Status
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Gene information
General information
TC006284 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: 6199612..6206930
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
    		TC006284
    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_04100

    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): 30% - 50%
    larval musculature irregular - 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): 30% - 50%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    cuticle remnants with some identifiable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

    Comment: about half of the remnants appear inside out
    head posterior ventralnot present - Penetrance (percentage of animals/eggs on slide): less than 30%
    head not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    head not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    thorax anterior not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    legs potentiallyfused - Penetrance (percentage of animals/eggs on slide): less than 30%
    thorax not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    thorax not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen bristle segmentation/division irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    abdomen not present - 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): 50% - 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)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC006284 RA
      MIISFRKPT VKYFVIALT AAIILAILG TIVYFLVKG 
ESSGKGAVV TNGHTCAHI GAAILAKGG SAVDAAIAA 
LFCEGVSMP QSMGLGGGF LMTVYFAEN RTAYSLNAR 
EVAPLAASK DMFDGNSSL STKGGLAVA VPGELRGYW 
EAYHRYGGK VAWADLVQP TIDLCESGV LVTEYLEKL 
YASQLESFK KDPVMAETF IDPSTNRTY KKGQVVKRP 
RLAKSLELM KSFGADALY DGTLTKGFV EDIRNKGGI 
ITVEDMKNY KVKWQEPIV VQMPNNQTL YTAPLPGSG 
VILSFIMNL LNNYLDNSQ PLSVTNWQR IVESFKFGY 
GKRTELGDI TDSNFANVT DLVKKLISP DYASEIRQK 
IHDGTTSQD PSYYGAKTV QPEDHGTAH ICVLAPNGD 
AVSVTSTIN LYFGAGFMS ESTGIILNN EMDDFSSPN 
MNNSFNVPP SEANYIEPG KRPLSSMVP SIVVGDGGV 
ELVIGAAGG TKITTSVAQ IAVKHLWFG APIGAAVQE 
KRIHHQLFP MEIEFENAF NETRDFVEA LHKIGHEYT 
IAEPGSGFS AVTAISRKG GDVATASDV RRTGDEVIV
    CDS sequence
    • >TC006284 RA
      atgattatt tccttcaga aaacccacc gtcaagtac 
ttcgtcatc gctttgacc gccgccatc atcctggca 
atcctcggc actattgtg tatttcctg gttaagggc 
gagtcgagc ggcaagggg gctgtggtc accaacggg 
cacacgtgc gcccacatc ggcgccgcc atcctcgcg 
aaagggggc tcggcggtg gacgccgcc atcgcagct 
ttgttctgc gagggcgtc tccatgccc cagagcatg 
gggctgggc gggggcttc ctgatgacg gtctacttc 
gccgagaac cgcacggcg tactcgctg aatgcgcgg 
gaggttgcc ccgctggcg gcctccaaa gacatgttc 
gatgggaac agctcgctg tcgacgaaa ggggggctt 
gcggtggcg gtgcccggg gagttgagg ggctactgg 
gaggcctac cacaggtat gggggcaag gtggcgtgg 
gccgatttg gtgcagcct accatagat ttgtgcgaa 
agtggggtc ctggtgacg gagtatttg gagaagttg 
tatgcgagt cagttggaa agcttcaag aaggatcct 
gtgatggct gagactttt atcgatccg agcactaat 
cgcacctat aagaaggga caagtggtt aagaggcca 
cggttggcc aaaagtttg gaactgatg aagagtttt 
ggggccgat gctttgtat gacggtact ttgacgaag 
gggtttgtt gaggatata cggaacaaa ggtgggatt 
atcacggtg gaggatatg aaaaactac aaggttaaa 
tggcaagaa cccatcgtg gttcaaatg cccaacaac 
cagacgctt tacacggca cctttgccc ggctctggt 
gtgatcctt agtttcata atgaacctc cttaacaat 
tacttggac aattcgcaa cccttgtcc gtcacaaac 
