Status
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Gene information
General information
TC003856 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: 23318792..23332435
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
    		TC003856
    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_03636

    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 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: 0.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 20.0% (includes death as larva, prepupa, pupa, adult)

    eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 2 (16 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC003856 RA
      MDCLVAYYT ERFKTVDGN VFEEFAKFY EKDLTRVHS 
WLESQFKKK TVKNNAISA LHRREGNNF YAEKNLIKS 
FDCYTKSLR FAIPYSKEY GLALANRSA VSFELKEYH 
NCLKDIELC FKSDYPTDL KPKVYVRKT ECYYELNQK 
EALNQCISE VLHFLETEN VVEKGKFVT RLNHIKKLK 
NAKPKTDSG QECLHEIPV FPDGENKCL AYASTKVKM 
SYNKDKGRH IIASTNIQR GDLLFIEKA FVFAPVFKE 
NKEFYSFKC YNCLSDIVS GVPCNTCTV CVYCDEKCR 
DQNWTKCHR WECDGMQAN IWFDLGIAL PAFKVMLEG 
ALSGFQTLE GGFEDDVKH FGDKENNYR YFNRLLSNI 
HKNKNLAPY IIMASVVTT YLQKYTDFF TWFLTQPSC 
PKEGLNELV KLVGGFITK HIAQLACNS STIEQWTCS 
SSDLLFPDV LITIASGIF PSVSIMNHS CRPNVTNYF 
MSDTIVVKA LEDIAQNEE IFNCYGIDY RGMEREQRQ 
YACKELYHF ECKCVICSD PAHELDMLD SYLCPKCKG 
LVPEIKNTI LSFCVNCGE KYHLKPFRK INYEAQKYM 
ESDSSNQLE LLIKSLKIR EKILYKHHK DFEEVYYRL 
YSFYVKLGD AENMFKYFH LWLENEKAR RGCNSRVVG 
TKLYEAALA ILHCLKGGQ QKNCTNLKD FLQNVEYMI 
KEAKAILNL YYPAFITNR LNKKIQFIS TK
    CDS sequence
    • >TC003856 RA
      atggattgt ttagtggct tattacacc gagaggttt 
aaaactgtt gatggcaac gtgtttgaa gagtttgcc 
aagttttat gaaaaagat ttgacacga gttcattcg 
tggttagaa agtcagttt aagaaaaaa acggtgaaa 
aataacgct atttcggcg ttacatagg cgagaaggg 
aataatttt tatgctgag aagaatcta attaagagt 
tttgattgt tatacaaag agtttacgt tttgccata 
ccatacagt aaagagtat ggactagct ttggccaat 
agatctgcc gtttcattt gaattgaaa gagtaccac 
aactgtctt aaagatatt gagttgtgt ttcaagagt 
gattatcca acagatctg aaaccaaaa gtttacgtt 
aggaagacc gaatgttat tatgagctg aatcaaaaa 
gaggctttg aatcagtgc atttctgag gtgctgcat 
tttctagag actgaaaac gttgtggaa aaaggtaaa 
tttgtcacg aggttaaac cacattaag aaattaaaa 
aatgcaaaa ccaaaaact gacagtggt caagagtgc 
cttcacgaa atcccggta tttcccgat ggagaaaac 
aaatgtttg gcctatgct tccactaaa gtaaaaatg 
agttacaat aaagacaaa ggacgtcac attattgct 
agtacaaac atccaaaga ggcgacctc ctctttata 
gaaaaagcg tttgttttc gccccagtt ttcaaagaa 
aacaaggaa ttctactcg ttcaagtgt tacaactgt 
cttagcgat attgtaagc ggtgtgcct tgcaacaca 
tgcaccgtt tgtgtttac tgcgacgaa aaatgtcgc 
gatcaaaat tggacaaag tgccatcgg tgggaatgc 
gatggaatg caagccaac atttggttt gacttagga 
attgcactt ccagcgttt aaagtcatg ttagaaggg 
gctttatca gggtttcaa acactggaa ggtggcttt 
gaagacgat gtgaaacat ttcggtgat aaagaaaac 
aactatcgg tacttcaac cgcctgctt tccaacatc 
cataagaac aaaaacctg gccccttat ataattatg 
gccagtgtt gtgactacg tatttgcaa aaatacacc 
gattttttc acctggttt ttgacacaa cccagctgt 
ccaaaggag ggtttaaat gagttggtg aaactcgtc 
gggggtttt attacaaaa cacatcgct cagcttgcg 
tgcaattcg agcacgatc gaacagtgg acgtgctct 
tcgtcggat ttgctcttc ccggatgtt ctcataacg 
atagcttct gggattttt ccgtcagtt agtataatg 
aaccattcg tgtcgacca aatgtcacg aattatttc 
atgagtgat actattgtt gttaaagcg ctcgaggat 
atcgctcaa aatgaggaa attttcaat tgttacgga 
atcgattat cgggggatg gagagggag caaagacag 
tacgcttgc aaggagttg taccatttc gaatgtaaa 
tgtgtcatt tgctcggat cctgcacac gaactggac 
atgctggac agctatttg tgcccaaaa tgcaaagga 
