60S ribosomal protein L39

Overview
Name60S ribosomal protein L39
Smed IDSMED30021433
Length (bp)1081
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We isolated X1 neoblasts cells enriched in high piwi-1 expression (Neoblast Population), and profiled ∼7,614 individual cells via scRNA-seq. Unsupervised analyses uncovered 12 distinct classes from 7,088 high-quality cells. We designated these classes Nb1 to Nb12 and ordered them based on high (Nb1) to low (Nb12) piwi-1 expression levels. We further defined groups of genes that best classified the cells parsed into 12 distinct cell clusters to generate a scaled expression heat map of discriminative gene sets for each cluster. Expression of each cluster’s gene signatures was validated using multiplex fluorescence in situ hybridization (FISH) co-stained with piwi-1 and largely confirmed the cell clusters revealed by scRNA-seq.

We also tested sub-lethal irradiation exposure. To profile rare pluripotent stem cells (PSCs) and avoid interference from immediate progenitor cells, we determined a time point after sub-lethal irradiation (7 DPI) with minimal piwi-1+ cells, followed by isolation and single-cell RNA-seq of 1,200 individual cells derived from X1 (Piwi-1 high) and X2 (Piwi-1 low) cell populations (Sub-lethal Irradiated Surviving X1 and X2 Cell Population)



Explore this single cell expression dataset with our NB Cluster Shiny App



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of 60S ribosomal protein L39 (SMED30021433) t-SNE clustered cells

Violin plots show distribution of expression levels for 60S ribosomal protein L39 (SMED30021433) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of 60S ribosomal protein L39 (SMED30021433) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for 60S ribosomal protein L39 (SMED30021433) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
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Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020



SMED30021433

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 14

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30021433 dd_Smed_v4_394_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30021433 dd_Smed_v4_394_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30021433 dd_Smed_v4_394_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30021433 dd_Smed_v4_394_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30021433 dd_Smed_v4_394_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30021433 dd_Smed_v4_394_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30021433 dd_Smed_v4_394_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30021433 dd_Smed_v4_394_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30021433 dd_Smed_v4_394_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30021433 dd_Smed_v4_394_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30021433 dd_Smed_v4_394_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30021433 dd_Smed_v6_394_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30021433 dd_Smed_v6_394_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
secretory systemSMED30021433 dd_Smed_v6_394_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of 60S ribosomal protein L39 vs. Planmine SMEST
Match: SMESG000065931.1 (SMESG000065931.1)

HSP 1 Score: 207.223 bits (526), Expect = 8.021e-66
Identity = 101/148 (68.24%), Postives = 119/148 (80.41%), Query Frame = 2 
Query:  221 KCRQAMWDAGFSISPVREIRPRNKGDSGEVDLSYVAIKREPGRNPAREIRGQAEFLLARLEEHQRETDHQVEKVRRYLAQINADIAEGRIPSTDGYAPSYKVSYELHDEKLRARTVAMDVVLPRKILPRELRDEGRHSNTYHDHPYAR 664
            +CRQAMWDAGFSIS VRE R  N+G S +V+L YVAIKREPG N AREIRGQAEFLL RLEEHQ+ET+ Q+ K RRYLAQ+N DIAEGRIPSTDGYAPSY VS+EL D  L  R   M+V+LPR++LPRELR+   +S++  DH +AR
Sbjct:   32 RCRQAMWDAGFSISTVRETRFGNQGSSEDVELPYVAIKREPGGNLAREIRGQAEFLLGRLEEHQKETERQIIKARRYLAQVNKDIAEGRIPSTDGYAPSYNVSFELDDPSLCNRLETMNVILPRRVLPRELRNVEENSDSRQDHSFAR 179
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BLAST of 60S ribosomal protein L39 vs. Planmine SMEST
Match: SMESG000013157.1 (SMESG000013157.1)

HSP 1 Score: 201.83 bits (512), Expect = 9.369e-63
Identity = 98/158 (62.03%), Postives = 119/158 (75.32%), Query Frame = 2 
Query:  194 VRLKTGNTIKCRQAMWDAGFSISPVREIRPRNKGDSGEVDLSYVAIKREPGRNPAREIRGQAEFLLARLEEHQRETDHQVEKVRRYLAQINADIAEGRIPSTDGYAPSYKVSYELHDEKLRARTVAMDVVLPRKILPRELRDEGRHSNTYHDHPYARE 667
             R    +  +CRQAMWDAGFSI PVRE R   +GDS EVDLSYVAIKREPGR+PARE+RGQAE+LLARLE HQ ET+ QVE+ R+YL ++N DIA GRIPSTDGYAP Y VS+EL D +L+ +   M V +PR ILP+E+R+E   +    +H YARE
Sbjct:  100 ARFPAHSAARCRQAMWDAGFSIFPVRETRGGTQGDSNEVDLSYVAIKREPGRSPAREMRGQAEYLLARLERHQAETNRQVEQARQYLRRVNEDIAAGRIPSTDGYAPQYNVSFELDDPRLQRQMSEMRVAVPRHILPKEMRNENDIAEPQREHSYARE 257
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BLAST of 60S ribosomal protein L39 vs. Planmine SMEST
Match: SMESG000032540.1 (SMESG000032540.1)

