SMED30014221

Overview
NameSMED30014221
Smed IDSMED30014221
Length (bp)706
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 SMED30014221 (SMED30014221) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30014221 (SMED30014221) 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 SMED30014221 (SMED30014221) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30014221 (SMED30014221) 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




SMED30014221

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermal cellSMED30014221SMESG000043379.1 dd_Smed_v4_8233_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30014221SMESG000043379.1 dd_Smed_v4_8233_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30014221SMESG000043379.1 dd_Smed_v4_8233_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30014221 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006515:3713..6021 -3466
Homology
BLAST of SMED30014221 vs. TrEMBL
Match: A0A1I8JF76 (PBPe domain-containing protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 1.947e-6
Identity = 44/158 (27.85%), Postives = 74/158 (46.84%), Query Frame = 2
Query:  200 YFYVGQCSSTNPII--SSIQPLDIYDMGGIFVLIAVGIIAAFPAAVIEYLLNKSKLQCQRKTTGNSLRFGQVYRAKVTGLDRNGVTVDIGRLNLFSTTNEGRIYYVPKKYLGI-KKKGEREILAPTDQGIMIGTKLLLKYMGNNPVDSKRIFVQVHKK 664
            Y+ V  CS++  +I  S +  + I  + GIF+++A   + +F    +EY+     LQ QR      L F + YRA VT +   GV V +           G   ++P + L     KG    +  +D  I  G+ + + Y+GN+P +  RIF   H++
Sbjct:  228 YWSVLLCSASENLITYSELTEVTIDQVAGIFMVLAGAFVLSFLVVAMEYIGYIIGLQVQRTRADPDLEFNKAYRALVTSITPTGVYVKL----------HGEKEFIPNQMLSPDASKG----MTASDLQISCGSMIEITYLGNDPAEGYRIF---HRR 368          
BLAST of SMED30014221 vs. TrEMBL
Match: A0A1I8JCZ2 (PBPe domain-containing protein OS=Macrostomum lignano OX=282301 PE=3 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 2.238e-6
Identity = 44/158 (27.85%), Postives = 74/158 (46.84%), Query Frame = 2
Query:  200 YFYVGQCSSTNPII--SSIQPLDIYDMGGIFVLIAVGIIAAFPAAVIEYLLNKSKLQCQRKTTGNSLRFGQVYRAKVTGLDRNGVTVDIGRLNLFSTTNEGRIYYVPKKYLGIK-KKGEREILAPTDQGIMIGTKLLLKYMGNNPVDSKRIFVQVHKK 664
            Y+ V  CS++  +I  S +  + I  + GIF+++A   + +F    +EY+     LQ QR      L F + YRA VT +   GV V +           G   ++P + L     KG    +  +D  I  G+ + + Y+GN+P +  RIF   H++
Sbjct:  555 YWSVLLCSASENLITYSELTEVTIDQVAGIFMVLAGAFVLSFLVVAMEYIGYIIGLQVQRTRADPDLEFNKAYRALVTSITPTGVYVKL----------HGEKEFIPNQMLSPDASKG----MTASDLQISCGSMIEITYLGNDPAEGYRIF---HRR 695          
