Status
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Gene information
General information
TC009440 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_007422.5: 1194906..1197714
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
    		TC009440
    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
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_01553

    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: 30.0% (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

    adult lethality - Number of animals showing the phenotype: 1 (9 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 leg musculature partially randomthinner - Penetrance (percentage of animals/eggs on slide): less than 30%

    leg musculature sometimes randomnot present - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    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: 50.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 50.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 5 (11 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC009440 RA
      MILLLAFSL SIFAFSEAS KWENVTIAV VEYKPILDS 
SLNEPEIVA KNAQKYIEI ITNVAKDRN LDLIVFPEE 
TLYVHRETA VTIKLDNPC DSDTYPQFL RNLSCAARS 
SHTYLALNL VDKVKCDQS QTNSSKNCK NSGFFYYNT 
DVVFDRNGT IVNRYHKYN LFGEREMDK PETAEEIVI 
ETDFGLKLG IFTCFDILF KAPAQELLK DGIDGAIYP 
SMWYSELPF LTAMQTQEM WASRHNTTL LAAGANSPL 
VGSGGSGVY RGAQGLVVG GIVAEGGTQ VFVYQGDKS 
VSETQDVDE LAKKMDAFN LQIDNSLEN YRWEVVNTS 
QRNYYNVLC AGDDDNTVC CHYSLTMSM DAIKPEMKH 
YTYILVAYA GIRSYTGVY NGGIEVCGV IACLNSSIS 
SCGQRFSNY DEIQWPLTF ESIAVSAKF VKSENRTQF 
PNSLLSSIR PIDSSETYW VEKEVEVNG TVFEEKQFA 
TNVDQKRLL TFAILGRNF DLDSPADSD DDDDSNHSS 
GNLSAAWIL LCCSLLILC KIK
    CDS sequence
    • >TC009440 RA
      atgattctt ctccttgcc ttttctcta tcgatattt 
gccttttcg gaggcgtca aaatgggag aacgtgacc 
attgcagtg gtggaatac aagccgatc ctcgacagc 
tcgttaaat gagcccgaa atagtggcc aaaaacgcg 
caaaaatac atcgagatt ataacaaat gtggcaaaa 
gacagaaat ttagaccta attgtgttt cccgaagag 
acgctctat gtccatcgc gaaacagca gttaccatc 
aaattagac aatccgtgt gattctgac acttatccc 
caatttctg aggaacctt tcttgcgca gctcggtca 
tcacacact tacctggcc ctaaacttg gtcgataaa 
gtaaaatgc gatcaatca caaactaat tcaagcaag 
aattgtaaa aattctggc tttttctac tataatact 
gacgttgtt tttgaccgg aacggcact attgttaat 
cgttaccac aaatataat ctttttggg gaacgggaa 
atggacaag cctgagacg gccgaagaa atcgtgatt 
gaaaccgat ttcgggctc aaacttggc attttcacc 
tgtttcgat attttgttt aaagcacca gcccaggag 
ttgctcaag gatgggatc gatggggcg atttacccc 
agcatgtgg tattcggag ctacccttc ttaactgct 
atgcagact caggaaatg tgggcaagt cgccacaac 
accactctg ttggctgcc ggtgccaac agccctctt 
gttggaagt ggaggaagt ggggtttac cgtggagct 
caaggttta gtggtgggt ggaattgtg gcagagggt 
ggtactcaa gttttcgtg taccaaggt gataaaagc 
gtttcggaa acgcaagac gtggacgaa ttggccaaa 
aaaatggac gcgtttaac ttacaaata gataacagt 
ttagaaaat tacagatgg gaggtggtg aacacctcg 
caacggaac tactacaac gttctttgt gcgggtgat 
