SMED30020024

Overview
NameSMED30020024
Smed IDSMED30020024
Length (bp)667
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 SMED30020024 (SMED30020024) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30020024 (SMED30020024) 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 SMED30020024 (SMED30020024) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30020024 (SMED30020024) 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



SMED30020024

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
nervous systemSMED30020024h1SMcG0017227 dd_Smed_v4_12949_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30020024h1SMcG0017227 dd_Smed_v4_12949_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30020024h1SMcG0017227 dd_Smed_v4_12949_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30020024h1SMcG0017227 OX_Smed_1.0.01959ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30020024 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001120:3053..3714 +3230
Homology
[Close]
BLAST of SMED30020024 vs. TrEMBL
Match: A0A183WIB0 (Uncharacterized protein OS=Trichobilharzia regenti OX=157069 GN=TRE_LOCUS11863 PE=4 SV=1)

HSP 1 Score: 70.4774 bits (171), Expect = 1.213e-10
Identity = 32/71 (45.07%), Postives = 51/71 (71.83%), Query Frame = 3 
Query:   96 KFRPQLLTLISMLSFVLLIMIIFMVLPMQYQNFIMEIFSSKVGK--FSYIDIGLYKTRHSMYRKEVYQHEM 302
            + +P L+ L+S+++FVLL+MI  ++LP   Q+ + ++  ++     F+YID+GLYKTRHS+YRKEVY   M
Sbjct:   37 ELQPGLIALVSLMAFVLLVMIATLLLPKSIQDNLFQLILNQTPDQTFNYIDVGLYKTRHSIYRKEVYSLAM 107
[Close]
BLAST of SMED30020024 vs. TrEMBL
Match: A0A183N1Y5 (Uncharacterized protein OS=Schistosoma margrebowiei OX=48269 GN=SMRZ_LOCUS22310 PE=4 SV=1)

HSP 1 Score: 67.0106 bits (162), Expect = 1.688e-9
Identity = 30/67 (44.78%), Postives = 47/67 (70.15%), Query Frame = 3 
Query:   96 KFRPQLLTLISMLSFVLLIMIIFMVLPMQYQNFIMEI--FSSKVGKFSYIDIGLYKTRHSMYRKEVY 290
            + +P L+ L+SM++ +LLIM   ++LP   Q+ + ++    +    F+YID+GLYKTRHS+YRKEVY
Sbjct:   37 ELQPGLIALVSMMALILLIMTAILLLPKSIQDNVFQLVLHQTPDQTFNYIDVGLYKTRHSIYRKEVY 103
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BLAST of SMED30020024 vs. TrEMBL
Match: A0A4Z2DKM1 (Uncharacterized protein OS=Schistosoma japonicum OX=6182 GN=EWB00_000070 PE=4 SV=1)

HSP 1 Score: 65.0846 bits (157), Expect = 1.924e-9
Identity = 30/67 (44.78%), Postives = 47/67 (70.15%), Query Frame = 3 
Query:   96 KFRPQLLTLISMLSFVLLIMIIFMVLPMQYQN--FIMEIFSSKVGKFSYIDIGLYKTRHSMYRKEVY 290
            + +P L+ L+S+++ +LLIM   ++LP   Q+  F + +  +    F+YID+GLYKTRHS+YRKEVY
Sbjct:   37 ELQPGLIALVSLMALILLIMTAVLLLPKSIQDNVFQLVLHQTPDQTFNYIDVGLYKTRHSIYRKEVY 103
[Close]
BLAST of SMED30020024 vs. TrEMBL
Match: A0A183JCE5 (Uncharacterized protein OS=Schistosoma curassoni OX=6186 GN=SCUD_LOCUS353 PE=4 SV=1)

HSP 1 Score: 65.855 bits (159), Expect = 1.926e-9
Identity = 29/67 (43.28%), Postives = 47/67 (70.15%), Query Frame = 3 
Query:   96 KFRPQLLTLISMLSFVLLIMIIFMVLPMQYQNFIMEI--FSSKVGKFSYIDIGLYKTRHSMYRKEVY 290
            + +P L+ L+S+++ +LLIM   ++LP   Q+ + ++    +    F+YID+GLYKTRHS+YRKEVY
Sbjct:   37 ELQPGLIALVSLMALILLIMTAILLLPKSIQDNVFQLVLHQTPDQTFNYIDVGLYKTRHSIYRKEVY 103
[Close]
BLAST of SMED30020024 vs. TrEMBL
Match: G4LZC0 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 GN=Smp_162390 PE=4 SV=1)

HSP 1 Score: 65.855 bits (159), Expect = 4.511e-9
Identity = 30/73 (41.10%), Postives = 51/73 (69.86%), Query Frame = 3 
Query:   84 LGDDK--FRPQLLTLISMLSFVLLIMIIFMVLPMQYQNFIMEIFSSKVGK--FSYIDIGLYKTRHSMYRKEVY 290
            +G +K   +P L+ L+S+++ +LLIM   ++LP   Q+ + ++  ++     F+YID+GLYKTRHS+YRKE+Y
Sbjct:   31 IGPEKVELQPGLIALVSLMALILLIMTAILLLPKSIQDNVFQLVLNQTPDQTFNYIDVGLYKTRHSIYRKEIY 103
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BLAST of SMED30020024 vs. Planmine SMEST
Match: SMESG000027441.1 (SMESG000027441.1)

