Status
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Gene information
General information
TC004836 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: 2664159..2666721
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
    		TC004836
    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
    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_03855

    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: 20.0% (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

    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: 30.0% (includes death as larva, prepupa, pupa, adult)

    larva lethality - Number of animals showing the phenotype: 2 (11 dpi)
    Days post injection

    eclosion not fulfilled (died as pupa) - Number of animals showing the phenotype: 1 (16 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004836 RA
      MLFKSTEAS KHIEANPHA KRLYDDLLS NYNRLIRPV 
ENHTQTLTV WLGLKLSQL IEMNLKNQV MTTNLWVVQ 
RWYDYKLKW EPEEYGGVE MLYVPSEHI WLPDIVLFN 
NADGNYEVT LMTKATLSY TGEVIWKPP SIYKSSCEI 
NVQYFPFDE QSCLMKFGS WTYNGLQVD LKHMDQVSG 
NNIVKVGID LSEFYLSVE WDILAVPAT RNEEYYPCC 
TEPYSDITF KITMRRKTL FYTVNLIIP CVGITFLTV 
LVFYLPSDS GEKVTLCVS ILLSLTVFF LLLAEIIPP 
TSLAVPLLG KYLLFTMIL VTSSIWVTV CVLNVHFRS 
PSTHKMSPI VRKIFLQFM PKLLIMRRT TYTLPEYDD 
SLPPRGYSG EIEMQLNMR DPFNTDFKM KAHSSMSSS 
NITPRFLSA NVLSALQGV RFIAQHIRD ADKDNEIVE 
DWKFVSMVL DRFFLWVFT LACIGGTFG IILQAPSLY 
DTRVPVHQQ LSEIPLTKI FQIPPSRTH IPTQ
    CDS sequence
    • >TC004836 RA
      atgctgttt aaatccact gaagcctcc aaacacatc 
gaggctaat cctcatgct aagcgatta tacgacgac 
ctcctcagt aattacaat cggctgatc agacctgtg 
gaaaaccat acgcaaact ctaactgta tggctgggc 
ctaaaactg tcacaattg atcgaaatg aacctaaaa 
aatcaagtc atgacgacc aatttatgg gtggtgcag 
agatggtac gactataaa ttaaagtgg gaaccggag 
gaatatggc ggtgtggaa atgctttac gtcccttct 
gagcatatt tggcttccg gacatcgtt ttattcaat 
aatgccgat ggtaattat gaggtgact ttgatgact 
aaagccact ttgtcttac accggcgaa gtaatttgg 
aagccacct tcgatctat aaatcttct tgcgaaata 
aacgtgcaa tattttccc ttcgacgag caaagttgt 
ctaatgaaa ttcggttct tggacttac aatggcctt 
caagtcgac ttgaagcac atggaccaa gtctccggc 
aacaatatt gtcaaagtc ggtattgac ttgtccgaa 
ttttacctt tccgtcgaa tgggacatc cttgcagtc 
cccgccacg cgaaacgaa gagtactat ccttgttgc 
acagagccg tattcagat atcactttc aagataaca 
atgcgtcgc aagacatta ttctataca gtcaacttg 
atcattcct tgcgtcggg atcacattt cttacagtt 
cttgttttc taccttcct tcggattcg ggcgagaaa 
gtcacactt tgtgtctca atcctatta tctctaact 
gtgtttttc ctgttgctc gctgaaatt attccgccg 
acttcgttg gccgtccct ttgttgggc aaatacctc 
ctctttacc atgattttg gtcacttcg tccatatgg 
gtcacggtg tgcgtgctc aacgtgcat ttcagatcc 
ccttcgact cacaaaatg tcgccgatt gtgcgaaaa 
atcttcctc caattcatg cccaaactg ctgattatg 
