Status
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Gene information
General information
TC006260 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: 5935575..5939483
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
    		TC006260
    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
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    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
    We will use your email address only for possible questions regarding this annotation. We will never show your address or give it away.
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_10451

    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 (11 dpi)
    Days post injection

    Fertility
    yolk sometimes amount decreased - Number of animals showing the phenotype: 4

    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%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 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: % (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: % (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC006260 RA
      MDSIATDSG KIVKMEVDY SSTCDEKIP ECQKLAQAG 
KLHDALDQL LALEKQTRT GADMVSTGR VLVAIVQIC 
KEARNWGAL NEHIVLLTK RRSQLKQAV AKMVQECCT 
YVDQTPDKD TMIKLIDTL RQVTEGKIY VEVERARLT 
HKLAKIREE EGNISEAAN IIQELQVET YGSMDKREK 
VELILEQMR LCLAKQDYI RTQIISKKI NTKFFDDEG 
TQDLKLKYY RLMMELDQH EGSYLATCK HYRAVLNTP 
NIQSEPLER QKAARAVVL YLILAPHDN EQADLTHRV 
LADKVLEEI PMYKQLLKL FTTSELIKW SGLCEIYEK 
ELLSTPVFS GNEQAKKRW NDLKNRVVE HNIRVMAKY 
YTRIKISRM ADLLDLSPA ETEEFLSQM VVSKSVQAK 
TDRPSGVVH FQQSKDPSD VLNDWAHDL ASLMQLVNK 
TTHLINKEE CVHKHLQAT A
    CDS sequence
    • >TC006260 RA
      atggactca atagcgacc gattccggc aaaatcgtc 
aaaatggaa gtcgattac agctcgact tgcgacgag 
aaaatcccc gaatgccag aaattggct caagctggg 
aaactccac gacgctctc gaccaactc ttggccctg 
gaaaagcaa actcggact ggggccgac atggtctcc 
actggtcgc gtcttagtc gcaatcgtc caaatttgt 
aaagaggcc agaaactgg ggggccctc aacgaacac 
attgttctc ctaaccaag agacggtcg cagttgaaa 
caagcggtg gccaaaatg gtgcaggaa tgttgcact 
tacgtggac caaaccccc gataaagac acaatgatt 
aagttgatt gatacacta cgccaggtt acggaaggc 
aaaatttac gttgaagtc gaaagggcg agattgacg 
cataaactg gcgaaaatt cgtgaggaa gaagggaat 
atttccgaa gcggcgaac ataatccaa gaattgcaa 
gtcgagact tacggttcc atggataaa cgtgagaaa 
gtcgagttg attttggaa caaatgagg ttgtgtttg 
gccaaacaa gactatatc aggactcaa atcatttcg 
aaaaaaatc aatacaaag tttttcgac gatgaaggc 
actcaagac ctcaaattg aagtactac cgactcatg 
atggagctg gaccagcat gagggctcc tatttggcc 
acttgtaag cactatcga gctgtttta aacactcca 
aatattcag tcggagcct ttggaacgt caaaaggcc 
gcacgtgcg gttgtttta tacttaata ctagcccct 
catgataac gaacaagcc gatttgact catcgtgtc 
ttggccgat aaagttctt gaagaaata ccaatgtac 
aaacaactg ttgaaactc ttcacgacc tcggaattg 
atcaagtgg tcgggtttg tgcgaaatt tacgaaaaa 
gaattgctc tcaactccg gttttcagc ggaaatgag 
caagcgaag aaacgatgg aatgattta aagaatcgt 
gtcgttgag cacaacatc cgtgtcatg gcaaaatat 
tacaccagg attaaaatt tcaagaatg gccgattta 
ttggactta tcaccggcc gaaaccgag gaatttttg 
tctcaaatg gtggtcagt aaaagtgtg caagccaag 
accgaccgg ccttcaggc gttgtacat tttcaacaa 
agtaaagat cccagtgat gtcctcaat gattgggcg 
cacgatttg gcatctctc atgcaactg gtcaacaaa 
accacgcat cttattaat aaagaagag tgtgttcac 
aagcatctc caagccacg gcttga
    mRNA sequence
    • >TC006260 RA
      gaacgaaaa ataaacccc aatttttta taccgattc 
aaaaacccg tgaaggtca caaacgtca aaccggcaa 
ctgtcaaaa gtgttttcg atgactggc tgtttattg 
tgacttgtg aaaaaaaat caggttcaa atcgtcaca 
aatttttca gtcatcaaa atggactca atagcgacc 
gattccggc aaaatcgtc aaaatggaa gtcgattac 
agctcgact tgcgacgag aaaatcccc gaatgccag 
aaattggct caagctggg aaactccac gacgctctc 
gaccaactc ttggccctg gaaaagcaa actcggact 
ggggccgac atggtctcc actggtcgc gtcttagtc 
gcaatcgtc caaatttgt aaagaggcc agaaactgg 
ggggccctc aacgaacac attgttctc ctaaccaag 
agacggtcg cagttgaaa caagcggtg gccaaaatg 
gtgcaggaa tgttgcact tacgtggac caaaccccc 
gataaagac acaatgatt aagttgatt gatacacta 
cgccaggtt acggaaggc aaaatttac gttgaagtc 
gaaagggcg agattgacg cataaactg gcgaaaatt 
cgtgaggaa gaagggaat atttccgaa gcggcgaac 
ataatccaa gaattgcaa gtcgagact tacggttcc 
atggataaa cgtgagaaa gtcgagttg attttggaa 
caaatgagg ttgtgtttg gccaaacaa gactatatc 
aggactcaa atcatttcg aaaaaaatc aatacaaag 
tttttcgac gatgaaggc actcaagac ctcaaattg 
aagtactac cgactcatg atggagctg gaccagcat 
gagggctcc tatttggcc acttgtaag cactatcga 
gctgtttta aacactcca aatattcag tcggagcct 
ttggaacgt caaaaggcc gcacgtgcg gttgtttta 
tacttaata ctagcccct catgataac gaacaagcc 
gatttgact catcgtgtc ttggccgat aaagttctt 
gaagaaata ccaatgtac aaacaactg ttgaaactc 
ttcacgacc tcggaattg atcaagtgg tcgggtttg 
tgcgaaatt tacgaaaaa gaattgctc tcaactccg 
gttttcagc ggaaatgag caagcgaag aaacgatgg 
aatgattta aagaatcgt gtcgttgag cacaacatc 
cgtgtcatg gcaaaatat tacaccagg attaaaatt 
tcaagaatg gccgattta ttggactta tcaccggcc 
gaaaccgag gaatttttg tctcaaatg gtggtcagt 
aaaagtgtg caagccaag accgaccgg ccttcaggc 
gttgtacat tttcaacaa agtaaagat cccagtgat 
gtcctcaat gattgggcg cacgatttg gcatctctc 
atgcaactg gtcaacaaa accacgcat cttattaat 
aaagaagag tgtgttcac aagcatctc caagccacg 
gcttgattt cttttttgt attatttta ctaataaat 
agtgtgcat tatttccga gtgttttct tgtgactgt 
tatctcatt tgtaacact tgataaaat acaattacg 
ttatttatc atcaatctt aaataaata catccttga 
gta

    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