Status
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Gene information
General information
TC005375 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: 13948455..13951493
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
    		TC005375
    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_00838

    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)

    eclosion not fulfilled (with pupal and adult features) - Number of animals showing the phenotype: 4 (3 dpi)
    Days post injection

    Analysis of embryonic musculature and early development
    number of eggs/embryos/larvae on slide: > 50 larval musculature irregular - Penetrance (percentage of animals/eggs on slide): 30% - 50%

    affected eggs/embryos/larvae total percentage of affected eggs/embryos/larvae on slide - 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
     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 some identifiable segments - Penetrance (percentage of animals/eggs on slide): less than 30%

    procephalic appendages partially remaining - Penetrance (percentage of animals/eggs on slide): less than 30%
    gnathal appendages partially remaining - Penetrance (percentage of animals/eggs on slide): less than 30%
    head capsule mostly not present - Penetrance (percentage of animals/eggs on slide): less than 30%
    head appendages position irregular - Penetrance (percentage of animals/eggs on slide): less than 30%
    head irregular - Penetrance (percentage of animals/eggs on slide): less than 30%

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

    Fertility
    egg production: number <50% of expected -
    ovary without detectable defects - Number of animals showing the phenotype: 4
    RNAi sequence
    Primers
    Left: Right:
    Protein sequence
    • >TC005375 RA
      MRFIVVAIL GCCALALAF PERKITNKQ FLERQRDIL 
RLFRHINQP SYYKDHQEI AQSFHLHDH YDHYTKPEI 
AKHYHQIYE YGLLPRGEV FSVFYEEHL QQAIALYKL 
FYYAKDYDT FYRTAVWAR QHVNEGVFL YSFSVAIVH 
REDTYGIVL PPIYEIYPH YFYNNEVIQ EAYRYKQQY 
YNQEHGYTI NANYSGFYL NLHPEQSLS YFTEDVGVN 
SFYYYYNIY YPHWLGGED FDFAHDRRG EQYYYVYQQ 
ILARYYLER LSNDFGEIP FFNYEVPFE NGYYPLLQY 
PNGLFFPQR PNYAKLYEY FYNYGQKYG NNRYAYSYT 
FVQDYERRI RDAIDRGYV FSHDGQRIN LFSEDGVNI 
LGNLIESNP DSPDRHFYG ALHVYARHL LGYSSQPLD 
KYHVAPSAL QHYETSLRD PAFYQFYKR IVLYFQKYK 
SYLPSYTEH DLHFQGVEV KSVEFDRLV TYFDHFYTD 
ISNAVYVTP QEYDSEKVQ VRVRQYRLN HKPFTYRVH 
VSSDKEQQA VVRIYLGPK YDEYGRYIN ISHNRLNFV 
EVDHFKYQL KVGENVIER NSHQNYFYQ NDRTSYRQL 
YKQVLGALN GNGEFNVNA NEAYFGFPR RFLLPKGNY 
GGQEFQFFV IVSPYVPYK YHQEGYDAS KYYYPRVGS 
GAHHIDNYA FGYPFDRPI HYDQIFHNV PNAYFYTTK 
IYHRHADDI NASTSAHQ
    CDS sequence
    • >TC005375 RA
      atgaggttc attgtagtg gcgatcctt ggctgttgt 
gccctggct ttggctttc cccgaacgt aaaataacc 
aataaacaa ttcctcgag agacaaaga gacatcctt 
cgcctgttc cgacacata aaccagcca agttactac 
aaagaccac caggagata gcccagagt ttccacctc 
catgaccac tacgaccac tacactaaa cctgaaatt 
gccaaacat taccaccaa atatacgag tatgggttg 
cttccaaga ggcgaagtc ttttcagtg ttttacgag 
gagcacctt cagcaagcc atagctttg tacaaactg 
ttctattat gccaaagat tacgacacg ttttatcgg 
acggccgtg tgggcaaga caacatgta aatgagggc 
gttttcttg tattctttt tcggtggca atcgtccac 
cgtgaggac acttacggg atagttttg cccccaatt 
tacgaaatc tacccccac tatttctac aacaacgag 
gtgatccag gaggcttac aggtacaaa caacagtat 
tacaaccag gaacacggt tacacaatc aatgccaat 
tactccggt ttttaccta aatctgcac cctgaacaa 
tctttgtcg tacttcact gaagatgta ggtgtcaat 
tccttctac tactactac aacatttac tacccccat 
tggttgggt ggggaggac tttgacttt gcccatgac 
aggcggggt gagcagtac tattacgtg taccaacaa 
attctggca aggtactac cttgaacgt ttgtccaac 
gatttcggg gaaataccg tttttcaac tatgaagta 
ccgttcgaa aatgggtac tacccttta ttgcagtac 
cccaatggt ctgtttttc ccccaaaga ccgaactat 
gccaagctt tacgagtac ttctacaac tatgggcaa 
aaatacggt aataatagg tatgcctac agttatact 
tttgtccag gattatgag aggaggatt cgggatgcc 
atcgatcgt ggatacgtc ttttcgcat gatggtcaa 
