Status
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Gene information
General information
TC012672 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_007424.3: 12839846..12844720
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
    		TC012672
    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
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    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_05294

    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: 30.0% (includes death as pupa, adult)

    pupa eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 1 (3 dpi)
    Days post injection

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 2 (3 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): less than 30%
    with embryonic tissue, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    embryo/egg with muscle fluorescence/pattern, but not hatched (pot. late embryonic lethality) - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    larval musculature partially not present - 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): more than 80%
    remarks: muscle pattern potentially obscured by segmentation defect,
    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): 30% - 50%
    cuticle remnants with some identifiable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

    appendages sometimes partially remaining - Penetrance (percentage of animals/eggs on slide): less than 30%
    legs shortened - Penetrance (percentage of animals/eggs on slide): less than 30%

    legs shape irregular - Penetrance (percentage of animals/eggs on slide): less than 30%
    abdomen partially not present - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 30% - 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: 20.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 40.0% (includes death as larva, prepupa, pupa, adult)

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

    pupal molt delayed (still larva) - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 2 (19 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC012672 RA
      MFHRKLVII SLFLVRLTN ALDWQYHNN TELEKYLKN 
FTATTRGIK TRLYSIGKS TKNNDLWVV RLTAAKESK 
LGVPNIKLI GTVHGNEPV GREILLHFM EFLRANYRT 
DPKITWLLD NTKIHFLPN LNPDGFALA SENMCEGEY 
GRNNALRGM DLNRNFPDY FRTNRIPEA PETKAVKKW 
LREVPFILS AALHGGALV ANYPFDTVQ ELTSFDTYP 
PSETPDNDV FVHLAGVYA RNHLKMHKG DACNKFQKF 
QGGIVNGAA WYPITGGMQ DYNYAFHGC MEITLEISC 
CKYPSAEDL PQFWEENRM ALLNYCVEA HRGVTGQIL 
DRATLKPIA HAALRVSGR NITFRTGKT GEFWRLLLP 
GNYELEVTA EGYYDQSAP FVVRNFNNS LPELTFLKI 
YLINSSFST TTQRTTRVT TELVRETLD GASTTDSFT 
EIIEEKQPI NARQIRLSE ESSASGNGT FVYFLFLLS 
FLTRLFVN
    CDS sequence
    • >TC012672 RA
      atgtttcat cgcaaattg gtgattatt tccctgttc 
ttggtgcgt ttaacgaac gcactcgac tggcaatac 
cacaacaac accgaactc gagaaatat ttgaaaaat 
ttcacggca acaacacgc gggattaaa acccgcctt 
tactccatc ggaaaatca acaaaaaac aacgactta 
tgggtggtg cgtttgacc gccgccaaa gagtcaaaa 
ctaggtgtt ccgaacatt aaactcata ggaactgtc 
catgggaat gagccagtt ggccgcgaa attttgctc 
cacttcatg gagtttttg cgcgccaat taccgcact 
gacccgaaa atcacctgg ctcttggac aacacaaaa 
atccacttt ttgcccaac ctgaacccg gacgggttc 
gcgctagct agcgagaac atgtgcgag ggcgaatac 
ggccggaat aacgctttg cgcggcatg gacttgaac 
cggaacttc ccggattat ttccgcacc aatcggatt 
