Status
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Gene information
General information
TC003598 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: 8684225..8686896
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
    		TC003598
    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_07980

    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: < 50
     embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): less than 30%
    cuticle remnants strongly fragmented (cuticle crumbs) - Penetrance (percentage of animals/eggs on slide): less than 30%

    head not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    thorax not present - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    abdomen not present - Penetrance (percentage of animals/eggs on slide): 50% - 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
    • >TC003598 RA
      MEKFDWRCP IRINLLLLR SVGLWPRGY GVYKRNYYL 
FYSIFTTIT IVGGHNLSQ VINIFYVYS DLEALTGTI 
FVATTNILA LVKRYVFVR NLPLIKEIL QTLNTYQFH 
PKTRQQLKI IQAPLRRWK LAYLCFSII VYFNVAMWT 
LEPLLDKMI KNRRLPFEA WYPFNSKQS PNYEIAYCY 
QFICIWNIT IANLNLDTL IFAFMMFIS AQCEILCDD 
LRSLDVGFG PKLIQCIKH HKEILRLAK VTNNIFNFI 
ILGQIATST AALALTMFQ LSLISSINT TALTHFAYM 
MGMLSEILL YCWFGNEIE VKSYLIPNA AYESQWMHQ 
DRSVAKNLL ILGCRCRKP IKITAINLF TLSLPTFIA 
ILRSAWSYF ALLSTINGK
    CDS sequence
    • >TC003598 RA
      atggaaaaa ttcgattgg agatgtccg atccgaata 
aacctcctt ctactaaga tctgtcggg ttgtggccc 
cgaggatac ggagtttac aaacgcaac tattacctc 
ttctactcc atattcacg acaattaca atcgtcggc 
ggccacaat ttatcgcaa gtcataaac attttctac 
gtttattcg gacttggag gctttgacg ggtaccata 
tttgtggca acaaccaac atcctggcc ctcgttaag 
agatacgtt ttcgtacgc aacctcccc ctcataaag 
gagattctg cagactttg aacacttac cagtttcac 
cccaaaact cggcaacag ctaaaaatc atccaagcg 
ccacttcgt cgctggaaa ctggcctac ctttgtttt 
tccattatt gtttatttc aacgtggcc atgtggacg 
cttgaaccg cttttggac aaaatgatc aaaaatcgg 
cggttgccc ttcgaagct tggtatcct ttcaacagc 
aagcaaagc cccaactac gaaatcgcc tactgctac 
cagttcatt tgcatttgg aacataact atcgctaat 
ttgaacttg gacactttg attttcgcc ttcatgatg 
ttcatttcg gcccaatgt gagattctt tgtgacgac 
ttgaggagt cttgacgtc ggttttggg ccaaaattg 
atacagtgt atcaaacac cacaaggaa attttacgc 
ctcgcaaag gtcactaac aacatcttc aattttatt 
attttaggg caaatagcc acaagtacg gccgctctc 
gctttaacc atgtttcag ctaagtcta atcagctcg 
ataaacacc accgctctc actcatttt gcctacatg 
atgggcatg ttgagtgag attttgttg tactgttgg 
ttcggtaac gaaattgaa gttaagagt tatttgatt 
ccgaacgca gcctacgag tcgcaatgg atgcaccag 
gaccgaagt gttgcgaaa aatttgctt attttgggc 
tgtcgttgt cgcaaaccg atcaaaatt acggcaatt 
aatttgttt acgctctct ttaccaacg tttattgcg 
attcttcgg tccgcatgg tcgtatttt gccttatta 