tggcaacga atcgtcgaa agcttcaaa ttcggctac 
ggcaaaagg acagaactc ggtgacatc accgacagc 
aactttgcc aatgtcaca gacttggtc aaaaagctc 
atttcgccg gattatgcc tccgaaatt cggcaaaaa 
atccacgac ggtaccacc tcccaagac ccgtcgtac 
tacggcgct aagacggtc caacccgag gaccatggt 
accgcccat atctgcgtc ctggccccc aatggggac 
gcagtctcc gtcacaagc accatcaat ttatatttc 
ggcgccggt ttcatgtcc gaaagcacc ggaatcatc 
ctcaacaac gaaatggac gacttctcc tcccccaac 
atgaacaac agcttcaac gtgccgccg tccgaagcc 
aactacatc gagcccggg aagcgcccg ttgtcctcc 
atggtgccc tcgattgtc gtgggggat ggcggggtt 
gagctcgtg ataggggcc gcaggaggg accaaaatc 
acgacctcg gtggcgcag atcgccgtc aagcatttg 
tggtttggg gctccgatc ggagcagca gtgcaggag 
aagcggatt caccatcag ttgttcccg atggagatt 
gagttcgag aatgcgttt aatgaaacg agagatttt 
gtggaagcg ttgcataaa attgggcat gagtatacg 
atagctgag ccggggtcg gggttttcg gcggtgacg 
gccatctcc cggaaaggg ggcgatgtg gcgacggcg 
agtgatgtg cggaggacg ggcgacgaa gttatagtt 
tga
    mRNA sequence
    • >TC006284 RA
      tctcgattc aaataatcc gattaaata aaacgcact 
tgaagttat ctcgcggca tttaattat tatcattac 
ctcaaatta ttatcattt taattacgc tcaagagcg 
gtaagagcc tcagtttgt ccgccggat tcgtcgcgg 
aaaagtgtt gcgtcgtac gaattaatt taatcaaac 
tatttttac taccgtgtt tatttcact attaccgcc 
tgataaccg caatgatta tttccttca gaaaaccca 
ccgtcaagt acttcgtca tcgctttga ccgccgcca 
tcatcctgg caatcctcg gcactattg tgtatttcc 
tggttaagg gcgagtcga gcggcaagg gggctgtgg 
tcaccaacg ggcacacgt gcgcccaca tcggcgccg 
ccatcctcg cgaaagggg gctcggcgg tggacgccg 
ccatcgcag ctttgttct gcgagggcg tctccatgc 
cccagagca tggggctgg gcgggggct tcctgatga 
cggtctact tcgccgaga accgcacgg cgtactcgc 
tgaatgcgc gggaggttg ccccgctgg cggcctcca 
aagacatgt tcgatggga acagctcgc tgtcgacga 
aaggggggc ttgcggtgg cggtgcccg gggagttga 
ggggctact gggaggcct accacaggt atgggggca 
aggtggcgt gggccgatt tggtgcagc ctaccatag 
atttgtgcg aaagtgggg tcctggtga cggagtatt 
tggagaagt tgtatgcga gtcagttgg aaagcttca 
agaaggatc ctgtgatgg ctgagactt ttatcgatc 
cgagcacta atcgcacct ataagaagg gacaagtgg 
ttaagaggc cacggttgg ccaaaagtt tggaactga 
tgaagagtt ttggggccg atgctttgt atgacggta 
ctttgacga aggggtttg ttgaggata tacggaaca 
aaggtggga ttatcacgg tggaggata tgaaaaact 
acaaggtta aatggcaag aacccatcg tggttcaaa 
tgcccaaca accagacgc tttacacgg cacctttgc 
ccggctctg gtgtgatcc ttagtttca taatgaacc 
tccttaaca attacttgg acaattcgc aacccttgt 
ccgtcacaa actggcaac gaatcgtcg aaagcttca 
aattcggct acggcaaaa ggacagaac tcggtgaca 
tcaccgaca gcaactttg ccaatgtca cagacttgg 
tcaaaaagc tcatttcgc cggattatg cctccgaaa 
ttcggcaaa aaatccacg acggtacca cctcccaag 
acccgtcgt actacggcg ctaagacgg tccaacccg 
aggaccatg gtaccgccc atatctgcg tcctggccc 
ccaatgggg acgcagtct ccgtcacaa gcaccatca 
atttatatt tcggcgccg gtttcatgt ccgaaagca 
ccggaatca tcctcaaca acgaaatgg acgacttct 
cctccccca acatgaaca acagcttca acgtgccgc 
cgtccgaag ccaactaca tcgagcccg ggaagcgcc 
cgttgtcct ccatggtgc cctcgattg tcgtggggg 
atggcgggg ttgagctcg tgatagggg ccgcaggag 
ggaccaaaa tcacgacct cggtggcgc agatcgccg 
tcaagcatt tgtggtttg gggctccga tcggagcag 
cagtgcagg agaagcgga ttcaccatc agttgttcc 
cgatggaga ttgagttcg agaatgcgt ttaatgaaa 
cgagagatt ttgtggaag cgttgcata aaattgggc 
atgagtata cgatagctg agccggggt cggggtttt 
cggcggtga cggccatct cccggaaag ggggcgatg 
tggcgacgg cgagtgatg tgcggagga cgggcgacg 
aagttatag tttgatggt ggagatagt taggtttat 
ttattatgg aaatttaat ttatttgca aataaaacc 
actgattcg ta

    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