Status
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Gene information
General information
TC004789 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_007416.3: 7235464..7240289
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
    		TC004789
    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 *
    {{ blurReferenceResult }}
    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_03846

    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)

    Fertility
    ovary without detectable defects - Number of animals showing the phenotype: 5
    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: < 50 embryo/egg with embryonic tissue, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    embryo/egg not developed/not fertilized - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): more than 80%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     egg without cuticle embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): more than 80%
    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): more than 80%
    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: 60.0% (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 (22 dpi)
    Days post injection

    Fertility
    egg production: number <50% of expected -
    Comment: No phenotpe found!
    ovary without detectable defects - Number of animals showing the phenotype: 4
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004789 RA
      MANQYHKLE AKAVQELKD IANKIRIHS VSSTQTAKS 
GHPTSCSSI AEILSVLFF NTMRYKISA PKDPSSDRF 
VLSKGHAAP ALYAVWAEA GLFPVADLQ NLRKLGSDL 
EGHPTPRLN FIDVGTGSL GQGLAIACG MAYVGKNFD 
KASYRVYCL VGDGESAEG SIWESLHFA TYYKLDNLC 
VIFDVNRLG QSEPTSLGH DIDTYRKRL EAFGFNVVA 
VDGHDVEEL VKAFHVSCN TKGKPTAII AKTFKGKNF 
PKIEDLENW HGKPLGDQA DRVLQHLKS LVKNTGPLQ 
LHPQKPLTD DAPIVDISN IKLSSPPSY KIGDSIATR 
VAYGTALVK LGQSNPRVI ALDGDMKNS TYSEALKKF 
DPTRYIECF IAEQNLVGV AIGATCRDR TVAFVSTFA 
TFLTRAYDQ IRMGAISQT NVNFCGSHC GVSIGEDGP 
SQMGLEDIA MFRTIPGST VFYPADAVS TERAVELAA 
NTKGVTFIR TNRPATAVI YPNNHVFQV GKSHVVKKS 
NNDQVLVIG GGVTLQEAI GAANELAKA GVGVRVLDL 
FTIKPIDKE GIIKNAKEC GGRILVVED HYYEGGIGE 
AVLSAVAQE RNIAVKHVA VPKVPRSGS PTALLDYYG 
LNSKHIVNY VQEAMKL
    CDS sequence
    • >TC004789 RA
      atggcaaat caataccac aaactcgaa gccaaggct 
gtccaagag ctgaaggac atcgccaac aaaatccgg 
atccattcg gtcagctcc acgcaaacg gcaaagtcg 
gggcatcca acatcatgc tcgtcaatc gccgaaatt 
ttatcggtc ctttttttc aacacaatg cgatacaaa 
atatcagca ccgaaagac ccctcaagt gaccgcttt 
gtcctttct aaaggtcac gccgctccg gcgctgtac 
gcagtatgg gccgaggcg ggtcttttc cccgttgct 
gatttacaa aacttgagg aaattgggg tcggacctc 
gagggtcat ccaactcct cgcttgaat ttcattgat 
gtagggaca ggctcgctg ggccaaggg ctggccatt 
