Status
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Gene information
General information
TC004782 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_007416.3: 6988869..7007734
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
    		TC004782
    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
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_00766

    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: 30.0% (includes death as pupa, adult)

    pupa eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 2 (3 dpi)
    Days post injection

    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 larval musculature pattern 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): less than 30%
    remarks: muscle pattern potentially obscured by segmentation defect,
    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): 30% - 50%
    cuticle remnants with some identifiable segments - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    head not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    legs shape irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    thorax not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen shape 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): 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)

    larva lethality early (L5/6) - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004782 RA
      MLKHMLTTN GGVANRVSR PDSSMVMEP RIDQGAHRY 
RSPNANSSR ISQQYPLNV SQLHSPNNL DASKHSIYS 
NTVLPQNKT LNGGLNISR VRNQSTVNK FMAKSKQVG 
VKEMLVSLG LLCLVSLLL ALLSLIFLL KISPVTASD 
IRELLRAEQ LTVITAEEY VVVYEVTLA LCALTLSLN 
LCCLLVCAI QFLFAVKLV KSPHGGNDR TNKYLQKSS 
VSRVCAVGG FFISIPVFL TGIILYTFI QFHSTPAIV 
TSVFIGLGI IFCGCAMVH NVFIWQREK TNAVKELAL 
AQHEQSYHT TTQLNHSHV SHVNHSFGH PVAVAPSTH 
TSPYVVRPA TTTPPTAEN LNLTKLSHP REASGSVSP 
GMPTATLEL SSVATTNSP HELSTLV
    CDS sequence
    • >TC004782 RA
      atgttgaag cacatgttg accacgaac gggggtgtc 
gcaaaccgc gtctcccgt ccagatagc tcgatggtg 
atggagccc cggatcgac cagggggcg caccggtac 
cgctctcca aacgcgaac agttcccgc atttcgcag 
cagtacccc ttgaacgtc tcccagctc cactccccc 
aacaatctg gacgcctcc aagcactcc atttactcc 
aatacggtc ctcccccaa aacaagacg ctcaatggg 
ggactcaac atctcccgg gtgcgcaac cagagcacc 
gttaacaaa tttatggca aagtcgaaa caagtcggc 
gttaaggag atgctcgtc agtttggga cttttgtgt 
ctagtgagt ctacttcta gcgttgttg tcgctcatt 
tttctactg aaaatatca ccagtgacc gccagtgac 
atcagagag ttgctaaga gctgaacaa ttaacggtg 
attacggcc gaggagtac gttgtggtg tatgaagtg 
acgttagcc ttatgtgca ctgacttta tcactcaat 
ttatgttgt ttgctggtg tgcgccatc cagtttttg 
ttcgccgtt aaactagtt aaaagccca cacggcgga 
aacgataga accaacaaa tatctccag aagtcatct 
gtaagccgc gtttgtgcg gttggcggt tttttcatc 
tcaattccc gtatttcta actggcatc atcctgtac 
actttcatc caattccac tcaaccccc gccatcgta 
accagcgta ttcatcggg cttgggatc atcttctgt 
ggttgtgcg atggttcac aacgtgttt atttggcag 
