Status
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Gene information
General information
TC008380 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: 9430900..9435654
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
    		TC008380
    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
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    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_07238

    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: 40.0% (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: 2 (9 dpi)
    Days post injection

    adult nutritional state potentially bad (cachectic) - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection

    Fertility
    ovary without detectable defects - Number of animals showing the phenotype: 3
    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: < 50 larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): more than 80%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 80%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     cuticle remnants with some identifiable segments - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    head size decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    posterior terminus not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen potentially partiallyeverted (inside-out) - Penetrance (percentage of animals/eggs on slide): less than 30%

    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
    • >TC008380 RA
      MSDETSNLL KLVFPNGFP SAWEYSTAF SDYISRLGT 
YKVEDLSRE PARLNEEKA SIHEQTQEL AVTNYKTFI 
ETAQCSRDL FTQFNTIEE KLDNLLEDI PEFEKKCQL 
FGEETSGIN NLRRLNSLT LTRNAQLLE ILELPQLMN 
SFINDGLYE DALELASYV RKLHNKHPD VPIFKSIVA 
DVDKAWLLM LHQLLTQLK QELTLPKCL QIVSHLRRM 
QVFTESELR LKFLQTRNT WLQSCLNAI PKDNANYHL 
NKTIEVTRV NLFNIITQY RAIFNDDEH SPLASIKSQ 
QVNQNVIFF TWIRDKISD FLATLEHDL NQGVSSIDT 
ILAQCMYFG VSFSKVGCD FRSSLIPIF TNKIVTDFE 
NAINDAIKR FELNMERFT LINKNHSNV PWKNKNEDP 
LQPPDSLLE FYPIAEFLN NVLTALNEL KLCAPIAAA 
KAVVDSLQH ALLVIAKSI LVLHGQEQQ AFTANAKDA 
FTRLCMCFA DDLVPYIQK CVHIIFPPS NIATVLGVN 
VQVLQNEGL TFLNKDVIV DPIRHLLPV KITPVLDLV 
ESETKIEAS DNRNELTSE
    CDS sequence
    • >TC008380 RA
      atgagtgat gagacgagt aatttatta aaactagtc 
ttccccaac ggatttccc agtgcatgg gaatacagc 
accgcattc agcgactac atttcccga ttaggcaca 
tacaaagtt gaggatttg tcacgagaa cccgctcgt 
ttgaacgag gaaaaggcc tcaattcat gaacagacc 
caggaattg gctgtcact aactataaa acgttcatt 
gaaacggca caatgttcg cgcgatttg ttcactcaa 
ttcaataca attgaggag aagttggat aatcttctc 
gaagatata cccgaattt gaaaagaag tgtcaatta 
tttggggaa gaaacaagc gggattaac aatttgcga 
cggttgaat tcgttgact ctgacacga aatgcacag 
ttgctcgaa attttagaa cttccacaa ttaatgaac 
tcgttcatt aatgacggt ttgtatgag gacgccttg 
gaattggcc agttacgtg cggaaattg cataataaa 
catccggat gtgcctata tttaaaagt attgttgct 
gatgttgat aaggcgtgg ttgttgatg ttacatcaa 
ttacttacg caattaaaa caagaattg actttaccg 
aaatgttta caaattgtt agtcatttg agacgtatg 
caagttttt accgaatct gagttgaga ttaaagttt 
ctgcaaacg agaaataca tggcttcag tcttgcttg 
aatgctatt cctaaggac aatgccaat tatcacttg 
aacaagacg attgaagtg accagagtc aacctgttc 
aacataatc acccagtat agagcaatt ttcaatgat 
gatgagcac agccctcta gcttcaatc aagagtcag 
caagtcaac caaaacgta attttcttc acttggatc 
cgagacaag atttccgat tttttggcg acacttgag 
cacgactta aaccaagga gtgtcatca attgataca 
attttggcc cagtgtatg tacttcggg gtttcgttc 
agtaaagtc gggtgtgat tttcggtcg tctttgatc 
ccgattttt acaaataaa atcgtcaca gatttcgag 
