Status
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Gene information
General information
TC013909 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: 432978..440282
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
    		TC013909
    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
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_05521

    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: 70.0% (includes death as pupa, adult)

    pupa eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 2 (3 dpi)
    Days post injection

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 2 (3 dpi)
    Days post injection

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

    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: 50.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality early (L5/6) - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection

    Pupal morphology
    antenna orientation irregular - Number of animals showing the phenotype: 8

    eyes not present - Number of animals showing the phenotype: 8

    Adult morphology
    ommatidia number decreased - Number of animals showing the phenotype: 5


    flagellomeres partiallynot present - Number of animals showing the phenotype: 5


    flagellomeres number decreased - Number of animals showing the phenotype: 5

    Fertility
    fertility after larval injection decreased (no living offspring) -
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC013909 RA
      MSSPNEYHM REVVFTDHS RFQSEEEAE TGSDEEQPI 
MFHYHQVEK SAIKRRGHL PKDAVKILK NWLYEHRFN 
AYPTEVEKN ILSQETNLT VLQISNWFI NARRRYLPE 
MMRREGYDS MHYTITRRR RVRRGVNGE VYHKGSKQM 
RIDGGSEDS QSDYEENTN GYEEVTSER KFNPWQADI 
HYGLTVNPA DRGTEALEV GHTEEVEST NDVTSVASY 
PSSLVMVKT TSGKNVILK VVPQQSDSD APKTFLLKT 
TKLIKQQQQ SASPCEIIP KQEVTVDEE VEEDDSKRD 
GTKTFDEEV FVNEVTLED NVNEVTIAG EVTVEGASS 
NEEDEEQQE QVVMLE
    CDS sequence
    • >TC013909 RA
      atgtcgagt ccgaacgag taccacatg cgggaagtg 
gtcttcacg gaccactcc aggttccag tcggaagag 
gaagccgaa acgggctca gacgaggag cagcccatc 
atgtttcac taccaccaa gtggagaaa tccgctata 
aaacggcgg ggccacttg cccaaagac gccgtcaaa 
atcctcaaa aactggctg tatgagcac aggttcaac 
gcctatccg accgaagtg gagaaaaac atactgtct 
caagaaacc aacttgaca gtgctgcag atcagtaat 
tggtttatc aacgcacga agacgctat ttgcccgaa 
atgatgcga agggagggc tacgattcc atgcactac 
acgatcaca aggcgtagg agagtaaga cgtggcgtg 
aacggggag gtttatcac aaggggagc aagcagatg 
aggatcgat gggggcagt gaagacagt cagtcagac 
tacgaggaa aacacaaac ggttatgag gaggtcacc 
agtgagagg aaattcaat ccctggcag gcggatatt 
cactatgga cttactgta aatccagct gatagagga 
accgaggct ttggaagtt ggccacact gaagaagtt 
gagagcaca aacgacgta accagtgtt gcttcatac 
ccttcgagt ttggtgatg gtgaaaact acatcgggt 
aaaaacgta atattaaaa gtggttccc caacagagc 
gactctgat gcacctaaa acttttctc ttgaaaact 
acaaagctt atcaagcaa caacaacaa tcggcttcg 
ccgtgcgaa atcatccca aaacaagaa gtaactgtt 
gatgaagaa gttgaagaa gacgatagt aaacgcgat 
ggtactaaa acttttgat gaagaagtg tttgtaaat 
gaggtgacc ttggaagat aatgtaaat gaggtaaca 
atagcaggt gaggtaact gtggaaggg gcgtcgagc 
aatgaagaa gacgaagaa cagcaggag caagttgtc 
atgctcgag taa
    mRNA sequence
    • >TC013909 RA
      taacagtaa tggcgtcgg tagctatac cacggtagg 
caaacaaaa gcatcctca aaactccgc agtccctag 
atgtgatgg tgaattcgg catcatatc catttccga 
gttgtaata aaatccagt aaaaagtgt aggtaattg 
gtgcaaaac ccccccaat tcgttattt tcgtgcaaa 
gtgtttgaa aaatcttga caaataccc aagctttcg 
acctaacct aattgtatt gacatttgt gtgaaattt 
gttttcaaa catcatcag cgtgtaatc gtttgccgt 
gttttgaat aaagccaat aaccaaaat cgaaattcg 
