Status
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Gene information
General information
TC000578 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: 9470561..9473736
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
    		TC000578
    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
    {{ blurEvidenceResult }}
    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_06621

    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

    remarks: eggs lost,
    Adult morphology
    remarks: eggs lost,
    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg with embryonic tissue potentially present, no cuticle, no fluorescence - Penetrance (percentage of animals/eggs on slide): less than 30%

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

    larval musculature fluorescence decreased - Penetrance (percentage of animals/eggs on slide): less than 30%

    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
    number of eggs/embryos/larvae on slide: > 50
     embryo/egg without visible larval cuticle in cuticle preparation - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    metathorax not present - Penetrance (percentage of animals/eggs on slide): less than 30%

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

    metathorax potentially transformed - Penetrance (percentage of animals/eggs on slide): less than 30%

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

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

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): 50% - 80%
    remarks: eggs lost,
    remarks - cuticles: later than schedule,
     
    8 days later, due to lost eggs in day 9
     

    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
    • >TC000578 RA
      MVLKSKGAL KGQPPLPGE ASEGAKQSR GRGRPKSPS 
RPKSPARPK SPARKSPSR TRKDSPPLQ SSTPKVSSP 
KARSPMRRS PSRKSPTRA VKTTVTKSA ETYFSERVT 
RPRRTRVDI DTDSDNPDG DVPHEKPQA AVRGRARRL 
EVQVEKLNL NATDSRSSP FNLIKRATR NSQNREVER 
VVHLKHFDS VAKKMGEFS DEDDSLMVR KSVSVDRGQ 
EFRQITEFG GVWGALFYM FTTPLTIIA LLAACNENQ 
CSFTQMPDL KKYSNLNTW FDLTSILGF FGYAIFLAI 
LSVIPFGGK QITGLATKQ GKFQYIMNG LFSCFVFLM 
IGIGLELRN IPICEFIVK HLFHLTIAS ILFGFILTF 
YAFVRSFYV PFNALNAHV VGRNKIYGF FMGRELNPQ 
AFGLLDLKM YVFRLALIG AALLDLTYL YTSLGLNTT 
PSIKTVDLK SLSINPTLV ILVLIHLVY YLDALAHEA 
TFVSSFEIQ YEGFGFMSG VGYLIYPIM MATVTKYVV 
DYDVTLPVW KLTWVNLIF VLGYILFRG SNNQKDAFR 
KNPYDPALS HLETIPTTK GKKLICSGF WGIVRHPNY 
LGDILMNLS FIPFAAHVP PVVTSISII LFMIHRSVR 
DNVRCKQKY GAAWDRYCS KVKYVLVPK VY
    CDS sequence
    • >TC000578 RA
      atggtactg aaatcgaaa ggggccttg aaaggccaa 
ccgcctctt cccggggaa gcttcggaa ggtgccaag 
cagtcgaga ggccgtggc agacccaaa agcccctcc 
aggcccaag agcccggcg cgccctaaa agcccggcc 
cgcaaaagc ccctcgagg acacgaaag gactcccct 
