Status
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Gene information
General information
TC013758 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: 4754165..4769116
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
    		TC013758
    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
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_02199

    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)

    adult lethality - Number of animals showing the phenotype: 2 (9 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (11 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): more than 80%

    embryo/egg with embryonic tissue, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 80%
    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): more than 80%
    cuticle remnants with unidentifyable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

    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: 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 - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection

    Fertility
    fertility after larval injection decreased (no living offspring) -
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC013758 RA
      MGDVEVHSN FTITEKKTK KVKKTTKRR ESSDHGGEV 
TITEMERTN GTQGGEYTK AMNKDWHGQ HFCCWQCDE 
SLTGQRYVL RDEHPYCVS CYESVFANA CEKCSRIIG 
IDSKDLSYK DKHWHEACF LCTTCGESL VDRQFGSKG 
DRIYCGRCY DEQFASRCD GCHEIFRAG TLSDQFKSR 
LNLQTKTVG EERIKKAKE RNEDVAILS MELPGEKKA 
FKCCLDQDC LLGDPTSLP LGTKKMEYK TRQWHEKCF 
CCCVCKVPI GTQSFIPRE QEIYCAKCY EEKFATRCI 
KCNKVITSG GVTYKNEPW HRECFTCTH CSKSLAGER 
FTSRDEKPY CAECFGELF AKRCFACNK PITGIGGTK 
FISFEDRHW HNDCFFCAS CRTSLVGRG FITDQEDII 
CPECAKQKL M
    CDS sequence
    • >TC013758 RA
      atgggagac gttgaagtt cattccaat tttaccatc 
accgaaaag aaaaccaaa aaagtcaag aagaccacc 
aaacgaagg gagagtagt gaccatggg ggcgaagtc 
accatcact gaaatggag cgcaccaac ggcacgcag 
ggtggcgag tacacaaag gccatgaac aaggactgg 
catgggcaa cacttttgc tgttggcag tgcgacgag 
agtttaact ggtcaacgc tacgtcctc cgtgacgag 
catccctat tgcgtgtct tgttacgaa tctgtcttc 
gccaatgct tgcgaaaag tgcagcaga atcatcgga 
atcgactca aaagacctt tcctacaaa gacaagcac 
tggcacgag gcctgcttc ctgtgcacg acttgcggg 
gaatccctc gtcgatagg caattcggg tcaaagggc 
gacaggatc tactgtggc cgctgctac gatgagcag 
ttcgcgtcc aggtgcgac ggctgccat gaaatcttc 
cgagcagga actctgagt gatcagttc aagtcgcgt 
ctgaacctc cagacgaaa actgtcggt gaggagcgg 
attaaaaag gccaaagag cggaatgaa gacgtcgcg 
attttgtcc atggaactg ccgggcgaa aaaaaggcc 
ttcaagtgc tgcctggac caggactgc ctgctgggg 
gaccccaca agcctgcct ctaggaaca aagaagatg 
gaatacaag acgaggcaa tggcacgag aagtgcttc 
tgctgttgc gtatgcaaa gtaccgatc ggtacccag 
agtttcatt cctcgcgag caagagatc tactgtgcc 
aagtgttac gaagagaaa ttcgccacg cgttgcatc 
aaatgcaac aaggtcatc accagcggc ggcgtgacg 
tacaagaac gagccctgg cacagggag tgcttcacc 