gcgtgcggc atggcctac gtgggcaaa aacttcgac 
aaggccagt tatagggtg tactgcctg gtcggggat 
ggggagagc gccgagggt tcaatctgg gaatcgctc 
cattttgcg acttactac aagctcgat aatctctgc 
gttatcttt gatgtgaac cgtctcggg caatctgag 
cccacttct ctgggtcat gatatcgac acttacagg 
aaacggttg gaagcgttc ggtttcaat gtagttgcc 
gtcgatgga cacgacgtc gaagagctg gtgaaagcc 
ttccacgtg tcgtgcaac accaaaggg aagcctacc 
gcaatcatt gcgaaaact ttcaaaggg aagaacttc 
cccaaaatt gaagatttg gaaaactgg cacgggaaa 
ccactagga gatcaggcc gatcgtgtc ctccaacac 
ctcaaatct cttgttaaa aacacgggg cctttgcaa 
ctccacccc cagaagccc ctcaccgac gatgctccc 
attgttgac atcagcaat attaaacta tcctcgcct 
ccatcttac aaaatcggc gatagtatt gctacgaga 
gtggcctac ggcactgct ttggtcaag ctcggccaa 
agcaacccc cgagtcatt gcccttgac ggcgatatg 
aaaaattca acatattcg gaagccctt aaaaaattt 
gaccccacg agatacatc gaatgtttc atcgccgaa 
cagaacctt gtcggggtt gccattggt gctacttgt 
cgcgaccgc acagttgcc ttcgtttcc acctttgct 
actttctta acccgtgct tatgaccag attcgtatg 
ggggctatt tctcagaca aatgtcaat ttctgcggc 
tctcattgt ggtgtcagt ataggcgaa gacggacca 
agccagatg gggctggaa gacatcgct atgttccgg 
accatcccc ggaagcact gtcttctac cccgctgat 
gcggtctcc actgaacgt gccgtcgaa ctggccgcg 
aacaccaaa ggagtcact ttcatcaga accaacaga 
ccggccact gctgtcatc taccccaac aatcacgta 
ttccaggtg ggcaagtcg cacgtggtg aagaagtcg 
aacaacgac caagtcctg gttattggt ggcggagtg 
accctgcag gaggccatc ggggccgcc aacgaattg 
gctaaagcc ggtgttggt gtccgtgtt ttggatctg 
ttcaccatc aagccaatt gacaaggag ggaataatc 
aaaaacgcg aaagaatgc ggtgggcgt attctcgtc 
gttgaagac cactactac gaggggggc attggcgag 
gctgtcctt tcggcggtc gctcaggag cgcaacatc 
gccgtgaaa cacgtggca gtgcccaaa gtgccccgc 
tccgggagc cccaccgcc cttttggac tactacggc 
ctcaacagc aaacacatt gtcaattac gtgcaagaa 
gcaatgaag ttgtaa
    mRNA sequence
    • >TC004789 RA
      atcattcaa gtatcaact tatcgactt atcgtcaat 
aattcagat ttgaaatat cgctaaata aaaacagat 
tcgactcat gaataatta cacacaaca tgtattttg 
caatggcct tgcaaatga taatgaaga gttattatt 
gttacataa ctggaaact tattttctt taattaatg 
caaaacatc aatcgcaaa atgcgccat tcttaattg 
ccggcaata aagttttgc acagatgta aataatttt 
atagcgttg ctatgggta gggaccctt taaatatcg 
tgagtcagc aatacggaa cctcatttt tcaaggata 
ggctctcat tgcagtaat tgcacttct attattgtc 
cctcgtgtc atcctgcgc attaaacaa tgcaagatg 
caccgtgtt tgtaaataa ataaaattc attcgagaa 
aaatacaaa gtcaaaatt ttgacccga ttatatcat 
ttttgatta tttataaac tctctgcag gggtgccgg 
ggttacttg atagcacag ttgtcgata gtttgggaa 
atttgggat gatttggcg ttattatat ctcagcttg 
cgttttttt cgattttta tttataaat tctctgctg 
gggttactc gataactta agcgttgat aatattgat 
cgttatgga aaataaaat catgtggaa aatgtgtga 
tttgatggt cacacaact gctgttacg gctgattcg 
agtcatttg attcaattt ttggcgcca aaactggcc 
catgtcttg cggtcattt cagtttgat tgaaaaata 
