SMED30031259

Overview
NameSMED30031259
Smed IDSMED30031259
Length (bp)570
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 SMED30031259 (SMED30031259) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30031259 (SMED30031259) 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 SMED30031259 (SMED30031259) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30031259 (SMED30031259) 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



SMED30031259

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
neoblastSMED30031259SMESG000007873.1 dd_Smed_v4_1289_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30031259SMESG000007873.1 dd_Smed_v4_1289_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior sideSMED30031259SMESG000007873.1 dd_Smed_v4_1289_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30031259SMESG000007873.1 dd_Smed_v4_1289_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30031259 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001367:67388..68021 -2502
Homology
[Close]
BLAST of SMED30031259 vs. Ensembl Human
Match: SH3BGRL3 (SH3 domain binding glutamate rich protein like 3 [Source:HGNC Symbol;Acc:HGNC:15568])

HSP 1 Score: 46.9802 bits (110), Expect = 8.276e-7
Identity = 26/76 (34.21%), Postives = 44/76 (57.89%), Query Frame = -1 
Query:  343 RVXXXXFSGSSKIKAEXTYVNDLLVKMKVTFQXIDISVETEKRDIMKEIVLAAGAKAFTPPRVLKDGKYIGGYDEF 570
            RV+    +GS +IK++ + V  +L   ++ +Q +DIS +   RD M+   LA   KA TPP+++   +Y G Y+ F
Sbjct:    5 RVYSTSVTGSREIKSQQSEVTRILDGKRIQYQLVDISQDNALRDEMR--ALAGNPKA-TPPQIVNGDQYCGDYELF 77
[Close]
BLAST of SMED30031259 vs. Ensembl Mouse
Match: Sh3bgrl3 (SH3 domain binding glutamic acid-rich protein-like 3 [Source:MGI Symbol;Acc:MGI:1920973])

HSP 1 Score: 46.9802 bits (110), Expect = 5.182e-7
Identity = 26/76 (34.21%), Postives = 43/76 (56.58%), Query Frame = -1 
Query:  343 RVXXXXFSGSSKIKAEXTYVNDLLVKMKVTFQXIDISVETEKRDIMKEIVLAAGAKAFTPPRVLKDGKYIGGYDEF 570
            RV+    +GS +IK++ + V  +L   ++ +Q +DIS +   RD M+   LA   KA TPP+++    Y G Y+ F
Sbjct:    5 RVYSTSVTGSREIKSQQSEVTRILDGKRIQYQLVDISQDNALRDEMR--TLAGNPKA-TPPQIVNGNHYCGDYELF 77
[Close]
BLAST of SMED30031259 vs. UniProt/SwissProt
Match: sp|Q91VW3|SH3L3_MOUSE (SH3 domain-binding glutamic acid-rich-like protein 3 OS=Mus musculus OX=10090 GN=Sh3bgrl3 PE=1 SV=1)

HSP 1 Score: 46.9802 bits (110), Expect = 3.625e-6
Identity = 26/76 (34.21%), Postives = 43/76 (56.58%), Query Frame = -1 
Query:  343 RVXXXXFSGSSKIKAEXTYVNDLLVKMKVTFQXIDISVETEKRDIMKEIVLAAGAKAFTPPRVLKDGKYIGGYDEF 570
            RV+    +GS +IK++ + V  +L   ++ +Q +DIS +   RD M+   LA   KA TPP+++    Y G Y+ F
Sbjct:    5 RVYSTSVTGSREIKSQQSEVTRILDGKRIQYQLVDISQDNALRDEMR--TLAGNPKA-TPPQIVNGNHYCGDYELF 77
[Close]
BLAST of SMED30031259 vs. UniProt/SwissProt
Match: sp|Q5RC61|SH3L3_PONAB (SH3 domain-binding glutamic acid-rich-like protein 3 OS=Pongo abelii OX=9601 GN=SH3BGRL3 PE=3 SV=1)

