Status
Please wait ...
Gene information
General information
TC006392 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: 8370410..8374458
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
    		TC006392
    Gene ontology

    GO terms for Tribolium

    • {{ goTerm.term }}
      ({{ goTerm.evidence }}){{ goTerm.evidenceTooltip }}
      {{goTerm.showAll ? '[-]' : '[+]'}}
      Status: {{ goTerm.status }}
      Evidence: {{ goTerm.evidence }} ({{ goTerm.evidenceTooltip }})
      Reference: {{ goTerm.referenceText }}
      Quotation: {{ goTerm.quotation }}
      Submitter: {{ goTerm.name }}

    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 *
    {{ blurIdResult }}
    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.
      {{ unavailableText }}

    * : mandatory fields
    For help on how to submit larger datasets or non experimental data please contact us.
    iBeetle screen iB_04130

    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: 1 (3 dpi)
    Days post injection

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

    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: < 50
     head mostly not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    gnathal appendages partiallypresent - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    head not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    thorax not present - 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): 30% - 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

    adult lethality - Number of animals showing the phenotype: 1 (22 dpi)
    Days post injection

    adult lethality - Number of animals showing the phenotype: 1 (41 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC006392 RA
      MLKWRLVTI CFFCLVYDW VISTSPPIS TTLASKDPK 
ITPAESLII NETDLIKTN TLPQTTPTT VEPNPSEPD 
CPVLKPSMS SLSQDQLTT ILTNPCRYD KLSKPATEG 
PLPVYMQID LTHIESADQ LQFKAHMLV QYLYKDSRL 
RYKDVFPQR GDLIGEELL RSKIWVPHV MVRNERDAR 
VMGIDGKDV FVLIKPTGD VVYSYRMTA TFYCWMNLQ 
KFPFDTQDC YLRWDSWTY NTTNLILHW DKNNPVKIA 
KNLHLTEFV LSGSLPQET VVPASFNNG AFVGNFSEL 
VFKFTLKRE VGYYVMDYF LPSILLVCT SWVTFWLQA 
DASAPRVTL GTSTMLAFI TLNGGINKN LPKVSYIKA 
SEIWFLACA CFIFCSMAE FAFVNVIWR RKKKVELKE 
RSGKHILKG ALTPSLARK QLRKAESVN SLYKTQSCT 
SLNGSENGS KESHNNYLT VHSFPASMK VPTITTQSN 
DDLIGGEDS VTTIPVPDT TRNKPQTQA WHTMTPHEV 
ANWIDRKSR IVFPLGFLI FNIMYWTFV YIL
    CDS sequence
    • >TC006392 RA
      atgctaaag tggcggctt gtgacaatt tgttttttt 
tgcctcgtt tatgactgg gtgattagt acttcacca 
ccaatttca acaacctta gcttcaaaa gacccgaaa 
ataacgccc gctgagagc ctaattatc aacgaaacg 
gacctaatt aaaacaaac actttgccg caaacgaca 
ccaactaca gtcgaacct aatcctagc gaacccgat 
tgtccggtc ttaaaaccc agtatgagt tctttaagc 
caggaccaa ctgactaca attttaacc aatccttgt 
cggtatgac aagcttagt aagcccgca actgagggg 
cccttgccc gtttacatg caaattgac ttgacccat 
atagaatcg gccgatcag ttgcaattt aaggcccat 
atgttggtg caatacttg tacaaggac tctagactg 
agatataag gatgtgttt ccccaacga ggggattta 
atcggggag gaactcctc aggagcaag atatgggtg 
ccccatgtc atggtacgt aacgaacgc gatgccaga 
gtgatgggt atcgatggt aaagacgtt tttgtgtta 
ataaaaccg acaggagat gtggtttat tcgtacaga 
atgaccgca actttctat tgttggatg aatctacaa 
aaattccct ttcgacacg caagattgt tacttgcga 
tgggatagc tggacgtac aacactacc aacttaatt 