cgggagaaa accaacgct gttaaagaa ctagcgttg 
gcccaacac gagcaatcc taccacaca accacgcaa 
ctaaaccat tcgcatgtc agtcatgtg aaccacagc 
tttggccac cctgtggct gtggcgcca tctacacat 
accagtccg tatgtggtc agaccggcg actacaacg 
ccgccaacg gccgaaaac ctgaacttg accaagttg 
tcgcaccct cgcgaggcc agcgggagc gtcagccca 
gggatgcca acagcgact ttggaactc agcagtgtt 
gccaccaca aactcgccg catgagttg tcaactcta 
gtttaa
    mRNA sequence
    • >TC004782 RA
      tggtgtatt agtagttgc ctaagcgtg aattgtgag 
ggagttttt gtggctttg ggggtgttt tcatttcga 
tttttttta aattgggtt tgtaagtgt ggggcttcc 
cccgcggcg ccctcctcc agtcgcaat ggttcgtca 
attaaccat tagacgcgc tgggatcgg ttcgtgggt 
accgttggt gtggagtgg tttagtggt tccgaatgc 
cgtgcgtac gcaccttcc ttaaaaccg tgctcaagc 
tcgaaacca gtaaaaaaa tcgaataag tgtcaggag 
agtggcatt gctgagaaa tttaaatga ttgtgtggt 
gtttgggca gtgtggtga acttccagc tcgaataat 
gcctttcga gccacgtat taaccttac tacctgcta 
cacagtgcc tgttaaaac ctgaagttc tgaacataa 
tgaaaccgc aggtggaca taaaaaact cccaaatca 
agtagcagc acaaaatga aagaaatat gttcacaag 
tgagcgcaa ccctcgctt ggagtggcg agttgaatc 
agtgaatcc cccaatggt tcaacatcg aaatgttga 
agcacatgt tgaccacga acgggggtg tcgcaaacc 
gcgtctccc gtccagata gctcgatgg tgatggagc 
cccggatcg accaggggg cgcaccggt accgctctc 
caaacgcga acagttccc gcatttcgc agcagtacc 
ccttgaacg tctcccagc tccactccc ccaacaatc 
tggacgcct ccaagcact ccatttact ccaatacgg 
tcctccccc aaaacaaga cgctcaatg ggggactca 
acatctccc gggtgcgca accagagca ccgttaaca 
aatttatgg caaagtcga aacaagtcg gcgttaagg 
agatgctcg tcagtttgg gacttttgt gtctagtga 
gtctacttc tagcgttgt tgtcgctca tttttctac 
tgaaaatat caccagtga ccgccagtg acatcagag 
agttgctaa gagctgaac aattaacgg tgattacgg 
ccgaggagt acgttgtgg tgtatgaag tgacgttag 
ccttatgtg cactgactt tatcactca atttatgtt 
gtttgctgg tgtgcgcca tccagtttt tgttcgccg 
ttaaactag ttaaaagcc cacacggcg gaaacgata 
gaaccaaca aatatctcc agaagtcat ctgtaagcc 
gcgtttgtg cggttggcg gttttttca tctcaattc 
ccgtatttc taactggca tcatcctgt acactttca 
tccaattcc actcaaccc ccgccatcg taaccagcg 
tattcatcg ggcttggga tcatcttct gtggttgtg 
cgatggttc acaacgtgt ttatttggc agcgggaga 
aaaccaacg ctgttaaag aactagcgt tggcccaac 
acgagcaat cctaccaca caaccacgc aactaaacc 
attcgcatg tcagtcatg tgaaccaca gctttggcc 
accctgtgg ctgtggcgc catctacac ataccagtc 
cgtatgtgg tcagaccgg cgactacaa cgccgccaa 
cggccgaaa acctgaact tgaccaagt tgtcgcacc 
ctcgcgagg ccagcggga gcgtcagcc cagggatgc 
caacagcga ctttggaac tcagcagtg ttgccacca 
caaactcgc cgcatgagt tgtcaactc tagtttaaa 
aaccagtca ttgttacta tgtgaagtt ttgctgtag 
gcacacggc gtgtgccta gagccaaac ttgccctat 
tatttatca gaagtttta ttattgtat atagagggc 
tagagggta tttaaagat tgtatatac cgcttgttt 
cacaacgat ttttgtgta catttgtga aatttcaaa 
gagttttag tacaaaaca gtctcactg cctacttca 
ggtttgata ttatgccgt ctgttactg gaatctaga 
ttaatatat tttatactg attttatat ctaacaaat 
tgcctttat atgaataaa cgtttgaaa aacac

    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