Status
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Gene information
General information
TC005712 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: 8574243..8579778
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
    		TC005712
    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
    If you have entered your name and agree by marking the checkbox. we might show your name on this page to honor your contribution.
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_03999

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

    larva lethality - Number of animals showing the phenotype: 5 (11 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (41 dpi)
    Days post injection

    Fertility
    egg production: number <50% of expected -
    Comment: No phenotype found!
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC005712 RA
      MVKLKAPPY RVWIAVMIF MTTFTNYML RANMSVSII 
SMVDKAKKN QTAVCATPA DNSTKPPPP PKSGSKKFK 
WSETDQGWI LAAYFYGYF LTLMPGGLI SNYIGPWHV 
LLWTGVGSA VLTGLTPIC ATSGGVGGV CANRFFIGF 
LGGPVYPAV NDLIAKWAP PKEKGKFLA AMMGNTLGT 
VLTWLAVAA ASSAWGWEW GFYVLAIFM LVFCATFGI 
VVRDRPDVH PWVSDDEKK HIFEAQEGH LTTKKGFPP 
YHKMLCFSI PFWALVIAQ FGNAWGLNL IITYVPKFM 
AETLGFNIK ASAGLAALP YIGRLLGSS VFGVIVDYM 
RKKEVMSVT KIRKLFITF SHFIPGLCL ILIRAFGCI 
KEGVIAMLV LNQGFNGAC VVSQLVNPQ DLSPNFAGA 
VFGIMNFFG MTTGLFVPK ITGYLNTTY TGFKGPTLI 
FMIGGIVYV ATGIVFILF GSGEVQPWN KKKGEEEAE 
TTEAK
    CDS sequence
    • >TC005712 RA
      atggttaaa ttaaaagcg ccaccatat cgggtatgg 
atcgcagtt atgattttc atgacgact tttacaaac 
tacatgctg agagccaac atgtccgtg agtataatc 
agcatggtt gacaaggca aagaaaaat cagacagca 
gtttgcgca actcctgcc gacaattca actaaacct 
cccccgcca cccaaatct gggagtaaa aaattcaaa 
tggagcgaa accgaccaa ggctggatc ctcgctgcc 
tatttctac ggctacttc ctcacactg atgcctgga 
ggtctgata tcaaattac atcggccct tggcacgtt 
ctcctgtgg acgggcgtt ggcagtgcc gtcttaact 
ggcttgact cccatttgc gccacatct ggaggtgtg 
ggtggggtt tgcgctaac cgatttttc atcggcttt 
cttgggggg ccagtgtac cccgccgtc aacgattta 
atcgcaaag tgggcgccg cccaaggaa aagggcaag 
tttctggcg gctatgatg ggcaacacc ttggggacg 
gtgctgacg tggctggcg gtggccgcg gcctcgtcg 
gcatggggc tgggagtgg gggttttac gttctggct 
attttcatg ttggttttt tgcgctacc tttggaata 
gttgtgagg gatagaccg gatgtacat ccttgggtt 
tccgatgac gaaaaaaag catattttc gaagcccaa 
gaagggcat cttacaacg aagaagggc tttcccccg 
taccacaaa atgttgtgt tttagcatc ccattctgg 
gctttagtt atagcccag tttggcaat gcctggggc 
ttgaatttg atcatcact tacgtcccc aaattcatg 
gccgaaacc ttaggcttc aatattaaa gcttcagcc 
ggtctcgct gcccttcca tacattggt cggcttctt 
ggtagtagt gtgttcggg gtcattgtt gattatatg 
cgtaaaaaa gaagtcatg tctgtgacc aaaatccga 
aaactcttt ataactttt tcccatttt atcccgggc 
ctctgtttg atactgatc cgagctttc ggttgtata 
aaagaaggc gtcatagcc atgctggtg ctaaaccag 
ggcttcaac ggtgcatgt gtggtcagc cagttggtt 
aacccacaa gatctctca ccgaatttc gctggagca 
gttttcgga atcatgaac tttttcggc atgactaca 
ggattattc gtgcccaag ataacagga tacttgaac 
acgacttat acaggattt aaaggcccg acgttaata 
ttcatgatt ggaggaatt gtttatgtg gctactggt 
attgtattt attcttttt ggatctggt gaggtgcag 
ccttggaat aaaaagaag ggcgaggaa gaggcggaa 
acgacagaa gcaaaataa
    mRNA sequence
    • >TC005712 RA
      atactctct ttacaatgg ttaaattaa aagcgccac 
catatcggg tatggatcg cagttatga ttttcatga 
cgactttta caaactaca tgctgagag ccaacatgt 
ccgtgagta taatcagca tggttgaca aggcaaaga 
aaaatcaga cagcagttt gcgcaactc ctgccgaca 
attcaacta aacctcccc cgccaccca aatctggga 
gtaaaaaat tcaaatgga gcgaaaccg accaaggct 
ggatcctcg ctgcctatt tctacggct acttcctca 
cactgatgc ctggaggtc tgatatcaa attacatcg 
gcccttggc acgttctcc tgtggacgg gcgttggca 
gtgccgtct taactggct tgactccca tttgcgcca 
catctggag gtgtgggtg gggtttgcg ctaaccgat 
ttttcatcg gctttcttg gggggccag tgtaccccg 
ccgtcaacg atttaatcg caaagtggg cgccgccca 
aggaaaagg gcaagtttc tggcggcta tgatgggca 
acaccttgg ggacggtgc tgacgtggc tggcggtgg 
ccgcggcct cgtcggcat ggggctggg agtgggggt 
tttacgttc tggctattt tcatgttgg ttttttgcg 
ctacctttg gaatagttg tgagggata gaccggatg 
tacatcctt gggtttccg atgacgaaa aaaagcata 
ttttcgaag cccaagaag ggcatctta caacgaaga 
agggctttc ccccgtacc acaaaatgt tgtgtttta 
gcatcccat tctgggctt tagttatag cccagtttg 
gcaatgcct ggggcttga atttgatca tcacttacg 
tccccaaat tcatggccg aaaccttag gcttcaata 
ttaaagctt cagccggtc tcgctgccc ttccataca 
ttggtcggc ttcttggta gtagtgtgt tcggggtca 
ttgttgatt atatgcgta aaaaagaag tcatgtctg 
tgaccaaaa tccgaaaac tctttataa ctttttccc 
attttatcc cgggcctct gtttgatac tgatccgag 
ctttcggtt gtataaaag aaggcgtca tagccatgc 
tggtgctaa accagggct tcaacggtg catgtgtgg 
tcagccagt tggttaacc cacaagatc tctcaccga 
atttcgctg gagcagttt tcggaatca tgaactttt 
tcggcatga ctacaggat tattcgtgc ccaagataa 
caggatact tgaacacga cttatacag gatttaaag 
gcccgacgt taatattca tgattggag gaattgttt 
atgtggcta ctggtattg tatttattc tttttggat 
ctggtgagg tgcagcctt ggaataaaa agaagggcg 
aggaagagg cggaaacga cagaagcaa aataattgc 
acatgaagt cgtttcctt gtttgtagt attttcgaa 
ataacagca aaacaaact caaaataca caatcttga 
ttaac

    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