Status
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Gene information
General information
TC006403 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: 8463659..8468622
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
    		TC006403
    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 *
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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
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    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_04132

    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: 40.0% (includes death as pupa, adult)

    adult lethality - Number of animals showing the phenotype: 3 (9 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection

    Fertility
    mature egg deposition blocked number 1st lateral oviduct: 2 number 2nd lateral oviduct: - Number of animals showing the phenotype: 1
    previtellogenic egg chamber orientation irregular - Number of animals showing the phenotype: 2

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 larval musculature pattern irregular - Penetrance (percentage of animals/eggs on slide): more than 80%

    affected eggs/embryos/larvae - Penetrance (percentage of animals/eggs on slide): more than 80%
    remarks: muscle pattern potentially obscured by segmentation defect,
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     larva everted (inside-out) - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    larva partially everted (inside-out) - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    affected eggs/embryos/larvae - 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: % (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
    • >TC006403 RA
      MDTEFYNLH KALSAYKTS ISTSMDKID DIFSQAAST 
FINPDCARG PNPKKYTIS LEIVTVLQH YIRILSTVE 
SLADGLATK LSNLDRDAE PERETACNP FTSALLSDS 
KECAVSCFF HNLKAQIAE RDVSSGVDS DNVSSDAET 
IVDLKTENL DEYARLNLF DVNVKPENA PESEISNSQ 
KATNNSKTQ IKFEVEADD SSGAETLVE QPVQGKNDL 
LDHSRLNPF KADSNEPKT GAKKKKTVR IKEEPPCEN 
AEIEYTALS KLLSMSVHD RRREAQKKF ENKSIKRDF 
NWRNVTSPP RDKKVREKF SIYDILEDQ LSVGQKCVF 
SHIISPAEF YLRTNQALF EMLQNSLNE DMNSQHQWV 
VNKYKTKED ARTHMGNFC FAFLPNKRK WYRVEVLDW 
LMEEELENI CIQLIDFGE TYYCKFEIL LPMTLFYSM 
FPRMAVRCH FAAIYSPDP SKWPESSIE ALEQMSEME 
AKTEFETIF VCKEGNSYG IDLLNEEKF GKKTLGQIL 
VDSELALQV DISDGLEAL EDEDFEEYE NINEAITGY 
DAKDEARLC PFTNAAGGC FKGARCKLE HGVLAKDGV 
TTDKVLTMN QAFTVTPLP PKGQCVDVL VTGYISTCR 
FYAQIVTAP SKTSNFNAN FQRLRESMN SNNIVHTYE 
PFKLYPGLG EVVLIKENS EWFRGICVG LAENDKIEV 
FFVDFGYKR EKKLKDLRQ MKEDLLYVP FQAVECMLE 
GCQEKKDAP KNASQTFFD SCMNLKVFK ALVVESEEP 
LRLSMWDSE GMEMGYVLK TCGLGEDRK KDVFPTKDC 
YLSCN
    CDS sequence
    • >TC006403 RA
      atggatacg gaattttac aatttacac aaagccctt 
tctgcctac aagacgtcc atcagcaca agtatggac 
aaaattgac gatatcttt tcgcaagct gcaagtact 
