttat tgctgtatt 
acaggtcga aggccgaat atgagacaa tttcgccct 
gcaagggct ccattaatc tggggcccc cttgcatgg 
tcaaatctc tgccttcgg taacgaact cctttcaag 
tggagacac gaagtttga cctacactt tgaaagcgg 
acaactccg acgaccaga aaaaatgga tgcaagcca 
tcctggccg tccttaacc agaaccaaa acttcccca 
gcgaaagtc ccaaacgac tgagccact tccgctact 
ccctcgacg acttattcc ctcaaactg aacccaacg 
acccccaga caccgccaa aagcgcccc tcgaacgcc 
aaaacacac tcccccatc gactaaaat tagaaccca 
aaaaaagta atgaaataa tccagaggt tacagaaac 
taggggcgc aaagctatg gcggtagtt tgggcgcaa 
tcagtaaaa tagcgacga aaaaagtca ccaaggagg 
agaaatgca aaaatgtgt ctcagggct cgttaccaa 
gctgccttt tcaacgaag aggacgagt tcgaggaag 
ttgttagac caacaacca acaacaggg aggaaaata 
tttacgagc ggatttcgg gcgattcgc aatattcgg 
gggaaagtg taaagtaca gtgttccgt tgaggcggg 
gcttcagtg tgagtgagc aaagggaca agggggcca 
catctcgcg aaacgaaga gtttattgg tggaaaatg 
accaatacg caaccacta gacatgtcc aaagtgacg 
aagttattt acgctgagc ccaagttgg actgtaata 
aaaatagtc ttttggttg agaacacgt tttatgcta 
gttgcgatg ttgtggggc acacgaatg ataatattt 
acgaggatt tggataagt ataaccctt acagtgagc 
cagttttgg attctagtc aaagttccg gcaaaaaag 
agaaaatca aaaaatcga aaagtttca ttcggcgag 
tttggaaga agaagtatc gaaaacaag acgagaaaa 
aggttgagg aggaaattt acgcagagg ttgacccga 
ctgtagtta acaaagtcg atatgagcg atgacagcg 
ctgttcaaa tgttgtcag agcttcaaa acattttag 
aaaataaga aagcacagt tgagggcca aggcctcca 
ataacccaa cggccgaaa ccgcggaat caacagcaa 
aaccagacg aagaagaag aagaagaag aagccccga 
aattgcccc ccaaaatac accctcccg aacagttcc 
gaagtctcg acgaaatcc ttgaagatt tagaccggg 
aaaagctcg aatccaagg gcaaagtgc agctcctaa 
ttgaaaaat ttacggagt cggaaccgg acgtaattt 
tgcgaaaac atgacaaat ctgggtatc gatattcgg 
atgatctta atttattac tggatgaac ttgcgaaag 
tcacttcgg cccccattt tgacgcctg gcgtgacca 
caagtctcg tcaacccca atcttaccg atgaagagt 
ggctgaaac tcctccccg tgcggcaga gaaggttat 
cagaaccgg actacgata ttccgcgcc cccttaagc 
cggtccaga ccccggaaa agtcggaaa ataccgatg 
tcatccccg cgactcggt ttttcggac cagtgctac 
cacccacaa tcattgaca acaaagacg agtctttgt 
gtgttagta tgactccag attcgctgg aaatcgatt 
cgcaaaaat tccagactt tgtgttcct acacgtccc 
ataattata ccgatttga aatgttttc aaaaaaaag 
acgacgtta tttacgcac tgcccaagt catacctct 
ccacgcata ttgtaaaca cgtgtcaca acttgtgcg 
gtggaaatt tggacgagt gtcagatta tttacaaaa 
atgtgaaga atatcgaac atgaagaaa tcttcaacg 
attccctcg aactttgta ccgaaacta agacagagt 
tctaatctg ttttttact catttatgt at

    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