SMED30004354

Overview
NameSMED30004354
Smed IDSMED30004354
Length (bp)347
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 SMED30004354 (SMED30004354) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30004354 (SMED30004354) 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 SMED30004354 (SMED30004354) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30004354 (SMED30004354) 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




SMED30004354

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30004354h1SMcG0009729 Contig45798newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004354h1SMcG0009729 Contig45798uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30004354 vs. TrEMBL
Match: D5JG59 (TNF receptor-associated factor-2-like protein A OS=Dugesia japonica OX=6161 GN=TRAF-2A PE=2 SV=1)

HSP 1 Score: 69.707 bits (169), Expect = 1.777e-11
Identity = 38/112 (33.93%), Postives = 61/112 (54.46%), Query Frame = 3
Query:    6 EILCEKCQISTTKKTMKEHHKVWIK-REEKCEFCGVIDEWIKIEMEHRNPKEEQICDLYEGVCANNCDRKEKVKLKEHWNECSGKPVKCPLELFNCQA-QLPIAEMQKHMIE 335
            EI CEKC I    K    H K   + R   C++CG+  +   + + H NP  +++C  Y G+C+NNC+   KV LK+H   C  K ++CP   F+C+  ++   ++ KH+ E
Sbjct:   12 EITCEKCGIKFGAKEKANHDKDKCEMRMVNCDYCGITMKSKDLNIIHLNPDRDELCSKYVGICSNNCNETRKVNLKDHLKICPNKKLECPFHQFDCKIDKMTKEKLMKHLDE 123          
BLAST of SMED30004354 vs. TrEMBL
Match: T1DBK6 (TRAF-4 OS=Dendrocoelum lacteum OX=27895 PE=2 SV=1)

HSP 1 Score: 57.3806 bits (137), Expect = 3.979e-7
Identity = 27/89 (30.34%), Postives = 46/89 (51.69%), Query Frame = 3
Query:   81 REEKCEFCGVIDEWIKIEMEHRNPKEEQICDLYEGVCANNCDRKEKVKLKEHWNECSGKPVKCPLELFNCQAQLPIAEMQKHMIENSIE 347
            RE  C++C  +  + +    H   +   +C  YE +C   C  + KV L  H   C  KP++CPL +F+C+  +P  +M +H+  +S E
Sbjct:  148 REVLCQYCRTLLTFKEYNESHLCFESRDLCGKYEAICPYGCTGESKVNLLHHRKSCENKPLECPLHVFDCKQLIPKDQMTEHLNTSSYE 236          
BLAST of SMED30004354 vs. TrEMBL
Match: A0A1I8G6V3 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=3 SV=1)

HSP 1 Score: 56.9954 bits (136), Expect = 6.065e-7
Identity = 28/112 (25.00%), Postives = 55/112 (49.11%), Query Frame = 3
Query:   15 CEKCQISTTKKTMKEHHKVWIK-REEKCEFCGVIDEWIKIEMEHRNPKEEQICDLYEGVCANNCDRKEKVKLK---EHWNECSGKPVKCPLELFNCQAQLPIAEMQKHMIEN 338
            CE+C+    KK M+ H     + R+E C+ C  +    ++E  HRN + +  C  +   C +  +R   +  +    H +EC  +PV+C      C+A +  +++++H  E+
Sbjct: 1762 CEQCKELILKKDMQRHTSSECRHRKETCDLCSQLVTHSEMETSHRNLQSDVCCPRFSARCPHCSERSTPMDRRGYVAHLSECPERPVECKYSHLGCRAMVRRSDLERHYRES 1873          
BLAST of SMED30004354 vs. TrEMBL
Match: A0A1I8J887 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=3 SV=1)

HSP 1 Score: 56.6102 bits (135), Expect = 8.961e-7
Identity = 28/112 (25.00%), Postives = 55/112 (49.11%), Query Frame = 3
Query:   15 CEKCQISTTKKTMKEHHKVWIK-REEKCEFCGVIDEWIKIEMEHRNPKEEQICDLYEGVCANNCDRKEKVKLK---EHWNECSGKPVKCPLELFNCQAQLPIAEMQKHMIEN 338
            CE+C+    KK M+ H     + R+E C+ C  +    ++E  HRN + +  C  +   C +  +R   +  +    H +EC  +PV+C      C+A +  +++++H  E+
Sbjct: 1861 CEQCKELILKKDMQRHTSSECRHRKETCDLCSQLVTHSEMETSHRNLQSDVCCPRFSARCPHCSERSTPMDRRGYVAHLSECPERPVECKYSHLGCRAMVRRSDLERHYRES 1972          
BLAST of SMED30004354 vs. TrEMBL
Match: A0A267FZZ5 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig012340g1 PE=4 SV=1)

