Status
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Gene information
General information
TC004143 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: 1621479..1627243
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
    		TC004143
    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
    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_00667

    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: 4 (9 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 embryo/egg with embryonic tissue, no cuticle, but muscle fluorescence - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    embryo/egg not developed/not fertilized - Penetrance (percentage of animals/eggs on slide): 50% - 80%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - Penetrance (percentage of animals/eggs on slide): more than 80%
    Analysis of larval stage 1 cuticle
    number of eggs/embryos/larvae on slide: > 50
     egg without cuticle 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%
    cuticle remnants with some identifiable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

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

    thorax fragmented - Penetrance (percentage of animals/eggs on slide): less than 30%
    thorax not present - Penetrance (percentage of animals/eggs on slide): 30% - 50%
    abdomen structure irregular - 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): 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)

    larva lethality early (L5/6) - Number of animals showing the phenotype: 1 (11 dpi)
    Days post injection

    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC004143 RA
      MLKFGSKHD SNIVYKCTV RLLEDTEIL ECEYKPHHK 
GKYLLEYVC QQLNLVEQD YLGLRYVDI QDQRHWLDL 
GKSICKQVK DLDPVLFSF RVKFYPPDP FRLKEEITR 
YQIFLQLKR DLLHGRLYC ATNEAAMLA ALILQGELG 
DYDPEIHVG NYMSELKIL LKQTETIEE KAMEIHQKQ 
LKGQSPSQV ENTFLKLAC QLDAYGVDP HPVKDHKGS 
QLYLGINYA GILTIQGSR KTHHFRWPD IQKINYEGK 
MFIIHLNYN DKKHTVGFK CPTGAACRH VWKCAVEQM 
LFFTLPASS DAPTVSGGG FFSWGTKFK YTGRTEKEI 
LEDSGSPTR EEPSIQRTS SLRRKASSV PATPSTPLQ 
PHLGYSSLP RSSHSDAGG SRMESSNST GLLSGLDGN 
PSQAYSDVA ALETVSEDQ EAMGASKLR TTVLKDDSM 
DRFSDYYFR DSFEHSSSE SQLIDSYRG YETTNPSHR 
SSRSQTPLS HSQVDGRIC LPNATHSVQ TNVKKTRKF 
NIVGAFIPT FIIVTIFVL IATVVMLET DCELFGSFR 
NIPEMVSLK YQFYEPIKQ YFRSKMSIF F
    CDS sequence
    • >TC004143 RA
      atgttaaag tttggctcc aaacatgac agtaatatt 
gtttacaaa tgcacggtc cgattattg gaagatacg 
gaaatccta gaatgtgaa tataagccc caccataag 
ggtaaatac ttgttggaa tatgtgtgt caacagttg 
aatttagta gaacaagac tacttaggg ctccgctat 
gttgatatt caagaccaa agacactgg ctggactta 
gggaaatca atctgtaaa caagtcaaa gatttggat 
ccggtcctg tttagtttt cgtgttaaa ttctaccct 
cctgatcca ttccgcctt aaggaagaa ataacacgt 
taccaaata tttttgcaa ttaaaacga gatctacta 
catgggcgc ttatattgc gccacgaac gaagccgca 
atgttggca gcacttatc ttacaaggt gaattgggc 
gattacgac cctgaaatt cacgttgga aattacatg 
agcgaatta aaaatacta cttaaacag actgaaacc 
atagaggag aaagcgatg gaaatccat cagaagcaa 
ctcaaaggc caaagcccc tcgcaagtg gaaaacacc 
ttcctcaaa ctggcctgc caactagac gcctacgga 
gttgacccg cacccagtg aaggaccat aaagggagt 
cagctctac ttgggcata aattatgcc ggaattttg 
acaattcaa ggtagtaga aaaacgcac cacttccgg 
tggcccgac atacagaaa atcaactac gagggaaaa 
atgttcata atccaccta aattacaat gataaaaag 
catacggtt ggttttaaa tgccccacg ggcgccgcc 
tgtcgccac gtttggaaa tgtgccgtt gaacaaatg 
ctatttttc actttgccg gcaagttcc gacgccccg 
actgtgagc ggcggtggg ttcttctca tggggtacg 
aagttcaaa tatacaggg cgtactgaa aaggaaatc 
ctggaagac agcggctcc ccaacacgg gaggagccc 
agcattcaa cgcacgtcc agtttgagg cgtaaagcg 
tccagtgta cctgcaact ccttcaacc ccccttcag 
ccccattta ggttatagt agtctgccg aggtcgagt 
cattcggac gccggaggc tcccgaatg gagtctagt 
aatagtaca gggttgctg tcagggtta gacgggaac 
ccgtcccaa gcttacagt gatgttgct gccttagaa 
actgtttcg gaagaccag gaggcgatg ggcgcctcc 
aaacttcga acaacagta ttgaaggat gattcgatg 
gatcgcttc agtgattat tatttccgg gactcgttc 
gaacattcg tcgtccgaa tcccagtta attgatagt 
