Status
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Gene information
General information
TC013340 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: 10911348..10914777
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
    		TC013340
    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_02113

    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: 40.0% (includes death as pupa, adult)

    adult lethality - Number of animals showing the phenotype: 3 (9 dpi)
    Days post injection

    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: 100.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 100.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 8 (11 dpi)
    Days post injection

    Comment: 3 died during a larval molt

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC013340 RA
      MPCPFLTRL SQNYVKNYG TLLLKMYGN QCPVVSSTM 
STIAGEDVK SQVLDTQKS NTPCPFLKE VNNVIKEVK 
NDDTIEMKS DVDLFPYDS FFHQQIMKK KKEHSYRVF 
KKVNRLAGP GQFPSALEY SWGEKPITV WCSNDYLGM 
SCHPKVKEA VREALDKYG TGAGGTRNI SGNSTLHEK 
LEGILAQLH QKERALLFT SCFVANDST LFTLAKTLP 
GCHIFSDAG NHASMIQGI RNSQVPKHI FKHNDPAHL 
EDLLKTVNK NIPKIVAFE TVHSMSGAV CPLEELCDV 
AHKYGALTF IDEVHAVGL YGEHGAGIG ERDGKLHKM 
DIISGTLGK AFGNVGGYI ASSATLVDM IRSYAAGFI 
FTTSLPPTV LSGAYKAIQ ILASDEGRE LRRRHQDNV 
KYLRGNLLN NGFPVEHTP SHIIPIKIG DPVQCGAVC 
DTLLKEKGH YIQAINYPT VARGQEKLR LAPTPHHTK 
EMMDTLVGD LKEVWQTLN LPFTGLQCG KNCPYCQKP 
LLFDYFESR SRLEQGCGK DLNCTIPNC PQLVGVV
    CDS sequence
    • >TC013340 RA
      atgccttgc ccatttcta acaagacta agccaaaac 
tacgttaaa aattatggg acccttttg cttaaaatg 
tacgggaac cagtgtccc gtggtgtca agcaccatg 
agcacaatt gccggagaa gacgtaaaa agtcaagtt 
ttagacacc caaaaatca aacaccccg tgtccattc 
ttgaaggaa gtcaacaat gttattaaa gaggtaaaa 
aacgacgac accattgaa atgaagagt gatgtagat 
ttatttcca tatgacagt tttttccac caacaaata 
atgaagaaa aaaaaggag cacagctac cgtgttttc 
aaaaaagtc aacaggcta gcaggccct ggacagttt 
ccaagtgct ttggagtac tcatggggc gaaaaaccc 
atcacggtt tggtgctcg aacgactat ttgggaatg 
tcttgccat cccaaggtt aaggaggct gtgagggaa 
gctcttgat aagtacggc acaggggct ggtggtact 
agaaatatt tcgggaaat tcaacattg cacgaaaag 
ctggaaggc attcttgca caactgcac caaaaagag 
agagctctg ctctttact tcttgtttc gttgcaaat 
gactctact cttttcacc ttggctaaa acactgcca 
ggatgtcat attttttcc gacgccgga aaccatgct 
tcaatgatt caaggcata agaaacagc caagtacca 
aaacacatt ttcaagcac aatgatccc gcacacttg 
gaagatctg ctgaagact gttaataaa aatattccg 
aaaatagtt gcatttgaa accgttcat tcaatgtca 
ggggctgtt tgtcccttg gaagaactt tgcgacgtt 
gctcacaaa tatggggcg ttaactttt attgatgaa 
gtccacgca gttggactt tatggtgaa catggagct 
ggaattggc gaacgtgac ggaaagctc cataaaatg 
gacataatc tcgggtact ttgggcaaa gccttcgga 
aacgttggt ggctatatc gcttcgtct gcgactctg 
gtcgatatg atcaggtct tacgctgct ggtttcatc 
ttcaccact tcgttacca cccactgtg ctgtcgggt 
gcttacaaa gcaatccag atcctggcc tcagatgag 
