Status
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Gene information
General information
TC004600 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: 6827774..6835773
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
    		TC004600
    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
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    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_06181

    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)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 1 (3 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg not developed/not fertilized - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    larva partially dorsalnot closed - Penetrance (percentage of animals/eggs on slide): less than 30%

    legs podomer number decreased - Penetrance (percentage of animals/eggs on slide): less than 30%

    legs shape irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

    abdomen number decreased - Penetrance (percentage of animals/eggs on slide): less than 30%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 50% - 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: 10.0% (includes death as larva, prepupa, pupa)
    Lethalities 22 days after larval injection: 10.0% (includes death as larva, prepupa, pupa, adult)

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004600 RA
      MSEGESKKL SELRVVDLK AELEKRGLD QKGIKRDLV 
DRLQKALQS EGLDPETYC FEIGEKKPV KRLSTSSSS 
YQGDDNVCT EKTETDSDA KEEETNVVT KEETEEQVG 
SGSNKTDAE PETINLTLE EEENIPEES AERESKNSG 
DKIVSDEKP TTPKQVQME ESTSPTSQQ ASKKTPETP 
GTSPSNGAE EPSQKKAQS NPRLLWITN VPKNTRANE 
LKQLLSSCG KVVCAKVVV NARFPGSCC FGYITMGSA 
EDAANVISK LNNTEFNGQ IIKIDKFEN IKSDINPTR 
KTKSEENKK SQTSEKKED KTKKSPEGK EKNEEKNDD 
NEKAAKSPA SPERRKSLN SDRSSRGRR RTTSKERQK 
ERPMHRSTS RGHKSSVLT FDKIKEERE RQRMRERER 
AIREESRRR REEAERMRE MREITRRQK SEADRLERE 
REKLRIERD RIEREKSEL IKLERERQR IEREKLEME 
KMELQRSRL RLEEDRRAV KRPLPVPYR REDTFEERK 
RPNNVRHFE DTTPRFEPP PPPTPVQQK KFAPSKDFK 
RMSYDKHES FSDKRRDYN SDRSHPGSS VRSNPSVNR 
YDNVRGRDS RDAPSRDSQ SNLMRSKER YNERDRSPH 
FRPLGESRD RHSSSQGKS DRDHHYSEQ NSDRWNHPT 
NSQSKFGSN NQKPWSGKS NWRPDPPTV DRWNSSRSS 
MNQQFSGNS NMAPTCPPP PGINNYSDR FDYKSSGLR 
KY
    CDS sequence
    • >TC004600 RA
      atgtctgaa ggcgagagc aagaaattg tcggaattg 
cgtgtagtg gatttaaaa gccgagttg gaaaaacgg 
ggtttggac caaaaagga atcaaacga gatctggtg 
gaccgcctt caaaaggca ctgcaaagc gaggggttg 
gaccccgaa acgtactgc tttgaaatc ggggagaag 
aaaccagtt aagaggctt tcaacttcg tcatcttct 
taccaaggg gatgacaat gtttgtact gaaaagact 
gaaactgat agcgacgca aaggaggaa gagacaaat 
gttgtcacg aaagaggaa acagaggaa caagttggt 