aggattaac ttattctcc gaagacggt gttaacatc 
cttggtaat ttaatcgaa tcaaaccct gactccccc 
gaccgccac ttctacggc gcccttcac gtgtacgcc 
cgccacctc ctggggtac tcctcccag cccttggac 
aaataccac gtggcccct tcggccctc caacactac 
gaaacgtcg ctccgtgac cccgctttc taccagttc 
tacaagcgc attgttttg tatttccag aagtacaag 
tcgtacctc ccgtcctac accgaacac gacttgcat 
ttccaaggg gtggaggtc aagagtgtt gaattcgac 
cgacttgtc acctacttc gaccacttt tacaccgat 
attagcaat gctgtttac gtcacgcct caggagtac 
gacagcgag aaggtccaa gtgagggta cgacagtac 
cgcctgaac cacaaaccg ttcacttac cgggttcat 
gtcagttcg gataaggag caacaagct gttgttaga 
atttatctg gggcctaaa tatgacgag tacgggcgt 
tatattaac attagtcac aacagactc aactttgtt 
gaagttgat cacttcaag taccagctc aaagttggg 
gaaaatgtg attgagagg aactcccat cagaactac 
ttctaccag aacgatcgt actagctat cggcagttg 
tacaagcaa gttttaggc gctttgaac ggcaatgga 
gagtttaac gtgaacgct aacgaggcc tattttgga 
tttcctcga agattcctt ttgcctaag ggtaattac 
gggggtcaa gaattccag ttctttgtc attgtgagc 
ccatatgtg ccctacaag taccaccaa gagggttat 
gacgctagc aagtactac tacccaagg gtggggtct 
ggtgcccat catatcgat aattatgcc tttggttat 
ccgtttgac cgacccatt cactatgac cagatcttc 
cacaatgta ccaaatgcc tatttctac actaccaag 
atttaccat agacatgcc gatgatatc aatgcgtca 
acttcggcc catcagtga
    mRNA sequence
    • >TC005375 RA
      ttgtttggc cgttcgaac aatcatgag gttcattgt 
agtggcgat ccttggctg ttgtgccct ggctttggc 
tttccccga acgtaaaat aaccaataa acaattcct 
cgagagaca aagagacat ccttcgcct gttccgaca 
cataaacca gccaagtta ctacaaaga ccaccagga 
gatagccca gagtttcca cctccatga ccactacga 
ccactacac taaacctga aattgccaa acattacca 
ccaaatata cgagtatgg gttgcttcc aagaggcga 
agtcttttc agtgtttta cgaggagca ccttcagca 
agccatagc tttgtacaa actgttcta ttatgccaa 
agattacga cacgtttta tcggacggc cgtgtgggc 
aagacaaca tgtaaatga gggcgtttt cttgtattc 
tttttcggt ggcaatcgt ccaccgtga ggacactta 
cgggatagt tttgccccc aatttacga aatctaccc 
ccactattt ctacaacaa cgaggtgat ccaggaggc 
ttacaggta caaacaaca gtattacaa ccaggaaca 
cggttacac aatcaatgc caattactc cggttttta 
cctaaatct gcaccctga acaatcttt gtcgtactt 
cactgaaga tgtaggtgt caattcctt ctactacta 
ctacaacat ttactaccc ccattggtt gggtgggga 
ggactttga ctttgccca tgacaggcg gggtgagca 
gtactatta cgtgtacca acaaattct ggcaaggta 
ctaccttga acgtttgtc caacgattt cggggaaat 
accgttttt caactatga agtaccgtt cgaaaatgg 
gtactaccc tttattgca gtaccccaa tggtctgtt 
tttccccca aagaccgaa ctatgccaa gctttacga 
gtacttcta caactatgg gcaaaaata cggtaataa 
taggtatgc ctacagtta tacttttgt ccaggatta 
tgagaggag gattcggga tgccatcga tcgtggata 
cgtcttttc gcatgatgg tcaaaggat taacttatt 
ctccgaaga cggtgttaa catccttgg taatttaat 
cgaatcaaa ccctgactc ccccgaccg ccacttcta 
cggcgccct tcacgtgta cgcccgcca cctcctggg 
gtactcctc ccagccctt ggacaaata ccacgtggc 
cccttcggc cctccaaca ctacgaaac gtcgctccg 
tgaccccgc tttctacca gttctacaa gcgcattgt 
tttgtattt ccagaagta caagtcgta cctcccgtc 
ctacaccga acacgactt gcatttcca aggggtgga 
ggtcaagag tgttgaatt cgaccgact tgtcaccta 
cttcgacca cttttacac cgatattag caatgctgt 
ttacgtcac gcctcagga gtacgacag cgagaaggt 
ccaagtgag ggtacgaca gtaccgcct gaaccacaa 
accgttcac ttaccgggt tcatgtcag ttcggataa 
ggagcaaca agctgttgt tagaattta tctggggcc 
taaatatga cgagtacgg gcgttatat taacattag 
tcacaacag actcaactt tgttgaagt tgatcactt 
caagtacca gctcaaagt tggggaaaa tgtgattga 
gaggaactc ccatcagaa ctacttcta ccagaacga 
tcgtactag ctatcggca gttgtacaa gcaagtttt 
aggcgcttt gaacggcaa tggagagtt taacgtgaa 
cgctaacga ggcctattt tggatttcc tcgaagatt 
ccttttgcc taagggtaa ttacggggg tcaagaatt 
ccagttctt tgtcattgt gagcccata tgtgcccta 
caagtacca ccaagaggg ttatgacgc tagcaagta 
ctactaccc aagggtggg gtctggtgc ccatcatat 
cgataatta tgcctttgg ttatccgtt tgaccgacc 
cattcacta tgaccagat cttccacaa tgtaccaaa 
tgcctattt ctacactac caagattta ccatagaca 
tgccgatga tatcaatgc gtcaacttc ggcccatca 
gtgatcaaa ataacgatt ttgtgtaac taattaact 
cttgttctg tatttagat taaataaag tgtattcaa 
aaaa

    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