tttgaatgt gtgagagtc tcctttgtt ctagacgtt 
gtcaaacgg ttcgattaa tgcatgagc gattgtgag 
taggaaaat gtcgagtcc gaacgagta ccacatgcg 
ggaagtggt cttcacgga ccactccag gttccagtc 
ggaagagga agccgaaac gggctcaga cgaggagca 
gcccatcat gtttcacta ccaccaagt ggagaaatc 
cgctataaa acggcgggg ccacttgcc caaagacgc 
cgtcaaaat cctcaaaaa ctggctgta tgagcacag 
gttcaacgc ctatccgac cgaagtgga gaaaaacat 
actgtctca agaaaccaa cttgacagt gctgcagat 
cagtaattg gtttatcaa cgcacgaag acgctattt 
gcccgaaat gatgcgaag ggagggcta cgattccat 
gcactacac gatcacaag gcgtaggag agtaagacg 
tggcgtgaa cggggaggt ttatcacaa ggggagcaa 
gcagatgag gatcgatgg gggcagtga agacagtca 
gtcagacta cgaggaaaa cacaaacgg ttatgagga 
ggtcaccag tgagaggaa attcaatcc ctggcaggc 
ggatattca ctatggact tactgtaaa tccagctga 
tagaggaac cgaggcttt ggaagttgg ccacactga 
agaagttga gagcacaaa cgacgtaac cagtgttgc 
ttcataccc ttcgagttt ggtgatggt gaaaactac 
atcgggtaa aaacgtaat attaaaagt ggttcccca 
acagagcga ctctgatgc acctaaaac ttttctctt 
gaaaactac aaagcttat caagcaaca acaacaatc 
ggcttcgcc gtgcgaaat catcccaaa acaagaagt 
aactgttga tgaagaagt tgaagaaga cgatagtaa 
acgcgatgg tactaaaac ttttgatga agaagtgtt 
tgtaaatga ggtgacctt ggaagataa tgtaaatga 
ggtaacaat agcaggtga ggtaactgt ggaaggggc 
gtcgagcaa tgaagaaga cgaagaaca gcaggagca 
agttgtcat gctcgagta ataacacac ttaactaat 
ttatttatt gcaagttga aagtaatct tcttacatg 
ttattgtaa gtttttttt gtacaatgt acaatttct 
tttatagga tttggatgt aattaattg tacccaaaa 
gtcaacata gttaaatag aatattttt tataaaact 
ttatttggt ttctaattt attcatcgc tatcctttt 
aatttgaca tgtgccgta cattcgtca agttgttaa 
caatacgat acaaaatat atctgaaaa aaataaatt 
acgtaaaat attgccgga caaaaccaa tttgtttta 
ctgacaata ttttgtaac aattgtttc gaacgagaa 
caagacact ggcaaaatt agttttcaa tcacagaca 
tgccactag aatctagtt cgccaaata atacaaaaa 
tattacaac tacggagga ctataaatt aggagactg 
aacgatatt caaaatcgc acccaaaag ttacagtat 
ggtagaatt aaaatgagg ttgtttcca gcgttatac 
tacctacgg taccatttt aatgggctt ttgcattca 
taataggct tagaaaaac tgacgacta aaattttcg 
cgagaaata taaaagaaa aaaagtatt aaaacaatt 
gaaattagc tgttcatcc tgaactttt caaaacgtt 
gcaaatacg gttaaaaat aataagaaa attatagag 
gattaaatt ttcgttaca aaaatccgc gagatcata 
tcattattt taaaccttt tggatataa taaatacgg 
tgtcgttga actgttaat gagaaaatt ttattctat 
actacttta ttcctttca cttttttgc atcttcatt 
cgtattcac cttattggc aaattgaaa tcagcttat 
agtttcaac aaaaggaat tgctacagc tataagtag 
tacagcatc ttgaaggca ttaatttga tttttcttt 
tgactagaa tgtattttt tatttaaaa ttttaaatg 
aacttcacg aacgaaaca aggaaacta gagttaaag 
aaaatccaa atgttagaa ttaatcaac ataacggaa 
ttgtcgaaa acaggaacg ttttatttg tacgtcgtt 
tcgaatcct aatatatag tactccgta ataaataca 
acctataca tttaaatac ctgggttag gcaaaacct 
ctaagcggt ttcacagga atagaaaaa taagagact 
ttttacgag gtggttcaa agagacgtc tacgtccaa 
attgtctag tctaacacc ttgttaacc aacattgat 
ttaaaattg cgatcatgc agataatac tcggaggtt 
acgtgcacg aagtcggtc ttaggccat tatgcagtg 
ctctaaagg gatgttttt ttgaccaat tttaaatga 
agcaaaatt tctagtcaa ttttcgaag gtactatat 
tttagtgac tgcagcgac gcttctaca acctcaaat 
atccaaaat tttgagtag acgtaagta ctacagggt 
ggcgcaaaa tcagtccag aatttttac aaatcgtgc 
aaccataaa tatttttag agggtttta tagttacaa 
gttttataa tggtgagta ataaaaaac accacagct 
ttggggtga aaaagaacc aaatcgaag aattttgta 
tttgatata aatttgatt ctcttggct gtttcgttc 
aaatatttt acttcctat agaagattt acatttgta 
tgaactttt aaggtttct gaagtttca gtggcttta 
aatgttttt ttcaaatga ccaaaaagt tagtgtaaa 
attttttcg gacagtgtg gttaaaaaa ttctaaggt 
acatttcaa gaggtacac aaattgtgc aaaaaaatc 
gtttatact ttaattcaa cccacgaag aagtaagag 
tta

    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