Status
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Gene information
General information
TC006230 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: 5480378..5487291
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
    		TC006230
    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.
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_04096

    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: 20.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 20.0% (includes death as larva, prepupa, pupa, adult)

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

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC006230 RA
      MAVSTSWFH QWNPPNLFP DPFFDNFTT GRSKQKNVD 
KYGQISNLL PFFLQLGLL EPPPPPTER TGHFTTWYK 
WKMLDYVYP SDEDRIAAI ASEDFIPEN NLPLGLEVY 
QDRIFVTMP KWKPGVPAT LAVIPKTRR ELSPKLVPY 
PNWDYHRTG SCEGITSVF RVQVDTCGR LWVLDSGQV 
DITIQPRQI CPVQIFLFD LKTDKLLLR YPLPDDFIK 
QDCLYSNIA IDIRDNDCL DVHAYLTDV WRYGLVVFS 
LKRRTSWRI TDHLFYPEP LAAAYNVHG LEFEWVDGI 
FGMALSPYN KKAKDRVLY FHPMSSFRE FFVKTSIIC 
NETGWSDVK DAFKVMGQS RGKFGHVSA SGMDRNGVM 
FFNMVTRDS IGCWDSRKP YKRDNIGII ARSTKTLVF 
PNDLKIDLE EKQSVWVLS NRLPFFLYR ELNKSDYNF 
RILTAYAED AIKDTVCDP HYRNHDTFR SFPDGEDCY
    CDS sequence
    • >TC006230 RA
      atggcagtg agcacctcc tggttccac cagtggaac 
cccccgaac ctcttcccg gaccccttt ttcgataac 
ttcaccacc ggaaggagc aagcaaaaa aatgtcgat 
aaatatggg caaatttcc aacctcctc ccatttttc 
ctgcaactg ggcctcctg gaaccccca cctccaccc 
acggagcgc accggccat tttaccaca tggtacaaa 
tggaaaatg ctggactac gtctaccca tcggacgag 
gaccggatc gcagccatc gcaagcgag gactttatt 
ccggaaaac aacctacca ttgggcctg gaggtgtac 
caggaccgg atttttgtc accatgccc aaatggaag 
cctggcgta ccagccaca ctggccgtc atacccaaa 
acacgacgg gaactgtcc ccaaaactg gtaccctac 
cccaactgg gactaccat aggactggt tcttgtgag 
ggcataacg tcggttttt agggtccaa gttgatact 
tgtggacgt ctgtgggtg ctagattcg ggtcaggtt 
gacataacc atccaaccc aggcaaata tgcccagtc 
caaattttt ctatttgac ctcaaaacg gacaaactt 
ttactccgg taccctcta ccggacgat ttcatcaaa 
caggattgt ctctatagc aacatcgcc atagatatc 
cgcgataat gactgtctg gacgtccac gcctacttg 
accgatgtc tggcggtat ggccttgtg gttttcagt 
ctcaaaaga aggacaagt tggcgcatc accgaccat 
ttgttttac cctgagccc ctcgctgcg gcttacaac 
gtccatgga ctcgagttc gaatgggtg gatggtatt 
ttcggtatg gccttaagt ccatacaac aagaaggcc 
aaagaccgc gtcctgtac tttcaccca atgtcgagc 
tttcgcgag tttttcgtc aagacttcg atcatttgt 
aacgagact ggatggagt gatgttaag gacgcgttc 
aaggtgatg gggcaaagc cgggggaag ttcgggcac 
gtgtcggcc tccgggatg gacaggaat ggggtgatg 
ttcttcaat atggtcaca agggactcg atcgggtgt 
tgggactcg cgaaagccg tacaagagg gataatatc 
gggattatt gccaggagt acgaagact ttggttttt 
cccaatgat ttgaagatt gatttggag gagaagcaa 
agtgtgtgg gtcttgtcg aaccgtttg ccatttttc 
ttataccgc gaactgaac aagagtgat tataatttt 
aggattttg actgcgtac gctgaagat gccataaaa 
gataccgtt tgtgatccg cattatcgc aatcatgac 
accttcagg agctttcct gatggcgaa gattgctac 
taa
    mRNA sequence
    • >TC006230 RA
      gtacgctgc aaaactcac tcaagccga agaaaatgc 
ttgaaaaac gccagtgtt gaaccagag tgtgaacag 
ctttcacag tcgttaccg atcaggcgt gctaacata 
acgagacaa aattttatt tctattatt acaattttt 
tttaataag ttttgtgac catggtcgg aagtgccca 
aacttttgc ccaaaaaaa gtgactctc taggccaaa 
aatgccggt ttaaccacc accatggca gtgagcacc 
tcctggttc caccagtgg aaccccccg aacctcttc 
ccggacccc tttttcgat aacttcacc accggaagg 
agcaagcaa aaaaatgtc gataaatat gggcaaatt 
tccaacctc ctcccattt ttcctgcaa ctgggcctc 
ctggaaccc ccacctcca cccacggag cgcaccggc 
cattttacc acatggtac aaatggaaa atgctggac 
tacgtctac ccatcggac gaggaccgg atcgcagcc 
atcgcaagc gaggacttt attccggaa aacaaccta 
ccattgggc ctggaggtg taccaggac cggattttt 
gtcaccatg cccaaatgg aagcctggc gtaccagcc 
acactggcc gtcataccc aaaacacga cgggaactg 
tccccaaaa ctggtaccc taccccaac tgggactac 
cataggact ggttcttgt gagggcata acgtcggtt 
tttagggtc caagttgat acttgtgga cgtctgtgg 
gtgctagat tcgggtcag gttgacata accatccaa 
cccaggcaa atatgccca gtccaaatt tttctattt 
gacctcaaa acggacaaa cttttactc cggtaccct 
ctaccggac gatttcatc aaacaggat tgtctctat 
agcaacatc gccatagat atccgcgat aatgactgt 
ctggacgtc cacgcctac ttgaccgat gtctggcgg 
tatggcctt gtggttttc agtctcaaa agaaggaca 
agttggcgc atcaccgac catttgttt taccctgag 
cccctcgct gcggcttac aacgtccat ggactcgag 
ttcgaatgg gtggatggt attttcggt atggcctta 
agtccatac aacaagaag gccaaagac cgcgtcctg 
tactttcac ccaatgtcg agctttcgc gagtttttc 
gtcaagact tcgatcatt tgtaacgag actggatgg 
agtgatgtt aaggacgcg ttcaaggtg atggggcaa 
agccggggg aagttcggg cacgtgtcg gcctccggg 
atggacagg aatggggtg atgttcttc aatatggtc 
acaagggac tcgatcggg tgttgggac tcgcgaaag 
ccgtacaag agggataat atcgggatt attgccagg 
agtacgaag actttggtt tttcccaat gatttgaag 
attgatttg gaggagaag caaagtgtg tgggtcttg 
tcgaaccgt ttgccattt ttcttatac cgcgaactg 
aacaagagt gattataat tttaggatt ttgactgcg 
tacgctgaa gatgccata aaagatacc gtttgtgat 
ccgcattat cgcaatcat gacaccttc aggagcttt 
cctgatggc gaagattgc tactaaatt attcaaata 
aatttttat tttctcaat tgttgttta cttaatcac 
ccaagacac aaaaaaccc taaataaat cctaataaa 
ttacattat gcgat

    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