Status
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Gene information
General information
TC008895 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: 11423221..11424976
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
    		TC008895
    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
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    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_01433

    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: 10.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 1 (3 dpi)
    Days post injection

    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 50
    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: 10.0% (includes death as larva, prepupa, pupa, adult)

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

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC008895 RA
      MAEQTLTQF TDKLLSEKI FSCAVCEKL LTLPIVLIE 
DVGNVCPNC CEDRDWKGL HNVKLEMIL KELQIPCKF 
QSTGCKKRV HFSALNEHE SNCKFHEKP CLLSHTGCE 
WTGVQSDFP SHFNECHSE HVIANPQSF FVIEININE 
ETNVTKLLK GKQECIIIV KKDREDLLH TICDVKNTE 
CNYDCTIKH FGQSSNCVE TKCKVSSFS SMHTTRINL 
AALKQMTEA ADVVTLQIK MSTQNEAAE FDEKVLQYF 
ECPVCKMLM KPPIYQCKF GHSFCSNCR PRLENCPNC 
RALFGTTRN YALEGLTAG ISYACMYHH LGCEEMLPA 
HDSGKHEAI CPFKPYPCP LDDCSFKGT HSNIGKHLD 
ENHKDKVIA ADFYKTTVE FRLEQMIDF YNFHQKYYM 
VFDENIFRL SFKRNSDYS FWAVEVLRK KEEDAVFIY 
EIGIIDMRK PDRRLIRCD VCFTDTNSE ELFKKCILF 
PNNILASYA CNGVFTYYC QIRKRQ
    CDS sequence
    • >TC008895 RA
      atggcagaa caaacccta actcagttc acagacaag 
ctactttcg gaaaaaata ttcagttgt gctgtttgc 
gagaaactg cttacgctc ccgatagtg ctgatagaa 
gatgtgggg aacgtttgc cccaattgt tgtgaggac 
agggactgg aaagggctg cacaatgtc aagctggag 
atgatttta aaggagctt caaatcccg tgcaagttt 
cagtcaacg ggttgcaag aaaagggtt catttcagt 
gctttaaac gagcacgaa agtaactgt aagtttcat 
gagaaacct tgtttgttg tcacacacc ggttgtgaa 
tggacagga gtccagagc gattttcct agtcacttt 
aacgaatgc cactctgag catgtgata gcaaaccct 
cagagcttc tttgtcatt gagatcaac ataaacgag 
gaaacgaac gtaacgaag ctgctcaaa ggcaagcaa 
gagtgcata ataattgtg aaaaaagat cgcgaagat 
ttgttgcac acaatctgt gatgtaaaa aacactgaa 
tgtaattat gattgtact atcaagcat ttcggacaa 
agtagcaac tgcgttgaa acaaagtgc aaagtttca 
tcattcagt agcatgcac accacaagg attaactta 
gcggctttg aaacagatg accgaggcc gctgatgtg 
gtcacactg caaataaaa atgtccacg cagaacgaa 
gccgcggaa tttgatgaa aaagtcctc caatatttc 
gaatgcccc gtttgcaaa atgctgatg aagccgcca 
atttatcag tgcaagttc ggccacagt ttttgtagc 
aactgtagg ccaagattg gaaaactgt ccgaattgt 
cgcgccctg ttcggaacc acgagaaat tacgccttg 
gaaggcttg actgcagga atcagttat gcgtgcatg 
taccaccat ctggggtgc gaggagatg ctgccagct 
catgattcg ggcaaacac gaggcgatt tgtccgttt 
aaaccgtac ccctgtcct ttggacgac tgttcattt 
aagggaacc cactcgaat attggaaaa cacctggat 
gagaatcac aaggataaa gtcattgcg gccgatttc 
tacaaaact accgtggag tttcgtttg gagcaaatg 
atcgacttt tacaacttc caccagaag tattacatg 
gtgtttgat gaaaatata tttagactg agtttcaag 
cgcaattca gattatagt ttctgggcg gttgaagtg 
ttgcgtaaa aaggaagaa gacgctgtt tttatttac 
gaaattgga atcattgat atgagaaaa cctgataga 
agactgata agatgcgat gtgtgcttt actgatact 
aattctgaa gaactgttt aaaaagtgt attttgttt 
ccgaataat atcctggct tcttatgct tgtaacggg 
gtgtttaca tactattgt caaatacgc aaacggcaa 
taa
    mRNA sequence
    • >TC008895 RA
      cgttcaaaa aatttttgt ttcgaaatt ggggttatc 
tgacctgtc acttcttaa cttatattg tgcaaaaac 
agcatgata gccagttca aatgtggtc atttagtgt 
ggagtcgca gcagggttt tggatatgg cagaacaaa 
ccctaactc agttcacag acaagctac tttcggaaa 
aaatattca gttgtgctg tttgcgaga aactgctta 
cgctcccga tagtgctga tagaagatg tggggaacg 
tttgcccca attgttgtg aggacaggg actggaaag 
ggctgcaca atgtcaagc tggagatga ttttaaagg 
agcttcaaa tcccgtgca agtttcagt caacgggtt 
gcaagaaaa gggttcatt tcagtgctt taaacgagc 
acgaaagta actgtaagt ttcatgaga aaccttgtt 
tgttgtcac acaccggtt gtgaatgga caggagtcc 
agagcgatt ttcctagtc actttaacg aatgccact 
ctgagcatg tgatagcaa accctcaga gcttctttg 
tcattgaga tcaacataa acgaggaaa cgaacgtaa 
cgaagctgc tcaaaggca agcaagagt gcataataa 
ttgtgaaaa aagatcgcg aagatttgt tgcacacaa 
tctgtgatg taaaaaaca ctgaatgta attatgatt 
gtactatca agcatttcg gacaaagta gcaactgcg 
ttgaaacaa agtgcaaag tttcatcat tcagtagca 
tgcacacca caaggatta acttagcgg ctttgaaac 
agatgaccg aggccgctg atgtggtca cactgcaaa 
taaaaatgt ccacgcaga acgaagccg cggaatttg 
atgaaaaag tcctccaat atttcgaat gccccgttt 
gcaaaatgc tgatgaagc cgccaattt atcagtgca 
agttcggcc acagttttt gtagcaact gtaggccaa 
gattggaaa actgtccga attgtcgcg ccctgttcg 
gaaccacga gaaattacg ccttggaag gcttgactg 
caggaatca gttatgcgt gcatgtacc accatctgg 
ggtgcgagg agatgctgc cagctcatg attcgggca 
aacacgagg cgatttgtc cgtttaaac cgtacccct 
gtcctttgg acgactgtt catttaagg gaacccact 
cgaatattg gaaaacacc tggatgaga atcacaagg 
ataaagtca ttgcggccg atttctaca aaactaccg 
tggagtttc gtttggagc aaatgatcg acttttaca 
acttccacc agaagtatt acatggtgt ttgatgaaa 
atatattta gactgagtt tcaagcgca attcagatt 
atagtttct gggcggttg aagtgttgc gtaaaaagg 
aagaagacg ctgttttta tttacgaaa ttggaatca 
ttgatatga gaaaacctg atagaagac tgataagat 
gcgatgtgt gctttactg atactaatt ctgaagaac 
tgtttaaaa agtgtattt tgtttccga ataatatcc 
tggcttctt atgcttgta acggggtgt ttacatact 
attgtcaaa tacgcaaac ggcaataaa ttgcaaagt 
acaaaaccg agttttctt taacaaaaa ataaatgtg 
gagataaaa c

    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