Status
Please wait ...
Gene information
General information
TC008016 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_007419.2: 3899845..3902196
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
    		TC008016
    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_09881

    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

    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): less than 30%

    larval musculature random not present - 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): less than 30%
    cuticle remnants with unidentifyable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

    head appendages position irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

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

    head not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    head shape irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    legs segment potentially fused - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    thorax not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    thorax shape irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    abdomen segment number decreased - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    abdomen not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    abdomen shape irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    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
    • >TC008016 RA
      MTNNELRRR KHRDQNGRP APNKKRKEI QPSSIHKSF 
FCLIISGTI LTLFILLYI DNIPWHLGH RAVDSIAKK 
LGYHKPVHA VVIDAGSTG SRVLAFTFH ESYFGGHLV 
LDKELFKYT KPGLSSFAD NPKKGAQTI ANLLEEAKN 
EIPKEYWNK TPLILKATA GLRLLPQEK AENLLNSVR 
ELFKKTPFL TNDDSVEIM DGTDEGIFS WFTVNFLLE 
RLYGNPAKT VAALDLGGG STQVTFSAL TPASLSQKQ 
YIHKAVAPR GLIPVYTHS YLGLGLMAA RKEVITFNQ 
PNQINVTSD CVNHIIEAR KFHYGGTDY YVSGPKVNY 
PVSKVKDST YQTGQETPV VDFATCSQI ITDYVVSKA 
TPPEELPTK IIFAFSYYF DRATEVGLI DEATGGSID 
VEAFKNAAK KSCADPNAD QPFMCLDLT FIWVLLEKG 
FGLQSDTKI YLFKKIDGH EISWALGAA YNLLRG
    CDS sequence
    • >TC008016 RA
      atgaccaac aacgaattg cgtcgacga aagcataga 
gaccaaaat gggcggccg gcacccaac aaaaaacgg 
aaggaaatt caaccttca agcatacac aagtcgttt 
ttttgcctc atcatcagc gggactatc ctgacattg 
tttatcttg ctttacatt gacaacatt ccatggcat 
ttgggacac agagccgta gacagcatt gccaaaaaa 
ttggggtac cacaaaccg gtacacgcc gttgtgata 
gacgctggt agcacggga tccagagtt ttagctttc 
acgttccat gaatcctac tttgggggc cacttagtc 
ttagataaa gaattattc aagtacacc aagcctggt 
ttatcatcg ttcgccgac aaccccaaa aagggggcc 
caaaccatt gccaacttg ttagaggaa gccaaaaac 
gaaattcca aaagagtat tggaacaaa acacccctc 
atcctcaaa gctacagca ggcctacgg ctgctcccc 
caagaaaaa gccgaaaat ttgctcaac tcagtccga 
gaactgttc aaaaagacc ccatttttg acaaacgat 
gacagtgtg gagattatg gacgggaca gacgaaggg 
attttctct tggttcact gttaacttc ctcctagag 
cgcttgtat ggaaaccct gccaagacc gtggcggcc 
ctcgatctg ggagggggc tccactcaa gtgactttc 
tcagccttg actcctgcc agtctttcg caaaaacag 
