EYE53-1

Overview
NameEYE53-1
Smed IDSMED30034479
Length (bp)370
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 EYE53-1 (SMED30034479) t-SNE clustered cells

Violin plots show distribution of expression levels for EYE53-1 (SMED30034479) 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 EYE53-1 (SMED30034479) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for EYE53-1 (SMED30034479) 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.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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



SMED30034479

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



PAGE Curations: 32

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30034479 SmedASXL_018952SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
cephalic gangliaSMED30034479 BK007033.1smed_ncbi_20200123PMID:22451003
González-Sastre et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
nervous systemSMED30034479 dd_Smed_v4_889_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30034479 dd_Smed_v4_889_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30034479 dd_Smed_v4_889_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30034479 dd_Smed_v4_889_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30034479 dd_Smed_v6_889_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30034479 BK007033.1smed_ncbi_20200123PMID:21806978
Iglesias et al., 2011		whole organism asexual adult colorimetric in situ hybridization evidence
eyeSMED30034479 BK007033.1smed_ncbi_20200123PMID:21806978
Iglesias et al., 2011		whole organism asexual adult colorimetric in situ hybridization evidence
cephalic gangliaSMED30034479 BK007033.1smed_ncbi_20200123PMID:21806978
Iglesias et al., 2011		whole organism asexual adult colorimetric in situ hybridization evidence
ventral nerve cordSMED30034479 BK007033.1smed_ncbi_20200123PMID:21806978
Iglesias et al., 2011		whole organism asexual adult colorimetric in situ hybridization evidence
central nervous systemSMED30034479 BK007033.1smed_ncbi_20200123PMID:21295481
Molina et al., 2011		whole organism asexual adult colorimetric in situ hybridization evidence
ventral region of the whole animalSMED30034479 BK007033.1smed_ncbi_20200123PMID:21295481
Molina et al., 2011		whole organism asexual adult colorimetric in situ hybridization evidence
eyeSMED30034479 BK007033.1smed_ncbi_20200123PMID:18287199
Iglesias et al., 2008		whole organism asexual adult colorimetric in situ hybridization evidence
cephalic gangliaSMED30034479 BK007033.1smed_ncbi_20200123PMID:18287199
Iglesias et al., 2008		whole organism asexual adult colorimetric in situ hybridization evidence
ventral nerve cordSMED30034479 BK007033.1smed_ncbi_20200123PMID:18287199
Iglesias et al., 2008		whole organism asexual adult colorimetric in situ hybridization evidence
ventral region of the whole animalSMED30034479 BK007033.1smed_ncbi_20200123PMID:18287199
Iglesias et al., 2008		whole organism asexual adult colorimetric in situ hybridization evidence
peripheral nervous system neuronSMED30034479 BK007033.1smed_ncbi_20200123PMID:18287199
Iglesias et al., 2008		whole organism asexual adult colorimetric in situ hybridization evidence
pharynxSMED30034479 BK007033smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
photoreceptor neuronSMED30034479 BK007033smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult fluorescence in situ hybridization evidence
cephalic gangliaSMED30034479 BK007033smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
ventral nerve cordSMED30034479 BK007033smed_ncbi_20200123PMID:20967238
Collins JJ et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
eyeSMED30034479 BK007033.1smed_ncbi_20200123PMID:26884331
Ong et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
pharynxSMED30034479 BK007033.1smed_ncbi_20200123PMID:21295483
Gaviño et al., 2011		whole organism asexual adult colorimetric in situ hybridization evidence
cephalic gangliaSMED30034479 BK007033.1smed_ncbi_20200123PMID:21295483
Gaviño et al., 2011		whole organism asexual adult colorimetric in situ hybridization evidence
ventral nerve cordSMED30034479 BK007033.1smed_ncbi_20200123PMID:21295483
Gaviño et al., 2011		whole organism asexual adult colorimetric in situ hybridization evidence
ventral region of the whole animalSMED30034479 BK007033.1smed_ncbi_20200123PMID:21295483
Gaviño et al., 2011		whole organism asexual adult colorimetric in situ hybridization evidence
eyeSMED30034479 BK007033.1smed_ncbi_20200123PMID:23318635
Blassberg et al., 2013		whole organism asexual adult colorimetric in situ hybridization evidence
eyeSMED30034479 BK007033.1smed_ncbi_20200123PMID:17905225
Molina et al., 2007		whole organism asexual adult colorimetric in situ hybridization evidence
cephalic gangliaSMED30034479 BK007033.1smed_ncbi_20200123PMID:17905225
Molina et al., 2007		whole organism asexual adult colorimetric in situ hybridization evidence
ventral nerve cordSMED30034479 BK007033.1smed_ncbi_20200123PMID:17905225
Molina et al., 2007		whole organism asexual adult colorimetric in situ hybridization evidence
ventral region of the whole animalSMED30034479 BK007033.1smed_ncbi_20200123PMID:17905225
Molina et al., 2007		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of EYE53-1 vs. TrEMBL
Match: E3CTK8 (EYE53-1 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 171.014 bits (432), Expect = 4.518e-53
Identity = 84/85 (98.82%), Postives = 84/85 (98.82%), Query Frame = 2 
Query:   50 MNLVPILTILCSLCLWLPRNADSMSMQKKLSIPTYWDDIDTSKRNAKRLSVPTYFDDWESRKKRSSAGKRLSVPSYWDEWESQRR 304
            MNLVPILTILCSLCLWLPRNADSMSMQKKLSIPTYWDDIDTSKRNAKRLSVPTYFDDWESRKKRSSAGKRLSVP YWDEWESQRR
Sbjct:    1 MNLVPILTILCSLCLWLPRNADSMSMQKKLSIPTYWDDIDTSKRNAKRLSVPTYFDDWESRKKRSSAGKRLSVPPYWDEWESQRR 85
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BLAST of EYE53-1 vs. TrEMBL
Match: Q6L8A4 (Eye53 OS=Dugesia japonica OX=6161 GN=eye53 PE=2 SV=1)

