Status
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Gene information
General information
TC003848 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: 23073973..23075580
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
    		TC003848
    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
    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_03630

    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: 0.0% (includes death as pupa, adult)

    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: 40.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 60.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 4 (11 dpi)
    Days post injection

    eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 1 (16 dpi)
    Days post injection

    eclosion not fulfilled (not completely eclosed) - Number of animals showing the phenotype: 1 (16 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (19 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC003848 RA
      MDEQNIPID INNNKLLDW LVSRRHVTK DWQNSILQV 
REKINNAIQ DMPAHEGII KLLSGQHIN YFHCLKIIE 
ILKETEADS KNLFGRYGS QRMKDWQQI VSMYQKDNI 
YLAEAAQIL IRNVSYEIP SLKKQVAKL EQSQTDAEK 
KIKDYSKNE ALALKEFNT SCEQLGITG KNIKSELIQ 
LLGELPKIY ENAAGKIKL VKPAIELYL AFNQYLSGK 
DTGVEVLPL LRFVAEKGN PTTYEYTYG EKPLKIELE 
EDTLEKNSE SEEQIDFGD NEIDFGENP DFELEESKI 
DWGTPSTDE EFEIVEHTD VDLSLEESG IVVEKSGMD 
GGVARGSEA LTVLDNPKM RDQVINELL ELDSFLKMR 
LFELSNDSD ILAMSQMQN APTMLQMQT VESITSMSD 
CVNVALAEL MNKRTLHLH NIKHSPKYV DILTANLKQ 
KLTLTERMR QSIGVLKEQ IEKYQSEIK NFEPAIRLL 
IEKTKQLQK EVQQDISKR YKGRVVNIV GGVNML
    CDS sequence
    • >TC003848 RA
      atggatgaa cagaacatt ccaatcgat attaacaac 
aacaagctc ctggactgg ttggtgagt cggcgtcac 
gtcaccaaa gactggcaa aacagcatc ctccaagtc 
cgcgaaaaa atcaacaat gcgatccaa gacatgcca 
gcccacgaa ggaataatc aaactacta tccggccaa 
cacatcaac tacttccac tgtttaaaa atcatcgag 
atcttgaaa gaaactgaa gcggacagt aagaattta 
ttcggccgt tacggctcc caacgcatg aaagactgg 
caacaaatc gtctccatg taccaaaaa gacaacatc 
tatttggcc gaagccgcg caaatcctg atccgaaac 
gtcagctac gaaatcccc agcttaaaa aaacaggtg 
gcaaaactg gaacaatcc caaacagac gccgaaaaa 
aaaatcaag gattattcc aagaacgaa gccctggcc 
cttaaggag ttcaacacg tcgtgcgaa cagctggga 
atcacgggc aaaaacatc aagagcgag ctaatccaa 
ctcctgggg gaactaccc aaaatttac gaaaacgca 
gctgggaaa atcaagttg gttaaaccg gccatcgag 
ctatacctt gcctttaac cagtacttg tctgggaaa 
gacacaggg gttgaggta cttcccctg ttgagattt 
gtggccgaa aaaggcaac cccaccact tatgagtac 
acatacggg gaaaaaccg ctcaaaatc gagctagag 
gaagacact cttgagaag aacagtgag agtgaagaa 
cagattgat ttcggtgat aatgaaatc gatttcggg 
gaaaacccc gacttcgag ctcgaagag tcgaaaatc 
gattggggg actcccagc actgacgaa gagttcgag 