ccgctgcag tcctccacg cccaaagtg tcctctccg 
aaagcgcgc agccctatg aggagaagc ccaagccgg 
aagtccccc acgagggcc gtcaaaacc actgttaca 
aaaagcgca gagacttat ttctcggag agagtgact 
agaccgcgc cggacgcgg gtcgatata gacacggac 
tcggacaac cccgacggg gatgtgccc cacgagaag 
ccccaagcc gccgtcagg ggacgcgcg aggcggctg 
gaggtccaa gtcgagaag ttaaatctg aatgcaact 
gactcaagg tcgagccct ttcaacctc atcaaacgc 
gcgacgaga aattcgcaa aatcgtgaa gttgagaga 
gtcgtccat ttgaagcat tttgatagt gtggcgaaa 
aaaatgggc gagttttcg gatgaggac gacagcttg 
atggtgagg aagtcggtc tcggttgat aggggacag 
gagtttcga caaattacc gaatttggg ggcgtttgg 
ggcgcgctt ttttacatg tttaccact cccttgacg 
atcattgcg ttattagcg gcgtgcaac gagaatcag 
tgctcgttc actcaaatg cccgatttg aagaaatat 
tcgaattta aacacctgg tttgatttg acttcgatt 
ttgggtttt ttcggttat gcgattttt ttggcgatt 
ttatcggtt atcccgttc ggtgggaaa cagattacc 
gggttggca acaaaacag ggaaaattt cagtacata 
atgaacggt cttttctcg tgttttgtt tttttaatg 
atcggaatt ggattagag ttgaggaat ataccgatt 
tgtgaattt atagtcaaa catttattc catttgaca 
atcgcgtcg attttattc ggttttatt ttaacgttt 
tacgctttt gtgagaagt ttttatgtt ccgtttaat 
gcgttaaat gctcatgtg gtcgggagg aataaaatt 
tatggtttc tttatgggg cgggaattg aatccacaa 
gcttttgga ctgcttgat ttgaaaatg tacgtcttt 
aggttggct ttaattgga gctgcactg ctggatcta 
acgtatctt tacacttcg ttgggtcta aacaccacg 
ccatcaata aaaacggtt gatttaaaa tcgttatca 
atcaaccca actttggtc attcttgta ctgattcat 
ttggtgtat tatttggat gctttggca catgaagct 
acctttgtt tcatcgttt gaaattcag tatgaagga 
tttggattt atgtcagga gttggttat ttgatttat 
ccaataatg atggctaca gtaacgaaa tacgttgtt 
gattacgac gtcacattg ccagtctgg aaattgact 
tgggtcaac cttattttt gtccttgga tatatttta 
tttagagga agtaataat caaaaagat gcctttaga 
aaaaatccc tacgatcct gcactttca catttggaa 
acaattccg acgaccaaa ggcaagaaa cttatctgt 
tccggtttt tggggcatc gtccgtcac ccgaattac 
cttggggat attttaatg aatctgtct tttattccc 
ttcgctgcc cacgtacca ccagttgtg acttcaatt 
tcgattata ttatttatg attcatcgt tctgttaga 
gataatgtt agatgtaaa cagaaatat ggggctgca 
tgggacagg tactgtagc aaagtaaaa tacgtgcta 
gtgccgaaa gtctactag
    mRNA sequence
    • >TC000578 RA
      actcttatt ttgactaac ttccaaacc ggccaatca 
aatcgccac atttcgaac gcgttgttt gcgatcaag 
tgagcgtct gtcgtgtta cggcgtctt ttggttgta 
aacacaaga atatttttc gaattattt tggaaatac 
cccaacaac accgccaca atttaagcg atggtactg 
aaatcgaaa ggggccttg aaaggccaa ccgcctctt 
cccggggaa gcttcggaa ggtgccaag cagtcgaga 
ggccgtggc agacccaaa agcccctcc aggcccaag 
agcccggcg cgccctaaa agcccggcc cgcaaaagc 
ccctcgagg acacgaaag gactcccct ccgctgcag 
tcctccacg cccaaagtg tcctctccg aaagcgcgc 
agccctatg aggagaagc ccaagccgg aagtccccc 
acgagggcc gtcaaaacc actgttaca aaaagcgca 
gagacttat ttctcggag agagtgact agaccgcgc 
cggacgcgg gtcgatata gacacggac tcggacaac 
cccgacggg gatgtgccc cacgagaag ccccaagcc 
gccgtcagg ggacgcgcg aggcggctg gaggtccaa 