HSP 1 Score: 125.561 bits (314), Expect = 3.610e-35
Identity = 55/85 (64.71%), Postives = 75/85 (88.24%), Query Frame = 2 
Query:   50 MNLVPILTILCSLCLWLPRNADSMSMQKKLSIPTYWDDIDTSKRNAKRLSVPTYFDDWESRKKRSSAGKRLSVPSYWDEWESQRR 304
            MN +PIL ++C LC  LP N +SM+MQKKLSIPTYWD++D +KR+ KRLSVPTY+D+W++RKKRSSA KRLSVPSY+++W++++R
Sbjct:    1 MNAIPILVVICYLCFMLPENMESMNMQKKLSIPTYWDEMDPNKRSDKRLSVPTYYDEWDARKKRSSAHKRLSVPSYYEDWDNKKR 85
The following BLAST results are available for this feature:
BLAST of EYE53-1 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 EYE53-1 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 EYE53-1 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 EYE53-1 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 EYE53-1 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 EYE53-1 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 EYE53-1 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 EYE53-1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
E3CTK84.518e-5398.82EYE53-1 OS=Schmidtea mediterranea OX=79327 PE=2 SV... [more]
Q6L8A43.610e-3564.71Eye53 OS=Dugesia japonica OX=6161 GN=eye53 PE=2 SV... [more]
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BLAST of EYE53-1 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 EYE53-1 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 EYE53-1 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 EYE53-1 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 EYE53-1 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 EYE53-1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034479 ID=SMED30034479|Name=EYE53-1|organism=Schmidtea mediterranea sexual|type=transcript|length=370bp
AAGAGACTATCAGTACCGTCCTAGTTCCATCACATATACGCCAAACAGAA
TGAACCTTGTTCCGATTCTCACGATCCTCTGCTCGCTGTGCTTGTGGCTC
CCAAGAAACGCCGACTCCATGAGCATGCAGAAGAAACTGTCGATTCCGAC
GTATTGGGATGACATTGATACCAGCAAGAGGAATGCCAAACGTCTATCTG
TTCCGACTTACTTCGATGATTGGGAGTCAAGGAAAAAGAGATCTTCAGCA
GGCAAGAGACTATCAGTACCGTCATACTGGGACGAATGGGAAAGTCAAAG
AAGATGATCCCGGACAGAATTGACTCTGGCAGATACATTTGAATGTTTAT
TAAATAAATATTTGTAGCTG
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protein sequence of SMED30034479-orf-1

>SMED30034479-orf-1 ID=SMED30034479-orf-1|Name=SMED30034479-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=102bp
RDYQYRPSSITYTPNRMNLVPILTILCSLCLWLPRNADSMSMQKKLSIPT
YWDDIDTSKRNAKRLSVPTYFDDWESRKKRSSAGKRLSVPSYWDEWESQR
R*
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Aliases
The feature 'EYE53-1' has the following synonyms
Synonym
EYE53-1
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000017photoreceptor neuron
PLANA:0000036eye
PLANA:0000044cephalic ganglia
PLANA:0000097ventral nerve cord
PLANA:0000099neuron
PLANA:0000103central nervous system
PLANA:0000143ventral region of the whole animal
PLANA:0000418head
PLANA:0000564peripheral nervous system neuron
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..30
score: 0.664
NoneNo IPR availableTMHMMTMhelixcoord: 10..27