Status
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Gene information
General information
TC002960 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_007418.3: 5777326..5782432
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
    		TC002960
    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_00481

    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)

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

    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 50
     abdomen shortened - 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): less than 30%
    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 early (L5/6) - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC002960 RA
      MTSEQVQEL RNAFLQQLA SKGNDAVHP KDLERVKKD 
DSWVNRFLM QHDNDQTEA LNMMWETLT WRKEFNVNE 
INDHVKMDI IVQGGFFPH GHDKDGSTL FVFKCKKYV 
KGTHNMDDL KRCVVYWFE RLERQDKGK PITLFFDME 
GCGLANMDL EFTKYLIGL FKQYYPYFL NYILIFEMP 
WILNAAFKI IKSWLPEKA VQKIKFVSK KDIKEYVPL 
DQALKCWGG QNDYTFSFL PEPQEEVPN NVGTASSRK 
VHFADGSSM SESPEGSGD RDHDGSALS VQPSSIITF 
VKEGGELVS TVELQNTDS SLILSFKLK TTSPEKFRV 
RPSVGCLTP GARATVHVT LLPGFQLGG LSRDKFLVM 
STVIESSEM NQDLAQLWR DTTGRKVNQ HRLKCAQSN 
DVSKNGNAV AVPGGSSDG DHTSSSQLM TKINNLTEC 
QSQLHGAVK RIQYFQMVI VLLVIVVGV MLSYVLHLE 
SQEGHTGSC SAP
    CDS sequence
    • >TC002960 RA
      atgacttcg gaacaagtt caggaactt agaaatgct 
tttctccag cagcttgcg tcaaaaggg aacgatgcc 
gttcatccc aaggacttg gaaagggtg aagaaggac 
gatagctgg gtgaaccga ttcttaatg caacatgat 
aatgaccaa actgaagcc ctaaacatg atgtgggag 
acgctcact tggagaaaa gagtttaac gtcaatgag 
attaatgac catgtaaag atggatatt atagtccag 
ggcggattt tttccacat gggcatgat aaggatggt 
agcaccttg tttgttttc aagtgtaag aaatacgtg 
aaagggaca cacaacatg gatgatttg aaaagatgc 
gtcgtatat tggtttgaa agattagaa cggcaagac 
aaaggcaaa cctatcacc ctcttcttt gatatggaa 
ggctgtggc ttagcaaat atggattta gaatttact 
aaatatcta ataggcctc ttcaaacaa tattacccc 
tatttttta aactacatt ctgattttt gaaatgcca 
tggattttg aacgcggcc ttcaaaata ataaagtct 
tggctaccc gagaaagcg gttcaaaaa atcaaattt 
gtgagtaaa aaagacata aaagagtac gtccctctg 
gatcaggca ctaaaatgt tggggtggg caaaacgac 
tacaccttc agcttcctg ccagaaccc caagaggaa 
gttccaaat aacgtcggc actgccagc agtaggaag 
gttcatttt gctgatggg tcttcgatg tcagagtca 
ccagaaggg agtggagac agggaccac gatggaagt 
gcccttagt gtacaacca tccagcatc atcaccttc 
gtcaaagag ggtggagag ctggttagt accgtggaa 
ttgcaaaac actgatagt tctctcata ctctccttc 
aagctaaaa accacatca ccggaaaaa ttccgcgtt 
aggcccagt gtcgggtgt ttgacgccg ggagcacgc 
gctacagtt catgtgact ctcttgccc ggttttcag 
ctaggtggc ctgtccaga gacaaattc cttgtgatg 
agcacagtc attgaatcc agtgaaatg aaccaggat 
ctagcccag ctatggagg gatacaact ggcaggaag 
gtcaaccag caccgtctg aagtgcgcc cagtcgaac 
gacgtctcc aaaaacggc aacgccgtt gccgtgcct 
gggggctcc tctgacggg gaccacacc agcagcagt 
caacttatg acaaaaata aataactta acggagtgc 
caaagtcag ctacatggg gctgtaaaa cgtattcag 
tatttccag atggtaatc gttctcttg gttatcgtt 
gtgggggtt atgttatct tatgtctta catttggaa 
agtcaagag gggcacacc ggttcctgc agcgcccca 
taa
    mRNA sequence
    • >TC002960 RA
      ggctgaact gcacatgtc ggatgattg cgattggtg 
tatttattt tagtttatc aacacaagt gtcactact 