gacgacaat acagtttgt tgccactac tccctcaca 
atgtccatg gacgcaatt aaaccagaa atgaaacat 
tacacttat attttagta gcgtatgct gggattcgt 
tcgtataca ggagtttac aatggtggt atcgaagtt 
tgcggtgtt atcgcttgt ttgaactcg tctatatcg 
tcctgtggt caaagattt tcgaattat gacgaaatt 
caatggcct ttgacgttt gaaagtatc gcagttagt 
gcgaaattt gtaaaaagt gagaatagg acgcagttt 
cccaactca cttttgagt tccattcga ccgattgat 
tcaagtgag acgtactgg gttgaaaag gaagtggaa 
gtgaatgga actgttttt gaggagaag caatttgca 
acaaatgtg gatcagaaa aggctgttg acgtttgca 
attcttgga aggaatttt gatttggat tcacctgct 
gatagtgac gatgacgat gattctaat cactcaagt 
gggaactta tcagcggcg tggattcta ttgtgttgc 
tcgttatta attttatgt aaaataaaa taa
    mRNA sequence
    • >TC009440 RA
      catgtcgca tcgcccgcc aactgtttt aatccccta 
ccgagaacc accgccgcc ctgccgcca caccacgcc 
gcccccacc gccaccaaa gcgacttct ctgattaaa 
ctttacaaa atggacgct ggcctaaac ccaactatg 
actaaacac taatcacta tctaatcac tcaatcatc 
aactgaagc acctactta atacaaaca cttttgaaa 
aatcaatca cagtcgtaa tgattcttc tccttgcct 
tttctctat cgatatttg ccttttcgg aggcgtcaa 
aatgggaga acgtgacca ttgcagtgg tggaataca 
agccgatcc tcgacagct cgttaaatg agcccgaaa 
tagtggcca aaaacgcgc aaaaataca tcgagatta 
taacaaatg tggcaaaag acagaaatt tagacctaa 
ttgtgtttc ccgaagaga cgctctatg tccatcgcg 
aaacagcag ttaccatca aattagaca atccgtgtg 
attctgaca cttatcccc aatttctga ggaaccttt 
cttgcgcag ctcggtcat cacacactt acctggccc 
taaacttgg tcgataaag taaaatgcg atcaatcac 
aaactaatt caagcaaga attgtaaaa attctggct 
ttttctact ataatactg acgttgttt ttgaccgga 
acggcacta ttgttaatc gttaccaca aatataatc 
tttttgggg aacgggaaa tggacaagc ctgagacgg 
ccgaagaaa tcgtgattg aaaccgatt tcgggctca 
aacttggca ttttcacct gtttcgata ttttgttta 
aagcaccag cccaggagt tgctcaagg atgggatcg 
atggggcga tttacccca gcatgtggt attcggagc 
tacccttct taactgcta tgcagactc aggaaatgt 
gggcaagtc gccacaaca ccactctgt tggctgccg 
gtgccaaca gccctcttg ttggaagtg gaggaagtg 
gggtttacc gtggagctc aaggtttag tggtgggtg 
gaattgtgg cagagggtg gtactcaag ttttcgtgt 
accaaggtg ataaaagcg tttcggaaa cgcaagacg 
tggacgaat tggccaaaa aaatggacg cgtttaact 
tacaaatag ataacagtt tagaaaatt acagatggg 
aggtggtga acacctcgc aacggaact actacaacg 
ttctttgtg cgggtgatg acgacaata cagtttgtt 
gccactact ccctcacaa tgtccatgg acgcaatta 
aaccagaaa tgaaacatt acacttata ttttagtag 
cgtatgctg ggattcgtt cgtatacag gagtttaca 
atggtggta tcgaagttt gcggtgtta tcgcttgtt 
tgaactcgt ctatatcgt cctgtggtc aaagatttt 
cgaattatg acgaaattc aatggcctt tgacgtttg 
aaagtatcg cagttagtg cgaaatttg taaaaagtg 
agaatagga cgcagtttc ccaactcac ttttgagtt 
ccattcgac cgattgatt caagtgaga cgtactggg 
ttgaaaagg aagtggaag tgaatggaa ctgtttttg 
aggagaagc aatttgcaa caaatgtgg atcagaaaa 
ggctgttga cgtttgcaa ttcttggaa ggaattttg 
atttggatt cacctgctg atagtgacg atgacgatg 
attctaatc actcaagtg ggaacttat cagcggcgt 
ggattctat tgtgttgct cgttattaa ttttatgta 
aaataaaat aaaatactt gagacgaga ttgttgtgt 
taattgaat tcgattaat taaaaaata aaacactgc 
ttcaaca

    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