aatgcaata aatgacgct attaaacga tttgaattg 
aatatggaa cggttcact ctcattaac aaaaatcac 
tcgaacgtt ccttggaaa aacaagaat gaagacccg 
ctgcaacct cctgatagt ttgttggag ttctaccca 
attgctgaa tttttgaat aatgttcta acagcactg 
aacgaactg aaattatgc gctcctatc gcggctgcg 
aaagctgtg gttgattca ttacaacat gcattgtta 
gttattgcc aaatcgatt ctggtgtta catgggcaa 
gagcaacaa gctttcaca gcgaatgcg aaagatgct 
tttaccaga ttgtgcatg tgttttgct gatgattta 
gttccctat attcagaaa tgtgtgcat attatcttc 
cctccgagc aatattgcg actgtgtta ggggtaaac 
gtgcaagtg ttgcaaaac gaagggctc acctttttg 
aataaggat gttattgtc gatccaatt agacacttg 
ctccctgtt aaaatcacc cctgtgtta gacttggtt 
gaaagtgaa acaaaaatc gaagctagt gataacaga 
aatgaatta acatcggag taa
    mRNA sequence
    • >TC008380 RA
      cgcgtcctg tgtttacca agtgacatg tcaacaatt 
cataataag tgcaaaaat gagtgatga gacgagtaa 
tttattaaa actagtctt ccccaacgg atttcccag 
tgcatggga atacagcac cgcattcag cgactacat 
ttcccgatt aggcacata caaagttga ggatttgtc 
acgagaacc cgctcgttt gaacgagga aaaggcctc 
aattcatga acagaccca ggaattggc tgtcactaa 
ctataaaac gttcattga aacggcaca atgttcgcg 
cgatttgtt cactcaatt caatacaat tgaggagaa 
gttggataa tcttctcga agatatacc cgaatttga 
aaagaagtg tcaattatt tggggaaga aacaagcgg 
gattaacaa tttgcgacg gttgaattc gttgactct 
gacacgaaa tgcacagtt gctcgaaat tttagaact 
tccacaatt aatgaactc gttcattaa tgacggttt 
gtatgagga cgccttgga attggccag ttacgtgcg 
gaaattgca taataaaca tccggatgt gcctatatt 
taaaagtat tgttgctga tgttgataa ggcgtggtt 
gttgatgtt acatcaatt acttacgca attaaaaca 
agaattgac tttaccgaa atgtttaca aattgttag 
tcatttgag acgtatgca agtttttac cgaatctga 
gttgagatt aaagtttct gcaaacgag aaatacatg 
gcttcagtc ttgcttgaa tgctattcc taaggacaa 
tgccaatta tcacttgaa caagacgat tgaagtgac 
cagagtcaa cctgttcaa cataatcac ccagtatag 
agcaatttt caatgatga tgagcacag ccctctagc 
ttcaatcaa gagtcagca agtcaacca aaacgtaat 
tttcttcac ttggatccg agacaagat ttccgattt 
tttggcgac acttgagca cgacttaaa ccaaggagt 
gtcatcaat tgatacaat tttggccca gtgtatgta 
cttcggggt ttcgttcag taaagtcgg gtgtgattt 
tcggtcgtc tttgatccc gatttttac aaataaaat 
cgtcacaga tttcgagaa tgcaataaa tgacgctat 
taaacgatt tgaattgaa tatggaacg gttcactct 
cattaacaa aaatcactc gaacgttcc ttggaaaaa 
caagaatga agacccgct gcaacctcc tgatagttt 
gttggagtt ctacccaat tgctgaatt tttgaataa 
tgttctaac agcactgaa cgaactgaa attatgcgc 
tcctatcgc ggctgcgaa agctgtggt tgattcatt 
acaacatgc attgttagt tattgccaa atcgattct 
ggtgttaca tgggcaaga gcaacaagc tttcacagc 
gaatgcgaa agatgcttt taccagatt gtgcatgtg 
ttttgctga tgatttagt tccctatat tcagaaatg 
tgtgcatat tatcttccc tccgagcaa tattgcgac 
tgtgttagg ggtaaacgt gcaagtgtt gcaaaacga 
agggctcac ctttttgaa taaggatgt tattgtcga 
tccaattag acacttgct ccctgttaa aatcacccc 
tgtgttaga cttggttga aagtgaaac aaaaatcga 
agctagtga taacagaaa tgaattaac atcggagta 
ataaaaata ttttttgta aaagttttg tcttttatt 
tatttcctt ccgtttgta cttccacat ttttgaaag 
ccttcgaac gtcggttag cgctgctgc gttcgcgtt 
ctttcagct ccaaacaca attcgtaaa ttccatcat 
cgtccaaaa gatcgcaac tatcaagca gtgtcagtt 
ttgtcgtcg aactgaaat gtaagcgta gctttcgtg 
gcaaatcta cgactttca cactgttct cttgaatat 
cgtggaagg gaatgtact caagcattg agtaaaaaa 
gtttatctt cctggtctg gggcgattg agacttcag 
tttgacact tgctttcgg agataacgt gcgctttta 
ttttattac tttcgagaa tgtggggat aaacgcgga 
tcattgttt gcacctctt tgtccatgg ttattttct 
cgggcggaa ggcggtgac gggaacccc acatttctc 
acaaaaatt ttgatttaa aatcaaaat ttttgacgt 
tttgggaaa aaaactaaa tacgcaagc gtaga

    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