tttatcaat cccgattgt gccagaggt ccaaacccg 
aaaaagtac acaatttcg ctcgaaatc gtaacagtt 
ttgcagcat tatattagg attcttagc actgttgag 
agcttagcc gacggtttg gcgaccaag ctctctaac 
ctagaccgt gacgcagag cctgaaaga gaaacagct 
tgcaatcct ttcacttcg gccctttta agcgactcg 
aaagagtgt gcagtttcg tgcttcttc cataacttg 
aaggcacaa attgccgaa agagatgtc agttcgggc 
gtcgattct gacaatgtt agttcagac gcggaaacg 
atagtggac ctaaaaacc gaaaatttg gacgaatac 
gcacgattg aatctgttt gatgtcaac gttaagcct 
gaaaatgcg cccgaaagt gaaatttcc aactctcaa 
aaagccaca aacaattcg aaaactcaa atcaaattc 
gaggttgaa gctgacgac agttcgggg gccgaaacg 
cttgtggaa caaccagtt cagggaaaa aacgatttg 
ttagatcac agtagactt aaccctttc aaagctgac 
tcgaatgag cccaaaaca ggggcaaaa aagaagaaa 
actgtaaga atcaaggag gagccgcct tgcgaaaac 
gccgaaatc gaatatacg gccctgagc aaacttttg 
tcgatgtct gtgcatgac aggcgtcgc gaggcgcag 
aaaaagttt gaaaacaaa tccatcaaa cgcgatttc 
aattggcgc aacgtcacc tcgccacca cgtgacaaa 
aaagtgcga gaaaaattc tcgatttac gatattctt 
gaggaccag ttaagtgtg ggccagaag tgtgttttc 
agtcacata atctcgccc gccgagttt tatcttcgc 
acgaatcag gcgttgttt gaaatgctg caaaatagc 
ttgaacgag gatatgaat agccaacac cagtgggtt 
gttaataaa tataaaacg aaggaggat gcaaggaca 
catatgggc aatttttgt ttcgcgttt ttgcccaat 
aagcggaag tggtacaga gtcgaggtg cttgattgg 
ctgatggag gaagaattg gagaatatc tgcatccag 
ttgattgat tttggcgaa acatactat tgcaaattt 
gagatactc ctccccatg accctattt tactcaatg 
tttccgcgt atggccgtc aggtgccac tttgcagcg 
atttattca cctgatcct agtaaatgg ccagaatcg 
agtatcgaa gccttggaa caaatgagc gaaatggag 
gctaaaacc gaattcgag acgattttt gtatgcaag 
gagggaaat tcgtatgga attgatctc ttgaatgag 
gagaaattt gggaagaaa acgttgggt cagattttg 
gtcgactcc gaacttgcc ctccaagtg gacatttca 
gacggactt gaagcatta gaggatgaa gatttcgaa 
gagtatgaa aacatcaac gaggccata actggatac 
gatgccaaa gatgaagca agactttgc cccttcact 
aatgcggca gggggctgt tttaaaggg gcaaggtgt 
aagctagaa cacggcgtt ttggcgaaa gatggcgtc 
acgacggat aaagttttg acgatgaat caagcgttc 
actgtgacg cctttgccc cccaaaggc cagtgtgtc 
gacgttttg gtaacgggg tacataagc acctgccgt 
ttttacgca caaattgtc acagcaccg tccaagact 
tcgaatttt aatgcaaac ttccagagg ctgagagag 
agcatgaac tcgaataat atagtccac acttacgag 
ccatttaaa ttgtatccc ggcctcggg gaggttgtt 
ttgatcaaa gaaaactcg gaatggttt cgggggatt 
tgcgttggc ttagccgaa aacgacaag attgaggtt 
ttctttgtg gattttggt tacaaaaga gagaaaaaa 
ctgaaagat cttagacaa atgaaagaa gatcttctt 
tatgtgcca ttccaagcg gttgaatgt atgttggag 
ggctgtcag gagaagaaa gatgcccca aaaaatgcc 
tcccaaaca tttttcgac tcgtgcatg aatttaaaa 
gtttttaag gctctagtt gttgaatca gaggaaccc 
ctgagactg tctatgtgg gactctgaa ggcatggag 
atgggctac gttctgaaa acgtgcggg ttaggagag 
gaccgcaag aaagatgtt ttcccaacc aaagactgt 
tatttaagt tgcaattga
    mRNA sequence
    • >TC006403 RA
      cggactcta acatggtga catctgaca tggacgttt 
atttgacag tgacagtca cgcttttgt aactttttt 
tgaaaactt ttttgtttg atgcatgat ggatacgga 
attttacaa tttacacaa agccctttc tgcctacaa 