BLAST of SMED30014221 vs. TrEMBL
Match: A0A267FB66 (PBPe domain-containing protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig012789g1 PE=4 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 4.334e-6
Identity = 43/152 (28.29%), Postives = 71/152 (46.71%), Query Frame = 2
Query:  200 YFYVGQCSSTNPII--SSIQPLDIYDMGGIFVLIAVGIIAAFPAAVIEYLLNKSKLQCQRKTTGNSLRFGQVYRAKVTGLDRNGVTVDIGRLNLFSTTNEGRIYYVPKKYLGIK-KKGEREILAPTDQGIMIGTKLLLKYMGNNPVDSKRIF 646
            Y+ V  CS++  +I  S +  + I  + GIF+++A   + +F    +EY+     LQ QR      L F + YRA VT +   GV V +           G   ++P + L     KG    +  +D  I  G+ + + Y+GN+P +  RIF
Sbjct:  750 YWSVLLCSASENLITYSELTEVTIDQVAGIFMVLAGAFVLSFLVVAMEYIGYIIGLQVQRTRADPDLEFNKAYRAIVTSITPTGVYVKL----------HGEKEFIPNQMLSPDASKG----MTASDLQISCGSMIEITYLGNDPAEGYRIF 887          
BLAST of SMED30014221 vs. TrEMBL
Match: A0A1I8JEA7 (PBPe domain-containing protein OS=Macrostomum lignano OX=282301 PE=3 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 4.670e-6
Identity = 43/152 (28.29%), Postives = 71/152 (46.71%), Query Frame = 2
Query:  200 YFYVGQCSSTNPII--SSIQPLDIYDMGGIFVLIAVGIIAAFPAAVIEYLLNKSKLQCQRKTTGNSLRFGQVYRAKVTGLDRNGVTVDIGRLNLFSTTNEGRIYYVPKKYLGIK-KKGEREILAPTDQGIMIGTKLLLKYMGNNPVDSKRIF 646
            Y+ V  CS++  +I  S +  + I  + GIF+++A   + +F    +EY+     LQ QR      L F + YRA VT +   GV V +           G   ++P + L     KG    +  +D  I  G+ + + Y+GN+P +  RIF
Sbjct:  711 YWSVLLCSASENLITYSELTEVTIDQVAGIFMVLAGAFVLSFLVVAMEYIGYIIGLQVQRTRADPDLEFNKAYRALVTSITPTGVYVKL----------HGEKEFIPNQMLSPDASKG----MTASDLQISCGSMIEITYLGNDPAEGYRIF 848          
BLAST of SMED30014221 vs. TrEMBL
Match: A0A267EIQ1 (PBPe domain-containing protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig012789g2 PE=4 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 4.835e-6
Identity = 43/152 (28.29%), Postives = 71/152 (46.71%), Query Frame = 2
Query:  200 YFYVGQCSSTNPII--SSIQPLDIYDMGGIFVLIAVGIIAAFPAAVIEYLLNKSKLQCQRKTTGNSLRFGQVYRAKVTGLDRNGVTVDIGRLNLFSTTNEGRIYYVPKKYLGIK-KKGEREILAPTDQGIMIGTKLLLKYMGNNPVDSKRIF 646
            Y+ V  CS++  +I  S +  + I  + GIF+++A   + +F    +EY+     LQ QR      L F + YRA VT +   GV V +           G   ++P + L     KG    +  +D  I  G+ + + Y+GN+P +  RIF
Sbjct:  741 YWSVLLCSASENLITYSELTEVTIDQVAGIFMVLAGAFVLSFLVVAMEYIGYIIGLQVQRTRADPDLEFNKAYRALVTSITPTGVYVKL----------HGEKEFIPNQMLSPDASKG----MTASDLQISCGSMIEITYLGNDPAEGYRIF 878          
BLAST of SMED30014221 vs. Planmine SMEST
Match: SMESG000043379.1 (SMESG000043379.1)

