Status
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Gene information
General information
TC008472 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_007419.2: 11127197..11133697
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
    		TC008472
    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_02778

    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: -1.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: -1.0% (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC008472 RA
      MVADTDHPA TTVNDTTEA DITEPSHKS IFDVVKSGE 
LSEIEELVD NLGTQILRE RDEWGYTPA HWAALDGSV 
EIMRYLVDR GAPIDLPCL GTQGPRPIH WACRKGHAA 
VVQVLLQAG VGVNAADFK GLTPLMTAC MFGRTATAA 
FLLGMGALN HLVDINGDT AMHWAAYKG HADLIRLLV 
YSGANLQKP DHFGSTPLH LACLSGSVT CVKLLCEKS 
NIDLEPLDK NDKTPLMLA QSHRHSDIV QVLESEKKR 
RSSWFPPVN EVWGLLFGK AGNSKAPLV FFMCSVLLW 
GYPMYVIRC IPITWNILR GSHYCFIYW NIVMWICWI 
TANRKNPGY IPVNTDSYH RAIKQIPYY DKWKKRYAV 
LNRLCHTCR CLRPLRAKH CRICNRCIS YFDHHCPFI 
YNCVGLRNR TWFFLFVMS VAINCSFTI YFATYCIAI 
EGFGILYIL GLFEAFVFS GLGWILTCT SILHACMNL 
TTNEMFNYK RYPYLRDKR GRYFNPFSR GPILNLIEF 
FFCTPEEYD DDYGYDYI
    CDS sequence
    • >TC008472 RA
      atggtcgca gacaccgac catcctgcc accaccgtc 
aacgacacc accgaagcc gacatcacc gaaccctcg 
cacaaatcc atcttcgac gttgtcaaa tcgggcgaa 
ctctccgaa atcgaagaa ctcgtcgat aacctcggc 
acacaaatc ctgcgagag cgcgatgaa tggggctat 
actccggcc cattgggcc gctctggac ggcagtgtg 
gagatcatg cggtatttg gtggacagg ggggccccc 
attgacctg ccatgtctc gggacgcag ggccccagg 
cccatacat tgggcctgt cgcaagggg catgcagcc 
gtggtccag gttttgctg caagcaggg gttggggtg 
aatgcggct gatttcaaa gggttgact ccgttgatg 
acggcttgc atgtttggg aggacggca acagcggcg 
tttttactg ggaatgggg gctttgaat catttggtt 
gatatcaac ggggacaca gcaatgcat tgggcggct 
tataaagga catgcggat ttgatcagg ctgttggtt 
tactcgggg gctaatttg caaaaaccg gatcatttt 
gggtccact cctctgcac ttggcgtgt ctttcgggg 
agtgtcacc tgtgtcaaa cttctctgc gagaagagt 
aatattgac ttggaacct ttggataag aacgacaaa 
acgccctta atgttagcc caaagccac cgccacagc 
gacattgtc caagtcctc gaatcggag aagaaacgc 
cgttcaagc tggtttcct ccagttaac gaagtttgg 
ggtcttttg ttcggaaaa gcagggaat tcgaaagcg 
ccactagtg ttcttcatg tgttcagtc ttactctgg 
gggtacccg atgtacgta attcggtgt atccccatc 
acttggaac attctacga ggctctcac tattgtttc 
atctattgg aacattgtc atgtggata tgttggata 
accgcaaac cggaaaaac ccaggctat atcccggtt 
aacaccgat tcctaccat cgagcaatc aaacaaatc 
ccttactac gacaaatgg aagaagaga tatgcggtt 
ttgaaccga ctctgtcac acttgtcgg tgtttgagg 
cctttaaga gccaaacac tgtcgaatt tgcaaccgg 
tgtatttct tactttgat catcattgt cccttcatt 
tacaactgt gtgggttta aggaatcga acttggttc 
ttccttttc gttatgagt gttgctatt aattgctcc 
tttacgatt tatttcgct acttattgc atagccatt 
gaagggttc ggcattttg tacattttg ggacttttt 
