Status
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Gene information
General information
TC003213 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_007418.3: 79203..85434
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
    		TC003213
    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_00535

    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 larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 20
    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: 10.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 10.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC003213 RA
      MTDLIVSRG DTFPRSFLD TYRASRTSE QLYNDLKSS 
KSDELVLQN PADIPIAPE IHHGHSENL LDASGCLSP 
TENDFLESS EMILRSNRR KVRPDYDRV DPEDSIRDI 
VTGNDFYRF VLFKKHYDK YVHLSQKYE EARNIAYYL 
EEKYHEVKM ERDDLIQQR DMLSKRLES NESLLREKE 
DEVFLQFER VVYLEEQCD KLKAEKEKF HQQKLAIEK 
EKEAAYRLL TEQARESEH TRRKLERAR QEVFHHMTR 
MKYEKESLE RENDQLKEA LEAERKGMR KYLNQMHQR 
KKQVDSLEG QLTDRQNTP LASQYQKAL QHLATCKKC 
SVCSYAKTA YRKNSRKYD RKLLGCLQT PFMEMRNMI 
KPPPSPIHG EGESLSEWF CHLNTPNPS ECSSLSVPF 
AELAITYMD DTSDTSSHC LRDHDVDDS SSQAACNSG 
KGFGSDSGF SSDICGDFK SNATTPKEK FSPNGTLDE 
ADCAKLTRT RWTASFRKL INRIRK
    CDS sequence
    • >TC003213 RA
      atgaccgat ttgatcgtt tctcgtggt gatacattc 
ccgcgatcc tttttggat acgtatcgt gcgagccgg 
accagtgag cagttgtac aatgactta aaatcaagc 
aaaagcgac gaattagtt ctgcaaaat ccggccgac 
attccaatt gcaccggaa atccatcat gggcattcg 
gagaattta ttggatgca tctgggtgt ttgtctccg 
actgagaat gacttcttg gagtcgtcg gagatgatc 
ttgaggagt aatagaagg aaggtcagg ccggattat 
gacagggtt gatccagag gatagtatc agggatatc 
gtcacagga aatgatttc tacagattc gtgcttttc 
aaaaaacac tatgataaa tacgttcac ttgtcgcaa 
aaatacgaa gaagccaga aacattgcc tattatctt 
gaagagaaa taccacgaa gtcaagatg gaaagggat 
gatctcatt caacagaga gacatgctg agcaaaaga 
ctggagtcg aacgaaagt ttattgagg gagaaagaa 
gacgaagtt tttcttcaa ttcgaacgt gtggtttat 
ttggaggaa cagtgtgat aagctaaaa gccgaaaaa 
gaaaaattc catcaacaa aaactggca atcgaaaag 
gagaaagaa gccgcttac agattactg acagaacag 
gcccgcgaa tcggaacat acacgtcgg aaactggaa 
agggcgcgt caggaagta tttcatcac atgacaaga 
atgaaatac gaaaaagaa agcttggaa cgagagaac 
gatcaactg aaagaggcc ttagaagcg gaacgtaaa 
ggtatgagg aagtatcta aaccagatg catcaaagg 
aaaaaacaa gtggacagt ctggaagga cagcttacg 
gatcgtcag aacacaccg ttggcttcg caataccaa 
aaggccctt caacatctt gccacttgt aagaaatgc 
tcggtctgt tcgtacgcc aaaacggcc tacaggaag 
aacagtcgc aaatacgat cgtaaactt ttgggttgt 
ctccaaaca ccgtttatg gaaatgcgc aatatgatc 
aaaccgcct ccttcaccc attcatggt gaaggcgaa 
agtctttct gagtggttt tgccacctt aatacaccc 
aatcctagc gaatgttcc tcgttgagt gtccctttt 
gctgaactg gccattacc tatatggac gatacttca 
gatacttca tcacactgt ctcagagat catgacgtg 
gacgattcg tcgagtcaa gcggcttgt aatagcggc 
