Status
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Gene information
General information
TC004900 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_007417.3: 4093626..4107139
Sequence information
Transcripts / Proteins (2) 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
    		TC004900
    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
    If you have entered your name and agree by marking the checkbox. we might show your name on this page to honor your contribution.
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_03870

    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 embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 larval musculature 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): less than 30%
    remarks: muscle pattern potentially obscured by segmentation defect,
    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: 30.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 70.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 3 (11 dpi)
    Days post injection

    eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 4 (16 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004900 RA
      MNASIKAQT GGTTPDGDS YVCVPPGYC NNGGTPTTP 
GIDPRIVTP GELCPSGTI PCYTQGPSS RCGERFVSP 
VSTADGQAT PGGHPWQAY LRNSTHPQY AGSGVLIDN 
YHVLTAAHK VYGDQNNPA NVIISMGVH NPSDLTSPN 
VQTRTASAI RVHPNYDPQ HLINDIAIV RVSSPFSLS 
QNNINSACL PTADASYTG QTCVVAGWG ETNFGVQDH 
PTNPMKQVN LSPVDIATC RAGLLPVLP TVDTYLDMT 
GGEICAGGE SMKDACTYD GGAPLTCPN TGKGNIAGL 
VIWGKSCGQ PSVYGVYVS VPFYRAWID STITQLNNS
    • >TC004900 RB
      MHAKEASIK AQTGGTTPD GDSYVCVPP GYCNNGGTP 
TTPGIDPRI VTPGELCPS GTIPCYTQG PSSRCGERF 
VSPVSTADG QATPGGHPW QAYLRNSTH PQYAGSGVL 
IDNYHVLTA AHKVYGDQN NPANVIISM GVHNPSDLT 
SPNVQTRTA SAIRVHPNY DPQHLINDI AIVRVSSPF 
SLSQNNINS ACLPTADAS YTGQTCVVA GWGETNFGV 
QDHPTNPMK QVNLSPVDI ATCRAGLLP VLPTVDTYL 
DMTGGEICA GGESMKDAC TYDGGAPLT CPNTGKGNI 
AGLVIWGKS CGQPSVYGV YVSVPFYRA WIDSTITQL 
NNS
    CDS sequence
    • >TC004900 RA
      atgaacgct tcaatcaaa gcacaaaca ggaggaacc 
acacctgac ggtgactcc tacgtgtgc gtacctccg 
ggatattgc aacaacggt ggcacccca acaactcca 
gggatcgat ccccggatt gttacaccc ggagaactt 
tgtccgagt ggaacaatc ccatgttac actcaaggg 
ccatcgagc cgatgtggc gaaagattc gtgtctcct 
gtttcaaca gccgatggg caagcaact ccaggcggt 
cacccatgg caagcttac ctacgaaat tccacccat 
ccacaatat gcgggcagt ggtgttcta atcgacaat 
taccacgtt cttacagca gcacacaaa gtctacgga 
gaccaaaat aatcccgcg aatgttatt ataagcatg 
ggtgtgcac aatcccagt gatttaacg tcgcccaat 
gttcagact cgaacagct tccgcgata agagttcat 
ccaaattac gacccccag catttgatc aacgacatt 
gcaatagtc agagtgtct tccccattt tctctaagt 
caaaacaat atcaattct gcttgtctt ccgacagct 
gacgcatca tacaccggt caaacatgt gttgtggct 
ggatggggc gaaacaaat tttggcgtc caagaccat 
cccactaat cccatgaaa caagtcaac ctatcacct 
gttgatatt gccacttgt cgagcagga ttattgcca 
gttttgcca acagttgac acgtatctg gatatgacc 
ggaggagaa atttgcgca ggaggcgaa tcaatgaag 
gatgcgtgc acgtacgac ggaggagca cctctcaca 
tgtcccaac actgggaaa ggcaacatt gctggattg 
gtcatttgg gggaaaagt tgcggacaa ccgagtgtc 
tatggagtc tacgtaagc gtgccgttt tatagggca 
tggatcgac agcaccata acacagctg aataattcg 
taa
    • >TC004900 RB
      atgcacgcg aaagaagct tcaatcaaa gcacaaaca 
ggaggaacc acacctgac ggtgactcc tacgtgtgc 
gtacctccg ggatattgc aacaacggt ggcacccca 
acaactcca gggatcgat ccccggatt gttacaccc 
ggagaactt tgtccgagt ggaacaatc ccatgttac 
actcaaggg ccatcgagc cgatgtggc gaaagattc 
gtgtctcct gtttcaaca gccgatggg caagcaact 
ccaggcggt cacccatgg caagcttac ctacgaaat 
