SMED30003229

Overview
NameSMED30003229
Smed IDSMED30003229
Length (bp)599
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 SMED30003229 (SMED30003229) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30003229 (SMED30003229) 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 SMED30003229 (SMED30003229) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30003229 (SMED30003229) 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



SMED30003229

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30003229SMESG000029274.1 SmedASXL_009129SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30003229SMESG000029274.1 dd_Smed_v4_16552_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30003229SMESG000029274.1 dd_Smed_v4_16552_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30003229SMESG000029274.1 dd_Smed_v6_16552_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30003229 vs. TrEMBL
Match: A0A3R7CTZ8 (Ephrin RBD domain-containing protein OS=Clonorchis sinensis OX=79923 GN=CSKR_3424s PE=4 SV=1)

HSP 1 Score: 69.3218 bits (168), Expect = 2.522e-10
Identity = 37/108 (34.26%), Postives = 55/108 (50.93%), Query Frame = 3 
Query:  135 HNIYWSPHNPLFKISSNHLIVKDGDNIELVCPKTYDIADKIYIFWTTNYNTYQNCGANSEAESEDLHLLFNCSLDRLNPQFRLQVSIYSWVISNPAFSNKQPVYFIRK 458
            HNI W P N LF      L V +GDN+  VCP+ + +   + IFWT +   Y  C  + E     +H L +C       +F L+VS +S +   P F ++ PVYF+ +
Sbjct:   32 HNILWGPENSLFDDKKAQLHVGEGDNLIFVCPEQFTL--HLLIFWTYSQTAYDYCDTSGEKR---VHPLMSCKQQERQTEFILKVSRFSELTHIPIFRSENPVYFLAQ 134
[Close]
BLAST of SMED30003229 vs. TrEMBL
Match: H2KQK3 (Ephrin RBD domain-containing protein OS=Clonorchis sinensis OX=79923 GN=CLF_104145 PE=4 SV=1)

HSP 1 Score: 69.3218 bits (168), Expect = 2.546e-10
Identity = 37/108 (34.26%), Postives = 55/108 (50.93%), Query Frame = 3 
Query:  135 HNIYWSPHNPLFKISSNHLIVKDGDNIELVCPKTYDIADKIYIFWTTNYNTYQNCGANSEAESEDLHLLFNCSLDRLNPQFRLQVSIYSWVISNPAFSNKQPVYFIRK 458
            HNI W P N LF      L V +GDN+  VCP+ + +   + IFWT +   Y  C  + E     +H L +C       +F L+VS +S +   P F ++ PVYF+ +
Sbjct:   32 HNILWGPENSLFDDKKAQLHVGEGDNLIFVCPEQFTL--HLLIFWTYSQTAYDYCDTSGEKR---VHPLMSCKQQERQTEFILKVSRFSELTHIPIFRSENPVYFLAQ 134
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BLAST of SMED30003229 vs. TrEMBL
Match: A0A3Q0KLD0 (Ephrin RBD domain-containing protein OS=Schistosoma mansoni OX=6183 PE=4 SV=1)

