Status
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Gene information
General information
TC010407 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_007420.3: 7601061..7629778
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
    		TC010407
    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
    If you have entered your name and agree by marking the checkbox. we might show your name on this page to honor your contribution.
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_09082

    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: 0.0% (includes death as pupa, adult)

    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): more than 80%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 80%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     larva dorsal bent - Penetrance (percentage of animals/eggs on slide): more than 80%

    vertex triplet vertex triplet posterior complete not present - Penetrance (percentage of animals/eggs on slide): more than 80%

    bell row number decreased - Penetrance (percentage of animals/eggs on slide): more than 80%

    affected eggs/embryos/larvae - 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: % (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
    • >TC010407 RA
      MFHTSGGGG GYSDGNAGF HQHLQQSPV YVPSSRAVP 
QYPSPASGH FGAAAHQSS WAHAGGTYG EMAAPSAHS 
LGTSPHAGA LSAGQFYAQ NMMMSSWRA YDGTGFQRT 
SPYDGSMEF QFGEGRECV NCGAISTPL WRRDGTGHY 
LCNACGLYH KMNGMNRPL IKPSKRLTA TRRLGLCCT 
NCGTRTTTL WRRNNDGEP VCNACGLYF KLHGVNRPL 
AMRKDGIQT RKRKPKKPV GGERDDSSS ASVEETKSL 
VHQSSQQHS SQSQSQTHH NHQLDKSSP VERPYLGQT 
SLLPATSTS AIKSEPGYE YSCIQNQPS YPYQQIFGF 
PGSANSSGE VAYHHQHHV TAAAKLMAS S
    CDS sequence
    • >TC010407 RA
      atgttccat acaagcggt ggtggtgga ggatacagc 
gacggcaac gcgggtttc caccagcat ctgcagcaa 
tctcccgtt tacgttcca agcagtaga gcagtgccc 
cagtatcct tctcctgcg agtgggcat ttcggggct 
gctgctcac cagagtagt tgggctcac gctggtgga 
acgtacggc gaaatggca gccccatct gcacacagc 
ttggggact tcgccacat gctggtgct ttatcagct 
gggcagttt tatgcccag aatatgatg atgagctcg 
tggagagcc tacgatggg actggattt caaaggacg 
tctccgtat gacggaagc atggagttt cagttcggc 
gaggggcgc gagtgtgta aactgcggc gccatttcg 
acgccgcta tggcgtcgc gacggcacg ggccattat 
ttgtgcaat gcttgtggg ctttaccac aaaatgaac 
ggcatgaac cgaccacta ataaaacca tcaaaacga 
ttgacggcg acccggaga ttagggctg tgctgcacg 
aactgtggg acgcggacg acgacatta tggcgtcgg 
aacaacgac ggagaacct gtttgtaac gcctgcgga 
ttatacttc aaattacac ggcgtgaac cggccttta 
gccatgagg aaggacggc atacaaaca cgcaaacgc 
aaaccgaag aagcctgtt ggcggggaa cgtgatgat 
agcagctcc gcctccgtt gaagaaaca aaatctctc 
gttcaccaa tcctcgcaa caacactcg tcgcaatct 
caatcgcaa acccatcac aaccatcag ctcgacaaa 
tcatcgccg gtggagcgc ccatatctg ggccaaacc 
tccctctta cctgccaca agtacaagt gccatcaaa 
agcgagccc gggtacgaa tacagctgc atacagaac 
cagccgtcg tatccttac caacaaata tttgggttt 
cctggttcg gccaacagc agcggggag gttgcctac 
caccaccaa caccacgtt actgccgcc gccaaacta 
atggcctcg tcttag
    mRNA sequence
    • >TC010407 RA
      agtcagttg ctacgaagg ttgaaagct ctcgtcacg 
ttgtccgtt caactttca actagctta attaagctc 
ggagctttc tcgttgttt atgccacag tggaccaga 
tttagtgaa gtttaaagt tgtttgttt attatttgt 
ttgttttgt tattaagtg acgaaaaaa caacgtttt 
gaataaccg gcaaaaggg atgattaga aaatagttt 
tccttctcc atcttcgac catgttcca tacaagcgg 
tggtggtgg aggatacag cgacggcaa cgcgggttt 
ccaccagca tctgcagca atctcccgt ttacgttcc 
aagcagtag agcagtgcc ccagtatcc ttctcctgc 
gagtgggca tttcggggc tgctgctca ccagagtag 
ttgggctca cgctggtgg aacgtacgg cgaaatggc 
agccccatc tgcacacag cttggggac ttcgccaca 
tgctggtgc tttatcagc tgggcagtt ttatgccca 
gaatatgat gatgagctc gtggagagc ctacgatgg 
gactggatt tcaaaggac gtctccgta tgacggaag 
catggagtt tcagttcgg cgaggggcg cgagtgtgt 
aaactgcgg cgccatttc gacgccgct atggcgtcg 
cgacggcac gggccatta tttgtgcaa tgcttgtgg 
gctttacca caaaatgaa cggcatgaa ccgaccact 
aataaaacc atcaaaacg attgacggc gacccggag 
attagggct gtgctgcac gaactgtgg gacgcggac 
gacgacatt atggcgtcg gaacaacga cggagaacc 
tgtttgtaa cgcctgcgg attatactt caaattaca 
cggcgtgaa ccggccttt agccatgag gaaggacgg 
catacaaac acgcaaacg caaaccgaa gaagcctgt 
tggcgggga acgtgatga tagcagctc cgcctccgt 
tgaagaaac aaaatctct cgttcacca atcctcgca 
acaacactc gtcgcaatc tcaatcgca aacccatca 
caaccatca gctcgacaa atcatcgcc ggtggagcg 
cccatatct gggccaaac ctccctctt acctgccac 
aagtacaag tgccatcaa aagcgagcc cgggtacga 
atacagctg catacagaa ccagccgtc gtatcctta 
ccaacaaat atttgggtt tcctggttc ggccaacag 
cagcgggga ggttgccta ccaccacca acaccacgt 
tactgccgc cgccaaact aatggcctc gtcttagtc 
taatggtat ttttatgga ctttgtaag tgctttcaa 
acaacaatt ttgcttaag tcttataaa tactcaggt 
cgaaacttc atgaatgac gaaattttt gaaacattg 
agagtgaaa cgatgagtt acaacagtg ttgagagac 
aactgaaat cttcttgta tgttcgtga tcactaaaa 
acttagtga atttattta tgtgatcgt aggaatagt 
tgtgtattt attgatttt atagaattg tttaaatta 
ttgtatcca cctagttat tgttataag ccgtcgctt 
tatttctat tattaattt ataatgctt aaatgtaac 
aagtattcc aggacaaca acagtattc tggccaaaa 
ttttattcg actgaacgt ttttcaatt ttttagtgc 
aatcctgaa tgttatgta ataatatta tttgcttat 
tagttaaaa tttaaaatt gtcatgtgt ttaaatcat 
tcaagctca tattgagcc gaactacaa caaaataaa 
taaataact tcactccct cggtctttt tcgctgtaa 
atattgact aattacgtg gtttcccgt actaaaagt 
tttcaaaaa attgtagtt gcactgttc taaaataaa 
taattgtaa atatgtgcg tctgtttaa tgttaaaaa 
atggaagtg taaatatta cttttatta ttaaattgt 
actagtaaa atataataa acatgtgac atacat

    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