cggcggacg acttacact ttgcctgag tatgacgac 
agtttgcct cccagagga tacagtggc gagatcgaa 
atgcaattg aatatgaga gatccattc aacactgat 
ttcaaaatg aaagcacat tcgtcgatg tcctcctcg 
aatataact cctcgtttc ctgtcggcg aacgttctc 
tcggctctg cagggtgtt aggtttatt gcacaacac 
atcagagat gccgataaa gataatgaa atcgttgaa 
gattggaag tttgtttcg atggtccta gatcgattc 
tttttatgg gtcttcact ctggcttgc atcggcgga 
actttcggg attatatta caagctcct tccttgtac 
gacacccga gtgcctgtt catcaacaa cttagcgaa 
attcctctc acgaaaatt ttccaaata cccccctcg 
cgcacacac atccccaca caataa
    mRNA sequence
    • >TC004836 RA
      cctggcgat gtgggagta aaacaacat ttccttaat 
tagcctagt tatgtattt aataaaatt agtttgttt 
cactttcat gctgtttaa atccactga agcctccaa 
acacatcga ggctaatcc tcatgctaa gcgattata 
cgacgacct cctcagtaa ttacaatcg gctgatcag 
acctgtgga aaaccatac gcaaactct aactgtatg 
gctgggcct aaaactgtc acaattgat cgaaatgaa 
cctaaaaaa tcaagtcat gacgaccaa tttatgggt 
ggtgcagag atggtacga ctataaatt aaagtggga 
accggagga atatggcgg tgtggaaat gctttacgt 
cccttctga gcatatttg gcttccgga catcgtttt 
attcaataa tgccgatgg taattatga ggtgacttt 
gatgactaa agccacttt gtcttacac cggcgaagt 
aatttggaa gccaccttc gatctataa atcttcttg 
cgaaataaa cgtgcaata ttttccctt cgacgagca 
aagttgtct aatgaaatt cggttcttg gacttacaa 
tggccttca agtcgactt gaagcacat ggaccaagt 
ctccggcaa caatattgt caaagtcgg tattgactt 
gtccgaatt ttacctttc cgtcgaatg ggacatcct 
tgcagtccc cgccacgcg aaacgaaga gtactatcc 
ttgttgcac agagccgta ttcagatat cactttcaa 
gataacaat gcgtcgcaa gacattatt ctatacagt 
caacttgat cattccttg cgtcgggat cacatttct 
tacagttct tgttttcta ccttccttc ggattcggg 
cgagaaagt cacactttg tgtctcaat cctattatc 
tctaactgt gtttttcct gttgctcgc tgaaattat 
tccgccgac ttcgttggc cgtcccttt gttgggcaa 
atacctcct ctttaccat gattttggt cacttcgtc 
catatgggt cacggtgtg cgtgctcaa cgtgcattt 
cagatcccc ttcgactca caaaatgtc gccgattgt 
gcgaaaaat cttcctcca attcatgcc caaactgct 
gattatgcg gcggacgac ttacacttt gcctgagta 
tgacgacag tttgcctcc cagaggata cagtggcga 
gatcgaaat gcaattgaa tatgagaga tccattcaa 
cactgattt caaaatgaa agcacattc gtcgatgtc 
ctcctcgaa tataactcc tcgtttcct gtcggcgaa 
cgttctctc ggctctgca gggtgttag gtttattgc 
acaacacat cagagatgc cgataaaga taatgaaat 
cgttgaaga ttggaagtt tgtttcgat ggtcctaga 
tcgattctt tttatgggt cttcactct ggcttgcat 
cggcggaac tttcgggat tatattaca agctccttc 
cttgtacga cacccgagt gcctgttca tcaacaact 
tagcgaaat tcctctcac gaaaatttt ccaaatacc 
cccctcgcg cacacacat ccccacaca ataaaccac 
agggtataa ccaaaaaac cttcttcct ctaaatggg 
accattgca caattctaa caaagcaca actactttt 
tgaatgttt tatggggca attttccaa aaatcgcac 
aatttttta cccaaacac ttcacactt ttgtggacc 
tagcctctg ttaccaaat gttatatgt gcttaaaat 
acaataaaa accgttaga acat

    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