gacgtccat cagcacaag tatggacaa aattgacga 
tatcttttc gcaagctgc aagtacttt tatcaatcc 
cgattgtgc cagaggtcc aaacccgaa aaagtacac 
aatttcgct cgaaatcgt aacagtttt gcagcatta 
tattaggat tcttagcac tgttgagag cttagccga 
cggtttggc gaccaagct ctctaacct agaccgtga 
cgcagagcc tgaaagaga aacagcttg caatccttt 
cacttcggc ccttttaag cgactcgaa agagtgtgc 
agtttcgtg cttcttcca taacttgaa ggcacaaat 
tgccgaaag agatgtcag ttcgggcgt cgattctga 
caatgttag ttcagacgc ggaaacgat agtggacct 
aaaaaccga aaatttgga cgaatacgc acgattgaa 
tctgtttga tgtcaacgt taagcctga aaatgcgcc 
cgaaagtga aatttccaa ctctcaaaa agccacaaa 
caattcgaa aactcaaat caaattcga ggttgaagc 
tgacgacag ttcgggggc cgaaacgct tgtggaaca 
accagttca gggaaaaaa cgatttgtt agatcacag 
tagacttaa ccctttcaa agctgactc gaatgagcc 
caaaacagg ggcaaaaaa gaagaaaac tgtaagaat 
caaggagga gccgccttg cgaaaacgc cgaaatcga 
atatacggc cctgagcaa acttttgtc gatgtctgt 
gcatgacag gcgtcgcga ggcgcagaa aaagtttga 
aaacaaatc catcaaacg cgatttcaa ttggcgcaa 
cgtcacctc gccaccacg tgacaaaaa agtgcgaga 
aaaattctc gatttacga tattcttga ggaccagtt 
aagtgtggg ccagaagtg tgttttcag tcacataat 
ctcgcccgc cgagtttta tcttcgcac gaatcaggc 
gttgtttga aatgctgca aaatagctt gaacgagga 
tatgaatag ccaacacca gtgggttgt taataaata 
taaaacgaa ggaggatgc aaggacaca tatgggcaa 
tttttgttt cgcgttttt gcccaataa gcggaagtg 
gtacagagt cgaggtgct tgattggct gatggagga 
agaattgga gaatatctg catccagtt gattgattt 
tggcgaaac atactattg caaatttga gatactcct 
ccccatgac cctatttta ctcaatgtt tccgcgtat 
ggccgtcag gtgccactt tgcagcgat ttattcacc 
tgatcctag taaatggcc agaatcgag tatcgaagc 
cttggaaca aatgagcga aatggaggc taaaaccga 
attcgagac gatttttgt atgcaagga gggaaattc 
gtatggaat tgatctctt gaatgagga gaaatttgg 
gaagaaaac gttgggtca gattttggt cgactccga 
acttgccct ccaagtgga catttcaga cggacttga 
agcattaga ggatgaaga tttcgaaga gtatgaaaa 
catcaacga ggccataac tggatacga tgccaaaga 
tgaagcaag actttgccc cttcactaa tgcggcagg 
gggctgttt taaaggggc aaggtgtaa gctagaaca 
cggcgtttt ggcgaaaga tggcgtcac gacggataa 
agttttgac gatgaatca agcgttcac tgtgacgcc 
tttgccccc caaaggcca gtgtgtcga cgttttggt 
aacggggta cataagcac ctgccgttt ttacgcaca 
aattgtcac agcaccgtc caagacttc gaattttaa 
tgcaaactt ccagaggct gagagagag catgaactc 
gaataatat agtccacac ttacgagcc atttaaatt 
gtatcccgg cctcgggga ggttgtttt gatcaaaga 
aaactcgga atggtttcg ggggatttg cgttggctt 
agccgaaaa cgacaagat tgaggtttt ctttgtgga 
ttttggtta caaaagaga gaaaaaact gaaagatct 
tagacaaat gaaagaaga tcttcttta tgtgccatt 
ccaagcggt tgaatgtat gttggaggg ctgtcagga 
gaagaaaga tgccccaaa aaatgcctc ccaaacatt 
tttcgactc gtgcatgaa tttaaaagt ttttaaggc 
tctagttgt tgaatcaga ggaacccct gagactgtc 
tatgtggga ctctgaagg catggagat gggctacgt 
tctgaaaac gtgcgggtt aggagagga ccgcaagaa 
agatgtttt cccaaccaa agactgtta tttaagttg 
caattgatt tttccatga ctgtttaga gtgtatttt 
aatttattt tattaaaga caattcaat ttt

    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