Status
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Gene information
General information
TC003984 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: 29244203..29260934
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
    		TC003984
    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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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_03663

    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: 20.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 2 (3 dpi)
    Days post injection

    Fertility
    mature egg deposition blocked number 1st lateral oviduct: >5 number 2nd lateral oviduct: - Number of animals showing the phenotype: 4
    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: 20.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 80.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection

    eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 4 (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: 2 (41 dpi)
    Days post injection

    Pupal morphology
    dorsal thoracic muscles pattern irregular - Number of animals showing the phenotype: 3

    Adult morphology
    head - Number of animals showing the phenotype: 4

    Comment: Head and pronotum bent inwards towards the ventral side!!!

    elytra surface irregular - Number of animals showing the phenotype: 4


    elytra dorsal orientation not closed - Number of animals showing the phenotype: 2


    thorax - Number of animals showing the phenotype: 4
    Comment: Head and pronotum bent inwards towards the ventral side!!!

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC003984 RA
      MPGSLTGSY RSLSGTSDV YRSTTVAGG GGGNAATGI 
LEGMKKAFS FMAGGTAAT KDQKLIERV ASGGPVVIS 
SRTENSNSN NRKMPASGV AEEAALLGT MPSDSMDDI 
ELKNIQLQF PSTRSLSRD DSSAQEEVV ETDRGNLVV 
AVQGSRNKP AILTYHDLG LNYVSSFQA FFNYIDMRA 
LLENFCVYH VNAPGQEEG SATLPEDYI YPTMDELAG 
QLGYVLSHF GLKQFIGFG VGAGANILA RFALNNPNQ 
VTALCLINC VSTQAGWIE WGYQKLNAR HLRSKGMTQ 
GVLDYLMWH HFGRNTEER NHDLVQVYK SYFERNVNP 
TNLALFIDS YVRRTDLNI QRELDPTKR KESTTLKMP 
VMNITGSLS PHVDDTVTF NGRLDPTNS SWMKISDCG 
MVLEEQPGK VAEAFRLFL QGEGYVAPL SPTKMALFR 
KTSLEELLK SKMPNGGQW PMNVIHITE NPISAVVC
    CDS sequence
    • >TC003984 RA
      atgccaggg agcctcacc ggctcttac cgctccttg 
tcgggcacg agcgacgtg taccgctcg accacggtg 
gcgggtggt ggcggtggg aacgccgcc accggaatc 
ctcgaaggc atgaagaaa gcttttagt ttcatggca 
ggtgggaca gccgccacc aaggaccaa aaactgatc 
gagagggtg gccagcggg gggcctgtc gtcatctca 
tccaggaca gaaaactcc aatagtaat aacaggaaa 
atgccagct tccggtgtg gctgaagaa gcggccctt 
ttgggcacg atgccttca gatagcatg gacgatatc 
gaactgaaa aatattcag cttcagttc ccttcgact 
cggtctttg tcacgggat gattcttca gctcaggag 
gaggtggtg gagaccgat cgagggaat ttggtggtg 
gcggtgcaa gggtcgagg aataagccg gcgatattg 
acctatcac gatttgggt ctcaactac gtctctagt 
ttccaagcc ttcttcaac tacatcgac atgcgggca 
ttactggag aacttctgc gtatatcac gtcaatgct 
ccaggtcaa gaggaaggt tctgcgaca cttcctgaa 
gattatatc tacccgacg atggacgag ctcgccggc 
caactcggc tacgtcctc tcccacttt ggtttgaaa 
caattcatc gggttcggc gtaggcgct ggtgccaat 
attttggct cgtttcgcc ctcaataac ccgaatcaa 
gtgaccgct ttgtgtctc atcaactgt gtgagcacc 
caagccggc tggattgaa tggggctat cagaaatta 
aacgcccgg catttgagg tccaaaggg atgactcag 
ggcgttttg gattatttg atgtggcat cattttgga 
cggaatacg gaggaaagg aaccacgac ttggtgcaa 
gtctacaag agctatttc gaacgcaat gttaatccg 