tccacccat ccacaatat gcgggcagt ggtgttcta 
atcgacaat taccacgtt cttacagca gcacacaaa 
gtctacgga gaccaaaat aatcccgcg aatgttatt 
ataagcatg ggtgtgcac aatcccagt gatttaacg 
tcgcccaat gttcagact cgaacagct tccgcgata 
agagttcat ccaaattac gacccccag catttgatc 
aacgacatt gcaatagtc agagtgtct tccccattt 
tctctaagt caaaacaat atcaattct gcttgtctt 
ccgacagct gacgcatca tacaccggt caaacatgt 
gttgtggct ggatggggc gaaacaaat tttggcgtc 
caagaccat cccactaat cccatgaaa caagtcaac 
ctatcacct gttgatatt gccacttgt cgagcagga 
ttattgcca gttttgcca acagttgac acgtatctg 
gatatgacc ggaggagaa atttgcgca ggaggcgaa 
tcaatgaag gatgcgtgc acgtacgac ggaggagca 
cctctcaca tgtcccaac actgggaaa ggcaacatt 
gctggattg gtcatttgg gggaaaagt tgcggacaa 
ccgagtgtc tatggagtc tacgtaagc gtgccgttt 
tatagggca tggatcgac agcaccata acacagctg 
aataattcg taa
    mRNA sequence
    • >TC004900 RA
      ttagtaatg atgaacgct tcaatcaaa gcacaaaca 
ggaggaacc acacctgac ggtgactcc tacgtgtgc 
gtacctccg ggatattgc aacaacggt ggcacccca 
acaactcca gggatcgat ccccggatt gttacaccc 
ggagaactt tgtccgagt ggaacaatc ccatgttac 
actcaaggg ccatcgagc cgatgtggc gaaagattc 
gtgtctcct gtttcaaca gccgatggg caagcaact 
ccaggcggt cacccatgg caagcttac ctacgaaat 
tccacccat ccacaatat gcgggcagt ggtgttcta 
atcgacaat taccacgtt cttacagca gcacacaaa 
gtctacgga gaccaaaat aatcccgcg aatgttatt 
ataagcatg ggtgtgcac aatcccagt gatttaacg 
tcgcccaat gttcagact cgaacagct tccgcgata 
agagttcat ccaaattac gacccccag catttgatc 
aacgacatt gcaatagtc agagtgtct tccccattt 
tctctaagt caaaacaat atcaattct gcttgtctt 
ccgacagct gacgcatca tacaccggt caaacatgt 
gttgtggct ggatggggc gaaacaaat tttggcgtc 
caagaccat cccactaat cccatgaaa caagtcaac 
ctatcacct gttgatatt gccacttgt cgagcagga 
ttattgcca gttttgcca acagttgac acgtatctg 
gatatgacc ggaggagaa atttgcgca ggaggcgaa 
tcaatgaag gatgcgtgc acgtacgac ggaggagca 
cctctcaca tgtcccaac actgggaaa ggcaacatt 
gctggattg gtcatttgg gggaaaagt tgcggacaa 
ccgagtgtc tatggagtc tacgtaagc gtgccgttt 
tatagggca tggatcgac agcaccata acacagctg 
aataattcg taataaagc gataatatt tatatgata 
tttatttgt gaaaactgg actgaataa atcaactaa 
attctt
    • >TC004900 RB
      gaccaggca tctctcggg cgttatcag caccggtcg 
cgtccatag atcaaggaa gagcctatc gggggaaag 
atattagag gctccatac aatgcagac attatgcac 
gcgaaagaa gcttcaatc aaagcacaa acaggagga 
accacacct gacggtgac tcctacgtg tgcgtacct 
ccgggatat tgcaacaac ggtggcacc ccaacaact 
ccagggatc gatccccgg attgttaca cccggagaa 
ctttgtccg agtggaaca atcccatgt tacactcaa 
gggccatcg agccgatgt ggcgaaaga ttcgtgtct 
cctgtttca acagccgat gggcaagca actccaggc 
ggtcaccca tggcaagct tacctacga aattccacc 
catccacaa tatgcgggc agtggtgtt ctaatcgac 
aattaccac gttcttaca gcagcacac aaagtctac 
ggagaccaa aataatccc gcgaatgtt attataagc 
atgggtgtg cacaatccc agtgattta acgtcgccc 
aatgttcag actcgaaca gcttccgcg ataagagtt 
catccaaat tacgacccc cagcatttg atcaacgac 
attgcaata gtcagagtg tcttcccca ttttctcta 
agtcaaaac aatatcaat tctgcttgt cttccgaca 
gctgacgca tcatacacc ggtcaaaca tgtgttgtg 
gctggatgg ggcgaaaca aattttggc gtccaagac 
catcccact aatcccatg aaacaagtc aacctatca 
cctgttgat attgccact tgtcgagca ggattattg 
ccagttttg ccaacagtt gacacgtat ctggatatg 
accggagga gaaatttgc gcaggaggc gaatcaatg 
aaggatgcg tgcacgtac gacggagga gcacctctc 
acatgtccc aacactggg aaaggcaac attgctgga 
ttggtcatt tgggggaaa agttgcgga caaccgagt 
gtctatgga gtctacgta agcgtgccg ttttatagg 
gcatggatc gacagcacc ataacacag ctgaataat 
tcgtaataa agcgataat atttatatg atatttatt 
tgtgaaaac tggactgaa taaatcaac taaattctt

    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