Status
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Gene information
General information
TC005842 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: 6758319..6760210
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
    		TC005842
    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
    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
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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_04020

    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: 10.0% (includes death as pupa, adult)

    adult lethality - Number of animals showing the phenotype: 1 (9 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 larval musculature irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): less than 30%
    remarks: muscle pattern potentially obscured by segmentation defect,
    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
    • >TC005842 RA
      MPPVVESRP TWSSNFRLY LAMFSYSTG ITIPKFASP 
WLLKTNVGI LLLIPVQLL VMFLTTIPC MFMELALGQ 
YSNRAVIRV WDLCPLLRG IGLCSFLTF LLYQSYYNF 
LCTCSLCFT FLSFTSEPQ WRSCNRSWN KINCFTLRD 
NYTKRLECS QRYGREKCD KMQWQSSVE QFYFNRVLN 
TDETSGYVG APQPELLVY GLVTIILIF FANYGGPKT 
TEKFLLVLA TVPTVQMVV LFFAPLSDQ NGFVTLNYL 
FTQLDVKNL SNFKTWTRI INLSLSSPG LGFGAFIAF 
GTQSTFRTP LHFKAIIIS VTSVLFTVL YSIIVQNFL 
ISLCIQSQM LFDDFFKLE QELEMPEAV FFLEHSSRF 
WITMWLSNC YMTGLRSLI VMMCLNTEV VYNSLPKAR 
KRHTLCVLT FSLIIYTGT IFLSTRIGY SVFKTIESV 
LNDFCVPFL NTLQLVGVV YFYGITKFR DDVHFMLGI 
RSSVYWNTL YVLNPLLLG IVLAYNLHD FFTGGSFNF 
HSLGIFRIS LIWFSLVVV TLYAFFYII VSFFGHHFK 
VCKSSPEWG PRHGSLFVS RKMFKAYNV AKEYLYRQE 
RFSQQ
    CDS sequence
    • >TC005842 RA
      atgcctccg gtggtggaa tcccgccca acgtggagc 
tccaatttc cggctctac ctggcaatg ttcagctac 
agtaccggg ataacgatc ccgaagttc gctagtcct 
tggctcctc aagaccaat gtcgggatc ctcctcctg 
atccccgtc cagctcctg gtcatgttc ctgacgacg 
atcccttgc atgttcatg gagctagcc ctggggcag 
tactccaac cgggcggtg atacgagtg tgggacttg 
tgcccgtta ctgcgagga atcggctta tgcagtttc 
ctcacgttt ctgctctac caatcgtat tacaatttc 
ctctgtaca tgtagtctt tgtttcacg tttttgtca 
ttcacgagc gaaccacaa tggagatct tgtaacagg 
agttggaat aagataaat tgcttcact ttgcgagac 
aattacacg aagcgactc gaatgcagc cagagatac 
ggcagggaa aagtgcgac aagatgcag tggcagtcg 
agcgtggag cagttttac ttcaaccgg gtgctgaac 
acggatgag acttccggt tatgtgggg gccccccag 
cctgaacta ctggtctat ggattggtc acaattatt 
ttgattttt tttgcgaac tatggtggc cccaaaacc 
accgaaaaa ttccttctg gtgttggca acggtgccc 
acggttcaa atggttgtc ttgtttttt gcccccttg 
tcggaccag aacggcttt gtgaccctt aattacttg 
ttcacccaa ctggatgtg aaaaatttg tccaatttt 
aagacctgg actaggatt ataaacttg tctctgagt 
agtccaggc ctggggttt ggtgccttc attgctttc 
ggcacgcag agcactttc aggacccct ctgcacttc 
aaggcgatc ataataagc gtcacttcg gttttattc 
acagtcttg tacagtatc atagtccag aacttttta 
atttcgttg tgcatccaa agccagatg ttgtttgac 
gattttttt aaactggaa caggagctg gagatgcct 
gaggccgtg tttttcctg gaacacagt tccaggttt 
