Status
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Gene information
General information
TC003656 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: 11714945..11717984
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
    		TC003656
    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
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    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
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    Email
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_00599

    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

    Fertility
    ovary present - Number of animals showing the phenotype: 4
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 20
    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: 10.0% (includes death as larva, prepupa, pupa, adult)

    pupal molt delayed (still prepupa) - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection

    eclosion delayed (still pupa) - Number of animals showing the phenotype: 1 (16 dpi)
    Days post injection

    eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 1 (19 dpi)
    Days post injection

    Fertility
    egg production: number no/almost no eggs -
    mature egg deposition blocked number 1st lateral oviduct: 2 number 2nd lateral oviduct: 3 - Number of animals showing the phenotype: 1
    ovary without detectable defects - Number of animals showing the phenotype: 3
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC003656 RA
      MSAQTITTT ETTQNAQKP QQYHWRMVW RNIILYIIM 
HLTGFYGLY LAMFYAQWK TVFYSWFLL VIALQGVTA 
GSHRLWAHK AYKARLPLR MLLCIFQTL SLQNHIYDW 
ATYHRVHHK FVDTNADPH NSRRGFFFS HMGWLFIEP 
HKDVEDKYK SIDFSDLHA DSVVMIQKK YYHTFFAPV 
IGFYLPAAI PWYFWGENF WTAFFVATM LRYCACTNI 
TFLVNSWAH IYGSRPYDK NIYPTESAT IAVLTGGEG 
WHNYHHTFP WDYKTGEFG KYRSNLTTG FLDFMAAIG 
WAYDLKTVS EEMIMKRVL RTGDGTRKF DKIDKILNV 
DDDHHHEDM LWGWGDSDM AKEEMNYVK IHNRKED
    CDS sequence
    • >TC003656 RA
      atgtcggcc cagaccatt accacgacc gagaccaca 
caaaatgcc cagaaaccg cagcagtac cattggagg 
atggtctgg aggaacatc atcctgtac attatcatg 
cacctcacc ggcttctat ggactgtac ctggccatg 
ttctacgcc cagtggaaa acagtcttt tacagttgg 
ttccttctg gtcatagcc ctccaagga gtgacagct 
ggtagtcac cgcctctgg gcccacaag gcctacaag 
gcgcgactc cccctccga atgcttctt tgtattttc 
caaaccctg tccctccag aaccacatc tacgactgg 
gccacgtac caccgcgtc caccacaag ttcgtcgat 
accaacgcc gacccacac aactcgcgc cgcggcttc 
ttcttctcc catatgggt tggttgttc atcgagccc 
cacaaagac gtggaggat aaatacaag tcgatcgac 
ttcagcgac ttgcatgcc gattccgtg gtcatgatc 
cagaaaaag tactaccac acgttcttt gccccagtc 
attgggttc tacctcccg gcggcgatc ccatggtac 
ttctggggc gagaacttc tggaccgcg tttttcgtt 
gcgaccatg ctgcggtac tgcgcctgc accaacatt 
acgttcctt gtgaacagt tgggcccat atctatggg 
tcccgccca tacgacaag aacatttat cccaccgaa 
agtgccacg attgcggtt ttgaccggt ggggagggt 
tggcacaac taccatcac actttcccg tgggattat 
aagaccggg gagtttggg aagtaccga agtaacctt 
accacgggc tttttggac tttatggcg gccataggc 
tgggcctat gacctcaag accgtgtcg gaagagatg 
ataatgaag agggtgctg cgcacgggt gatggtact 
cggaagttt gataagatc gataagata ctcaatgtg 
gacgatgac caccaccat gaagacatg ctctggggg 
tggggggat agtgatatg gccaaagag gaaatgaac 
tacgtcaaa attcacaac aggaaggag gattaa
    mRNA sequence
    • >TC003656 RA
      gagacttcg taaagctgg tgcacatta ggattcact 
tttgttgaa gtcacaccg acatcacga acgcagcaa 
gtgtgttaa ttatcgaaa taactacgt gatcacaac 
aacggtcga ataaataat taaatagga accaatagg 
aattttttt ttgacatat tcataacaa ctgtaagat 
atttttgac attagaagg gagcaagga acattaaag 
tcataaaaa aggataaat agcgcgatg tcggcccag 
accattacc acgaccgag accacacaa aatgcccag 
aaaccgcag cagtaccat tggaggatg gtctggagg 
aacatcatc ctgtacatt atcatgcac ctcaccggc 
ttctatgga ctgtacctg gccatgttc tacgcccag 
tggaaaaca gtcttttac agttggttc cttctggtc 
atagccctc caaggagtg acagctggt agtcaccgc 
ctctgggcc cacaaggcc tacaaggcg cgactcccc 
ctccgaatg cttctttgt attttccaa accctgtcc 
ctccagaac cacatctac gactgggcc acgtaccac 
cgcgtccac cacaagttc gtcgatacc aacgccgac 
ccacacaac tcgcgccgc ggcttcttc ttctcccat 
atgggttgg ttgttcatc gagccccac aaagacgtg 
gaggataaa tacaagtcg atcgacttc agcgacttg 
catgccgat tccgtggtc atgatccag aaaaagtac 
taccacacg ttctttgcc ccagtcatt gggttctac 
ctcccggcg gcgatccca tggtacttc tggggcgag 
aacttctgg accgcgttt ttcgttgcg accatgctg 
cggtactgc gcctgcacc aacattacg ttccttgtg 
aacagttgg gcccatatc tatgggtcc cgcccatac 
gacaagaac atttatccc accgaaagt gccacgatt 
gcggttttg accggtggg gagggttgg cacaactac 
catcacact ttcccgtgg gattataag accggggag 
tttgggaag taccgaagt aaccttacc acgggcttt 
ttggacttt atggcggcc ataggctgg gcctatgac 
ctcaagacc gtgtcggaa gagatgata atgaagagg 
gtgctgcgc acgggtgat ggtactcgg aagtttgat 
aagatcgat aagatactc aatgtggac gatgaccac 
caccatgaa gacatgctc tgggggtgg ggggatagt 
gatatggcc aaagaggaa atgaactac gtcaaaatt 
cacaacagg aaggaggat taagtctag ctcgtgtta 
attaattta ttatcaaat ggttcagtc atgtacaat 
aacagctct ggagggagc gattcaatt cccattatt 
agcgaattt ttttcaccg agacaaaga ccagattgg 
agcacttaa tcttgtgca gcagaacgt tttaataat 
aatcagatg tttcacatt acacggtgg cctgttttc 
ctctgtggc ataatctga tattcttca gtggtaaaa 
aatttcaaa cggaacata aaatttata tttacgatg 
acagcctgc attattttt aatgcgagc tattaataa 
gttaataaa caaatgtca gagttattt atcgcgtta 
ttaaggttt tttatgcag gacagttaa tggaaaatt 
gtttcggga gattggacg gtttcagca cgagagaga 
tttattttt gccaacgag gaaataaaa attgacgct 
gaaaatcac ttttgcccg gttacatga gctcatcaa 
atttttcag ctttttaca ataatcact ttacgtgga 
tctatcgaa aaatttgaa ttaaaagca aatttcagt 
ttttatata ataaacaaa gtttaatat a

    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