ccggaggcg ccggagacc aaagctgtg aaaaagtgg 
ctacgtgag gtgcccttt attctatcg gcggctctc 
catggcggg gctctggtc gcgaattac ccattcgat 
acagtgcaa gaattgact tcgttcgat acgtatccg 
ccctcggag acccccgat aacgatgtt ttcgtgcat 
ttggccggg gtttatgcc aggaatcac ctgaaaatg 
cacaagggt gatgcttgt aacaagttt caaaaattc 
caggggggg attgttaac ggggctgcg tggtatccg 
attacagga ggaatgcaa gattacaat tatgcattc 
cacggctgt atggaaatc actctagaa atctcgtgt 
tgtaaatat ccaagcgcg gaagacctg ccacagttc 
tgggaagaa aacagaatg gccttgcta aattactgt 
gtggaggcc cacaggggc gtaacgggc caaatcctc 
gacagggcc accctcaag cccatcgca cacgcagct 
ctgcgagtt tcaggccga aatatcaca ttccgcacc 
ggaaaaacc ggagaattc tggcgactc cttctgccc 
ggaaactac gaacttgaa gtcacggcg gagggatat 
tacgaccaa agtgctcct ttcgttgtc aggaatttc 
aataattcg ttgccggaa ttgaccttt ttgaaaatc 
tatttgata aattcaagt tttagcacc acgacgcag 
agaactaca agagtgacg acggaactt gtaagagag 
actttagat ggcgcttcc acaaccgat tctttcact 
gaaataatc gaagagaag cagccgata aatgccaga 
caaattcgc ttgagcgaa gaaagttcg gccagtggg 
aatggcact tttgtttat ttcctgttt ttactttct 
tttctgacg agactgttt gtcaactga
    mRNA sequence
    • >TC012672 RA
      cgtgctgaa tttatgaga agttatgtt tacaatcag 
ttaaaggtg aaacattta ttatcgttt agaacatcc 
gttgtggtt tccgttccg gtcaaagta aatattaat 
caaaagaaa ataattcaa aatgataat aaatcgccg 
cgataaagt gatttgttt ctgttccac acgtctgtc 
atgtgcgaa acttgctga agaaacact tcattatct 
ctattttgc tgaaaagca tcgaacgac cacaacgat 
atcactata ccaaagtgc aaaatcgcg ccaaaagtt 
ccagtgaca atgtttcat cgcaaattg gtgattatt 
tccctgttc ttggtgcgt ttaacgaac gcactcgac 
tggcaatac cacaacaac accgaactc gagaaatat 
ttgaaaaat ttcacggca acaacacgc gggattaaa 
acccgcctt tactccatc ggaaaatca acaaaaaac 
aacgactta tgggtggtg cgtttgacc gccgccaaa 
gagtcaaaa ctaggtgtt ccgaacatt aaactcata 
ggaactgtc catgggaat gagccagtt ggccgcgaa 
attttgctc cacttcatg gagtttttg cgcgccaat 
taccgcact gacccgaaa atcacctgg ctcttggac 
aacacaaaa atccacttt ttgcccaac ctgaacccg 
gacgggttc gcgctagct agcgagaac atgtgcgag 
ggcgaatac ggccggaat aacgctttg cgcggcatg 
gacttgaac cggaacttc ccggattat ttccgcacc 
aatcggatt ccggaggcg ccggagacc aaagctgtg 
aaaaagtgg ctacgtgag gtgcccttt attctatcg 
gcggctctc catggcggg gctctggtc gcgaattac 
ccattcgat acagtgcaa gaattgact tcgttcgat 
acgtatccg ccctcggag acccccgat aacgatgtt 
ttcgtgcat ttggccggg gtttatgcc aggaatcac 
ctgaaaatg cacaagggt gatgcttgt aacaagttt 
caaaaattc caggggggg attgttaac ggggctgcg 
tggtatccg attacagga ggaatgcaa gattacaat 
tatgcattc cacggctgt atggaaatc actctagaa 
atctcgtgt tgtaaatat ccaagcgcg gaagacctg 
ccacagttc tgggaagaa aacagaatg gccttgcta 
aattactgt gtggaggcc cacaggggc gtaacgggc 
caaatcctc gacagggcc accctcaag cccatcgca 
cacgcagct ctgcgagtt tcaggccga aatatcaca 
ttccgcacc ggaaaaacc ggagaattc tggcgactc 
cttctgccc ggaaactac gaacttgaa gtcacggcg 
gagggatat tacgaccaa agtgctcct ttcgttgtc 
aggaatttc aataattcg ttgccggaa ttgaccttt 
ttgaaaatc tatttgata aattcaagt tttagcacc 
acgacgcag agaactaca agagtgacg acggaactt 
gtaagagag actttagat ggcgcttcc acaaccgat 
tctttcact gaaataatc gaagagaag cagccgata 
aatgccaga caaattcgc ttgagcgaa gaaagttcg 
gccagtggg aatggcact tttgtttat ttcctgttt 
ttactttct tttctgacg agactgttt gtcaactga 
aggctaaaa ataccaata cggggcctg agatggttt 
ttgggtcat tatgagcgt caaaaaata attaattag 
tgccttgtt gttgttgta cataattat ttctttatg 
ttttacgta atattgtac aaataattg atgaataaa 
tgctaatgt tccac

    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