HSP 1 Score: 197.593 bits (501), Expect = 4.234e-62
Identity = 95/159 (59.75%), Postives = 121/159 (76.10%), Query Frame = 2 
Query:  194 VRLKTGNTIKCRQAMWDAGFSISPVREIRPRNKGDSGEVDLSYVAIKREPGRNPAREIRGQAEFLLARLEEHQRETDHQVEKVRRYLAQINADIAEGRIPSTDGYAPSYKVSYELHDEKLRARTVAMDVVLPRKILPRELRDEGRHSNTYHDHPYAREQ 670
            +R    + ++CRQAMWDAGFSISPVRE R  ++ ++ +VDL +VAIKREPGRNPAREIRGQAE+LLARLEEH+R+TDH+V+K RR+L +IN DIA G IPSTDGYAP Y   + L D +L   + AM VV+PR+ L R   +    +N +HDHPYARE+
Sbjct:   17 LRFPAHSAVRCRQAMWDAGFSISPVRESRMGSRSNTDDVDLPFVAIKREPGRNPAREIRGQAEYLLARLEEHKRQTDHEVDKARRHLEEINWDIAAGIIPSTDGYAPPYNTPFNLDDPRLNRSSSAMKVVVPRETLIRGWGEANEPANEHHDHPYARER 175
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BLAST of 60S ribosomal protein L39 vs. Planmine SMEST
Match: SMESG000063851.1 (SMESG000063851.1)

HSP 1 Score: 196.823 bits (499), Expect = 5.803e-62
Identity = 99/158 (62.66%), Postives = 118/158 (74.68%), Query Frame = 2 
Query:  194 VRLKTGNTIKCRQAMWDAGFSISPVREIRPRNKGDSGEVDLSYVAIKREPGRNPAREIRGQAEFLLARLEEHQRETDHQVEKVRRYLAQINADIAEGRIPSTDGYAPSYKVSYELHDEKLRARTVAMDVVLPRKILPRELRDEGRHSNTYHDHPYARE 667
             R  T +  +CRQAMWDAGFSISPVRE R   +GDS EV L YVAIKRE GR+PAREIRGQAE LLARLE HQ ET+ QVE+ R+YL ++N DIA G IPSTDGYAP Y VSYEL+D +L+ R   M V +PR ILP+E+R+E   +  + +H YARE
Sbjct:   23 ARFPTHSAARCRQAMWDAGFSISPVREARGGTQGDSDEVYLPYVAIKRESGRSPAREIRGQAEHLLARLEHHQAETNRQVEQARQYLQRVNEDIAAGWIPSTDGYAPQYNVSYELNDPRLQRRMPEMRVAVPRHILPKEMRNEDEITELHREHSYARE 180
[Close]
BLAST of 60S ribosomal protein L39 vs. Planmine SMEST
Match: SMESG000029442.1 (SMESG000029442.1)