HSP 1 Score: 53.5286 bits (127), Expect = 9.730e-6
Identity = 28/112 (25.00%), Postives = 55/112 (49.11%), Query Frame = 3
Query:   15 CEKCQISTTKKTMKEHHKVWIK-REEKCEFCGVIDEWIKIEMEHRNPKEEQICDLYEGVCANNCDRKEKVKLK---EHWNECSGKPVKCPLELFNCQAQLPIAEMQKHMIEN 338
            CE+C+    KK M+ H     + R+E C+ C  +    ++E  HRN + +  C  +   C +  +R   +  +    H +EC  +PV+C      C+A +  +++++H  E+
Sbjct:  201 CEQCKELILKKDMQRHTSSECRHRKETCDLCSQLVTHSEMETSHRNLQSDVCCPRFSARCPHCSERSTPMDRRGYVAHLSECPERPVECKYSHLGCRAMVRRSDLERHYRES 312          
BLAST of SMED30004354 vs. Planmine SMEST
Match: SMESG000025043.1 (SMESG000025043.1)

HSP 1 Score: 229.565 bits (584), Expect = 6.653e-71
Identity = 108/115 (93.91%), Postives = 112/115 (97.39%), Query Frame = 3
Query:    3 NEILCEKCQISTTKKTMKEHHKVWIKREEKCEFCGVIDEWIKIEMEHRNPKEEQICDLYEGVCANNCDRKEKVKLKEHWNECSGKPVKCPLELFNCQAQLPIAEMQKHMIENSIE 347
            NEILCEKCQ STTKKTMKEHHKV IKREEKCEFCGVI EWIKIEMEHRNPKEEQICDLYEG+CANNCDRK+KVKLKEHWNECSGKPVKCPLELFNCQAQLP+AEMQKHM+ENSIE
Sbjct: 1282 NEILCEKCQTSTTKKTMKEHHKVCIKREEKCEFCGVIGEWIKIEMEHRNPKEEQICDLYEGICANNCDRKDKVKLKEHWNECSGKPVKCPLELFNCQAQLPVAEMQKHMMENSIE 1396          
BLAST of SMED30004354 vs. Planmine SMEST
Match: SMESG000025043.1 (SMESG000025043.1)

HSP 1 Score: 229.565 bits (584), Expect = 6.984e-71
Identity = 108/115 (93.91%), Postives = 112/115 (97.39%), Query Frame = 3
Query:    3 NEILCEKCQISTTKKTMKEHHKVWIKREEKCEFCGVIDEWIKIEMEHRNPKEEQICDLYEGVCANNCDRKEKVKLKEHWNECSGKPVKCPLELFNCQAQLPIAEMQKHMIENSIE 347
            NEILCEKCQ STTKKTMKEHHKV IKREEKCEFCGVI EWIKIEMEHRNPKEEQICDLYEG+CANNCDRK+KVKLKEHWNECSGKPVKCPLELFNCQAQLP+AEMQKHM+ENSIE
Sbjct: 1280 NEILCEKCQTSTTKKTMKEHHKVCIKREEKCEFCGVIGEWIKIEMEHRNPKEEQICDLYEGICANNCDRKDKVKLKEHWNECSGKPVKCPLELFNCQAQLPVAEMQKHMMENSIE 1394          
BLAST of SMED30004354 vs. Planmine SMEST
Match: SMESG000025043.1 (SMESG000025043.1)

HSP 1 Score: 229.565 bits (584), Expect = 7.547e-71
Identity = 108/115 (93.91%), Postives = 112/115 (97.39%), Query Frame = 3
Query:    3 NEILCEKCQISTTKKTMKEHHKVWIKREEKCEFCGVIDEWIKIEMEHRNPKEEQICDLYEGVCANNCDRKEKVKLKEHWNECSGKPVKCPLELFNCQAQLPIAEMQKHMIENSIE 347
            NEILCEKCQ STTKKTMKEHHKV IKREEKCEFCGVI EWIKIEMEHRNPKEEQICDLYEG+CANNCDRK+KVKLKEHWNECSGKPVKCPLELFNCQAQLP+AEMQKHM+ENSIE
Sbjct: 1280 NEILCEKCQTSTTKKTMKEHHKVCIKREEKCEFCGVIGEWIKIEMEHRNPKEEQICDLYEGICANNCDRKDKVKLKEHWNECSGKPVKCPLELFNCQAQLPVAEMQKHMMENSIE 1394          
BLAST of SMED30004354 vs. Planmine SMEST
Match: SMESG000025043.1 (SMESG000025043.1)