tggataacc atgtggtta tccaattgt tacatgacc 
ggtctccga agtttgatt gtgatgatg tgcctgaac 
accgaagtg gtttataac tcgttacca aaggccaga 
aaacgacac acactctgt gttctaacg ttctctctt 
ataatctac accgggacg attttcctg tcaacgaga 
attggttac tccgtgttt aaaaccatc gaaagtgtg 
ttaaacgac ttttgtgtt ccgttcctc aacacttta 
caactcgtc ggagttgtg tatttttac ggtattact 
aaatttaga gacgatgtc cactttatg ttagggata 
cggtcgtca gtgtactgg aacacgctc tacgtcctt 
aatcccctt cttctgggg attgtgttg gcctacaac 
ttgcacgat ttcttcact ggggggagt ttcaatttt 
cacagtctt ggtattttt aggataagt cttatttgg 
tttagtctt gttgttgtc acgttgtat gcttttttc 
tacattatt gttagtttc tttgggcac cattttaaa 
gtttgtaag tcgtcacct gagtggggc cctcgacac 
ggctccctg tttgtgagc cgaaaaatg ttcaaggcc 
tataacgtg gccaaggag tatttgtat cgtcaagaa 
cggttcagt cagcaataa
    mRNA sequence
    • >TC005842 RA
      aaagttgac gcgcgcgtt tcaaatcca tgcctccgg 
tggtggaat cccgcccaa cgtggagct ccaatttcc 
ggctctacc tggcaatgt tcagctaca gtaccggga 
taacgatcc cgaagttcg ctagtcctt ggctcctca 
agaccaatg tcgggatcc tcctcctga tccccgtcc 
agctcctgg tcatgttcc tgacgacga tcccttgca 
tgttcatgg agctagccc tggggcagt actccaacc 
gggcggtga tacgagtgt gggacttgt gcccgttac 
tgcgaggaa tcggcttat gcagtttcc tcacgtttc 
tgctctacc aatcgtatt acaatttcc tctgtacat 
gtagtcttt gtttcacgt ttttgtcat tcacgagcg 
aaccacaat ggagatctt gtaacagga gttggaata 
agataaatt gcttcactt tgcgagaca attacacga 
agcgactcg aatgcagcc agagatacg gcagggaaa 
agtgcgaca agatgcagt ggcagtcga gcgtggagc 
agttttact tcaaccggg tgctgaaca cggatgaga 
cttccggtt atgtggggg ccccccagc ctgaactac 
tggtctatg gattggtca caattattt tgatttttt 
ttgcgaact atggtggcc ccaaaacca ccgaaaaat 
tccttctgg tgttggcaa cggtgccca cggttcaaa 
tggttgtct tgttttttg cccccttgt cggaccaga 
acggctttg tgaccctta attacttgt tcacccaac 
tggatgtga aaaatttgt ccaatttta agacctgga 
ctaggatta taaacttgt ctctgagta gtccaggcc 
tggggtttg gtgccttca ttgctttcg gcacgcaga 
gcactttca ggacccctc tgcacttca aggcgatca 
taataagcg tcacttcgg ttttattca cagtcttgt 
acagtatca tagtccaga actttttaa tttcgttgt 
gcatccaaa gccagatgt tgtttgacg attttttta 
aactggaac aggagctgg agatgcctg aggccgtgt 
ttttcctgg aacacagtt ccaggtttt ggataacca 
tgtggttat ccaattgtt acatgaccg gtctccgaa 
gtttgattg tgatgatgt gcctgaaca ccgaagtgg 
tttataact cgttaccaa aggccagaa aacgacaca 
cactctgtg ttctaacgt tctctctta taatctaca 
ccgggacga ttttcctgt caacgagaa ttggttact 
ccgtgttta aaaccatcg aaagtgtgt taaacgact 
tttgtgttc cgttcctca acactttac aactcgtcg 
gagttgtgt atttttacg gtattacta aatttagag 
acgatgtcc actttatgt tagggatac ggtcgtcag 
tgtactgga acacgctct acgtcctta atccccttc 
ttctgggga ttgtgttgg cctacaact tgcacgatt 
tcttcactg gggggagtt tcaattttc acagtcttg 
gtattttta ggataagtc ttatttggt ttagtcttg 
ttgttgtca cgttgtatg cttttttct acattattg 
ttagtttct ttgggcacc attttaaag tttgtaagt 
cgtcacctg agtggggcc ctcgacacg gctccctgt 
ttgtgagcc gaaaaatgt tcaaggcct ataacgtgg 
ccaaggagt atttgtatc gtcaagaac ggttcagtc 
agcaataac ttgtgcaat aaaatattt caaataac

    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