gaagcgttc gttttctca ggattaggt tggattctg 
acgtgtact tcgatttta cacgcttgc atgaacttg 
accacaaac gaaatgttc aattacaaa cgttatcct 
tatttgagg gacaagagg gggcgttat tttaatcca 
ttctcaaga ggacctatc ttaaatcta atcgagttc 
tttttttgt acaccggaa gaatatgac gacgattac 
ggctacgat tatatatga
    mRNA sequence
    • >TC008472 RA
      agcatattt ttccatttg ttctgagtt tttatattt 
taaatttta ataacagtt gtgcccact ttaactgag 
tcgaaattt ttgattttg agccaccct tgcgcgcgc 
tccttaaaa atcaatacc caagtgaaa caacttggc 
acgctacgc aaatatctg cattaaatc aatcataaa 
taatttaca ccggagtgg taaacagtc gtcagaacg 
ctttgcaaa gtgtttcca agtccgggc actgcccga 
agcgtgtgg gctttgccc caaacctcc tgcaacatg 
gtcgcagac accgaccat cctgccacc accgtcaac 
gacaccacc gaagccgac atcaccgaa ccctcgcac 
aaatccatc ttcgacgtt gtcaaatcg ggcgaactc 
tccgaaatc gaagaactc gtcgataac ctcggcaca 
caaatcctg cgagagcgc gatgaatgg ggctatact 
ccggcccat tgggccgct ctggacggc agtgtggag 
atcatgcgg tatttggtg gacaggggg gcccccatt 
gacctgcca tgtctcggg acgcagggc cccaggccc 
atacattgg gcctgtcgc aaggggcat gcagccgtg 
gtccaggtt ttgctgcaa gcaggggtt ggggtgaat 
gcggctgat ttcaaaggg ttgactccg ttgatgacg 
gcttgcatg tttgggagg acggcaaca gcggcgttt 
ttactggga atgggggct ttgaatcat ttggttgat 
atcaacggg gacacagca atgcattgg gcggcttat 
aaaggacat gcggatttg atcaggctg ttggtttac 
tcgggggct aatttgcaa aaaccggat cattttggg 
tccactcct ctgcacttg gcgtgtctt tcggggagt 
gtcacctgt gtcaaactt ctctgcgag aagagtaat 
attgacttg gaacctttg gataagaac gacaaaacg 
cccttaatg ttagcccaa agccaccgc cacagcgac 
attgtccaa gtcctcgaa tcggagaag aaacgccgt 
tcaagctgg tttcctcca gttaacgaa gtttggggt 
cttttgttc ggaaaagca gggaattcg aaagcgcca 
ctagtgttc ttcatgtgt tcagtctta ctctggggg 
tacccgatg tacgtaatt cggtgtatc cccatcact 
tggaacatt ctacgaggc tctcactat tgtttcatc 
tattggaac attgtcatg tggatatgt tggataacc 
gcaaaccgg aaaaaccca ggctatatc ccggttaac 
accgattcc taccatcga gcaatcaaa caaatccct 
tactacgac aaatggaag aagagatat gcggttttg 
aaccgactc tgtcacact tgtcggtgt ttgaggcct 
ttaagagcc aaacactgt cgaatttgc aaccggtgt 
atttcttac tttgatcat cattgtccc ttcatttac 
aactgtgtg ggtttaagg aatcgaact tggttcttc 
cttttcgtt atgagtgtt gctattaat tgctccttt 
acgatttat ttcgctact tattgcata gccattgaa 
gggttcggc attttgtac attttggga ctttttgaa 
gcgttcgtt ttctcagga ttaggttgg attctgacg 
tgtacttcg attttacac gcttgcatg aacttgacc 
acaaacgaa atgttcaat tacaaacgt tatccttat 
ttgagggac aagaggggg cgttatttt aatccattc 
tcaagagga cctatctta aatctaatc gagttcttt 
ttttgtaca ccggaagaa tatgacgac gattacggc 
tacgattat atatgatat acaagaaat aatagttgt 
aagaaaaat gtcaccaca aaatagcta ttttccact 
gtattatag acattattt gctgactac acttattca 
agtggcttg gtttttgca atgcaaaat cttgtattt 
attatatga aataaattt tatcagaaa ac

    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