ggtagagaa ctgcgaaga cgtcaccag gataatgta 
aaatattta agaggcaat ttattgaat aacggattc 
cccgtggaa catacgcct agtcatatc atcccgatt 
aaaatcgga gacccggtg cagtgtgga gccgtttgt 
gacactttg ttgaaagaa aaaggtcac tacatacaa 
gctatcaac taccccact gttgccaga gggcaagaa 
aaactgaga ttggcgccg acccctcat catactaaa 
gagatgatg gatacgctt gttggcgat cttaaagaa 
gtgtggcaa actttaaat ttgccgttt accggactt 
cagtgcgga aagaactgt ccctactgt caaaagccg 
cttctattt gactacttt gaatccaga tcaagactt 
gaacaaggt tgtgggaag gatcttaac tgtactatt 
ccaaactgt ccacagttg gttggtgtt gtgtaa
    mRNA sequence
    • >TC013340 RA
      ttcacttcg caccgtcga gtagtgcac ttgaactca 
actactttc tagcgctct ccatattga cctacatct 
acaaaaatc actttctaa ttctcaaaa taacctaag 
atttttgac caagtaatt gctacgcaa cgtacacgg 
aataattgg agaaaatgc cttgcccat ttctaacaa 
gactaagcc aaaactacg ttaaaaatt atgggaccc 
ttttgctta aaatgtacg ggaaccagt gtcccgtgg 
tgtcaagca ccatgagca caattgccg gagaagacg 
taaaaagtc aagttttag acacccaaa aatcaaaca 
ccccgtgtc cattcttga aggaagtca acaatgtta 
ttaaagagg taaaaaacg acgacacca ttgaaatga 
agagtgatg tagatttat ttccatatg acagttttt 
tccaccaac aaataatga agaaaaaaa aggagcaca 
gctaccgtg ttttcaaaa aagtcaaca ggctagcag 
gccctggac agtttccaa gtgctttgg agtactcat 
ggggcgaaa aacccatca cggtttggt gctcgaacg 
actatttgg gaatgtctt gccatccca aggttaagg 
aggctgtga gggaagctc ttgataagt acggcacag 
gggctggtg gtactagaa atatttcgg gaaattcaa 
cattgcacg aaaagctgg aaggcattc ttgcacaac 
tgcaccaaa aagagagag ctctgctct ttacttctt 
gtttcgttg caaatgact ctactcttt tcaccttgg 
ctaaaacac tgccaggat gtcatattt tttccgacg 
ccggaaacc atgcttcaa tgattcaag gcataagaa 
acagccaag taccaaaac acattttca agcacaatg 
atcccgcac acttggaag atctgctga agactgtta 
ataaaaata ttccgaaaa tagttgcat ttgaaaccg 
ttcattcaa tgtcagggg ctgtttgtc ccttggaag 
aactttgcg acgttgctc acaaatatg gggcgttaa 
cttttattg atgaagtcc acgcagttg gactttatg 
gtgaacatg gagctggaa ttggcgaac gtgacggaa 
agctccata aaatggaca taatctcgg gtactttgg 
gcaaagcct tcggaaacg ttggtggct atatcgctt 
cgtctgcga ctctggtcg atatgatca ggtcttacg 
ctgctggtt tcatcttca ccacttcgt taccaccca 
ctgtgctgt cgggtgctt acaaagcaa tccagatcc 
tggcctcag atgagggta gagaactgc gaagacgtc 
accaggata atgtaaaat atttaagag gcaatttat 
tgaataacg gattccccg tggaacata cgcctagtc 
atatcatcc cgattaaaa tcggagacc cggtgcagt 
gtggagccg tttgtgaca ctttgttga aagaaaaag 
gtcactaca tacaagcta tcaactacc ccactgttg 
ccagagggc aagaaaaac tgagattgg cgccgaccc 
ctcatcata ctaaagaga tgatggata cgcttgttg 
gcgatctta aagaagtgt ggcaaactt taaatttgc 
cgtttaccg gacttcagt gcggaaaga actgtccct 
actgtcaaa agccgcttc tatttgact actttgaat 
ccagatcaa gacttgaac aaggttgtg ggaaggatc 
ttaactgta ctattccaa actgtccac agttggttg 
gtgttgtgt aaaaaaact ggagattat ttttatgga 
agttaaagg tgttggtac attttattc tcaagttat 
ggaagatgt taaaaatgt attgtcaat ttatggaac 
tattatact agataagca aatataaaa agttgaaag 
at

    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