aaaggtttc gggagcgat tcaggtttt tcgtccgac 
atttgcggc gattttaag agtaacgca acaacgcca 
aaagagaag tttagtccg aacggaact ttggatgaa 
gcggactgt gccaaatta actcgtaca agatggacc 
gcttcattt aggaagcta atcaatcgt attagaaag 
tag
    mRNA sequence
    • >TC003213 RA
      cgtaattga ataatgacc gatttgatc gtttctcgt 
ggtgataca ttcccgcga tcctttttg gatacgtat 
cgtgcgagc cggaccagt gagcagttg tacaatgac 
ttaaaatca agcaaaagc gacgaatta gttctgcaa 
aatccggcc gacattcca attgcaccg gaaatccat 
catgggcat tcggagaat ttattggat gcatctggg 
tgtttgtct ccgactgag aatgacttc ttggagtcg 
tcggagatg atcttgagg agtaataga aggaaggtc 
aggccggat tatgacagg gttgatcca gaggatagt 
atcagggat atcgtcaca ggaaatgat ttctacaga 
ttcgtgctt ttcaaaaaa cactatgat aaatacgtt 
cacttgtcg caaaaatac gaagaagcc agaaacatt 
gcctattat cttgaagag aaataccac gaagtcaag 
atggaaagg gatgatctc attcaacag agagacatg 
ctgagcaaa agactggag tcgaacgaa agtttattg 
agggagaaa gaagacgaa gtttttctt caattcgaa 
cgtgtggtt tatttggag gaacagtgt gataagcta 
aaagccgaa aaagaaaaa ttccatcaa caaaaactg 
gcaatcgaa aaggagaaa gaagccgct tacagatta 
ctgacagaa caggcccgc gaatcggaa catacacgt 
cggaaactg gaaagggcg cgtcaggaa gtatttcat 
cacatgaca agaatgaaa tacgaaaaa gaaagcttg 
gaacgagag aacgatcaa ctgaaagag gccttagaa 
gcggaacgt aaaggtatg aggaagtat ctaaaccag 
atgcatcaa aggaaaaaa caagtggac agtctggaa 
ggacagctt acggatcgt cagaacaca ccgttggct 
tcgcaatac caaaaggcc cttcaacat cttgccact 
tgtaagaaa tgctcggtc tgttcgtac gccaaaacg 
gcctacagg aagaacagt cgcaaatac gatcgtaaa 
cttttgggt tgtctccaa acaccgttt atggaaatg 
cgcaatatg atcaaaccg cctccttca cccattcat 
ggtgaaggc gaaagtctt tctgagtgg ttttgccac 
cttaataca cccaatcct agcgaatgt tcctcgttg 
agtgtccct tttgctgaa ctggccatt acctatatg 
gacgatact tcagatact tcatcacac tgtctcaga 
gatcatgac gtggacgat tcgtcgagt caagcggct 
tgtaatagc ggcaaaggt ttcgggagc gattcaggt 
ttttcgtcc gacatttgc ggcgatttt aagagtaac 
gcaacaacg ccaaaagag aagtttagt ccgaacgga 
actttggat gaagcggac tgtgccaaa ttaactcgt 
acaagatgg accgcttca tttaggaag ctaatcaat 
cgtattaga aagtagact gatgaagaa aaataaaag 
cacaaattg aaaacaata gtaggtgtt aacggttta 
taagacttg atagatcga atatcaaat gttttttcg 
aaatttatt aaatcacgt tttgtgtct aattaaata 
cgacgtatc tcctgtttt ttcatgtaa caggttttt 
tcgtagggg aattatata atactccgc ccgtaggca 
ccaacattt tatagttaa tgttaaaag tgaatgtta 
aaaatatat acaaagtga aacacctat ttctacttt 
gttagacga tgaaatcat tttacaaat ttgttgaaa 
tcaatttga gtattgagt gctatttta aagtattta 
caagtttgt tcttgcctt ctaaatgtt ttaagtgcc 
gtccaagta ttttttaaa gctgtttat gatttttaa 
gtattactt ttttcattt atttaattg gtggcagtc 
ttagtttta atgactatt tatttcaac cattccaat 
attacgatt acataagta gaaattcat taagtgtga 
acacataat tgcatctaa cgtttttca ggtgcagat 
tggcagcat ttgtgataa aataaaaca atttttgtc 
tg

    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