HSP 1 Score: 63.5438 bits (153), Expect = 2.914e-8
Identity = 38/108 (35.19%), Postives = 55/108 (50.93%), Query Frame = 3 
Query:  135 HNIYWSPHNPLFKISSNHLIVKDGDNIELVCPKTYDIADKIYIFWTTNYNTYQNCGANSEAESEDLHLLFNCSLDRLNPQFRLQVSIYSWVISNPAFSNKQPVYFIRK 458
            H I W   N LF  +     VK+GDNI  VCP   D+     +FWT +  TY  CGA S +++     L +CS    N +F L+V+ +S +  +P F     VYF+ +
Sbjct:   25 HIIMWDITNKLFSSNVTMFRVKEGDNIVFVCPS--DVRRSQKLFWTMSKETYDECGAPSSSQTVK---LLDCSQSPKNTEFILKVAQFSEIPYSPHFRENDFVYFLGQ 127
[Close]
BLAST of SMED30003229 vs. TrEMBL
Match: A0A095A5G5 (Ephrin RBD domain-containing protein (Fragment) OS=Schistosoma haematobium OX=6185 GN=MS3_10717 PE=4 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 5.250e-8
Identity = 35/100 (35.00%), Postives = 56/100 (56.00%), Query Frame = 3 
Query:  165 LFKISSNHLI--VKDGDNIELVCPKTYDIADKIYIFWTTNYNTYQNCGANSEAESEDLHLLFNCSLDRLNPQFRLQVSIYSWVISNPAFSNKQPVYFIRK 458
            +++ SSN  +  VK+GDNI  +CP   D+     +FWT +  TY +CGA S +++     L +CS    N +F L+V+ +S +  +P F     VYF+ K
Sbjct:    6 VYRFSSNVTMFRVKEGDNIVFICPS--DVRRSQKLFWTMSKKTYDDCGAPSSSQTVK---LLDCSQSPKNTEFILKVAQFSEIPYSPHFRENDFVYFLGK 100
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BLAST of SMED30003229 vs. TrEMBL
Match: A0A4Z2DW92 (Coiled coil domain-containing protein isoform 2 OS=Schistosoma japonicum OX=6182 GN=EWB00_002901 PE=4 SV=1)

HSP 1 Score: 60.077 bits (144), Expect = 3.706e-7
Identity = 35/108 (32.41%), Postives = 59/108 (54.63%), Query Frame = 3 
Query:  135 HNIYWSPHNPLFKISSNHLIVKDGDNIELVCPKTYDIADKIYIFWTTNYNTYQNCGANSEAESEDLHLLFNCSLDRLNPQFRLQVSIYSWVISNPAFSNKQPVYFIRK 458
            H I W  +N LF  ++    V +GDNI  +C  + D+     +FWT +  TY++CGA+S +++     L +CS    + +F L+VS +S +  +P F     VYF+ +
Sbjct:   25 HIITWDINNKLFSSNATIFKVNEGDNIVFIC--SSDVKRNQKLFWTMSRETYEDCGASSSSQTVK---LLDCSQSPQSSEFILKVSQFSEIPYSPHFRENDYVYFLGQ 127
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BLAST of SMED30003229 vs. Planmine SMEST
Match: SMESG000029274.1 (SMESG000029274.1)

HSP 1 Score: 275.018 bits (702), Expect = 7.758e-95
Identity = 132/133 (99.25%), Postives = 132/133 (99.25%), Query Frame = 3 
Query:   54 MPIFLMFLKASLAVISLFFDLVISTVSHNIYWSPHNPLFKISSNHLIVKDGDNIELVCPKTYDIADKIYIFWTTNYNTYQNCGANSEAESEDLHLLFNCSLDRLNPQFRLQVSIYSWVISNPAFSNKQPVYFI 452
            MPIFLMFLKASLAVISLFFDLVISTVSHNIYWSPHNPLFKISSNHLIVKDGDNIELVCPKTYDI DKIYIFWTTNYNTYQNCGANSEAESEDLHLLFNCSLDRLNPQFRLQVSIYSWVISNPAFSNKQPVYFI
Sbjct:    1 MPIFLMFLKASLAVISLFFDLVISTVSHNIYWSPHNPLFKISSNHLIVKDGDNIELVCPKTYDIVDKIYIFWTTNYNTYQNCGANSEAESEDLHLLFNCSLDRLNPQFRLQVSIYSWVISNPAFSNKQPVYFI 133
[Close]
BLAST of SMED30003229 vs. Planmine SMEST
Match: SMESG000029274.1 (SMESG000029274.1)