gtcgagaag ttaaatctg aatgcaact gactcaagg 
tcgagccct ttcaacctc atcaaacgc gcgacgaga 
aattcgcaa aatcgtgaa gttgagaga gtcgtccat 
ttgaagcat tttgatagt gtggcgaaa aaaatgggc 
gagttttcg gatgaggac gacagcttg atggtgagg 
aagtcggtc tcggttgat aggggacag gagtttcga 
caaattacc gaatttggg ggcgtttgg ggcgcgctt 
ttttacatg tttaccact cccttgacg atcattgcg 
ttattagcg gcgtgcaac gagaatcag tgctcgttc 
actcaaatg cccgatttg aagaaatat tcgaattta 
aacacctgg tttgatttg acttcgatt ttgggtttt 
ttcggttat gcgattttt ttggcgatt ttatcggtt 
atcccgttc ggtgggaaa cagattacc gggttggca 
acaaaacag ggaaaattt cagtacata atgaacggt 
cttttctcg tgttttgtt tttttaatg atcggaatt 
ggattagag ttgaggaat ataccgatt tgtgaattt 
atagtcaaa catttattc catttgaca atcgcgtcg 
attttattc ggttttatt ttaacgttt tacgctttt 
gtgagaagt ttttatgtt ccgtttaat gcgttaaat 
gctcatgtg gtcgggagg aataaaatt tatggtttc 
tttatgggg cgggaattg aatccacaa gcttttgga 
ctgcttgat ttgaaaatg tacgtcttt aggttggct 
ttaattgga gctgcactg ctggatcta acgtatctt 
tacacttcg ttgggtcta aacaccacg ccatcaata 
aaaacggtt gatttaaaa tcgttatca atcaaccca 
actttggtc attcttgta ctgattcat ttggtgtat 
tatttggat gctttggca catgaagct acctttgtt 
tcatcgttt gaaattcag tatgaagga tttggattt 
atgtcagga gttggttat ttgatttat ccaataatg 
atggctaca gtaacgaaa tacgttgtt gattacgac 
gtcacattg ccagtctgg aaattgact tgggtcaac 
cttattttt gtccttgga tatatttta tttagagga 
agtaataat caaaaagat gcctttaga aaaaatccc 
tacgatcct gcactttca catttggaa acaattccg 
acgaccaaa ggcaagaaa cttatctgt tccggtttt 
tggggcatc gtccgtcac ccgaattac cttggggat 
attttaatg aatctgtct tttattccc ttcgctgcc 
cacgtacca ccagttgtg acttcaatt tcgattata 
ttatttatg attcatcgt tctgttaga gataatgtt 
agatgtaaa cagaaatat ggggctgca tgggacagg 
tactgtagc aaagtaaaa tacgtgcta gtgccgaaa 
gtctactag ttttaaaaa aagtactgt taattgcct 
gaatgttta tgtacatac ttttaacac tacacaaag 
gtgttcaga cttatcagt aaattttgt acaatctga 
acacgacta ttttttaga tgtacccaa tcagagtgt 
atgtgtaat atttacatg ttattttta tgcaaagtt 
gctcaacaa tctttttgc ataaaaatc tgattgggt 
ttgaagaaa ttgaaaatt tcttgatca cgtttagaa 
ttaagttat cgtaggtgt aggtcataa tttttattt 
tattggtgt gagtttata agttttttg ccatacttt 
accaatgaa atgacaaag tacaaactg aacacattg 
taccaaact tatgttata gtcacagtg gggtttttg 
ctctctcat acaacaatt atattttca tttttcgtg 
atctcaact agattgtgc aatgttttt gacaaaaag 
gaataagta tggaaataa aaaaaggag gttcaaaac 
gtaactaaa atcgaaaat tatagtatt tttgtaatt 
acagtatgg agatgcgcg gtttataat gcgacttgt 
atgaatttt atcaatttt tagataact taaattttt 
ataacaatg aaacatatt agcccaaat ttttaatac 
agtggtgta taataaggg ggccccatg gcgtccttt 
tttatgtgt tttattttc catacactt aactgacat 
attttaaat aaataggaa attagtatt taaaatttt 
aaattttat gattttttt gaaagtgcc ctagtagta 
aaagaacag attgatttc tacttatag attgtttta 
gaataaatt tttttaaag tga

    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