ctggtccca gaaattaag aacacaatt ttgagtttt 
tgcgttaac tgtggcgaa aaataccat ttgaaaccg 
tttaggaaa atcaattat gaggcccaa aaatacatg 
gaaagcgat tcttctaat cagttagaa cttttaata 
aagagttta aaaatcaga gaaaaaatt ctctataaa 
catcacaaa gatttcgag gaagtttac taccgactg 
tatagtttt tacgtaaag cttggagac gctgaaaat 
atgttcaaa tatttccac ttatggcta gagaatgag 
aaagcgcgt cggggttgc aactcaagg gttgtaggg 
acaaagtta tacgaagct gcgcttgca atccttcat 
tgtttgaag gggggacag caaaaaaat tgcacaaat 
ctcaaggat tttctacaa aatgtcgaa tatatgatt 
aaagaagcc aaagccatc ctgaattta tattatcca 
gcgttcatc acaaacagg ctgaataag aaaatacaa 
tttatttcg acgaaataa
    mRNA sequence
    • >TC003856 RA
      tcttttgta ccatttcaa tcacgagtt ttgtcaccg 
gcgaagtga tggatgtca ttagtgaca tgtgttatt 
tattacgca aatatttca aaaagtttc agtttttgt 
gctttagac ttcaacaca ttgtgttct aattttttt 
caatacgta cgaacattt tgtagtttt ttaaaataa 
tctacaaat ccagaaatg gattgttta gtggcttat 
tacaccgag aggtttaaa actgttgat ggcaacgtg 
tttgaagag tttgccaag ttttatgaa aaagatttg 
acacgagtt cattcgtgg ttagaaagt cagtttaag 
aaaaaaacg gtgaaaaat aacgctatt tcggcgtta 
cataggcga gaagggaat aatttttat gctgagaag 
aatctaatt aagagtttt gattgttat acaaagagt 
ttacgtttt gccatacca tacagtaaa gagtatgga 
ctagctttg gccaataga tctgccgtt tcatttgaa 
ttgaaagag taccacaac tgtcttaaa gatattgag 
ttgtgtttc aagagtgat tatccaaca gatctgaaa 
ccaaaagtt tacgttagg aagaccgaa tgttattat 
gagctgaat caaaaagag gctttgaat cagtgcatt 
tctgaggtg ctgcatttt ctagagact gaaaacgtt 
gtggaaaaa ggtaaattt gtcacgagg ttaaaccac 
attaagaaa ttaaaaaat gcaaaacca aaaactgac 
agtggtcaa gagtgcctt cacgaaatc ccggtattt 
cccgatgga gaaaacaaa tgtttggcc tatgcttcc 
actaaagta aaaatgagt tacaataaa gacaaagga 
cgtcacatt attgctagt acaaacatc caaagaggc 
gacctcctc tttatagaa aaagcgttt gttttcgcc 
ccagttttc aaagaaaac aaggaattc tactcgttc 
aagtgttac aactgtctt agcgatatt gtaagcggt 
gtgccttgc aacacatgc accgtttgt gtttactgc 
gacgaaaaa tgtcgcgat caaaattgg acaaagtgc 
catcggtgg gaatgcgat ggaatgcaa gccaacatt 
tggtttgac ttaggaatt gcacttcca gcgtttaaa 
gtcatgtta gaaggggct ttatcaggg tttcaaaca 
ctggaaggt ggctttgaa gacgatgtg aaacatttc 
ggtgataaa gaaaacaac tatcggtac ttcaaccgc 
ctgctttcc aacatccat aagaacaaa aacctggcc 
ccttatata attatggcc agtgttgtg actacgtat 
ttgcaaaaa tacaccgat tttttcacc tggtttttg 
acacaaccc agctgtcca aaggagggt ttaaatgag 
ttggtgaaa ctcgtcggg ggttttatt acaaaacac 
atcgctcag cttgcgtgc aattcgagc acgatcgaa 
cagtggacg tgctcttcg tcggatttg ctcttcccg 
gatgttctc ataacgata gcttctggg atttttccg 
tcagttagt ataatgaac cattcgtgt cgaccaaat 
gtcacgaat tatttcatg agtgatact attgttgtt 
aaagcgctc gaggatatc gctcaaaat gaggaaatt 
ttcaattgt tacggaatc gattatcgg gggatggag 
agggagcaa agacagtac gcttgcaag gagttgtac 
catttcgaa tgtaaatgt gtcatttgc tcggatcct 
gcacacgaa ctggacatg ctggacagc tatttgtgc 
ccaaaatgc aaaggactg gtcccagaa attaagaac 
acaattttg agtttttgc gttaactgt ggcgaaaaa 
taccatttg aaaccgttt aggaaaatc aattatgag 
gcccaaaaa tacatggaa agcgattct tctaatcag 
ttagaactt ttaataaag agtttaaaa atcagagaa 
aaaattctc tataaacat cacaaagat ttcgaggaa 
gtttactac cgactgtat agtttttac gtaaagctt 
ggagacgct gaaaatatg ttcaaatat ttccactta 
tggctagag aatgagaaa gcgcgtcgg ggttgcaac 
tcaagggtt gtagggaca aagttatac gaagctgcg 
cttgcaatc cttcattgt ttgaagggg ggacagcaa 
aaaaattgc acaaatctc aaggatttt ctacaaaat 
gtcgaatat atgattaaa gaagccaaa gccatcctg 
aatttatat tatccagcg ttcatcaca aacaggctg 
aataagaaa atacaattt atttcgacg aaataaaaa 
aatgtgtta ctactcttt

    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