attgttgaa cacaccgac gttgattta tccctggaa 
gagtcggga attgtcgtt gaaaagtcg ggaatggac 
ggaggggtg gccaggggc tccgaagcc ctaactgtc 
ctcgataac cccaaaatg cgcgatcag gtcataaat 
gaattgctc gagttggat tcgttcctc aaaatgcgc 
ctctttgag ttatcgaac gattccgat attttggcg 
atgtctcaa atgcaaaat gcgccaacg atgcttcag 
atgcaaacg gttgagtcg atcacgtcg atgagcgat 
tgtgtgaac gtggctttg gctgagttg atgaataag 
cggacgctg catttgcac aatatcaag cattcgccc 
aagtatgta gatattttg accgcgaat ttgaagcaa 
aagttgacg ctgaccgag aggatgagg cagagtatt 
ggggtgttg aaggaacag atcgagaag tatcaaagc 
gaaattaag aattttgag cctgctatt aggcttcta 
attgagaaa accaagcag ttgcaaaag gaggtgcag 
caggatatt tccaagagg tacaaagga cgtgttgtt 
aatattgtc ggaggtgtc aatatgttg taa
    mRNA sequence
    • >TC003848 RA
      tcaaacaac tgtcaaaac actcaaaat aattcaaca 
tatgtttaa tcattttta ggaataaga aattgttga 
aaatggatg aacagaaca ttccaatcg atattaaca 
acaacaagc tcctggact ggttggtga gtcggcgtc 
acgtcacca aagactggc aaaacagca tcctccaag 
tccgcgaaa aaatcaaca atgcgatcc aagacatgc 
cagcccacg aaggaataa tcaaactac tatccggcc 
aacacatca actacttcc actgtttaa aaatcatcg 
agatcttga aagaaactg aagcggaca gtaagaatt 
tattcggcc gttacggct cccaacgca tgaaagact 
ggcaacaaa tcgtctcca tgtaccaaa aagacaaca 
tctatttgg ccgaagccg cgcaaatcc tgatccgaa 
acgtcagct acgaaatcc ccagcttaa aaaaacagg 
tggcaaaac tggaacaat cccaaacag acgccgaaa 
aaaaaatca aggattatt ccaagaacg aagccctgg 
cccttaagg agttcaaca cgtcgtgcg aacagctgg 
gaatcacgg gcaaaaaca tcaagagcg agctaatcc 
aactcctgg gggaactac ccaaaattt acgaaaacg 
cagctggga aaatcaagt tggttaaac cggccatcg 
agctatacc ttgccttta accagtact tgtctggga 
aagacacag gggttgagg tacttcccc tgttgagat 
ttgtggccg aaaaaggca accccacca cttatgagt 
acacatacg gggaaaaac cgctcaaaa tcgagctag 
aggaagaca ctcttgaga agaacagtg agagtgaag 
aacagattg atttcggtg ataatgaaa tcgatttcg 
gggaaaacc ccgacttcg agctcgaag agtcgaaaa 
tcgattggg ggactccca gcactgacg aagagttcg 
agattgttg aacacaccg acgttgatt tatccctgg 
aagagtcgg gaattgtcg ttgaaaagt cgggaatgg 
acggagggg tggccaggg gctccgaag ccctaactg 
tcctcgata accccaaaa tgcgcgatc aggtcataa 
atgaattgc tcgagttgg attcgttcc tcaaaatgc 
gcctctttg agttatcga acgattccg atattttgg 
cgatgtctc aaatgcaaa atgcgccaa cgatgcttc 
agatgcaaa cggttgagt cgatcacgt cgatgagcg 
attgtgtga acgtggctt tggctgagt tgatgaata 
agcggacgc tgcatttgc acaatatca agcattcgc 
ccaagtatg tagatattt tgaccgcga atttgaagc 
aaaagttga cgctgaccg agaggatga ggcagagta 
ttggggtgt tgaaggaac agatcgaga agtatcaaa 
gcgaaatta agaattttg agcctgcta ttaggcttc 
taattgaga aaaccaagc agttgcaaa aggaggtgc 
agcaggata tttccaaga ggtacaaag gacgtgttg 
ttaatattg tcggaggtg tcaatatgt tgtaattaa 
tgtaaataa aaggattac taattt

    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