ctacactgg gataagaac aatccggtc aaaatcgca 
aaaaacttg catttgacc gagtttgtc ctcagcggg 
agtttacca caggagact gtagtacca gcctcattc 
aataacgga gctttcgtt ggcaacttc agcgaacta 
gttttcaaa ttcacacta aaacgagaa gttggctat 
tacgtcatg gactacttt ttgccctcg attctcctc 
gtttgtact tcttgggtg actttttgg ctgcaagcc 
gacgcgtca gcgcctcgt gtcacgtta ggcacttcc 
acaatgttg gcttttatc acactaaac ggcggaatt 
aataaaaat ttaccgaaa gtgtcatac atcaaagca 
agcgagatt tggttccta gcttgcgct tgtttcata 
ttttgttca atggcggaa ttcgccttc gtcaatgtg 
atttggaga cgcaagaaa aaagtggag ttgaaggaa 
cgtagcggt aaacacatc cttaaaggc gcccttacg 
ccaagtctg gcaagaaaa caattacga aaagctgag 
tctgtcaat agtttatac aaaacccag tcatgtacg 
agtttaaac ggaagcgaa aacggaagt aaagagtca 
cataataat tatttgaca gttcatagt tttcccgcc 
agtatgaag gtaccaacc attacaacg caaagcaac 
gatgacttg atcggcggc gaggacagt gttaccacc 
atcccggtg cccgatacc accagaaac aaaccacaa 
acgcaagca tggcacact atgacgccc cacgaagtg 
gccaactgg atcgacagg aaatcaaga atcgtgttc 
ccgctcggt tttctcatt tttaacatc atgtattgg 
acttttgtt tacattttg taa
    mRNA sequence
    • >TC006392 RA
      tttgagggc aatttattc cggtgtgtc cgactgaaa 
ggtagtacg gattgtacg tttgattgt ggtctgcat 
aaacatata gtttaaagc ggccgtgat aacggggta 
taagagtct aaataacct tggatcatc ttagtttat 
tgttttgtg cgtggcttg aaaatgcta aagtggcgg 
cttgtgaca atttgtttt ttttgcctc gtttatgac 
tgggtgatt agtacttca ccaccaatt tcaacaacc 
ttagcttca aaagacccg aaaataacg cccgctgag 
agcctaatt atcaacgaa acggaccta attaaaaca 
aacactttg ccgcaaacg acaccaact acagtcgaa 
cctaatcct agcgaaccc gattgtccg gtcttaaaa 
cccagtatg agttcttta agccaggac caactgact 
acaatttta accaatcct tgtcggtat gacaagctt 
agtaagccc gcaactgag gggcccttg cccgtttac 
atgcaaatt gacttgacc catatagaa tcggccgat 
cagttgcaa tttaaggcc catatgttg gtgcaatac 
ttgtacaag gactctaga ctgagatat aaggatgtg 
tttccccaa cgaggggat ttaatcggg gaggaactc 
ctcaggagc aagatatgg gtgccccat gtcatggta 
cgtaacgaa cgcgatgcc agagtgatg ggtatcgat 
ggtaaagac gtttttgtg ttaataaaa ccgacagga 
gatgtggtt tattcgtac agaatgacc gcaactttc 
tattgttgg atgaatcta caaaaattc cctttcgac 
acgcaagat tgttacttg cgatgggat agctggacg 
tacaacact accaactta attctacac tgggataag 
aacaatccg gtcaaaatc gcaaaaaac ttgcatttg 
accgagttt gtcctcagc gggagttta ccacaggag 
actgtagta ccagcctca ttcaataac ggagctttc 
gttggcaac ttcagcgaa ctagttttc aaattcaca 
ctaaaacga gaagttggc tattacgtc atggactac 
tttttgccc tcgattctc ctcgtttgt acttcttgg 
gtgactttt tggctgcaa gccgacgcg tcagcgcct 
cgtgtcacg ttaggcact tccacaatg ttggctttt 
atcacacta aacggcgga attaataaa aatttaccg 
aaagtgtca tacatcaaa gcaagcgag atttggttc 
ctagcttgc gcttgtttc atattttgt tcaatggcg 
gaattcgcc ttcgtcaat gtgatttgg agacgcaag 
aaaaaagtg gagttgaag gaacgtagc ggtaaacac 
atccttaaa ggcgccctt acgccaagt ctggcaaga 
aaacaatta cgaaaagct gagtctgtc aatagttta 
tacaaaacc cagtcatgt acgagttta aacggaagc 
gaaaacgga agtaaagag tcacataat aattatttg 
acagttcat agttttccc gccagtatg aaggtacca 
accattaca acgcaaagc aacgatgac ttgatcggc 
ggcgaggac agtgttacc accatcccg gtgcccgat 
accaccaga aacaaacca caaacgcaa gcatggcac 
actatgacg ccccacgaa gtggccaac tggatcgac 
aggaaatca agaatcgtg ttcccgctc ggttttctc 
atttttaac atcatgtat tggactttt gtttacatt 
ttgtaaact ttggcctca cttttgtat ttattctag 
tcttctgtc tcaccctta tttattgct ttttcaata 
aaaagtttt ctcaacg

    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