HSP 1 Score: 194.512 bits (493), Expect = 1.893e-61
Identity = 96/143 (67.13%), Postives = 116/143 (81.12%), Query Frame = 2 
Query:  236 MWDAGFSISPVREIRPRNKGDSGEVDLSYVAIKREPGRNPAREIRGQAEFLLARLEEHQRETDHQVEKVRRYLAQINADIAEGRIPSTDGYAPSYKVSYELHDEKLRARTVAMDVVLPRKILPRELRDEGRHSNTYHDHPYAR 664
            MW AGF IS VRE R  N+G S +V+L YVAIKREPGRNPA EIRGQAEF+LARLEEHQ+ET+ Q+ K RRYLAQ+NADIAEG+IPSTD YAP+Y VS+EL D +LR +T AM+VV+PR++LPRELR+     +  +DH YAR
Sbjct:    1 MWVAGFLISRVRETRSGNQGSSEDVELPYVAIKREPGRNPAWEIRGQAEFILARLEEHQKETNRQIAKARRYLAQVNADIAEGKIPSTDRYAPNYNVSFELDDPRLRGQTGAMNVVVPRRVLPRELRNVEEKPDHRYDHSYAR 143
The following BLAST results are available for this feature:
BLAST of 60S ribosomal protein L39 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of 60S ribosomal protein L39 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of 60S ribosomal protein L39 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of 60S ribosomal protein L39 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of 60S ribosomal protein L39 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of 60S ribosomal protein L39 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of 60S ribosomal protein L39 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of 60S ribosomal protein L39 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of 60S ribosomal protein L39 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of 60S ribosomal protein L39 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of 60S ribosomal protein L39 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of 60S ribosomal protein L39 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of 60S ribosomal protein L39 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of 60S ribosomal protein L39 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000065931.18.021e-6668.24SMESG000065931.1[more]
SMESG000013157.19.369e-6362.03SMESG000013157.1[more]
SMESG000032540.14.234e-6259.75SMESG000032540.1[more]
SMESG000063851.15.803e-6262.66SMESG000063851.1[more]
SMESG000029442.11.893e-6167.13SMESG000029442.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30021433 ID=SMED30021433|Name=60S ribosomal protein L39|organism=Schmidtea mediterranea sexual|type=transcript|length=1081bp
TTTTAAATAAATTAATATATTTTAAAGTTTGTTTAAATATACAGTTTTAG
TTATATTCAGCAATTTTAAATGGTAAGTAATATTTTTAAAGTAATATTTT
AATTATTATTCTTAATAGGCTGCACATAAAAGTTTAATAATTAAAAAGAA
ACTTGCAAAGAAGCAAGGACAAAACCGTCCAATTCCCCAATGGGTTAGAT
TGAAGACTGGAAATACGATAAAGTGCAGGCAAGCGATGTGGGACGCGGGA
TTTTCGATATCGCCAGTTCGAGAAATCAGACCAAGGAATAAAGGAGATTC
GGGAGAAGTCGATCTTTCATACGTAGCAATAAAACGTGAACCCGGCCGTA
ACCCGGCTCGAGAAATCCGAGGCCAAGCCGAGTTCCTGTTGGCTCGCCTC
GAAGAACACCAGCGGGAAACCGATCACCAAGTGGAGAAAGTCAGGCGGTA
CCTGGCGCAGATAAACGCGGACATTGCGGAGGGCAGAATACCCAGTACGG
ATGGGTATGCCCCTAGCTACAAAGTGTCATATGAATTACACGATGAGAAA
CTACGCGCACGGACCGTGGCAATGGATGTGGTATTACCACGGAAAATTCT
TCCCCGAGAACTACGGGATGAAGGAAGACACTCAAATACTTATCACGATC
ACCCATATGCTCGCGAACAAACTAGACTTTCTGTTTTATTTTACTTAATC
TTTAGAGTAGTAGATAGGAGAACAATTTTCCACCCGCCTGATGATAACCT
TAGCATAAACCGATCAATAACAGATGAATCCTTACCAAATCTTACAACAA
GAATTAATGCGGACGCAGAAAACAAACGCAGGGCTTCACCAACAGGTCCT
ACAGTTGGTCAAGGAAATCCAGCAAATCAAAGCCACCTGGTTGGAGCCGG
GCCGAGTAAAGCGTCTTTACCAAAAGATGACAACTGCACAGAAAGAACTT
CGCGCCAGCCAGAAGAAATGCCGAAGAGGAACAGACAACGGAATTGGCCT
GGCAAGAAGGAGCGCGAAAGAAAGTACAAGCTCAAGAAGGCTCGTATGGT
ATATCACATTCTCAAATCAAATAGGATTTGA
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protein sequence of SMED30021433-orf-1

>SMED30021433-orf-1 ID=SMED30021433-orf-1|Name=SMED30021433-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=282bp
MWDAGFSISPVREIRPRNKGDSGEVDLSYVAIKREPGRNPAREIRGQAEF
LLARLEEHQRETDHQVEKVRRYLAQINADIAEGRIPSTDGYAPSYKVSYE
LHDEKLRARTVAMDVVLPRKILPRELRDEGRHSNTYHDHPYAREQTRLSV
LFYLIFRVVDRRTIFHPPDDNLSINRSITDESLPNLTTRINADAENKRRA
SPTGPTVGQGNPANQSHLVGAGPSKASLPKDDNCTERTSRQPEEMPKRNR
QRNWPGKKERERKYKLKKARMVYHILKSNRI*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0000429neoblast
PLANA:0000484secretory system
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR000077Ribosomal_L39
IPR023626Ribosomal_L39e_dom
Vocabulary: cellular component
TermDefinition
GO:0005622intracellular
GO:0005840ribosome
Vocabulary: molecular function
TermDefinition
GO:0003735structural constituent of ribosome
Vocabulary: biological process
TermDefinition
GO:0006412translation