acgaattta gcgttgttt attgatagt tatgtgcgc 
cgtacagat ttgaatata cagagggag ttggatccg 
acgaagcgg aaagaatcg actacgttg aagatgccg 
gttatgaat attacgggg tcgttgagt ccccatgtt 
gatgatact gtcactttt aatgggcgc ttggatccc 
accaactcg tcatggatg aagatttca gactgcggt 
atggtcctc gaagaacaa cccggcaaa gtggccgaa 
gctttccga ctatttctt caaggagaa ggctacgtg 
gcgcccctg tctcccaca aaaatggct cttttccgc 
aaaacgtcg ctggaagaa ctgctcaaa tcgaaaatg 
cctaatggc ggacaatgg ccaatgaat gtcatccat 
atcaccgaa aatccgata tcggctgtc gtctgttaa
    mRNA sequence
    • >TC003984 RA
      tatcagtta cctgataaa ccgccaaca aaaacccgt 
ctccgcccc tgtccttct tcgtgaaac caagtcacg 
tggtcttct aacgaccaa tcaggtctc atttagcat 
tacaacatt agtgcatcc gtagaaacg tcactcttc 
gccagtcga agcctcctc cgactgtcc caaaaatcg 
tgttagtgt tgtgtttgc atagattca ttaaatcaa 
aactgccat ttccaaagg cctaaccca cgatgccag 
ggagcctca ccggctctt accgctcct tgtcgggca 
cgagcgacg tgtaccgct cgaccacgg tggcgggtg 
gtggcggtg ggaacgccg ccaccggaa tcctcgaag 
gcatgaaga aagctttta gtttcatgg caggtggga 
cagccgcca ccaaggacc aaaaactga tcgagaggg 
tggccagcg gggggcctg tcgtcatct catccagga 
cagaaaact ccaatagta ataacagga aaatgccag 
cttccggtg tggctgaag aagcggccc ttttgggca 
cgatgcctt cagatagca tggacgata tcgaactga 
aaaatattc agcttcagt tcccttcga ctcggtctt 
tgtcacggg atgattctt cagctcagg aggaggtgg 
tggagaccg atcgaggga atttggtgg tggcggtgc 
aagggtcga ggaataagc cggcgatat tgacctatc 
acgatttgg gtctcaact acgtctcta gtttccaag 
ccttcttca actacatcg acatgcggg cattactgg 
agaacttct gcgtatatc acgtcaatg ctccaggtc 
aagaggaag gttctgcga cacttcctg aagattata 
tctacccga cgatggacg agctcgccg gccaactcg 
gctacgtcc tctcccact ttggtttga aacaattca 
tcgggttcg gcgtaggcg ctggtgcca atattttgg 
ctcgtttcg ccctcaata acccgaatc aagtgaccg 
ctttgtgtc tcatcaact gtgtgagca cccaagccg 
gctggattg aatggggct atcagaaat taaacgccc 
ggcatttga ggtccaaag ggatgactc agggcgttt 
tggattatt tgatgtggc atcattttg gacggaata 
cggaggaaa ggaaccacg acttggtgc aagtctaca 
agagctatt tcgaacgca atgttaatc cgacgaatt 
tagcgttgt ttattgata gttatgtgc gccgtacag 
atttgaata tacagaggg agttggatc cgacgaagc 
ggaaagaat cgactacgt tgaagatgc cggttatga 
atattacgg ggtcgttga gtccccatg ttgatgata 
ctgtcactt ttaatgggc gcttggatc ccaccaact 
cgtcatgga tgaagattt cagactgcg gtatggtcc 
tcgaagaac aacccggca aagtggccg aagctttcc 
gactatttc ttcaaggag aaggctacg tggcgcccc 
tgtctccca caaaaatgg ctcttttcc gcaaaacgt 
cgctggaag aactgctca aatcgaaaa tgcctaatg 
gcggacaat ggccaatga atgtcatcc atatcaccg 
aaaatccga tatcggctg tcgtctgtt aaattaata 
ataataata accgccgcc actgctcac acaatcaca 
ctatcaaca catatacac acacttatt tgagctgta 
ttggaattt atggaggat ttgtcgggc gggaagctg 
gcggacgct tcgaggaat ccccctgta tatcaagcg 
ggacgcatt aagcatgtg atgttttcg aaaataggc 
gctaaacta gactagaat cgattattt tttaagaga 
tatataaag ttaggtttg aaaatggcg gcgacagtc 
ggtataaca ggaaactat aagaaaaat gagcttaaa 
ttttcggtc atagggggc gtgagttgt gataaattt 
caatacaga cgtttcgtt ggccactgc ccttctgaa 
gcacatatc taggcccag attgagtta tttaggccc 
gcaacgaaa ttctatcac gccatatcg actaggtgc 
gcttaacta ggacctaac aacagtgtt ttgagtttc 
tgttgtgat tagttgacg attacgtat ttaagaaaa 
atagctgta ggtggagct ttacctgtt gatagaaag 
cctactatt taatgaatt ttaaggaga acccctcac 
gaacaagca gttcttatc atttcgtaa ggttatgta 
agataagat cggtgtcgt tggatgctg ttcggtttt 
tatattgtt gcgatgtag ttttatgtt ttgaaatgt 
gatgaataa tcgtattgt gcctcactt tgttaatgg 
tttaagtta agcactatt taattttaa taaaatgtt 
taaaacgtt

    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