taccgcggc tacgagact acgaatccc tctcatcgc 
tccagtcgt agccaaact ccgttatct cattctcag 
gttgatggt cgaatttgc ctgccaaat gctacacat 
agtgtacaa acaaatgtt aagaaaact agaaaattt 
aacatcgtg ggcgcgttc atacccacg ttcattata 
gtaacgata tttgtacta attgctacc gttgtaatg 
ttagaaact gattgtgaa ttatttggt agctttagg 
aacattccg gagatggtc tcgctaaaa taccaattc 
tatgaacca attaaacaa tattttcga agtaaaatg 
tcgatattt ttctga
    mRNA sequence
    • >TC004143 RA
      tgtaaataa atgacgata cagacagat gtgctcgca 
gaaagagta tgtgaaggt attggcttt tttcaaggg 
gtgtacaat cggagtatg taatattga ttgcatttt 
tctggcgca gtacaaata aacgaatca ccctgtgta 
aaaaccagc ccttgtaac tttttacga aagttggcg 
aaattaatg gtggggcaa ttgctttta ttgggacat 
tttgtgatg aatgaaacg tagaaagtt ggcaatgaa 
gtgaactcg tgttgtgac tccgcccaa caggtgaac 
tatgcgcca aaatgggcg gggtttagc ggggaggag 
tattgcagt tgtgttgat tgttgtctt gttaaaaaa 
ataatttag gaattgttt tttcttggg atgatcgcc 
ggatttgtc ctttcaggc aaccgagtt gtctcgttg 
ttgtgggga gtttcgatg ttgttcatg cgcagctac 
gtcacgtag tattcaagc ttctgtcaa aaatatgtg 
tcaaatgct gtcttgtgt tatttacgt aaataattg 
tctgttgta aaataagat aataaattt tataaaaag 
ttgcgaatt ataaatgaa ctagacata tgtttaaag 
tggaaaatg ttaaagttt ggctccaaa catgacagt 
aatattgtt tacaaatgc acggtccga ttattggaa 
gatacggaa atcctagaa tgtgaatat aagccccac 
cataagggt aaatacttg ttggaatat gtgtgtcaa 
cagttgaat ttagtagaa caagactac ttagggctc 
cgctatgtt gatattcaa gaccaaaga cactggctg 
gacttaggg aaatcaatc tgtaaacaa gtcaaagat 
ttggatccg gtcctgttt agttttcgt gttaaattc 
taccctcct gatccattc cgccttaag gaagaaata 
acacgttac caaatattt ttgcaatta aaacgagat 
ctactacat gggcgctta tattgcgcc acgaacgaa 
gccgcaatg ttggcagca cttatctta caaggtgaa 
ttgggcgat tacgaccct gaaattcac gttggaaat 
tacatgagc gaattaaaa atactactt aaacagact 
gaaaccata gaggagaaa gcgatggaa atccatcag 
aagcaactc aaaggccaa agcccctcg caagtggaa 
aacaccttc ctcaaactg gcctgccaa ctagacgcc 
tacggagtt gacccgcac ccagtgaag gaccataaa 
gggagtcag ctctacttg ggcataaat tatgccgga 
attttgaca attcaaggt agtagaaaa acgcaccac 
ttccggtgg cccgacata cagaaaatc aactacgag 
ggaaaaatg ttcataatc cacctaaat tacaatgat 
aaaaagcat acggttggt tttaaatgc cccacgggc 
gccgcctgt cgccacgtt tggaaatgt gccgttgaa 
caaatgcta tttttcact ttgccggca agttccgac 
gccccgact gtgagcggc ggtgggttc ttctcatgg 
ggtacgaag ttcaaatat acagggcgt actgaaaag 
gaaatcctg gaagacagc ggctcccca acacgggag 
gagcccagc attcaacgc acgtccagt ttgaggcgt 
aaagcgtcc agtgtacct gcaactcct tcaaccccc 
cttcagccc catttaggt tatagtagt ctgccgagg 
tcgagtcat tcggacgcc ggaggctcc cgaatggag 
tctagtaat agtacaggg ttgctgtca gggttagac 
gggaacccg tcccaagct tacagtgat gttgctgcc 
ttagaaact gtttcggaa gaccaggag gcgatgggc 
gcctccaaa cttcgaaca acagtattg aaggatgat 
tcgatggat cgcttcagt gattattat ttccgggac 
tcgttcgaa cattcgtcg tccgaatcc cagttaatt 
gatagttac cgcggctac gagactacg aatccctct 
catcgctcc agtcgtagc caaactccg ttatctcat 
tctcaggtt gatggtcga atttgcctg ccaaatgct 
acacatagt gtacaaaca aatgttaag aaaactaga 
aaatttaac atcgtgggc gcgttcata cccacgttc 
attatagta acgatattt gtactaatt gctaccgtt 
gtaatgtta gaaactgat tgtgaatta tttggtagc 
tttaggaac attccggag atggtctcg ctaaaatac 
caattctat gaaccaatt aaacaatat tttcgaagt 
aaaatgtcg atatttttc tgattattt aagctctct 
catttgcat ttcgaattc agcttgaag aactctttg 
aagtagcaa cagattagt ttagttgca tagagtaag 
gaatccaat tattaaaat agttcctgc aatactaaa 
tcattagac taggttacg gtttcttta acgacaaaa 
tcagttttg tgttctaat ggctttaag caaaatgca 
ctgttttgt gatacattc gttgaacga actaaagtg 
taacattcc gttcagggc gcttcaacg ttattgtgg 
gcgttcctc attttttta atttattga acaaatgta 
caattttta tacaaaagt actcgggca gaaatattt 
tgttggcaa ttaaattta agaaatctg tgatctttt 
ctcaatctg ctgctatag taatagaaa taatcgtac 
aaagaagtg caatcaaaa tctattttc cgttgaatt 
tgtaactcg aatcataat tgctactta cgccaacaa 
tttgtgatt gtgttatac ttttgtgta cacagactt 
gcttagcga ggctatata attttgtat gtatgtatg 
atgatttaa ggggccaca gattcagaa gcacttagt 
tcatctatt tttatacgt tttattatt ttcaatttt 
atttttgtt atctttcta tgatgtaac tcatttcgc 
caaataaac ttaagtcaa ttaa

    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