Status
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Gene information
General information
TC034842 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_007423.3: 9702163..9714803
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
    		TC034842
    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_02479

    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: 40.0% (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

    adult lethality - Number of animals showing the phenotype: 3 (9 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg not developed/not fertilized - Penetrance (percentage of animals/eggs on slide): more than 80%
    affected eggs/embryos/larvae - 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%
    affected eggs/embryos/larvae -
    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: 10.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 10.0% (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC034842 RA
      MSEIRRSLR LQSKNHFVK TEPKARRKI LRSFGSFDV 
PFNNCKYKY RGCKERFPE DELKRHELE CHFRWYKCE 
GKIFAGWSC NWKGYHEDI MNHFKKEHR ERTYMKDQN 
VIEMSLILD QDSYDLQLI RKRKQLFWF KHRLLSEEK 
AAYWLCQYV GPQKEALTY CYELVVSSN EVRKFAVTE 
LCYTDALDA NKIYEAGRC VVMTFDQIK SFMNGEGKV 
TVYFRIKKN VKAKNIKYE QINAEIFTS NMTETITIK 
NFSSLLSLP PSKKLKECK IARLTAPGE NYGSLMLKV 
DVTLTTTSG GSETLHLVA KMVPPNPDI QEIFNTSVT 
FRNEIEFYR KIVPALRNF QKKFGPEVV NFFPKYFGS 
RLNLTGSDH VDPDAVLLL DNLKIANYV GLDRCAGLD 
ISVTRLILR NLATLHAVP IGLKLQQPE VFASEVRPF 
LSPWLPKRE MHDKYRAAI AKMAAEIPE IAHLTQRIL 
DGFDRELIP EVPREPFAT IAHNDCWAS NSLVKFESG 
EAVDCKLVD YQVCGYGSP ARDVIFFLF SSVGIEGLE 
QLEHLLKFY HDCFISTLK KVGCDVGRF GFEEFGKEL 
DFEARNSQF GHVAFMLFV VFTDKTLIK EIKEFSVDN 
IIAGAGSEE HKRKFAFVV EEFAKRNWI
    CDS sequence
    • >TC034842 RA
      atgtcagag ataaggcgt tcattacgt ttacaaagc 
aagaatcat ttcgtcaaa actgagcca aaggcaagg 
agaaagata ttacggtct tttggtagc tttgacgtc 
ccttttaac aactgtaaa tacaaatac cgcggttgc 
aaggaacgc ttccctgaa gatgagctc aaaaggcat 
gagctggaa tgccacttt cgttggtac aaatgcgag 
gggaaaata tttgcggga tggtcctgt aactggaaa 
ggctatcac gaggacatc atgaaccac ttcaagaag 
gagcaccgg gaaagaacc tacatgaaa gaccaaaac 
gttatagaa atgtcgctg atcctggac caggactcg 
tacgatttg caattgatt cgaaagcga aagcagctt 
ttctggttc aaacaccga cttttgagt gaggagaag 
gcggcgtat tggttgtgt caatacgta gggccgcag 
aaagaagca ctaacttac tgttacgag ctggttgtg 
agcagtaat gaagtacgg aaatttgcg gtaaccgaa 
ttgtgttac acggatgct ttagacgcg aataaaatt 
tacgaagcc ggaaggtgt gtcgttatg acgttcgat 
cagattaag agtttcatg aatggagag gggaaggta 
acagtttat ttcaggatc aagaagaat gttaaggcg 
aagaatata aaatatgaa caaatcaat gctgaaatt 
ttcacatca aacatgact gaaacaatc acgatcaaa 
aacttctcc tccttacta tcacttcca ccgtcaaaa 
aaactcaag gaatgtaaa atcgcgcgt ctcacagct 
ccgggtgaa aactacgga agtttaatg ctaaaggtg 
gacgtaacc ctgaccaca acttccggc ggaagtgaa 
accctccat cttgtcgcc aaaatggtg ccgccgaac 
cccgacatc caggaaatc ttcaacact tcggtcact 
ttccgcaac gaaatcgaa ttctaccga aaaatcgtg 
cccgcctta cgcaacttt caaaaaaaa tttggaccg 
gaagtcgtc aacttcttc ccgaaatat ttcggaagt 
cggcttaac ctcaccgga agtgaccac gtggacccc 
gacgccgtc ctcctattg gacaatttg aaaatcgca 
aactatgtc ggactggac cgatgtgct ggactcgac 
atttccgtg actcgccta attttgcga aacttggca 
acactgcac gccgtcccc attggctta aaactgcaa 