agtggatcg aataagact gatgcggag ccagaaacc 
ataaattta actttggaa gaggaggaa aatattccc 
gaagagagc gccgagcgg gagagtaag aattctggc 
gataaaata gtttccgat gagaagcca acaacacct 
aaacaagtc cagatggaa gagtcgacg tcacccact 
tcacagcag gcctccaag aaaacgcca gaaacacca 
gggactagc cctagcaat ggagcggaa gaaccgagt 
cagaagaag gcccagtca aaccctcgc ctactctgg 
attactaac gtccctaaa aacacgcgc gctaacgaa 
ctcaaacaa ctgctttcg tcttgtgga aaagtcgtt 
tgcgctaaa gtcgtcgtt aacgcaagg tttcccgga 
tcatgttgc ttcggatac atcacaatg ggatcggct 
gaggatgcg gctaatgtc atttccaaa ctaaataat 
accgaattt aacggacag attatcaag attgataaa 
tttgagaat atcaaatcg gatattaat ccgacacgg 
aaaactaaa agcgaagaa aataagaaa tcacaaacg 
agtgaaaag aaggaggat aaaactaag aaaagtcca 
gagggcaaa gaaaagaat gaagagaaa aatgatgat 
aatgagaaa gcggcgaaa agtccagcc agccctgaa 
agaaggaag tccttaaat tccgaccga tctagtcgc 
ggacgcaga cgtaccacc tcaaaagag cggcagaaa 
gaaaggccg atgcatcgc tccacctct cgagggcat 
aagtccagt gtcctaact ttcgacaaa attaaagag 
gaacgagag cggcagcgc atgcgcgag cgcgaacgc 
gccattcgc gaagagagc cgacgccgt cgagaggag 
gcagagcgc atgcgcgaa atgcgtgaa atcacccgt 
cgccagaaa agcgaagca gaccgatta gaacgcgaa 
cgcgagaaa ttgcgaatc gaacgcgac cgaatcgag 
cgcgaaaaa agcgaattg ataaaactg gagcgagag 
cgtcaacga atcgaacgc gagaagcta gaaatggaa 
aaaatggag ttacaaagg tcacgtttg aggcttgag 
gaggaccgc agggctgtg aaacgtcca cttcctgtg 
ccctacaga cgggaggac acattcgag gagcgaaaa 
cgtccaaac aatgtgcgt cattttgag gacacaacg 
ccgcggttt gaaccgccg ccgccgcct actccggtg 
caacagaag aagtttgca ccttcgaaa gattttaaa 
cgaatgtcc tatgataag catgagtcg ttttcggac 
aaacgcagg gattataat tcggacagg tcgcatcca 
gggtcgtcg gttaggtcg aacccttcg gttaatcgg 
tatgataac gtcagaggg cgcgattcg cgggatgcg 
ccatctagg gactcgcaa tcgaacttg atgaggtcg 
aaggagcgg tacaatgag agggacagg agcccccat 
tttaggccc cttggggag agcagggac cgccatagt 
tcgtctcag gggaaatca gatcgagat catcactac 
tcagaacaa aattctgat cgttggaac cacccaact 
aactcacaa tcgaagttc ggttcaaat aaccaaaag 
ccttggtct ggcaaaagc aactggcgt ccagaccca 
cctacggtc gacagatgg aactcaagt aggtcttca 
atgaatcaa cagttctct ggaaattcc aatatggcg 
ccgacttgt ccacctccg ccaggaatt aataattat 
tcagatcga ttcgactac aagtccagt ggacttaga 
aaatattaa
    mRNA sequence
    • >TC004600 RA
      tgcaaccta aatggctgg tgtctgtgt gaaaaatta 
gcatttttt ctaaattta ttgaaatgt ctgaaggcg 
agagcaaga aattgtcgg aattgcgtg tagtggatt 
taaaagccg agttggaaa aacggggtt tggaccaaa 
aaggaatca aacgagatc tggtggacc gccttcaaa 
aggcactgc aaagcgagg ggttggacc ccgaaacgt 
actgctttg aaatcgggg agaagaaac cagttaaga 
ggctttcaa cttcgtcat cttcttacc aaggggatg 
acaatgttt gtactgaaa agactgaaa ctgatagcg 
acgcaaagg aggaagaga caaatgttg tcacgaaag 
aggaaacag aggaacaag ttggtagtg gatcgaata 
agactgatg cggagccag aaaccataa atttaactt 