HSP 1 Score: 229.565 bits (584), Expect = 7.921e-71
Identity = 108/115 (93.91%), Postives = 112/115 (97.39%), Query Frame = 3
Query:    3 NEILCEKCQISTTKKTMKEHHKVWIKREEKCEFCGVIDEWIKIEMEHRNPKEEQICDLYEGVCANNCDRKEKVKLKEHWNECSGKPVKCPLELFNCQAQLPIAEMQKHMIENSIE 347
            NEILCEKCQ STTKKTMKEHHKV IKREEKCEFCGVI EWIKIEMEHRNPKEEQICDLYEG+CANNCDRK+KVKLKEHWNECSGKPVKCPLELFNCQAQLP+AEMQKHM+ENSIE
Sbjct: 1271 NEILCEKCQTSTTKKTMKEHHKVCIKREEKCEFCGVIGEWIKIEMEHRNPKEEQICDLYEGICANNCDRKDKVKLKEHWNECSGKPVKCPLELFNCQAQLPVAEMQKHMMENSIE 1385          
BLAST of SMED30004354 vs. Planmine SMEST
Match: SMESG000025043.1 (SMESG000025043.1)

HSP 1 Score: 229.18 bits (583), Expect = 8.556e-71
Identity = 108/115 (93.91%), Postives = 112/115 (97.39%), Query Frame = 3
Query:    3 NEILCEKCQISTTKKTMKEHHKVWIKREEKCEFCGVIDEWIKIEMEHRNPKEEQICDLYEGVCANNCDRKEKVKLKEHWNECSGKPVKCPLELFNCQAQLPIAEMQKHMIENSIE 347
            NEILCEKCQ STTKKTMKEHHKV IKREEKCEFCGVI EWIKIEMEHRNPKEEQICDLYEG+CANNCDRK+KVKLKEHWNECSGKPVKCPLELFNCQAQLP+AEMQKHM+ENSIE
Sbjct: 1229 NEILCEKCQTSTTKKTMKEHHKVCIKREEKCEFCGVIGEWIKIEMEHRNPKEEQICDLYEGICANNCDRKDKVKLKEHWNECSGKPVKCPLELFNCQAQLPVAEMQKHMMENSIE 1343          
The following BLAST results are available for this feature:
BLAST of SMED30004354 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 SMED30004354 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 SMED30004354 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 SMED30004354 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 SMED30004354 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 SMED30004354 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 SMED30004354 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 SMED30004354 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
D5JG591.777e-1133.93TNF receptor-associated factor-2-like protein A OS... [more]
T1DBK63.979e-730.34TRAF-4 OS=Dendrocoelum lacteum OX=27895 PE=2 SV=1[more]
A0A1I8G6V36.065e-725.00Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8J8878.961e-725.00Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267FZZ59.730e-625.00Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
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BLAST of SMED30004354 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 SMED30004354 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 SMED30004354 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 SMED30004354 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 SMED30004354 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 SMED30004354 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000025043.16.653e-7193.91SMESG000025043.1[more]
SMESG000025043.16.984e-7193.91SMESG000025043.1[more]
SMESG000025043.17.547e-7193.91SMESG000025043.1[more]
SMESG000025043.17.921e-7193.91SMESG000025043.1[more]
SMESG000025043.18.556e-7193.91SMESG000025043.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004354 ID=SMED30004354|Name=SMED30004354|organism=Schmidtea mediterranea sexual|type=transcript|length=347bp
ATAATGAGATATTATGCGAAAAATGCCAAATCAGCACAACAAAAAAGACT
ATGAAAGAACATCACAAAGTATGGATTAAGAGAGAGGAAAAATGCGAATT
CTGTGGAGTCATCGACGAATGGATAAAAATAGAAATGGAACATCGGAATC
CAAAAGAGGAACAAATATGTGATCTATATGAAGGAGTATGCGCAAACAAC
TGCGACAGGAAAGAGAAAGTCAAATTAAAGGAACATTGGAACGAATGTAG
CGGCAAACCAGTCAAGTGCCCGTTAGAATTATTCAATTGTCAAGCGCAAC
TACCAATTGCGGAAATGCAAAAGCACATGATAGAAAATAGTATCGAG
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protein sequence of SMED30004354-orf-1

>SMED30004354-orf-1 ID=SMED30004354-orf-1|Name=SMED30004354-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=115bp
NEILCEKCQISTTKKTMKEHHKVWIKREEKCEFCGVIDEWIKIEMEHRNP
KEEQICDLYEGVCANNCDRKEKVKLKEHWNECSGKPVKCPLELFNCQAQL
PIAEMQKHMIENSIE
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR001293Znf_TRAF
IPR013323SIAH-type
IPR008974TRAF-like
Vocabulary: molecular function
TermDefinition
GO:0008270zinc ion binding
GO:0004842ubiquitin-protein transferase activity
GO:0005515protein binding
GO:0046872metal ion binding
Vocabulary: biological process
TermDefinition
GO:0016567protein ubiquitination