Status
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Gene information
General information
TC004920 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_007417.3: 4611770..4617327
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
    		TC004920
    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
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    Name
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    Email
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_08981

    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: 40.0% (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: 2 (9 dpi)
    Days post injection

    Fertility
    ovary without detectable defects - Number of animals showing the phenotype: 3
    mature egg structure irregular - Number of animals showing the phenotype: 1

    mature egg number increased - Number of animals showing the phenotype: 1
    yolk potentially latedeposition irregular - Number of animals showing the phenotype: 1
    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: % (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: % (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004920 RA
      MGLGGCYAI LKYLLVLLN LIFALLGIA GTVFAIWML 
VDPSFSLSL TQDYIISVV IILIASLLL LVVAIFGIV 
GALKESQCA LTTFFCLLL IIFVAEVSA GVWVHINRD 
SLKLQIKNA VELTVEQEY YTSDNRKAI FDTFQQKLQ 
CCGAKAASD WIGNKKVVL TVTSNQENY SIPMSCCRE 
GTTMEDCKK ATLNIKPTS SIDYTAIYD KGCYYAIMT 
KLEELSWVL IVGIVLAVI QILGLIFAL ILAFAVNRS 
NRYKA
    CDS sequence
    • >TC004920 RA
      atggggctt gggggctgc tacgccatc ttaaaatac 
ctcctggtg ctcctaaat ttgatattt gcgttgttg 
ggcattgct ggcaccgtc ttcgcaata tggatgctc 
gtcgacccc tcattttcg ctatcgctc actcaagac 
tacataatt tcggtcgta ataattctc atcgcttca 
cttctcctc ctcgttgtg gctattttc ggcattgtt 
ggcgctttg aaagagagc cagtgtgcc ctaacgacc 
ttcttctgt ctcctctta atcattttc gtagctgag 
gtatcagcc ggagtttgg gtgcacatc aatcgagac 
agcctcaaa ctgcaaatt aaaaatgct gttgaactc 
accgtggaa caggaatac tacaccagc gacaatcgc 
aaggctatt tttgacacc tttcagcaa aaattgcaa 
tgttgcggc gccaaagcg gctagcgac tggatcggg 
aataagaaa gtggtgctt acggtgacc tcaaaccag 
gagaattat agcattccc atgagttgc tgtcgcgaa 
gggactacg atggaagat tgcaaaaaa gcaacgcta 
aatattaag ccgacaagc tcgattgac tacacagcg 
atttacgac aaaggttgc tactacgcc attatgacc 
aagttggaa gagctttcg tgggttttg atcgttgga 
atagttcta gcggtgatc cagattttg ggtttgatc 
tttgctctg attcttgca tttgccgtt aaccgatct 
aataggtac aaagcctaa
    mRNA sequence
    • >TC004920 RA
      tggttcatg aatgaagct gcgtttatt tcgaattta 
ttgcccaat ttcgggttt cgagtcggc gcgatttcg 
gccgaagcg gcttcggcg gtatccgca tgtgcaaca 
tccgttgac aaatcccag tgatcgctt tcggttgaa 
tccaaaaca aacagaatc tcatctcaa catttgtga 
aagaattgt gaatctcac tgaaaaatg gggcttggg 
ggctgctac gccatctta aaatacctc ctggtgctc 
ctaaatttg atatttgcg ttgttgggc attgctggc 
accgtcttc gcaatatgg atgctcgtc gacccctca 
ttttcgcta tcgctcact caagactac ataatttcg 
gtcgtaata attctcatc gcttcactt ctcctcctc 
gttgtggct attttcggc attgttggc gctttgaaa 
gagagccag tgtgcccta acgaccttc ttctgtctc 
ctcttaatc attttcgta gctgaggta tcagccgga 
gtttgggtg cacatcaat cgagacagc ctcaaactg 
caaattaaa aatgctgtt gaactcacc gtggaacag 
gaatactac accagcgac aatcgcaag gctattttt 
gacaccttt cagcaaaaa ttgcaatgt tgcggcgcc 
aaagcggct agcgactgg atcgggaat aagaaagtg 
gtgcttacg gtgacctca aaccaggag aattatagc 
attcccatg agttgctgt cgcgaaggg actacgatg 
gaagattgc aaaaaagca acgctaaat attaagccg 
acaagctcg attgactac acagcgatt tacgacaaa 
ggttgctac tacgccatt atgaccaag ttggaagag 
ctttcgtgg gttttgatc gttggaata gttctagcg 
gtgatccag attttgggt ttgatcttt gctctgatt 
cttgcattt gccgttaac cgatctaat aggtacaaa 
gcctaaaat taaaacata caaaggata tttttcttc 
tacaaattt attttcgga tcaagagtt tatattaaa 
atgcagaag aatcgcaca tattttcga ttgtgtaca 
aattgtata tccttaaac ttcaagtgt tgtaacatg 
tgtgccata tattgtgac cgacggttt tgcacgaaa 
cggccgatt gaagctcat tagagtcaa aattgtcca 
aattttaca atggttgtt tcgtgcaaa aacgcccgg 
atgtgtaac ttagcttta cctttagat atagtttgg 
tgtacaacc tttctaagc actgtacct aaaatatat 
tttcttaaa agaaaattt ttcgacatg cactagcat 
ttactcatg acatttaac tttagactg atatttatt 
ttcactgtt cgaatgtcc agtaatctc atttactgt 
ctctcaagt tttagttga tgatttaga cgagagcat 
tccattttt gatgaatgc tgttagaaa tcctagcat 
gccagtgtt aaatacgta gtgtaagta gtatagagt 
tgccaaaat gtttttagt tctgatgtg aataatcag 
tattgtagt ctaattttt ttattataa acagttgtg 
tgccaaaaa ctttcaaat ttacagagt tgcctattt 
ggttatata ttttatcaa atatttaag aaaattctt 
tgttaccat accatttca gcagccagt cagtgatag 
tgaagaaac gagccaagg aattgtcag tactaataa 
tattaatta gaatttatc gaagttgat gctatttaa 
atggtatat tgtgagtcg tgattcatt cagttttcc 
ggcatttat attagtttc agcattgta tattcagat 
atttaatgg aataagatg tgttttagc ttattttgt 
taataaaca aatacaacc aat

    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