tgtcaccag tcgtcatac atcactttt tatttcgtt 
ggttgatag ttgtgattt agtttaagt tcaaggatc 
gttaataac gtaagagtg gattaaagt gttatattg 
tcaatgtct tatttaaat tccgtgtca ttaaaccca 
gtgtaatct tattgaagt gttgaatta tttgttgtc 
aaatcgaaa accaaagaa atgacttcg gaacaagtt 
caggaactt agaaatgct tttctccag cagcttgcg 
tcaaaaggg aacgatgcc gttcatccc aaggacttg 
gaaagggtg aagaaggac gatagctgg gtgaaccga 
ttcttaatg caacatgat aatgaccaa actgaagcc 
ctaaacatg atgtgggag acgctcact tggagaaaa 
gagtttaac gtcaatgag attaatgac catgtaaag 
atggatatt atagtccag ggcggattt tttccacat 
gggcatgat aaggatggt agcaccttg tttgttttc 
aagtgtaag aaatacgtg aaagggaca cacaacatg 
gatgatttg aaaagatgc gtcgtatat tggtttgaa 
agattagaa cggcaagac aaaggcaaa cctatcacc 
ctcttcttt gatatggaa ggctgtggc ttagcaaat 
atggattta gaatttact aaatatcta ataggcctc 
ttcaaacaa tattacccc tatttttta aactacatt 
ctgattttt gaaatgcca tggattttg aacgcggcc 
ttcaaaata ataaagtct tggctaccc gagaaagcg 
gttcaaaaa atcaaattt gtgagtaaa aaagacata 
aaagagtac gtccctctg gatcaggca ctaaaatgt 
tggggtggg caaaacgac tacaccttc agcttcctg 
ccagaaccc caagaggaa gttccaaat aacgtcggc 
actgccagc agtaggaag gttcatttt gctgatggg 
tcttcgatg tcagagtca ccagaaggg agtggagac 
agggaccac gatggaagt gcccttagt gtacaacca 
tccagcatc atcaccttc gtcaaagag ggtggagag 
ctggttagt accgtggaa ttgcaaaac actgatagt 
tctctcata ctctccttc aagctaaaa accacatca 
ccggaaaaa ttccgcgtt aggcccagt gtcgggtgt 
ttgacgccg ggagcacgc gctacagtt catgtgact 
ctcttgccc ggttttcag ctaggtggc ctgtccaga 
gacaaattc cttgtgatg agcacagtc attgaatcc 
agtgaaatg aaccaggat ctagcccag ctatggagg 
gatacaact ggcaggaag gtcaaccag caccgtctg 
aagtgcgcc cagtcgaac gacgtctcc aaaaacggc 
aacgccgtt gccgtgcct gggggctcc tctgacggg 
gaccacacc agcagcagt caacttatg acaaaaata 
aataactta acggagtgc caaagtcag ctacatggg 
gctgtaaaa cgtattcag tatttccag atggtaatc 
gttctcttg gttatcgtt gtgggggtt atgttatct 
tatgtctta catttggaa agtcaagag gggcacacc 
ggttcctgc agcgcccca taacaataa ctatcagac 
gcaggcccg atcgaaata aatttggtt cgtaaactg 
gtgcaaaat tcattgtac attgttttg tatttgatt 
tgtatttta aaactggtt ttacgtttc taaccggtg 
cctgcagtt catgacaat ataccacat tcctataaa 
atttatttt tgttaaaag taaagtgct ttattttgg 
gtattttaa tgtattaaa tcagtttga gtgatattg 
ttaaaatgt gtgttgttg cgttggtat atgttacta 
gcgccacaa cgtactgtt ttgtctagt gaatatatt 
ttgtttaca cttttaaag gttatattg ttacaatat 
ttaacttaa attagattt tatacctta gttaagata 
ttttcatgc tatgtacaa tcgcattaa aagaactga 
aaaaatgct aattgtata tattttgcc tatgtgtaa 
gttacacaa ctatgtata gtgattttt atattgaag 
gtcgtacat tctgtttaa cagtttgaa attatatct 
ctttgtttg acatttaat aagagttta atcgatatt 
atatttttt ttgaaaata ttttcttaa tgagacgta 
ctgccacaa aaatttatt taagtagta ttaatatgt 
atcaaatca accaatcaa aatttatat ttaggcaac 
tcttttata taagtcaaa caaaaaccg aaaaatcag 
tcaagtgct acaaattac caaatacac tcattgtta 
aagcctacg ctacgaata ttgccttac ctaattgta 
caacaaaaa aggacaaac tgtggtttt ctaaagcta 
gttaggcag ctgatctcc aactcattt tttactctt 
atagcgaat caaatgtct aaaaacagt tgcctaagc 
taaaatttt gaagcatgt agttaaaaa aggctagaa 
acgtaaatg tagtaatta tttttaatc cacaaaatt 
cgtttgttc ataagtgat gaataaatt gatgaaaaa 
act

    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