HSP 1 Score: 46.9802 bits (110), Expect = 3.975e-6
Identity = 26/76 (34.21%), Postives = 44/76 (57.89%), Query Frame = -1 
Query:  343 RVXXXXFSGSSKIKAEXTYVNDLLVKMKVTFQXIDISVETEKRDIMKEIVLAAGAKAFTPPRVLKDGKYIGGYDEF 570
            RV+    +GS +IK++ + V  +L   ++ +Q +DIS +   RD M+   LA   KA TPP+++   +Y G Y+ F
Sbjct:    5 RVYSTSVTGSREIKSQQSEVTRILDGKRIQYQLVDISQDNALRDEMR--ALAGNPKA-TPPQIVNGDQYCGDYELF 77
[Close]
BLAST of SMED30031259 vs. UniProt/SwissProt
Match: sp|Q9H299|SH3L3_HUMAN (SH3 domain-binding glutamic acid-rich-like protein 3 OS=Homo sapiens OX=9606 GN=SH3BGRL3 PE=1 SV=1)

HSP 1 Score: 46.9802 bits (110), Expect = 3.975e-6
Identity = 26/76 (34.21%), Postives = 44/76 (57.89%), Query Frame = -1 
Query:  343 RVXXXXFSGSSKIKAEXTYVNDLLVKMKVTFQXIDISVETEKRDIMKEIVLAAGAKAFTPPRVLKDGKYIGGYDEF 570
            RV+    +GS +IK++ + V  +L   ++ +Q +DIS +   RD M+   LA   KA TPP+++   +Y G Y+ F
Sbjct:    5 RVYSTSVTGSREIKSQQSEVTRILDGKRIQYQLVDISQDNALRDEMR--ALAGNPKA-TPPQIVNGDQYCGDYELF 77
[Close]
BLAST of SMED30031259 vs. UniProt/SwissProt
Match: sp|Q3ZCL8|SH3L3_BOVIN (SH3 domain-binding glutamic acid-rich-like protein 3 OS=Bos taurus OX=9913 GN=SH3BGRL3 PE=3 SV=1)

HSP 1 Score: 46.9802 bits (110), Expect = 3.975e-6
Identity = 26/76 (34.21%), Postives = 44/76 (57.89%), Query Frame = -1 
Query:  343 RVXXXXFSGSSKIKAEXTYVNDLLVKMKVTFQXIDISVETEKRDIMKEIVLAAGAKAFTPPRVLKDGKYIGGYDEF 570
            RV+    +GS +IK++ + V  +L   ++ +Q +DIS +   RD M+   LA   KA TPP+++   +Y G Y+ F
Sbjct:    5 RVYSTSVTGSREIKSQQSEVTRILDGKRIQYQLVDISQDNALRDEMR--ALAGNPKA-TPPQIVNGDQYCGDYELF 77
[Close]
BLAST of SMED30031259 vs. Planmine SMEST
Match: SMESG000007873.1 (SMESG000007873.1)

