Status
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Gene information
General information
TC006625 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: 12075261..12077981
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
    		TC006625
    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_01070

    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: 50.0% (includes death as pupa, adult)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 2 (3 dpi)
    Days post injection

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

    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: 50.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 70.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality early (L5/6) - Number of animals showing the phenotype: 4 (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
    • >TC006625 RA
      MFAIRNEDF ESDSDSNFE DEDELTRII PPEVEDTRE 
CMKARHILG ILGFLGFAN VYAMRVNLS VAIVAMVNN 
TAIPQPSTN SNIYDHCLV PNATNSTQP NTSDGEFAW 
DEAKQGIVL GSFFYGYVL TQVPGGRLA ELFGGKLVY 
GVGVLVTAV FTLLSPIAA RINFPLFIL VRVLEGMGE 
GVTFPSMHA MLARWIPPL ERSKFAAYV YAGANFGTV 
ISLPLSGWL CSLELDGGW PLCFYLFGF LGIIWFVFW 
CFLIYDSPS SHPRINPQE RAFILASIG PQDEDDKAS 
IPWLKMLTC VPLWAILIT QCGQSWAFY TQLTELPTY 
MSQILHFDI QANAFLSAI PYLTSWWCG ILISFVADW 
LLSRGYLSL STSYKVFNS LASIVPSLG ILGVAYVGC 
DRVAVQLLL AIPGALAGA VYAGNQMNH IALSPKYAG 
TMYGITNAA SNMCGFLAP YVIGVIIEG RETLGQWRL 
VFYLAAGIN IGANLFYIA FASAREQPW SRSQRLSTI 
N
    CDS sequence
    • >TC006625 RA
      atgtttgca atccgaaat gaggatttc gaaagcgac 
tccgacagc aactttgaa gacgaagac gaactaact 
cgtataatc ccacctgaa gtggaagac acccgagag 
tgcatgaaa gcgcggcat attctagga atcctcggt 
tttctgggc tttgccaat gtgtacgct atgcgtgtc 
aacctgtct gtggccatt gtggccatg gtgaataac 
acagcaatt ccgcaacct tccactaac agcaacatc 
tacgaccac tgtttggtc ccaaacgcc acaaactca 
acacagcca aatacatct gatggggaa tttgcgtgg 
gacgaagcc aagcaaggg attgttttg gggtcgttt 
ttctatggg tatgtgctt acccaggta ccggggggc 
cgtttggcc gagctgttt ggggggaag ttggtgtac 
ggtgtgggg gttttagtg acggcggtt ttcacgtta 
ttgagtccc attgcagcg aggattaat tttccactg 
tttatcctt gtgcgcgtt ctggagggc atgggcgaa 
ggggtcacg tttccctca atgcatgcc atgctggcg 
aggtggatt cctccactg gagaggagc aaatttgca 
gcatatgtt tatgcagga gccaacttt ggcaccgtc 
atatcgctc ccgctatcg ggttggctg tgctcgctg 
gaactggac ggcggttgg ccgctgtgt ttctactta 
ttcgggttc cttggcata atttggttc gtattttgg 
tgctttctc atctacgac tcgccttcg tcccatccg 
aggataaac ccgcaagag cgagctttc atcttagcc 
agcatcggc cctcaagac gaagacgac aaggcctcc 
atcccctgg ctcaaaatg ctaacttgc gtcccactt 
tgggcaatt ctgataacc cagtgtggc cagtcgtgg 
gctttttac acccagttg actgaactg cctacttac 
atgagccaa atcctccac tttgacatt caagctaac 
gcatttttg tccgcaatt ccgtatctt acaagttgg 
tggtgcggg attcttatc agtttcgtg gccgattgg 
ctgttgagt cgtggatat ttgtcgctc tctacttcg 
tacaaagtc tttaattct ttagcttca attgtccca 
tcgctgggt attttgggc gtggcgtat gttgggtgt 
gacagagtg gcggtgcag ctgcttttg gccattccg 
ggggctctt gcgggggcg gtttatgcc ggcaatcaa 
atgaatcac attgctctc agccccaag tatgcgggg 