HSP 1 Score: 282.337 bits (721), Expect = 3.874e-98
Identity = 150/150 (100.00%), Postives = 150/150 (100.00%), Query Frame = 3 
Query:   36 MHTSTGKVFTNVTSLTLGDDKFRPQLLTLISMLSFVLLIMIIFMVLPMQYQNFIMEIFSSKVGKFSYIDIGLYKTRHSMYRKEVYQHEMXXXXXXXXXXAKIDELNSKMLTKDIELPRIVTTSYDQMSIEPDESSSRILVENSQKNQVLA 485
            MHTSTGKVFTNVTSLTLGDDKFRPQLLTLISMLSFVLLIMIIFMVLPMQYQNFIMEIFSSKVGKFSYIDIGLYKTRHSMYRKEVYQHEMSKSNNLKKNSAKIDELNSKMLTKDIELPRIVTTSYDQMSIEPDESSSRILVENSQKNQVLA
Sbjct:    1 MHTSTGKVFTNVTSLTLGDDKFRPQLLTLISMLSFVLLIMIIFMVLPMQYQNFIMEIFSSKVGKFSYIDIGLYKTRHSMYRKEVYQHEMSKSNNLKKNSAKIDELNSKMLTKDIELPRIVTTSYDQMSIEPDESSSRILVENSQKNQVLA 150
[Close]
BLAST of SMED30020024 vs. Planmine SMEST
Match: SMESG000009120.1 (SMESG000009120.1)

HSP 1 Score: 57.3806 bits (137), Expect = 1.912e-10
Identity = 23/50 (46.00%), Postives = 36/50 (72.00%), Query Frame = 3 
Query:  153 MIIFMVLPMQYQNFIMEIFSSKVGKFSYIDIGLYKTRHSMYRKEVYQHEM 302
            MII +++P + Q+F + +  ++  KF+YID  LY+ RHSMYRKE+Y  +M
Sbjct:    1 MIIALIIPKEKQDFFLNMCKAEDVKFNYIDTALYRARHSMYRKEIYLQQM 50
[Close]
BLAST of SMED30020024 vs. Planmine SMEST
Match: SMESG000023107.1 (SMESG000023107.1)

HSP 1 Score: 52.7582 bits (125), Expect = 1.267e-8
Identity = 33/83 (39.76%), Postives = 50/83 (60.24%), Query Frame = 3 
Query:   60 FTNVTSLTLGDDKFRPQLLTLISMLSFVLLIMIIFMVLPMQYQNFIMEIFSSKVG--KFSYIDIGLYKTRHSMYRKEVYQHEM 302
            F   T+L   ++++   L+ LI  LS VL++M+  +V         + IF    G  KF+YI++GL+KTRHS+YR EVY+H M
Sbjct:   18 FNRSTNLLTNENQYNLPLIILIIFLSSVLIVMMFSLVNHSGMFGKSINIFGKCRGPKKFNYINVGLFKTRHSIYRSEVYKHSM 100
The following BLAST results are available for this feature:
BLAST of SMED30020024 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 SMED30020024 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 SMED30020024 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 SMED30020024 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 SMED30020024 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 SMED30020024 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 SMED30020024 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 SMED30020024 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A183WIB01.213e-1045.07Uncharacterized protein OS=Trichobilharzia regenti... [more]
A0A183N1Y51.688e-944.78Uncharacterized protein OS=Schistosoma margrebowie... [more]
A0A4Z2DKM11.924e-944.78Uncharacterized protein OS=Schistosoma japonicum O... [more]
A0A183JCE51.926e-943.28Uncharacterized protein OS=Schistosoma curassoni O... [more]
G4LZC04.511e-941.10Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
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BLAST of SMED30020024 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 SMED30020024 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 SMED30020024 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 SMED30020024 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 SMED30020024 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 SMED30020024 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000027441.13.874e-98100.00SMESG000027441.1[more]
SMESG000009120.11.912e-1046.00SMESG000009120.1[more]
SMESG000023107.11.267e-839.76SMESG000023107.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020024 ID=SMED30020024|Name=SMED30020024|organism=Schmidtea mediterranea sexual|type=transcript|length=667bp
ATTCCTTCAAATTGAAAAAATAGACTCCCGCCTAAATGCACACTAGTACA
GGAAAGGTTTTCACAAATGTCACCAGTCTCACATTGGGAGATGATAAATT
TCGACCGCAATTGCTCACCTTGATCTCGATGTTGTCATTTGTTTTATTGA
TCATGATAATTTTCATGGTGCTGCCAATGCAGTATCAAAACTTCATCATG
GAAATATTTTCCAGCAAAGTCGGTAAGTTCAGTTACATAGACATCGGCTT
GTACAAAACTCGACATTCCATGTACCGGAAAGAAGTTTATCAGCATGAAA
TGAGCAAATCAAATAATCTGAAAAAGAATTCCGCGAAAATCGACGAACTG
AATTCGAAAATGTTAACTAAAGACATTGAGTTGCCAAGAATCGTCACGAC
CAGTTACGATCAAATGAGCATTGAGCCTGACGAGTCTAGCAGTCGAATTC
TAGTGGAAAATTCACAGAAAAATCAAGTTCTAGCATAAATCTAGCATTAT
TTGCTTTGCTCAAATTGTATTGTAGCACTTCTGGTAAATCGGATCGGATT
TTTATTTTGTGTTGTTTTTTTAAATAATCAATCATTTGTATAATTAATAT
AATTTTTATCACTTTTTCAATGATTTGGATAAATAATTGTGAGACATTGG
AAGATCAAAATAAACAA
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protein sequence of SMED30020024-orf-1

>SMED30020024-orf-1 ID=SMED30020024-orf-1|Name=SMED30020024-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=151bp
MHTSTGKVFTNVTSLTLGDDKFRPQLLTLISMLSFVLLIMIIFMVLPMQY
QNFIMEIFSSKVGKFSYIDIGLYKTRHSMYRKEVYQHEMSKSNNLKKNSA
KIDELNSKMLTKDIELPRIVTTSYDQMSIEPDESSSRILVENSQKNQVLA
*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 26..48