tgtgttttt gactattgg aaaattgtg tgcgcatgc 
ttccaggtg aaacgcgat tgccttgac tccgggcac 
ctaaaaaat gtctcagag aaagtcccg agtcgaaaa 
attggtgta ttttattta gaaatgtct tagcgttac 
gtaattgtt atctgaccc agcttccaa tagcgtcaa 
tgtacgtaa catagcttg atgttagcg aggtccgca 
ttggctgtc cctcaaggt gtgtgcacg cctgccatt 
taaccactt gttgattac atgctggtg ccaagtgaa 
cgggttagc tctagctcc tgaccggtc tttccctcg 
atgtccgct gatataatg gcaaatcaa taccacaaa 
ctcgaagcc aaggctgtc caagagctg aaggacatc 
gccaacaaa atccggatc cattcggtc agctccacg 
caaacggca aagtcgggg catccaaca tcatgctcg 
tcaatcgcc gaaatttta tcggtcctt tttttcaac 
acaatgcga tacaaaata tcagcaccg aaagacccc 
tcaagtgac cgctttgtc ctttctaaa ggtcacgcc 
gctccggcg ctgtacgca gtatgggcc gaggcgggt 
cttttcccc gttgctgat ttacaaaac ttgaggaaa 
ttggggtcg gacctcgag ggtcatcca actcctcgc 
ttgaatttc attgatgta gggacaggc tcgctgggc 
caagggctg gccattgcg tgcggcatg gcctacgtg 
ggcaaaaac ttcgacaag gccagttat agggtgtac 
tgcctggtc ggggatggg gagagcgcc gagggttca 
atctgggaa tcgctccat tttgcgact tactacaag 
ctcgataat ctctgcgtt atctttgat gtgaaccgt 
ctcgggcaa tctgagccc acttctctg ggtcatgat 
atcgacact tacaggaaa cggttggaa gcgttcggt 
ttcaatgta gttgccgtc gatggacac gacgtcgaa 
gagctggtg aaagccttc cacgtgtcg tgcaacacc 
aaagggaag cctaccgca atcattgcg aaaactttc 
aaagggaag aacttcccc aaaattgaa gatttggaa 
aactggcac gggaaacca ctaggagat caggccgat 
cgtgtcctc caacacctc aaatctctt gttaaaaac 
acggggcct ttgcaactc cacccccag aagcccctc 
accgacgat gctcccatt gttgacatc agcaatatt 
aaactatcc tcgcctcca tcttacaaa atcggcgat 
agtattgct acgagagtg gcctacggc actgctttg 
gtcaagctc ggccaaagc aacccccga gtcattgcc 
cttgacggc gatatgaaa aattcaaca tattcggaa 
gcccttaaa aaatttgac cccacgaga tacatcgaa 
tgtttcatc gccgaacag aaccttgtc ggggttgcc 
attggtgct acttgtcgc gaccgcaca gttgccttc 
gtttccacc tttgctact ttcttaacc cgtgcttat 
gaccagatt cgtatgggg gctatttct cagacaaat 
gtcaatttc tgcggctct cattgtggt gtcagtata 
ggcgaagac ggaccaagc cagatgggg ctggaagac 
atcgctatg ttccggacc atccccgga agcactgtc 
ttctacccc gctgatgcg gtctccact gaacgtgcc 
gtcgaactg gccgcgaac accaaagga gtcactttc 
atcagaacc aacagaccg gccactgct gtcatctac 
cccaacaat cacgtattc caggtgggc aagtcgcac 
gtggtgaag aagtcgaac aacgaccaa gtcctggtt 
attggtggc ggagtgacc ctgcaggag gccatcggg 
gccgccaac gaattggct aaagccggt gttggtgtc 
cgtgttttg gatctgttc accatcaag ccaattgac 
aaggaggga ataatcaaa aacgcgaaa gaatgcggt 
gggcgtatt ctcgtcgtt gaagaccac tactacgag 
gggggcatt ggcgaggct gtcctttcg gcggtcgct 
caggagcgc aacatcgcc gtgaaacac gtggcagtg 
cccaaagtg ccccgctcc gggagcccc accgccctt 
ttggactac tacggcctc aacagcaaa cacattgtc 
aattacgtg caagaagca atgaagttg taattttat 
catgtttac taatggagc ggtgtaaca ttccatttt 
aataaaaaa attctaagt ta

    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