Status
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Gene information
General information
TC008685 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: 13973273..13975771
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
    		TC008685
    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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    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_01389

    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 embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg with muscle fluorescence/pattern, but not hatched (pot. late embryonic lethality) - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    embryo/egg with embryonic tissue, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): less than 30%

    larval musculature fluorescence decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    larval musculature shape irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    larval musculature mostly fluorescence not 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): 50% - 80%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     larva cuticle dorsal irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    head capsule mostly not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    vertex triplet irregular - 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%
    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: 40.0% (includes death as larva, prepupa, pupa, adult)

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

    eclosion delayed (still pupa) - Number of animals showing the phenotype: 3 (16 dpi)
    Days post injection

    eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 3 (19 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (41 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC008685 RA
      MAFLRNILA KQSPITNAF TNTIWHRQM SGGNPVECK 
VAVITGGAI GIGVACAKS LLENGARGV MLGDIREKE 
GKELAAELN KTYGKDKAL FMKCDVTKK DEFENLFKC 
TYQRFPSMD IVINNAGLL QDKYWPLEL AVNVNGLVQ 
GTLFGFHYM GKHGKHEKG RGGVIVNMA SIYGLQQAY 
ACPVYNGTK GFVIRFSNA MSHEYYEKM TGVKVLTMC 
PGVTDTNMI DESSTYALD GFGDLGKLV SEGLANLPP 
QPASACGDC LIKMLCSGE NGGIWVIEE SECYKVRLP 
DRQTLRTVS IMFRLLFLK NIRNIASIF LAKRLQWPR 
NTLQKSSLA RGRNEAQPE QPPKPHKEI FFPQLGRDG 
IKDKVALVT GGTDGIGLR CVRELLRTG ARGVMIADT 
NESKGFNRV IEFSKDYGQ SRIAFIQIN PANYVLLKN 
AFISTLNFY EGLDIVINN VRFKEKNWE DQVDENIKG 
IVLSTQLCL EFMGRNNGG KGGILLNIV SEYEENTDS 
CPLHSACQD FVVRFDRSV ATSHFDTTN VKVLTICRA 
SFDTIGCDL TTILTKGTN GCVWMPCTC ASDS
    CDS sequence
    • >TC008685 RA
      atggctttc ctcaggaat attcttgca aaacagagc 
ccaataaca aacgcgttt actaacaca atatggcat 
cgccaaatg tctgggggg aatcctgtc gaatgcaaa 
gttgctgtt ataactggc ggtgctatt ggcattggg 
gttgcttgt gctaagtca cttttggaa aacggtgct 
aggggcgta atgttgggt gatattcga gaaaaagaa 
ggcaaagaa ctcgcggct gaattaaat aagacctac 
ggtaaagat aaagccctt ttcatgaaa tgtgacgtc 
accaaaaag gatgaattt gaaaacttg ttcaaatgc 
acctatcag aggtttcca agtatggat atcgtaatc 
aataacgct ggtctgttg caagacaaa tattggccc 
cttgaacta gccgtgaac gtgaacggc ttggtacaa 
gggacacta tttggtttc cactacatg ggaaaacat 
gggaaacac gaaaagggc agaggtgga gttattgtg 
aacatggcg tccatctat gggctccaa caagcctac 
gcatgtcct gtttacaac ggcactaaa ggatttgta 
attcgattt agcaacgct atgtcccat gaatattac 
gagaaaatg acaggcgtt aaagtcctg acaatgtgt 
cctggggtg actgacacg aacatgatt gacgaatca 
agcacctat gccctggat ggctttgga gacctgggc 