tacatccac aaagccgtc gccccccgc ggtctcatc 
ccggtgtac acccacagt tacctaggt ttaggtcta 
atggcagct cggaaggaa gtgattacg tttaaccag 
cctaaccaa attaacgtg acctcggat tgcgtcaat 
catatcatt gaagcgcgc aaatttcat tatgggggc 
acggattac tacgtcagt ggccctaaa gtcaactac 
ccggtctcc aaggtaaaa gactcgact taccagact 
gggcaggag acccccgtt gtcgatttc gccacgtgt 
tcacaaatc ataaccgat tatgttgtg tccaaagca 
acgccgcct gaggagctc cccacgaaa atcattttc 
gccttcagt tattatttt gatagggcg acggaagtt 
ggcctaatt gatgaagcg acggggggc agcattgac 
gtcgaagcg tttaaaaat gccgccaaa aaatcatgt 
gctgaccca aacgcagac caacctttt atgtgcctt 
gaccttacg ttcatttgg gttttattg gagaaagga 
tttgggttg cagagtgac actaagatt tatttattc 
aaaaaaatt gatggtcac gagattagt tgggcacta 
ggtgcagct tacaattta ctgagaggt tga
    mRNA sequence
    • >TC008016 RA
      gtacgaaag tgcaagtaa tgactgttt tgaggttag 
ataccaatt gttggcgac cttatcaaa tcgttagaa 
aatgagtag ctgtaaaga taaactagt gaaggacat 
gatagtgca acttctgcc gatttaatt gcatttatt 
tagtcaatt tctgcgagt caaagtgcg cagacacgt 
cctttttga gaattccat gccaatcaa taataaggc 
aattgtgta aaatcttcg ccggcctat ataatttta 
tttctccga taaaagcat cattaaaac atgaccaac 
aacgaattg cgtcgacga aagcataga gaccaaaat 
gggcggccg gcacccaac aaaaaacgg aaggaaatt 
caaccttca agcatacac aagtcgttt ttttgcctc 
atcatcagc gggactatc ctgacattg tttatcttg 
ctttacatt gacaacatt ccatggcat ttgggacac 
agagccgta gacagcatt gccaaaaaa ttggggtac 
cacaaaccg gtacacgcc gttgtgata gacgctggt 
agcacggga tccagagtt ttagctttc acgttccat 
gaatcctac tttgggggc cacttagtc ttagataaa 
gaattattc aagtacacc aagcctggt ttatcatcg 
ttcgccgac aaccccaaa aagggggcc caaaccatt 
gccaacttg ttagaggaa gccaaaaac gaaattcca 
aaagagtat tggaacaaa acacccctc atcctcaaa 
gctacagca ggcctacgg ctgctcccc caagaaaaa 
gccgaaaat ttgctcaac tcagtccga gaactgttc 
aaaaagacc ccatttttg acaaacgat gacagtgtg 
gagattatg gacgggaca gacgaaggg attttctct 
tggttcact gttaacttc ctcctagag cgcttgtat 
ggaaaccct gccaagacc gtggcggcc ctcgatctg 
ggagggggc tccactcaa gtgactttc tcagccttg 
actcctgcc agtctttcg caaaaacag tacatccac 
aaagccgtc gccccccgc ggtctcatc ccggtgtac 
acccacagt tacctaggt ttaggtcta atggcagct 
cggaaggaa gtgattacg tttaaccag cctaaccaa 
attaacgtg acctcggat tgcgtcaat catatcatt 
gaagcgcgc aaatttcat tatgggggc acggattac 
tacgtcagt ggccctaaa gtcaactac ccggtctcc 
aaggtaaaa gactcgact taccagact gggcaggag 
acccccgtt gtcgatttc gccacgtgt tcacaaatc 
ataaccgat tatgttgtg tccaaagca acgccgcct 
gaggagctc cccacgaaa atcattttc gccttcagt 
tattatttt gatagggcg acggaagtt ggcctaatt 
gatgaagcg acggggggc agcattgac gtcgaagcg 
tttaaaaat gccgccaaa aaatcatgt gctgaccca 
aacgcagac caacctttt atgtgcctt gaccttacg 
ttcatttgg gttttattg gagaaagga tttgggttg 
cagagtgac actaagatt tatttattc aaaaaaatt 
gatggtcac gagattagt tgggcacta ggtgcagct 
tacaattta ctgagaggt tgattcgtt ttaactgta 
attaaacgc acgattttt attcacaaa atttgactg 
tgccttaac tgtaaataa gtatttagt tgataggct 
gtgcaataa tttgttttt atccatcaa cgtttgtaa 
tttttccaa ttaataaaa tcacttttg tttt

    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