accatgtac gggatcacg aatgcagcg tccaacatg 
tgcgggttt ctagccccc tatgtcatt ggtgtaatt 
attgaagga cgggaaacg ttgggtcag tggagactg 
gtgttttac ctagctgct ggtattaac attggggcg 
aatttgttt tacatagcg ttcgccagt gcaagggaa 
caaccgtgg tcaaggtca caaagactg agcaccatc 
aactga
    mRNA sequence
    • >TC006625 RA
      gtagaacag ctgataaca ccagtgttt gggaagttg 
taaatacgg ttttaaaaa atatcgtaa cttatcatt 
gattttatt atttattta atgtcacat aatcagtat 
taatcgccg tctacgcat tacatatcg tgttattcc 
gttccgagt gactcattg ctggtgcga agagtcaag 
ctttgtcct agctctgtg tcagttatt atcatcgca 
aaaccatgt ttgcaatcc gaaatgagg atttcgaaa 
gcgactccg acagcaact ttgaagacg aagacgaac 
taactcgta taatcccac ctgaagtgg aagacaccc 
gagagtgca tgaaagcgc ggcatattc taggaatcc 
tcggttttc tgggctttg ccaatgtgt acgctatgc 
gtgtcaacc tgtctgtgg ccattgtgg ccatggtga 
ataacacag caattccgc aaccttcca ctaacagca 
acatctacg accactgtt tggtcccaa acgccacaa 
actcaacac agccaaata catctgatg gggaatttg 
cgtgggacg aagccaagc aagggattg ttttggggt 
cgtttttct atgggtatg tgcttaccc aggtaccgg 
ggggccgtt tggccgagc tgtttgggg ggaagttgg 
tgtacggtg tgggggttt tagtgacgg cggttttca 
cgttattga gtcccattg cagcgagga ttaattttc 
cactgttta tccttgtgc gcgttctgg agggcatgg 
gcgaagggg tcacgtttc cctcaatgc atgccatgc 
tggcgaggt ggattcctc cactggaga ggagcaaat 
ttgcagcat atgtttatg caggagcca actttggca 
ccgtcatat cgctcccgc tatcgggtt ggctgtgct 
cgctggaac tggacggcg gttggccgc tgtgtttct 
acttattcg ggttccttg gcataattt ggttcgtat 
tttggtgct ttctcatct acgactcgc cttcgtccc 
atccgagga taaacccgc aagagcgag ctttcatct 
tagccagca tcggccctc aagacgaag acgacaagg 
cctccatcc cctggctca aaatgctaa cttgcgtcc 
cactttggg caattctga taacccagt gtggccagt 
cgtgggctt tttacaccc agttgactg aactgccta 
cttacatga gccaaatcc tccactttg acattcaag 
ctaacgcat ttttgtccg caattccgt atcttacaa 
gttggtggt gcgggattc ttatcagtt tcgtggccg 
attggctgt tgagtcgtg gatatttgt cgctctcta 
cttcgtaca aagtcttta attctttag cttcaattg 
tcccatcgc tgggtattt tgggcgtgg cgtatgttg 
ggtgtgaca gagtggcgg tgcagctgc ttttggcca 
ttccggggg ctcttgcgg gggcggttt atgccggca 
atcaaatga atcacattg ctctcagcc ccaagtatg 
cggggacca tgtacggga tcacgaatg cagcgtcca 
acatgtgcg ggtttctag ccccctatg tcattggtg 
taattattg aaggacggg aaacgttgg gtcagtgga 
gactggtgt tttacctag ctgctggta ttaacattg 
gggcgaatt tgttttaca tagcgttcg ccagtgcaa 
gggaacaac cgtggtcaa ggtcacaaa gactgagca 
ccatcaact gacaggcgc tttatttgg cgatgcttg 
tcgatgcct agatcaaga ttttttaat accaatgaa 
aggttaaac ttctgctta agcggaagt ttacagtat 
cgttaaata gttaagtat tgaaaaatg tgattccct 
agaattatc caattcatt tactaggtg caatgaata 
ttacaaaaa tatttggtt ttgttcctt tcatattaa 
cccgattat agaatgtat acaggtttt acgggaaat 
caattatta aaaagtcaa attgtgaag actaatttt 
tgagtaatt tagaatcaa atattttat taaaatgtg 
taccttcta taatcatag cataattaa atgtgataa 
agccttatc tcacttttt atttattgt ttttttaag 
tttcttagc cagtgtaaa attggtgtt tacacctcc 
atgtatgaa caattttac gataatgtt tagatctat 
cgaacgggg taccgacta cgaaaggcc cactgaaag 
tttttaatt tccatatta atattgtat ataaatttt 
attgtaaaa tatattttt tctatttat

    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