Status
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Gene information
General information
TC014238 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: 3549434..3551258
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
    		TC014238
    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
    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_10205

    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)

    Adult morphology
    abdominal odoriferous glands colour darker - Number of animals showing the phenotype: 4 (13 dpi)
    Days post injection

    Fertility
    mature egg deposition blocked number 1st lateral oviduct: number 2nd lateral oviduct: - Number of animals showing the phenotype: 2
    previtellogenic egg chamber number decreased - Number of animals showing the phenotype: 1

    vitellarium size shortened - Number of animals showing the phenotype: 1

    mature egg not present - Number of animals showing the phenotype: 2

    egg chamber number decreased - Number of animals showing the phenotype: 2

    vitellogenic egg chamber potentially degenerated - Number of animals showing the phenotype: 2
    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
    • >TC014238 RA
      MKFSTILLC TLFTIFVIA SKVVFDKIY QTARLIIDE 
EFHFQLGEA YCRYEFDKW HPKITTFPG LYLFSNLLL 
GPFDLCSSY WLRLTSLVS SFANLILFY CLLNLNNEQ 
PKWQNAISA TSLSLLPPM YFFGHLYYT DTVSLTMVS 
VLFLLSQRK HHYFASIFG LFSVLCRQT NIIWVLMAF 
GCYVLKDVN NICNKSRKT DCVSAKELV ELLKLAKGK 
NLLMTIKKM PFVFWLNAT CYGSLLLIF ALFVYMHGS 
IVVGDKTAH EATIHLPQL FYFSLFCLF FAWPHFVTE 
ITGFLKFVK RHKIISLAV VLSSVAIVH FNTLVHPYV 
LADNRHYIF YIWNRFYGR YFWFRYCVV PVYLFAWFV 
IVRKLWDRL DVTFLLFFI PCTTVVLVT QKLLEFRYF 
FIPYVLFRT HLKNADVRF VLCEFVTYC VLNFCTLYI 
FFNKTIEWE NFDCPQRLI W
    CDS sequence
    • >TC014238 RA
      atgaaattt tccacgatt ttgttgtgt accttgttc 
acaatcttt gtcatagct tcgaaagtt gtattcgac 
aaaatatat caaaccgca agacttatt attgatgaa 
gagtttcat tttcaactt ggagaagct tattgcaga 
tacgaattc gacaagtgg cacccgaaa ataacaaca 
tttccaggc ctctatcta ttcagtaac ttgttactg 
gggcctttt gatttgtgt tcaagttat tggctaaga 
ctgacttca ttggtttcc tcattcgcg aatttaata 
cttttttat tgcttacta aacctaaat aatgaacaa 
cccaagtgg caaaatgcc atttcagca accagttta 
tcattatta ccaccgatg tactttttt ggccatctc 
tattacaca gatactgtc tcgcttacg atggtttcc 
gtgcttttt ttactgtca caaagaaag caccactat 
tttgcgtcg atctttgga ttattttcc gttttgtgc 
cgacaaacc aacataata tgggttctg atggctttc 
gggtgctat gtcctaaaa gacgtaaac aacatttgc 
aacaagtct agaaaaact gactgcgtt tctgcaaag 
gaattggtc gagttgtta aaactggcg aaagggaaa 
aatctattg atgacgatc aaaaaaatg ccgttcgtt 
ttttggtta aacgccact tgttacggc tctttgttg 
ctaattttt gcattgttt gtctacatg catggaagt 
atagttgtg ggtgataaa acagcgcat gaggccacc 
attcatttg ccccaatta ttttatttt tcgcttttt 
tgcctgttt tttgcttgg cctcacttc gttactgaa 
attactggt ttccttaaa tttgtgaag cgacataaa 
attatcagt ctggctgtt gtgttatca agtgtggct 
atagtgcat ttcaacact ttggttcat ccgtatgtt 
ttggccgac aacaggcat tacattttt tacatttgg 
aaccgattt tacgggagg tatttttgg ttccgctat 
tgcgttgtt ccagtgtat ttatttgca tggtttgtg 
atagttaga aaactgtgg gatagacta gatgtgacg 
ttccttctg tttttcatt ccatgtaca acggtggtt 
ttagtaaca cagaaacta ctagagttt cggtatttt 
tttattcca tatgttctc ttccgaacg catttgaaa 
aatgctgat gttcggttc gtgttatgc gagttcgta 
acttactgt gtacttaat ttttgcaca ctgtatata 
tttttcaac aagactata gaatgggaa aatttcgat 
tgtccccaa aggctgatt tggtaa
    mRNA sequence
    • >TC014238 RA
      ctcccaaaa ataatgttt caaatgaaa ttttccacg 
attttgttg tgtaccttg ttcacaatc tttgtcata 
gcttcgaaa gttgtattc gacaaaata tatcaaacc 
gcaagactt attattgat gaagagttt cattttcaa 
cttggagaa gcttattgc agatacgaa ttcgacaag 
tggcacccg aaaataaca acatttcca ggcctctat 
ctattcagt aacttgtta ctggggcct tttgatttg 
tgttcaagt tattggcta agactgact tcattggtt 
tcctcattc gcgaattta atacttttt tattgctta 
ctaaaccta aataatgaa caacccaag tggcaaaat 
gccatttca gcaaccagt ttatcatta ttaccaccg 
atgtacttt tttggccat ctctattac acagatact 
gtctcgctt acgatggtt tccgtgctt tttttactg 
tcacaaaga aagcaccac tattttgcg tcgatcttt 
ggattattt tccgttttg tgccgacaa accaacata 
atatgggtt ctgatggct ttcgggtgc tatgtccta 
aaagacgta aacaacatt tgcaacaag tctagaaaa 
actgactgc gtttctgca aaggaattg gtcgagttg 
ttaaaactg gcgaaaggg aaaaatcta ttgatgacg 
atcaaaaaa atgccgttc gttttttgg ttaaacgcc 
acttgttac ggctctttg ttgctaatt tttgcattg 
tttgtctac atgcatgga agtatagtt gtgggtgat 
aaaacagcg catgaggcc accattcat ttgccccaa 
ttattttat ttttcgctt ttttgcctg ttttttgct 
tggcctcac ttcgttact gaaattact ggtttcctt 
aaatttgtg aagcgacat aaaattatc agtctggct 
gttgtgtta tcaagtgtg gctatagtg catttcaac 
actttggtt catccgtat gttttggcc gacaacagg 
cattacatt ttttacatt tggaaccga ttttacggg 
aggtatttt tggttccgc tattgcgtt gttccagtg 
tatttattt gcatggttt gtgatagtt agaaaactg 
tgggataga ctagatgtg acgttcctt ctgtttttc 
attccatgt acaacggtg gttttagta acacagaaa 
ctactagag tttcggtat ttttttatt ccatatgtt 
ctcttccga acgcatttg aaaaatgct gatgttcgg 
ttcgtgtta tgcgagttc gtaacttac tgtgtactt 
aatttttgc acactgtat atatttttc aacaagact 
atagaatgg gaaaatttc gattgtccc caaaggctg 
atttggtaa ggcgtattt atttttgtg gctgttaat 
taaatgtac caataaata

    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