aaacttgtg agcgaagga ctggccaat ctgccaccc 
caaccagct tcagcttgt ggggactgt ttgatcaaa 
atgctgtgc tccggcgaa aatgggggt atttgggtg 
attgaagaa agcgagtgc tacaaagtc cggcttccg 
gaccgccag actctgcgt accgtttcg ataatgttt 
aggttgctg tttttaaaa aacattaga aatatcgcc 
tctattttc ctagccaaa aggctgcaa tggcccaga 
aacaccttg cagaaatcg tcactggca cggggcaga 
aacgaggct cagccggaa cagcccccg aagccgcac 
aaggagata tttttcccg cagttgggg cgcgatggt 
attaaggac aaagtagct ttagtgact gggggcacg 
gacggaatt ggcttgcga tgtgtgaga gaattgcta 
agaaccggg gctaggggg gtaatgatt gcagacaca 
aacgagagc aagggtttc aatcgggtg atagagttt 
tcaaaggac tatggccaa agtaggata gcgttcatt 
cagatcaac ccggctaat tatgttttg cttaaaaat 
gcgtttatt agcacccta aatttctac gagggcttg 
gacattgtg attaacaac gtcaggttc aaggaaaaa 
aattgggag gatcaggtt gatgagaat attaaagga 
atcgtgttg agtacacag ctctgtttg gaatttatg 
ggtcgtaat aatggagga aaaggcggg attttgctg 
aacatagtc tcagaatat gaggaaaac accgactcc 
tgtccactg cacagtgct tgtcaagac tttgttgtc 
cgctttgac cgatcagtt gcaacgtca catttcgac 
accacgaac gtcaaagta ttaacaatt tgcagagcc 
agttttgac acgatcggg tgcgactta accacgata 
ctaacaaaa ggaaccaac ggctgtgtt tggatgcct 
tgcacttgt gcgtcggat tcctaa
    mRNA sequence
    • >TC008685 RA
      tgtttgtgt cgtgcaaaa tggctttcc tcaggaata 
ttcttgcaa aacagagcc caataacaa acgcgttta 
ctaacacaa tatggcatc gccaaatgt ctgggggga 
atcctgtcg aatgcaaag ttgctgtta taactggcg 
gtgctattg gcattgggg ttgcttgtg ctaagtcac 
ttttggaaa acggtgcta ggggcgtaa tgttgggtg 
atattcgag aaaaagaag gcaaagaac tcgcggctg 
aattaaata agacctacg gtaaagata aagcccttt 
tcatgaaat gtgacgtca ccaaaaagg atgaatttg 
aaaacttgt tcaaatgca cctatcaga ggtttccaa 
gtatggata tcgtaatca ataacgctg gtctgttgc 
aagacaaat attggcccc ttgaactag ccgtgaacg 
tgaacggct tggtacaag ggacactat ttggtttcc 
actacatgg gaaaacatg ggaaacacg aaaagggca 
gaggtggag ttattgtga acatggcgt ccatctatg 
ggctccaac aagcctacg catgtcctg tttacaacg 
gcactaaag gatttgtaa ttcgattta gcaacgcta 
tgtcccatg aatattacg agaaaatga caggcgtta 
aagtcctga caatgtgtc ctggggtga ctgacacga 
acatgattg acgaatcaa gcacctatg ccctggatg 
gctttggag acctgggca aacttgtga gcgaaggac 
tggccaatc tgccacccc aaccagctt cagcttgtg 
gggactgtt tgatcaaaa tgctgtgct ccggcgaaa 
atgggggta tttgggtga ttgaagaaa gcgagtgct 
acaaagtcc ggcttccgg accgccaga ctctgcgta 
ccgtttcga taatgttta ggttgctgt ttttaaaaa 
acattagaa atatcgcct ctattttcc tagccaaaa 
ggctgcaat ggcccagaa acaccttgc agaaatcgt 
cactggcac ggggcagaa acgaggctc agccggaac 
agcccccga agccgcaca aggagatat ttttcccgc 
agttggggc gcgatggta ttaaggaca aagtagctt 
tagtgactg ggggcacgg acggaattg gcttgcgat 
gtgtgagag aattgctaa gaaccgggg ctagggggg 
taatgattg cagacacaa acgagagca agggtttca 
atcgggtga tagagtttt caaaggact atggccaaa 
gtaggatag cgttcattc agatcaacc cggctaatt 
atgttttgc ttaaaaatg cgtttatta gcaccctaa 
atttctacg agggcttgg acattgtga ttaacaacg 
tcaggttca aggaaaaaa attgggagg atcaggttg 
atgagaata ttaaaggaa tcgtgttga gtacacagc 
tctgtttgg aatttatgg gtcgtaata atggaggaa 
aaggcggga ttttgctga acatagtct cagaatatg 
aggaaaaca ccgactcct gtccactgc acagtgctt 
gtcaagact ttgttgtcc gctttgacc gatcagttg 
caacgtcac atttcgaca ccacgaacg tcaaagtat 
taacaattt gcagagcca gttttgaca cgatcgggt 
gcgacttaa ccacgatac taacaaaag gaaccaacg 
gctgtgttt ggatgcctt gcacttgtg cgtcggatt 
cctaattag aatacttta attatttgt gtatgaatg 
aacaaggtg tttttttcc caatgactg tctttttct 
gtttgaatc aatacaaat taatgaacg ct

    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