caaccggaa gtcttcgct tcggaagtg cgcccattt 
ctatcacca tggttacca aagcgcgaa atgcacgac 
aagtatcgc gccgccatt gccaaaatg gcggccgaa 
attcccgaa atcgcccac ttgacgcag cgaatcctt 
gacgggttc gaccgggaa cttatcccg gaagtcccg 
cgggaaccg ttcgccacc atagcccac aacgattgc 
tgggctagc aacagtttg gtgaaattc gagtcaggg 
gaggctgtg gattgcaaa ctcgttgat tatcaagtg 
tgcggttac ggatcgccg gctcgtgac gtcattttc 
ttccttttt tcaagtgta gggattgag ggtttggaa 
cagttggaa cacctcctt aagttttac cacgattgt 
ttcatctcc actctcaag aaagttggc tgtgatgtt 
gggcggttt ggttttgag gagtttggc aaggagttg 
gattttgag gcgaggaat tcgcagttt gggcacgtg 
gcttttatg cttttcgtt gttttcacc gataaaacc 
ttgattaag gagattaag gagttttcc gttgataat 
atcatagca ggcgctggg agcgaggag cataagagg 
aagtttgcg tttgttgtg gaggagttt gctaaaagg 
aattggatt tga
    mRNA sequence
    • >TC034842 RA
      atagttcct cttctgaaa ctgaaatgt cagagataa 
ggcgttcat tacgtttac aaagcaaga atcatttcg 
tcaaaactg agccaaagg caaggagaa agatattac 
ggtcttttg gtagctttg acgtccctt ttaacaact 
gtaaataca aataccgcg gttgcaagg aacgcttcc 
ctgaagatg agctcaaaa ggcatgagc tggaatgcc 
actttcgtt ggtacaaat gcgagggga aaatatttg 
cgggatggt cctgtaact ggaaaggct atcacgagg 
acatcatga accacttca agaaggagc accgggaaa 
gaacctaca tgaaagacc aaaacgtta tagaaatgt 
cgctgatcc tggaccagg actcgtacg atttgcaat 
tgattcgaa agcgaaagc agcttttct ggttcaaac 
accgacttt tgagtgagg agaaggcgg cgtattggt 
tgtgtcaat acgtagggc cgcagaaag aagcactaa 
cttactgtt acgagctgg ttgtgagca gtaatgaag 
tacggaaat ttgcggtaa ccgaattgt gttacacgg 
atgctttag acgcgaata aaatttacg aagccggaa 
ggtgtgtcg ttatgacgt tcgatcaga ttaagagtt 
tcatgaatg gagagggga aggtaacag tttatttca 
ggatcaaga agaatgtta aggcgaaga atataaaat 
atgaacaaa tcaatgctg aaattttca catcaaaca 
tgactgaaa caatcacga tcaaaaact tctcctcct 
tactatcac ttccaccgt caaaaaaac tcaaggaat 
gtaaaatcg cgcgtctca cagctccgg gtgaaaact 
acggaagtt taatgctaa aggtggacg taaccctga 
ccacaactt ccggcggaa gtgaaaccc tccatcttg 
tcgccaaaa tggtgccgc cgaaccccg acatccagg 
aaatcttca acacttcgg tcactttcc gcaacgaaa 
tcgaattct accgaaaaa tcgtgcccg ccttacgca 
actttcaaa aaaaatttg gaccggaag tcgtcaact 
tcttcccga aatatttcg gaagtcggc ttaacctca 
ccggaagtg accacgtgg accccgacg ccgtcctcc 
tattggaca atttgaaaa tcgcaaact atgtcggac 
tggaccgat gtgctggac tcgacattt ccgtgactc 
gcctaattt tgcgaaact tggcaacac tgcacgccg 
tccccattg gcttaaaac tgcaacaac cggaagtct 
tcgcttcgg aagtgcgcc catttctat caccatggt 
taccaaagc gcgaaatgc acgacaagt atcgcgccg 
ccattgcca aaatggcgg ccgaaattc ccgaaatcg 
cccacttga cgcagcgaa tccttgacg ggttcgacc 
gggaactta tcccggaag tcccgcggg aaccgttcg 
ccaccatag cccacaacg attgctggg ctagcaaca 
gtttggtga aattcgagt caggggagg ctgtggatt 
gcaaactcg ttgattatc aagtgtgcg gttacggat 
cgccggctc gtgacgtca ttttcttcc ttttttcaa 
gtgtaggga ttgagggtt tggaacagt tggaacacc 
tccttaagt tttaccacg attgtttca tctccactc 
tcaagaaag ttggctgtg atgttgggc ggtttggtt 
ttgaggagt ttggcaagg agttggatt ttgaggcga 
ggaattcgc agtttgggc acgtggctt ttatgcttt 
tcgttgttt tcaccgata aaaccttga ttaaggaga 
ttaaggagt tttccgttg ataatatca tagcaggcg 
ctgggagcg aggagcata agaggaagt ttgcgtttg 
ttgtggagg agtttgcta aaaggaatt ggatttgag 
gggcagctg aagaaaaat tgtgtttgg actgtgata 
agcaaaaat ataaatact tgcactgta gataaggtt 
gcaaaatat tggtttgtg gcaataaaa tttgaaaaa 
atta

    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