HSP 1 Score: 144.05 bits (362), Expect = 6.664e-45
Identity = 80/83 (96.39%), Postives = 80/83 (96.39%), Query Frame = -1 
Query:  301 SGSSKIKAEXTYVNDLLVKMKVTFQXIDISVETEKRDIMKEIVLAAGAKAFTPPRVLKDGKYIGGYDEFYXXXXXXXXESILQ 549
            SGSSKIKAE TYVNDLLVKMKVTFQ IDISVETEKRDIMKEIVLAAGAKAFTPPRVLKDGKYIGGYDEFYEAAEAEN ESILQ
Sbjct:   11 SGSSKIKAEQTYVNDLLVKMKVTFQTIDISVETEKRDIMKEIVLAAGAKAFTPPRVLKDGKYIGGYDEFYEAAEAENLESILQ 93
The following BLAST results are available for this feature:
BLAST of SMED30031259 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 1
Match NameE-valueIdentityDescription
SH3BGRL38.276e-734.21SH3 domain binding glutamate rich protein like 3 [... [more]
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BLAST of SMED30031259 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 SMED30031259 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 SMED30031259 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 SMED30031259 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 SMED30031259 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 1
Match NameE-valueIdentityDescription
Sh3bgrl35.182e-734.21SH3 domain binding glutamic acid-rich protein-like... [more]
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BLAST of SMED30031259 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 4
Match NameE-valueIdentityDescription
sp|Q91VW3|SH3L3_MOUSE3.625e-634.21SH3 domain-binding glutamic acid-rich-like protein... [more]
sp|Q5RC61|SH3L3_PONAB3.975e-634.21SH3 domain-binding glutamic acid-rich-like protein... [more]
sp|Q9H299|SH3L3_HUMAN3.975e-634.21SH3 domain-binding glutamic acid-rich-like protein... [more]
sp|Q3ZCL8|SH3L3_BOVIN3.975e-634.21SH3 domain-binding glutamic acid-rich-like protein... [more]
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BLAST of SMED30031259 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 SMED30031259 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 SMED30031259 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 SMED30031259 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 SMED30031259 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 SMED30031259 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 SMED30031259 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000007873.16.664e-4596.39SMESG000007873.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031259 ID=SMED30031259|Name=SMED30031259|organism=Schmidtea mediterranea sexual|type=transcript|length=570bp
TTTTTTTTTTTTTTTTTTTTTTTTGAGAAAATTCATAATATATTTGAAAC
ATCGACNCAATATTGTNTTTTTGGAATTATAAAAATTTGCNCAAAAAATT
NATATTATTCAATATTAACTAATAAAAATAAAAAAACTAAAAAAATATAT
ACCAATTATAAAGTCTAAAAAATCATAAATTTGATTTTTCAGTATTAGAA
AATTTCAAGTTATAGGAATAAAATCAATATNCCAAATTAATGCCAATGTC
ATTTATAGNGGTATTGNCATTTATTATTTAATTTAAATAACTTTAAATCA
TTGTAATATGCTTTCCANATTTTCAGCTTCGGCAGCTTCATAAAACTCAT
CATAACCCCCAATATATTTTCCATCTTTTAAAACTCTNGGNGGGGTAAAT
GCTTTAGCTCCTGCTGCTAGCACTATTTCTTTCATAATATCTCGTTTCTC
AGTTTCAACTGAAATATCTATTGNTTGAAATGTCACTTTCATCTTAACTA
AAAGATCGTTGACATATGTTNGCTCGGCTTTAATTTTTGAACTACCAGAA
AAAAAAAAAAAAAAAACTCG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell
PLANA:0000142posterior region of the whole animal
Vocabulary: INTERPRO
TermDefinition
IPR036249Thioredoxin-like_sf
IPR012336Thioredoxin-like_fold
IPR006993Glut_rich_SH3-bd
IPR002109Glutaredoxin
Vocabulary: molecular function
TermDefinition
GO:0009055electron carrier activity
GO:0015035protein disulfide oxidoreductase activity
Vocabulary: biological process
TermDefinition
GO:0045454cell redox homeostasis
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR006993SH3-binding, glutamic acid-rich proteinPFAMPF04908SH3BGRcoord: 1..77
e-value: 2.2E-13
score: 50.2
IPR036249Thioredoxin-like superfamilyGENE3DG3DSA:3.40.30.10coord: 1..78
e-value: 6.7E-17
score: 63.2
IPR036249Thioredoxin-like superfamilySUPERFAMILYSSF52833Thioredoxin-likecoord: 5..77
NoneNo IPR availablePANTHERPTHR12232SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH-LIKE PROTEINcoord: 1..77
IPR002109GlutaredoxinPROSITEPS51354GLUTAREDOXIN_2coord: 1..78
score: 10.739