HSP 1 Score: 324.324 bits (830), Expect = 1.313e-105
Identity = 155/156 (99.36%), Postives = 156/156 (100.00%), Query Frame = 2
Query:  197 RYFYVGQCSSTNPIISSIQPLDIYDMGGIFVLIAVGIIAAFPAAVIEYLLNKSKLQCQRKTTGNSLRFGQVYRAKVTGLDRNGVTVDIGRLNLFSTTNEGRIYYVPKKYLGIKKKGEREILAPTDQGIMIGTKLLLKYMGNNPVDSKRIFVQVHKK 664
            +YFYVGQCSSTNPIISSIQPLDIYDMGGIFVLIAVGIIAAFPAAVIEYLLNKSKLQCQRKTTGNSLRFGQVYRAKVTGLDRNGVTVDIGRLNLFSTTNEGRIYYVPKKYLGIKKKGEREILAPTDQGIMIGTKLLLKYMGNNPVDSKRIFVQVHKK
Sbjct:  708 KYFYVGQCSSTNPIISSIQPLDIYDMGGIFVLIAVGIIAAFPAAVIEYLLNKSKLQCQRKTTGNSLRFGQVYRAKVTGLDRNGVTVDIGRLNLFSTTNEGRIYYVPKKYLGIKKKGEREILAPTDQGIMIGTKLLLKYMGNNPVDSKRIFVQVHKK 863          
The following BLAST results are available for this feature:
BLAST of SMED30014221 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 SMED30014221 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 SMED30014221 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 SMED30014221 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 SMED30014221 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 SMED30014221 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 SMED30014221 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 SMED30014221 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1I8JF761.947e-627.85PBPe domain-containing protein OS=Macrostomum lign... [more]
A0A1I8JCZ22.238e-627.85PBPe domain-containing protein OS=Macrostomum lign... [more]
A0A267FB664.334e-628.29PBPe domain-containing protein (Fragment) OS=Macro... [more]
A0A1I8JEA74.670e-628.29PBPe domain-containing protein OS=Macrostomum lign... [more]
A0A267EIQ14.835e-628.29PBPe domain-containing protein (Fragment) OS=Macro... [more]
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BLAST of SMED30014221 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 SMED30014221 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 SMED30014221 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 SMED30014221 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 SMED30014221 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 SMED30014221 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000043379.11.313e-10599.36SMESG000043379.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014221 ID=SMED30014221|Name=SMED30014221|organism=Schmidtea mediterranea sexual|type=transcript|length=706bp
CCAAAATCCGTTCTTGCACCGGGGCCTCCAAAATGGCTAGATCCACAGCT
GCAGACTTGCTATTGTTTAACCTCTTTAAACTACTACGAACCTGAATTTA
CAAATTTTGTGAATAAATTTTTATAGCTTATTTCTTCATTTTGATTGTTC
CAAAACTCGAATTTAGCGGAAATTTTCATGGCTGAAATTGATGTTTAGAT
ATTTTTATGTTGGTCAATGTTCAAGCACAAATCCTATAATATCAAGCATA
CAGCCTTTGGATATTTATGACATGGGAGGCATATTCGTTTTGATTGCCGT
GGGAATAATAGCGGCGTTTCCAGCGGCTGTAATTGAATATTTGCTTAACA
AATCTAAATTGCAGTGTCAAAGAAAAACGACCGGGAATTCATTACGATTT
GGACAAGTTTATAGGGCTAAAGTCACTGGGTTGGATCGAAATGGCGTTAC
TGTCGATATTGGAAGATTAAATCTATTTTCAACCACCAACGAAGGAAGAA
TATACTATGTTCCTAAAAAGTACCTTGGAATAAAAAAAAAAGGAGAACGA
GAAATTTTGGCGCCGACCGATCAAGGAATTATGATTGGAACGAAATTACT
GTTGAAGTATATGGGGAACAATCCTGTAGATTCCAAAAGAATATTTGTCC
AAGTTCATAAAAAATAAATTTTGGATCAAAGAGATTATTTTAGATTTCAT
TAATGC
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protein sequence of SMED30014221-orf-1

>SMED30014221-orf-1 ID=SMED30014221-orf-1|Name=SMED30014221-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=159bp
MFRYFYVGQCSSTNPIISSIQPLDIYDMGGIFVLIAVGIIAAFPAAVIEY
LLNKSKLQCQRKTTGNSLRFGQVYRAKVTGLDRNGVTVDIGRLNLFSTTN
EGRIYYVPKKYLGIKKKGEREILAPTDQGIMIGTKLLLKYMGNNPVDSKR
IFVQVHKK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0002032epidermal cell
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
GO:0004970ionotropic glutamate receptor activity
GO:0016740transferase activity
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: biological process
TermDefinition
GO:0035235ionotropic glutamate receptor signaling pathway
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 30..52