Status
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Gene information
General information
TC005444 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: 13098921..13102785
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
    		TC005444
    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_03953

    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: < 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: 0.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 0.0% (includes death as larva, prepupa, pupa, adult)

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

    Pupal morphology
    head completeorientation bent - Number of animals showing the phenotype: 10

    antenna orientation bent - Number of animals showing the phenotype: 10

    Adult morphology
    antenna orientation bent - Number of animals showing the phenotype: 9


    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC005444 RA
      MNTLTFLLL TFCTSIHTQ TSKFYVIRQ WKYLNFTWP 
DEDALKTAT ATGDYIPEN NIVSGIKYF EDYYYLTLP 
RMKKGVPAT LARIKAGPT RDTAPPLEP FPSWGMNQL 
GDCNNLQNV QNVEIDAKG QVWIIDGGR VQTLVEPVV 
KCGAKLVVY GLREGRVST VFHFPEEVA ARNGSYLYD 
LVVDDTDGG FAYITDNSA IDPGIIVFS VKENRAWKI 
RHSKTMTAD PSARHFTAN GVPISVPIN IAGIALGPK 
IHTSNEKLI VNEDREVYF SPLSSLHLY SINTSSLRN 
PANFSDSSV TDLGLKSSQ SVGMVMDNQ GILYYTLLA 
NNAIGRWDS HTPFQSGQK LIAQDSKYL EWPNSLTLE 
TMGNLTVLM NRLNQFVYD KFDLNKYNF RLITAFVGG 
RSYVYDDNF NYDMNRDER MFHNESKTT PEPLPTPAP 
EPHYDDITS TMSNNVEIV KSASHKLAS SLFTLILCF 
LLVRR
    CDS sequence
    • >TC005444 RA
      atgaacact ctcaccttc ctcctgctc accttttgc 
acctcaatc cacactcaa acgagcaaa ttttacgtc 
atccgccaa tggaagtac ctcaacttc acatggccg 
gacgaagac gccctcaaa acggccaca gccaccgga 
gactacatc ccggaaaat aacatcgtt tccgggatc 
aagtacttc gaggattac tactacttg acgctcccg 
aggatgaag aagggagta ccggcgacg ctggcacgg 
atcaaggct gggcccacc cgggacacg gcgccgcct 
ctggagccc ttcccctcc tgggggatg aaccagctg 
ggggattgc aacaatttg cagaatgtg caaaacgtg 
gagattgac gccaagggc caggtgtgg attattgac 
ggagggagg gtgcagacg ttggtggag ccggtggtt 
aagtgcggg gccaagttg gtggtgtat gggctgagg 
gagggaagg gtgagcacg gtgtttcat ttcccggag 
gaagtcgca gcgagaaat gggagttat ttgtacgat 
cttgtggtg gatgatact gatggcggg tttgcttat 
attacggat aatagtgcc atcgatcca ggaataatc 
gtcttttcg gtgaaagaa aaccgcgcg tggaaaatc 
cgccactca aaaaccatg acagcagat ccctccgcc 
cgccatttc accgccaat ggagtgccc atttccgtc 
cccatcaac atagctggc atagcccta ggccccaaa 
attcacaca agcaacgaa aaactaata gtcaacgag 
gacagggag gtttatttc agtccgttg tcaagcctc 
cacctttac tcaatcaac acttcgagt ctccgaaac 
cctgctaat ttctccgac agctccgtc accgacttg 
gggctgaaa tcctcacag tcggtgggg atggtgatg 
gacaaccaa gggatactt tattacacc cttttggcc 
aacaacgcc atagggcga tgggacagt cacaccccg 
ttccaatcc gggcagaaa ttaatcgcc caggacagc 
aaataccta gagtggccc aactctcta actttggaa 
actatgggc aacttgacc gtgcttatg aatcggctc 
aaccaattc gtttacgat aagttcgac ttaaacaag 
tacaatttt agactgatt acggccttt gtgggcggg 
agaagttac gtgtacgac gataatttc aattatgat 
atgaatagg gacgaaagg atgtttcac aatgaaagt 
aaaacgact ccagaacca cttccaact cctgcaccg 
gagccgcat tacgatgac ataacatca acgatgagc 
aataacgtg gaaatagtt aaatcagca agtcataaa 
ttagcgagt agtttgttt actttgatt ttgtgtttt 
ctgctagtg cgacggtga
    mRNA sequence
    • >TC005444 RA
      tgaacttga ccactcgca atgaacact ctcaccttc 
ctcctgctc accttttgc acctcaatc cacactcaa 
acgagcaaa ttttacgtc atccgccaa tggaagtac 
ctcaacttc acatggccg gacgaagac gccctcaaa 
acggccaca gccaccgga gactacatc ccggaaaat 
aacatcgtt tccgggatc aagtacttc gaggattac 
tactacttg acgctcccg aggatgaag aagggagta 
ccggcgacg ctggcacgg atcaaggct gggcccacc 
cgggacacg gcgccgcct ctggagccc ttcccctcc 
tgggggatg aaccagctg ggggattgc aacaatttg 
cagaatgtg caaaacgtg gagattgac gccaagggc 
caggtgtgg attattgac ggagggagg gtgcagacg 
ttggtggag ccggtggtt aagtgcggg gccaagttg 
gtggtgtat gggctgagg gagggaagg gtgagcacg 
gtgtttcat ttcccggag gaagtcgca gcgagaaat 
gggagttat ttgtacgat cttgtggtg gatgatact 
gatggcggg tttgcttat attacggat aatagtgcc 
atcgatcca ggaataatc gtcttttcg gtgaaagaa 
aaccgcgcg tggaaaatc cgccactca aaaaccatg 
acagcagat ccctccgcc cgccatttc accgccaat 
ggagtgccc atttccgtc cccatcaac atagctggc 
atagcccta ggccccaaa attcacaca agcaacgaa 
aaactaata gtcaacgag gacagggag gtttatttc 
agtccgttg tcaagcctc cacctttac tcaatcaac 
acttcgagt ctccgaaac cctgctaat ttctccgac 
agctccgtc accgacttg gggctgaaa tcctcacag 
tcggtgggg atggtgatg gacaaccaa gggatactt 
tattacacc cttttggcc aacaacgcc atagggcga 
tgggacagt cacaccccg ttccaatcc gggcagaaa 
ttaatcgcc caggacagc aaataccta gagtggccc 
aactctcta actttggaa actatgggc aacttgacc 
gtgcttatg aatcggctc aaccaattc gtttacgat 
aagttcgac ttaaacaag tacaatttt agactgatt 
acggccttt gtgggcggg agaagttac gtgtacgac 
gataatttc aattatgat atgaatagg gacgaaagg 
atgtttcac aatgaaagt aaaacgact ccagaacca 
cttccaact cctgcaccg gagccgcat tacgatgac 
ataacatca acgatgagc aataacgtg gaaatagtt 
aaatcagca agtcataaa ttagcgagt agtttgttt 
actttgatt ttgtgtttt ctgctagtg cgacggtga 
aacaacgag aaatttcgg tcgggtcgc tcaaaatgg 
cccccggac ggccatttt gagcctgta aatatactc 
tgtttagga tagtcatta gcttgatca gactgtttt 
gttttgtaa tcattatta attctgttg cgttgttgt 
ctagtgttt tagttacca aagccatta acacgtaat 
aaaatatcg aaaacaaa

    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