HSP 1 Score: 265.388 bits (677), Expect = 5.664e-91
Identity = 127/128 (99.22%), Postives = 127/128 (99.22%), Query Frame = 3 
Query:   69 MFLKASLAVISLFFDLVISTVSHNIYWSPHNPLFKISSNHLIVKDGDNIELVCPKTYDIADKIYIFWTTNYNTYQNCGANSEAESEDLHLLFNCSLDRLNPQFRLQVSIYSWVISNPAFSNKQPVYFI 452
            MFLKASLAVISLFFDLVISTVSHNIYWSPHNPLFKISSNHLIVKDGDNIELVCPKTYDI DKIYIFWTTNYNTYQNCGANSEAESEDLHLLFNCSLDRLNPQFRLQVSIYSWVISNPAFSNKQPVYFI
Sbjct:    1 MFLKASLAVISLFFDLVISTVSHNIYWSPHNPLFKISSNHLIVKDGDNIELVCPKTYDIVDKIYIFWTTNYNTYQNCGANSEAESEDLHLLFNCSLDRLNPQFRLQVSIYSWVISNPAFSNKQPVYFI 128
[Close]
BLAST of SMED30003229 vs. Planmine SMEST
Match: SMESG000031186.1 (SMESG000031186.1)

HSP 1 Score: 61.2326 bits (147), Expect = 2.331e-11
Identity = 34/126 (26.98%), Postives = 66/126 (52.38%), Query Frame = 3 
Query:   81 ASLAVISLFFDLVISTV--SHNIYWSPHNPLFKISSNHLIVKDGDNIELVCPKTYDIADKIYIFWTTNYNTYQNCGANSEAESEDLHLLFNCSLDRLNPQFRLQVSIYSWVISNPAFSNKQPVYFI 452
            +++ VI L F +  ++   +H ++W   NP+F   +N + V++GD+I +VCP      + IY  W+     +  C    ++ S    ++ +C    +  +F  QV+ +SWV  NP+F   +P+Y +
Sbjct:   58 SNMIVIMLLFGIPSASTQRTHRLFWDDKNPVFNPGNNRMFVEEGDDITIVCPSNSPEHNNIY--WSKKNEVFDLCEPTFDSNS---IMMIHCEPYSIK-EFNFQVTKFSWVSLNPSFLRNKPIYLL 177
[Close]
BLAST of SMED30003229 vs. Planmine SMEST
Match: SMESG000031186.1 (SMESG000031186.1)

HSP 1 Score: 61.2326 bits (147), Expect = 2.331e-11
Identity = 34/126 (26.98%), Postives = 66/126 (52.38%), Query Frame = 3 
Query:   81 ASLAVISLFFDLVISTV--SHNIYWSPHNPLFKISSNHLIVKDGDNIELVCPKTYDIADKIYIFWTTNYNTYQNCGANSEAESEDLHLLFNCSLDRLNPQFRLQVSIYSWVISNPAFSNKQPVYFI 452
            +++ VI L F +  ++   +H ++W   NP+F   +N + V++GD+I +VCP      + IY  W+     +  C    ++ S    ++ +C    +  +F  QV+ +SWV  NP+F   +P+Y +
Sbjct:   58 SNMIVIMLLFGIPSASTQRTHRLFWDDKNPVFNPGNNRMFVEEGDDITIVCPSNSPEHNNIY--WSKKNEVFDLCEPTFDSNS---IMMIHCEPYSIK-EFNFQVTKFSWVSLNPSFLRNKPIYLL 177
[Close]
BLAST of SMED30003229 vs. Planmine SMEST
Match: SMESG000063175.1 (SMESG000063175.1)

