Status
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Gene information
General information
TC004005 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: 28592477..28601491
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
    		TC004005
    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_03669

    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: 3 (3 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg with embryonic tissue, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): more than 80%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): more than 80%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     egg without cuticle embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): more than 80%

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

    legs segment shortened - Penetrance (percentage of animals/eggs on slide): less than 30%
    thorax segment sometimes not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    thorax not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen segment number decreased - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen 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): 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: 0.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 40.0% (includes death as larva, prepupa, pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 2 (16 dpi)
    Days post injection


    adult lethality - Number of animals showing the phenotype: 2 (19 dpi)
    Days post injection

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

    Adult morphology
    elytra dorsal orientation not closed - Number of animals showing the phenotype: 8


    Fertility
    egg production: number no/almost no eggs -
    vitellogenic egg chamber shape irregular - Number of animals showing the phenotype: 4

    tropharium size shortened - Number of animals showing the phenotype: 4

    egg chamber position anteriorized - Number of animals showing the phenotype: 4

    mature egg not present - Number of animals showing the phenotype: 4

    egg chamber number decreased - Number of animals showing the phenotype: 4
    vitellogenic egg chamber partially not present - Number of animals showing the phenotype: 4
    previtellogenic egg chamber number decreased - Number of animals showing the phenotype: 4
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004005 RA
      MASGEDRKV ALLTGITGQ DGSYLTEFL LGKGYEVHG 
IIRRASTFN TSRIEHLHT NVYQHKGGK MHLHYGDMT 
DSSSLVKLI NKIKPMEIY NLAAQSHVK VSFDLSEYT 
AEVDAVGTL RLLDAIRTC GLEKEVKFY QASTSELYG 
KVAEIPQSE KTPFYPRSP YACAKLYAY WIVVNYREA 
YGMFACNGI LFNHESPRR GETFVTRKI TREVAKIHL 
GLTQCLELG NLDSKRDWG HAKDYVEAM WLMLQQPEP 
DDFVIASGE THSVREFVE AAFRHVGKE ILWEGSGVD 
EVGKEKDTG VVRVRINPR YFRPTEVDL LLGDASKAR 
SKFNWAPKV SFPELVKDM MEADIDLMK RNPLA
    CDS sequence
    • >TC004005 RA
      atggcaagt ggtgaggac cgcaaagtg gcccttttg 
accggaatt acgggtcag gacggttcg tatcttact 
gagtttctt ctgggcaaa ggctacgaa gttcatggg 
attattcgc agagctagt acttttaat acgagcaga 
attgagcat ttgcacaca aatgtttac cagcataag 
ggcggaaaa atgcattta cattatggg gacatgacc 
gattctagc tcacttgtg aagcttata aataaaata 
aaaccaatg gaaatttat aatttggcg gctcaaagc 
cacgttaag gtgtctttt gatttgagc gagtacacg 
gcagaggtg gacgctgtg ggaactttg cgacttttg 
gatgccata aggacttgt gggttggag aaagaagtc 
aagttttat caagcttcc acctcggaa ttgtacgga 
aaagtcgcc gaaattcca cagagtgaa aaaacgccg 
ttttatccc aggtctcca tacgcttgt gcaaagctt 
tacgcttac tggatcgtg gtgaactac cgtgaagct 
tacggcatg ttcgcctgc aacggcatc ctcttcaac 
cacgaaagc ccccgacgt ggtgaaacc ttcgtcacg 
cgcaaaatc acccgagaa gtggccaaa atccacctg 
gggctcact cagtgcctt gaattaggc aacctggac 
tcgaagcgc gactggggc catgccaag gactacgtg 
gaggccatg tggctcatg ctgcagcag cccgagccg 
gacgacttc gtcatagct tccggggag acgcacagt 
gtgcgggag tttgttgag gcggctttc agacacgtg 
gggaaggag attctgtgg gaagggagc ggcgtggac 
gaggtgggg aaggagaag gacaccgga gttgtccgg 
gttaggatc aacccgagg tatttccgg cccacggaa 
gtggatttg ttgttgggg gatgcgtcc aaagccagg 
agcaagttt aattgggcg ccgaaagtg tcgtttcct 
gagctggtg aaggatatg atggaggcg gatattgat 
ttaatgaag aggaatcct ttggcttag
    mRNA sequence
    • >TC004005 RA
      cctgtaatc ggttaaacc aaaataatc tcgattgtg 
ggcttgtct gtagataaa taagaaaat ctgcttgtt 
taaacacaa ttcgggtgt taattgcgg taataaatc 
acacaattg tgtaacaag acacgtcat ggcaagtgg 
tgaggaccg caaagtggc ccttttgac cggaattac 
gggtcagga cggttcgta tcttactga gtttcttct 
gggcaaagg ctacgaagt tcatgggat tattcgcag 
agctagtac ttttaatac gagcagaat tgagcattt 
gcacacaaa tgtttacca gcataaggg cggaaaaat 
gcatttaca ttatgggga catgaccga ttctagctc 
acttgtgaa gcttataaa taaaataaa accaatgga 
aatttataa tttggcggc tcaaagcca cgttaaggt 
gtcttttga tttgagcga gtacacggc agaggtgga 
cgctgtggg aactttgcg acttttgga tgccataag 
gacttgtgg gttggagaa agaagtcaa gttttatca 
agcttccac ctcggaatt gtacggaaa agtcgccga 
aattccaca gagtgaaaa aacgccgtt ttatcccag 
gtctccata cgcttgtgc aaagcttta cgcttactg 
gatcgtggt gaactaccg tgaagctta cggcatgtt 
cgcctgcaa cggcatcct cttcaacca cgaaagccc 
ccgacgtgg tgaaacctt cgtcacgcg caaaatcac 
ccgagaagt ggccaaaat ccacctggg gctcactca 
gtgccttga attaggcaa cctggactc gaagcgcga 
ctggggcca tgccaagga ctacgtgga ggccatgtg 
gctcatgct gcagcagcc cgagccgga cgacttcgt 
catagcttc cggggagac gcacagtgt gcgggagtt 
tgttgaggc ggctttcag acacgtggg gaaggagat 
tctgtggga agggagcgg cgtggacga ggtggggaa 
ggagaagga caccggagt tgtccgggt taggatcaa 
cccgaggta tttccggcc cacggaagt ggatttgtt 
gttggggga tgcgtccaa agccaggag caagtttaa 
ttgggcgcc gaaagtgtc gtttcctga gctggtgaa 
ggatatgat ggaggcgga tattgattt aatgaagag 
gaatccttt ggcttagtt tttgatttt ttagcacaa 
cattccgtt ttttatttt ttttttaac tagtcttcc 
taatggcat attgattgt tttattttt tgacactta 
cgtaaattg tcacgtgct cgcattgta atttaaatg 
caaatggaa gtattttta taaagtatg tccaaagga 
aattggccg atttaatcg ttgtaatga ctgaaatgt 
atgtaaatt tgtctaaat aaaattaac tttgaaat

    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