tgcacccac tgctccaag agcctggcg ggcgagcgc 
ttcaccagc cgcgacgag aagccctat tgcgccgag 
tgcttcggc gagctgttc gccaaacgg tgcttcgcc 
tgcaataag cccatcacc ggcatcggg ggcacgaag 
ttcatctcg ttcgaggac aggcattgg cacaacgac 
tgcttcttc tgcgcctcg tgccgcacc agtctagtg 
ggccgtggc ttcatcacc gaccaggaa gacatcatc 
tgtcccgaa tgcgccaag caaaagttg atgtag
    mRNA sequence
    • >TC013758 RA
      acagaattc agtcgcagt tcactgtta gaaccgggt 
gtgtgtatt gtcctcgaa aatgggaga cgttgaagt 
tcattccaa ttttaccat caccgaaaa gaaaaccaa 
aaaagtcaa gaagaccac caaacgaag ggagagtag 
tgaccatgg gggcgaagt caccatcac tgaaatgga 
gcgcaccaa cggcacgca gggtggcga gtacacaaa 
ggccatgaa caaggactg gcatgggca acacttttg 
ctgttggca gtgcgacga gagtttaac tggtcaacg 
ctacgtcct ccgtgacga gcatcccta ttgcgtgtc 
ttgttacga atctgtctt cgccaatgc ttgcgaaaa 
gtgcagcag aatcatcgg aatcgactc aaaagacct 
ttcctacaa agacaagca ctggcacga ggcctgctt 
cctgtgcac gacttgcgg ggaatccct cgtcgatag 
gcaattcgg gtcaaaggg cgacaggat ctactgtgg 
ccgctgcta cgatgagca gttcgcgtc caggtgcga 
cggctgcca tgaaatctt ccgagcagg aactctgag 
tgatcagtt caagtcgcg tctgaacct ccagacgaa 
aactgtcgg tgaggagcg gattaaaaa ggccaaaga 
gcggaatga agacgtcgc gattttgtc catggaact 
gccgggcga aaaaaaggc cttcaagtg ctgcctgga 
ccaggactg cctgctggg ggaccccac aagcctgcc 
tctaggaac aaagaagat ggaatacaa gacgaggca 
atggcacga gaagtgctt ctgctgttg cgtatgcaa 
agtaccgat cggtaccca gagtttcat tcctcgcga 
gcaagagat ctactgtgc caagtgtta cgaagagaa 
attcgccac gcgttgcat caaatgcaa caaggtcat 
caccagcgg cggcgtgac gtacaagaa cgagccctg 
gcacaggga gtgcttcac ctgcaccca ctgctccaa 
gagcctggc gggcgagcg cttcaccag ccgcgacga 
gaagcccta ttgcgccga gtgcttcgg cgagctgtt 
cgccaaacg gtgcttcgc ctgcaataa gcccatcac 
cggcatcgg gggcacgaa gttcatctc gttcgagga 
caggcattg gcacaacga ctgcttctt ctgcgcctc 
gtgccgcac cagtctagt gggccgtgg cttcatcac 
cgaccagga agacatcat ctgtcccga atgcgccaa 
gcaaaagtt gatgtagat tttacagat ttctgtttt 
tttttaatc agtgaccat agcaccgtg acacgcaca 
cactacaca cacacacat cttacacca ccgaaaaaa 
acataaaag aaaaataca aaaaaaaac gaggatacg 
ctgttttta gagtaaatg tatttattt ttggaggat 
ttatttttg tttgccata ttataacat gacgtcaga 
gttgattgg gacgtagga tattctaaa ttttgacat 
tacaccaca gcttccttg attcgtgca atgacagta 
cgtcgagga tcaaggaag ctgtgccct atccaaaca 
gttgcctta aaaatttag tagtagaga cccatgaat 
attaaacat atatatttg ttataaatt acggttgtt 
attgcttct taactgtta atgtaagtg ttttgacaa 
ttttttatt gtatattat tattactat tgtagataa 
tgtacacag cttcatagc atttatgaa atgagcaac 
tttggtgct atttgagta gttagatta attttttta 
ttattattt tcctaattt ctagttact gtttttcag 
taaattcta tctaaatgc ttcattaac agaaatgtt 
actattaat attgataaa taaacatac ataatattc 
gtttagagt ttaactttc agttgtaaa atgtacgta 
ttggtaaat ttggattgt taaaaattt gttatgctt 
ttaaataca agtacaggg ctttgcttt agggatatt 
gttatattt aattccaca ataaatatc tgaaagaaa 
a

    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