tccacaatt aatggcaaa taa
    mRNA sequence
    • >TC003598 RA
      ttaggcctg tgagtgacc gaaagcact ataaaaagc 
tcgacatga atttgtttt acgcattta tttgttgtc 
ccgagtgct ccaaacaat atttcaatg gaaaaattc 
gattggaga tgtccgatc cgaataaac ctccttcta 
ctaagatct gtcgggttg tggccccga ggatacgga 
gtttacaaa cgcaactat tacctcttc tactccata 
ttcacgaca attacaatc gtcggcggc cacaattta 
tcgcaagtc ataaacatt ttctacgtt tattcggac 
ttggaggct ttgacgggt accatattt gtggcaaca 
accaacatc ctggccctc gttaagaga tacgttttc 
gtacgcaac ctccccctc ataaaggag attctgcag 
actttgaac acttaccag tttcacccc aaaactcgg 
caacagcta aaaatcatc caagcgcca cttcgtcgc 
tggaaactg gcctacctt tgtttttcc attattgtt 
tatttcaac gtggccatg tggacgctt gaaccgctt 
ttggacaaa atgatcaaa aatcggcgg ttgcccttc 
gaagcttgg tatcctttc aacagcaag caaagcccc 
aactacgaa atcgcctac tgctaccag ttcatttgc 
atttggaac ataactatc gctaatttg aacttggac 
actttgatt ttcgccttc atgatgttc atttcggcc 
caatgtgag attctttgt gacgacttg aggagtctt 
gacgtcggt tttgggcca aaattgata cagtgtatc 
aaacaccac aaggaaatt ttacgcctc gcaaaggtc 
actaacaac atcttcaat tttattatt ttagggcaa 
atagccaca agtacggcc gctctcgct ttaaccatg 
tttcagcta agtctaatc agctcgata aacaccacc 
gctctcact cattttgcc tacatgatg ggcatgttg 
agtgagatt ttgttgtac tgttggttc ggtaacgaa 
attgaagtt aagagttat ttgattccg aacgcagcc 
tacgagtcg caatggatg caccaggac cgaagtgtt 
gcgaaaaat ttgcttatt ttgggctgt cgttgtcgc 
aaaccgatc aaaattacg gcaattaat ttgtttacg 
ctctcttta ccaacgttt attgcgatt cttcggtcc 
gcatggtcg tattttgcc ttattatcc acaattaat 
ggcaaataa tacactaaa taacttgaa cttgtaaag 
tagggaaaa cacaaaaat agtagtcaa aattgcgtc 
acttttatg taatagttt aatttataa aattcaaaa 
aggagaaga ccaacgaat tttgttcat ttaacgatt 
ttattgtaa ttttttagt cgcaagtca aattagaga 
cgggcttgt tgcaagaaa acactcagt tgggctata 
atatttttc ttcattaaa gttgtttgt atttttatt 
agagacttc tggtatgtc tactttgta atttactgt 
catttcaga cggaatatt tataaggca gtaagccaa 
gtccccttt tattttatt ctaaacgat gtaaaaaac 
ttaaaaaaa tccttataa atcactttc aatcaagat 
aaacaacac atgttctaa gggaaaaat gtctgggcc 
tgttttttc caatttttt tgatttttt tccaaaaat 
aattaaaaa attccttgt tactatttt ataaaataa 
taagcaggt atttgaatg gcataattt tgtctagtt 
aaagtaaat gtagctcgt tatgtctta gtaaggtat 
aaaaagcca acttcatta tttttcttt tcattcaag 
tttaccttc agccgcacg tttgtgaaa acttttagg 
agatgtttc atatttttt gtgtcgagt ggaatattg 
ttcacattt tatatttat tacaagttt tactaatcc 
ttgttttaa atcatttac taacacgca gctggattt 
ttaacttct gcaacgagt tattaaaaa tttttaaaa 
ttaagtgtt tttgtgaaa tttctttga agtttaatt 
tagacggtt tagtgctag atcttacac ttgaatatt 
ttcctcgat aatttataa gtcagtgag ttttgcatt 
ttgttgtta ttttaattt taatttata tttttcagg 
ctactcgta tgtttagat ctttgctta ccaataaaa 
taatgctta tact

    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