HSP 1 Score: 56.9954 bits (136), Expect = 4.149e-10
Identity = 40/112 (35.71%), Postives = 57/112 (50.89%), Query Frame = 3 
Query:  132 SHNIYWSPHNPLFKISSNHLIVKDGDNIELVCPKTYDIADKIY-IFWTTNYNTYQNCGANSEAESEDLHLLFNCSLDRLNPQ--FRLQVSIYSWVISNPAFSNKQPVYFIRK 458
             H I W   +PLF+ S+N L V   DNI + CP    + ++I+ I+W+ + N +  C       +  L   F C     NP   F L V+ +SWV  NP FS  +PVYFI +
Sbjct:   37 EHIIEWKKFSPLFERSANILKVNHDDNILIKCPV---LENEIFAIYWSYDRNDFIKCDPEDSLTTTPL---FTC-----NPMKSFSLLVTRFSWVSLNPTFSQNRPVYFIAQ 137
The following BLAST results are available for this feature:
BLAST of SMED30003229 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 SMED30003229 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 SMED30003229 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 SMED30003229 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 SMED30003229 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 SMED30003229 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 SMED30003229 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 SMED30003229 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A3R7CTZ82.522e-1034.26Ephrin RBD domain-containing protein OS=Clonorchis... [more]
H2KQK32.546e-1034.26Ephrin RBD domain-containing protein OS=Clonorchis... [more]
A0A3Q0KLD02.914e-835.19Ephrin RBD domain-containing protein OS=Schistosom... [more]
A0A095A5G55.250e-835.00Ephrin RBD domain-containing protein (Fragment) OS... [more]
A0A4Z2DW923.706e-732.41Coiled coil domain-containing protein isoform 2 OS... [more]
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BLAST of SMED30003229 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 SMED30003229 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 SMED30003229 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 SMED30003229 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 SMED30003229 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 SMED30003229 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000029274.17.758e-9599.25SMESG000029274.1[more]
SMESG000029274.15.664e-9199.22SMESG000029274.1[more]
SMESG000031186.12.331e-1126.98SMESG000031186.1[more]
SMESG000031186.12.331e-1126.98SMESG000031186.1[more]
SMESG000063175.14.149e-1035.71SMESG000063175.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003229 ID=SMED30003229|Name=SMED30003229|organism=Schmidtea mediterranea sexual|type=transcript|length=599bp
ATATTTTAATGAGGATGATTTGAATAATTAAATATAAGAAACTCCAGCAA
GATATGCCGATATTTCTCATGTTTCTCAAAGCAAGTTTGGCAGTTATTAG
CTTATTTTTCGATCTAGTCATTAGCACTGTCAGCCACAACATTTATTGGA
GCCCCCATAACCCGTTGTTTAAAATTTCCTCCAACCATTTAATTGTCAAA
GATGGCGATAATATCGAATTGGTTTGTCCAAAAACATACGACATTGCCGA
TAAAATTTATATTTTTTGGACAACAAACTATAATACCTATCAAAACTGTG
GGGCAAATTCAGAAGCTGAAAGTGAAGACTTACATCTGTTATTCAATTGC
TCCTTAGATCGTCTCAACCCCCAATTTCGTCTTCAAGTATCAATTTATTC
CTGGGTCATTTCTAATCCAGCTTTCAGCAATAAACAGCCAGTTTATTTTA
TTCGTAAGTCACACTAGAAATAAAATTTAATTTTTTTGTTCACTTTTGAT
CTGTTTAATTTTTCGAATCGGGAACTCTTACTTAGCAAATGTGATGGTAA
AGGTCTTCGAGAGGCCGAGAAGATACCATTCGCGCATGATTGGCTCAGG
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protein sequence of SMED30003229-orf-1

>SMED30003229-orf-1 ID=SMED30003229-orf-1|Name=SMED30003229-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=138bp
MPIFLMFLKASLAVISLFFDLVISTVSHNIYWSPHNPLFKISSNHLIVKD
GDNIELVCPKTYDIADKIYIFWTTNYNTYQNCGANSEAESEDLHLLFNCS
LDRLNPQFRLQVSIYSWVISNPAFSNKQPVYFIRKSH*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR008972Cupredoxin
IPR001799Ephrin_RBD
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR001799Ephrin receptor-binding domainPFAMPF00812Ephrincoord: 27..136
e-value: 2.3E-9
score: 37.4
IPR008972CupredoxinGENE3DG3DSA:2.60.40.420coord: 22..137
e-value: 1.7E-10
score: 42.5
IPR008972CupredoxinSUPERFAMILYSSF49503Cupredoxinscoord: 27..134