Status
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Gene information
General information
TC003160 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: 1008839..1011756
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
    		TC003160
    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_03512

    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: 20.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 2 (3 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): 50% - 80%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): 50% - 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): 50% - 80%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): 50% - 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

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC003160 RA
      MAVKNETVL YSQLQPWST VGADPCMEQ VGGPPVPVR 
IGQYYQTPR PHPWRPTLG YENVEVTPL PSQPVTNAL 
IDPCYTPHG MATEPLKFP NLVTGFERN PAHAARAAL 
YTRYTPIEW THNNLRNYG ESDTNRNYS ERLRGEFIR 
VMRETDEKT AQGQREVGR RLGERITDL TFWRNEART 
ELERLLTES DLLQEARRS LEKAISDIE GPLHIAQEC 
LYQRENRQG IDLVHDNAE HSLLKEIEI YRNSQEQLK 
CLYERIKDQ LRNNRAAQH ELETDVRSK EGALGIDNM 
CHQLNNFSK GINYYGGIE KYDPTVSTV QTWAENSNR 
IVQRSQSER GKSAQLRSD IENLINTVA TQIWDAWSN 
TNNALARRA AETLEAKSK LQMHLHKIQ QEIFDVEKN 
IELIKKAIM DKSNPMKVA HTRLEARTH RKNVELCRD 
TAQDRLVRE VVDIQDSIE YLHRKLQEA EAQHQQLLK 
TRSNLESDL HNKVNSLFI DREKCMGMR RSFPITATI 
KY
    CDS sequence
    • >TC003160 RA
      atggcggta aaaaacgag acagtgtta tattcacaa 
cttcaacca tggagtacc gtgggggcc gatccttgc 
atggagcag gtcgggggg ccgccagtg ccggtccgc 
attggtcag tactaccaa actccaagg ccccaccct 
tggaggccc acgctgggt tacgaaaac gtggaagtg 
accccattg ccgagtcaa ccggtcaca aatgcgctc 
atcgatccc tgttatact ccgcatggg atggccacc 
gagccgttg aaatttccg aatttggtg accggtttt 
gagcgaaat ccggcccat gcagctagg gctgccctt 
tatacgaga tatacgccc attgagtgg acgcataat 
aatttgcgg aattatggc gagtcggat acgaatcgg 
aattattcg gagcggctc aggggcgaa tttattcgg 
gtcatgaga gaaactgat gaaaaaacg gcgcaaggt 
cagcgcgag gtgggccga agacttggt gaaagaatc 
accgatttg acgttttgg cggaatgag gcccgcact 
gagctcgag agacttttg actgagagt gatttgctg 
caagaagct cgcaggtct ttagagaag gctatttcg 
gacattgag gggcccctc catatcgct caggagtgc 
ctctaccaa agagaaaac cgccaggga attgatcta 
gtccacgat aatgccgaa cactccctt ctaaaagaa 
atcgaaatt tatcgaaac tctcaggaa caactcaaa 
tgtctctac gaacgcatc aaggaccag ctcagaaat 
aacagagcg gctcagcac gaactcgaa actgacgtt 
cggagcaaa gaaggggct cttggaatt gacaacatg 
tgccaccaa ctcaataat ttctccaaa ggaatcaac 
tactacgga gggatagaa aaatacgac cctacggtt 
tcaacggtt caaacgtgg gccgaaaac agcaaccga 
atcgttcaa agatcacaa tcagaaaga ggcaaatcg 
gctcagtta cgttccgat attgaaaat ttaataaac 
acagttgct actcaaatt tgggatgct tggagtaat 
acgaataat gcgttagca agacgggca gcagaaaca 
ttagaagcc aaaagtaaa ctccaaatg catttgcat 
aaaatccaa caggaaatt ttcgatgtt gagaaaaat 
atcgaattg atcaagaag gcaattatg gataagagc 
aatccaatg aaagtggca cacacaaga cttgaagcg 
agaactcat cggaaaaac gtcgagttg tgcagagat 
acggcccaa gacagactt gtgcgagaa gtggttgat 
attcaagac agcattgaa tatctccac agaaagctc 
caagaagcg gaagctcag catcaacaa ctgctcaaa 
actcgatca aatctcgag tcagatttg cacaataaa 
gtcaattcg ttgtttatt gatcgagaa aaatgcatg 
gggatgaga aggtcattc cctatcact gccaccatc 
aaatactaa
    mRNA sequence
    • >TC003160 RA
      aaagtcaaa attatttcg cttttttag atgtttagt 
gagtagttg ggtgaatgg cggtaaaaa acgagacag 
tgttatatt cacaacttc aaccatgga gtaccgtgg 
gggccgatc cttgcatgg agcaggtcg gggggccgc 
cagtgccgg tccgcattg gtcagtact accaaactc 
caaggcccc acccttgga ggcccacgc tgggttacg 
aaaacgtgg aagtgaccc cattgccga gtcaaccgg 
tcacaaatg cgctcatcg atccctgtt atactccgc 
atgggatgg ccaccgagc cgttgaaat ttccgaatt 
tggtgaccg gttttgagc gaaatccgg cccatgcag 
ctagggctg ccctttata cgagatata cgcccattg 
agtggacgc ataataatt tgcggaatt atggcgagt 
cggatacga atcggaatt attcggagc ggctcaggg 
gcgaattta ttcgggtca tgagagaaa ctgatgaaa 
aaacggcgc aaggtcagc gcgaggtgg gccgaagac 
ttggtgaaa gaatcaccg atttgacgt tttggcgga 
atgaggccc gcactgagc tcgagagac ttttgactg 
agagtgatt tgctgcaag aagctcgca ggtctttag 
agaaggcta tttcggaca ttgaggggc ccctccata 
tcgctcagg agtgcctct accaaagag aaaaccgcc 
agggaattg atctagtcc acgataatg ccgaacact 
cccttctaa aagaaatcg aaatttatc gaaactctc 
aggaacaac tcaaatgtc tctacgaac gcatcaagg 
accagctca gaaataaca gagcggctc agcacgaac 
tcgaaactg acgttcgga gcaaagaag gggctcttg 
gaattgaca acatgtgcc accaactca ataatttct 
ccaaaggaa tcaactact acggaggga tagaaaaat 
acgacccta cggtttcaa cggttcaaa cgtgggccg 
aaaacagca accgaatcg ttcaaagat cacaatcag 
aaagaggca aatcggctc agttacgtt ccgatattg 
aaaatttaa taaacacag ttgctactc aaatttggg 
atgcttgga gtaatacga ataatgcgt tagcaagac 
gggcagcag aaacattag aagccaaaa gtaaactcc 
aaatgcatt tgcataaaa tccaacagg aaattttcg 
atgttgaga aaaatatcg aattgatca agaaggcaa 
ttatggata agagcaatc caatgaaag tggcacaca 
caagacttg aagcgagaa ctcatcgga aaaacgtcg 
agttgtgca gagatacgg cccaagaca gacttgtgc 
gagaagtgg ttgatattc aagacagca ttgaatatc 
tccacagaa agctccaag aagcggaag ctcagcatc 
aacaactgc tcaaaactc gatcaaatc tcgagtcag 
atttgcaca ataaagtca attcgttgt ttattgatc 
gagaaaaat gcatgggga tgagaaggt cattcccta 
tcactgcca ccatcaaat actaacaca ttcagtcca 
aaaataaat cgtgc

    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