tggaagagg aggaaaata ttcccgaag agagcgccg 
agcgggaga gtaagaatt ctggcgata aaatagttt 
ccgatgaga agccaacaa cacctaaac aagtccaga 
tggaagagt cgacgtcac ccacttcac agcaggcct 
ccaagaaaa cgccagaaa caccaggga ctagcccta 
gcaatggag cggaagaac cgagtcaga agaaggccc 
agtcaaacc ctcgcctac tctggatta ctaacgtcc 
ctaaaaaca cgcgcgcta acgaactca aacaactgc 
tttcgtctt gtggaaaag tcgtttgcg ctaaagtcg 
tcgttaacg caaggtttc ccggatcat gttgcttcg 
gatacatca caatgggat cggctgagg atgcggcta 
atgtcattt ccaaactaa ataataccg aatttaacg 
gacagatta tcaagattg ataaatttg agaatatca 
aatcggata ttaatccga cacggaaaa ctaaaagcg 
aagaaaata agaaatcac aaacgagtg aaaagaagg 
aggataaaa ctaagaaaa gtccagagg gcaaagaaa 
agaatgaag agaaaaatg atgataatg agaaagcgg 
cgaaaagtc cagccagcc ctgaaagaa ggaagtcct 
taaattccg accgatcta gtcgcggac gcagacgta 
ccacctcaa aagagcggc agaaagaaa ggccgatgc 
atcgctcca cctctcgag ggcataagt ccagtgtcc 
taactttcg acaaaatta aagaggaac gagagcggc 
agcgcatgc gcgagcgcg aacgcgcca ttcgcgaag 
agagccgac gccgtcgag aggaggcag agcgcatgc 
gcgaaatgc gtgaaatca cccgtcgcc agaaaagcg 
aagcagacc gattagaac gcgaacgcg agaaattgc 
gaatcgaac gcgaccgaa tcgagcgcg aaaaaagcg 
aattgataa aactggagc gagagcgtc aacgaatcg 
aacgcgaga agctagaaa tggaaaaaa tggagttac 
aaaggtcac gtttgaggc ttgaggagg accgcaggg 
ctgtgaaac gtccacttc ctgtgccct acagacggg 
aggacacat tcgaggagc gaaaacgtc caaacaatg 
tgcgtcatt ttgaggaca caacgccgc ggtttgaac 
cgccgccgc cgcctactc cggtgcaac agaagaagt 
ttgcacctt cgaaagatt ttaaacgaa tgtcctatg 
ataagcatg agtcgtttt cggacaaac gcagggatt 
ataattcgg acaggtcgc atccagggt cgtcggtta 
ggtcgaacc cttcggtta atcggtatg ataacgtca 
gagggcgcg attcgcggg atgcgccat ctagggact 
cgcaatcga acttgatga ggtcgaagg agcggtaca 
atgagaggg acaggagcc cccatttta ggccccttg 
gggagagca gggaccgcc atagttcgt ctcagggga 
aatcagatc gagatcatc actactcag aacaaaatt 
ctgatcgtt ggaaccacc caactaact cacaatcga 
agttcggtt caaataacc aaaagcctt ggtctggca 
aaagcaact ggcgtccag acccaccta cggtcgaca 
gatggaact caagtaggt cttcaatga atcaacagt 
tctctggaa attccaata tggcgccga cttgtccac 
ctccgccag gaattaata attattcag atcgattcg 
actacaagt ccagtggac ttagaaaat attaatttt 
gtatttatt agccacctg ttttttttg tttgttaca 
attaattat gtgtttgac caatttaat aaataatat 
ttaaagtaa cacgctttt tgtttcatt tatttttta 
cattagaat tacaacaat caacaataa aaataacaa 
gacacgaaa ttaatccaa gccgtgttc tacaacgga 
cagcattga acttgtttt agacggagc caaaaggta 
cgatttttt gtccattcg gaacggtac caaaacctt 
gactccgtc caactgacc gcttgattc gagcttcca 
acctgcgat aaactggaa cgaaaagat gaaatattt 
gttgttttg cgtcacgac gcttaaata ggcatcgct 
aatcccaaa acctgaaac aaaaaatag tgaagtcag 
gctaggacc actttagaa acataacaa gagaaataa 
agacgtttg tctgca

    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