SMED30018547

Overview
NameSMED30018547
Smed IDSMED30018547
Length (bp)393
Neoblast Clusters

Zeng et. al., 2018



 

 

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



Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
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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



SMED30018547

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30018547h1SMcG0003033 Contig4735newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30018547h1SMcG0003033 Contig4735uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30018547h1SMcG0004916 Contig939GPL15192PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30018547h1SMcG0004916 Contig4735newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30018547h1SMcG0004916 Contig4735uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
protonephridiaSMED30018547h1SMcG0004916 dd_Smed_v4_8385_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30018547h1SMcG0004916 dd_Smed_v4_8385_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30018547h1SMcG0004916 dd_Smed_v4_8385_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
Homology
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BLAST of SMED30018547 vs. Planmine SMEST
Match: SMESG000060548.1 (SMESG000060548.1)

HSP 1 Score: 194.512 bits (493), Expect = 1.668e-61
Identity = 98/113 (86.73%), Postives = 99/113 (87.61%), Query Frame = 3 
Query:   54 MSLYFWEGVAWVFILYMKLTYCXXXXXXXXXXXXVAEYHIRESHGDSYLYTEINYINGANYQIELKFSLNKIEGSLLYFFDKYDNQLIISLSDDLEERMKIEFRGEEYHSTLS 392
            MSLYFWEGVAWVFILYMKLTY              +EYHIRESHGDSYLYTEINYINGANYQIELKFSLNKIEGSLLYFFDKYDNQLIISLSDDLEERMKIEFRGEEYHSTLS
Sbjct:    1 MSLYFWEGVAWVFILYMKLTY--------------SEYHIRESHGDSYLYTEINYINGANYQIELKFSLNKIEGSLLYFFDKYDNQLIISLSDDLEERMKIEFRGEEYHSTLS 99
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BLAST of SMED30018547 vs. Planmine SMEST
Match: SMESG000060548.1 (SMESG000060548.1)

HSP 1 Score: 195.282 bits (495), Expect = 3.050e-61
Identity = 98/113 (86.73%), Postives = 99/113 (87.61%), Query Frame = 3 
Query:   54 MSLYFWEGVAWVFILYMKLTYCXXXXXXXXXXXXVAEYHIRESHGDSYLYTEINYINGANYQIELKFSLNKIEGSLLYFFDKYDNQLIISLSDDLEERMKIEFRGEEYHSTLS 392
            MSLYFWEGVAWVFILYMKLTY              +EYHIRESHGDSYLYTEINYINGANYQIELKFSLNKIEGSLLYFFDKYDNQLIISLSDDLEERMKIEFRGEEYHSTLS
Sbjct:    1 MSLYFWEGVAWVFILYMKLTY--------------SEYHIRESHGDSYLYTEINYINGANYQIELKFSLNKIEGSLLYFFDKYDNQLIISLSDDLEERMKIEFRGEEYHSTLS 99
[Close]
BLAST of SMED30018547 vs. Planmine SMEST
Match: SMESG000060548.1 (SMESG000060548.1)

HSP 1 Score: 194.512 bits (493), Expect = 2.009e-60
Identity = 98/113 (86.73%), Postives = 99/113 (87.61%), Query Frame = 3 
Query:   54 MSLYFWEGVAWVFILYMKLTYCXXXXXXXXXXXXVAEYHIRESHGDSYLYTEINYINGANYQIELKFSLNKIEGSLLYFFDKYDNQLIISLSDDLEERMKIEFRGEEYHSTLS 392
            MSLYFWEGVAWVFILYMKLTY              +EYHIRESHGDSYLYTEINYINGANYQIELKFSLNKIEGSLLYFFDKYDNQLIISLSDDLEERMKIEFRGEEYHSTLS
Sbjct:    1 MSLYFWEGVAWVFILYMKLTY--------------SEYHIRESHGDSYLYTEINYINGANYQIELKFSLNKIEGSLLYFFDKYDNQLIISLSDDLEERMKIEFRGEEYHSTLS 99
[Close]
BLAST of SMED30018547 vs. Planmine SMEST
Match: SMESG000060548.1 (SMESG000060548.1)

HSP 1 Score: 159.844 bits (403), Expect = 3.049e-48
Identity = 82/97 (84.54%), Postives = 83/97 (85.57%), Query Frame = 3 
Query:  102 MKLTYCXXXXXXXXXXXXVAEYHIRESHGDSYLYTEINYINGANYQIELKFSLNKIEGSLLYFFDKYDNQLIISLSDDLEERMKIEFRGEEYHSTLS 392
            MKLTY              +EYHIRESHGDSYLYTEINYINGANYQIELKFSLNKIEGSLLYFFDKYDNQLIISLSDDLEERMKIEFRGEEYHSTLS
Sbjct:    1 MKLTY--------------SEYHIRESHGDSYLYTEINYINGANYQIELKFSLNKIEGSLLYFFDKYDNQLIISLSDDLEERMKIEFRGEEYHSTLS 83
[Close]
BLAST of SMED30018547 vs. Planmine SMEST
Match: SMESG000060548.1 (SMESG000060548.1)

HSP 1 Score: 159.073 bits (401), Expect = 1.907e-47
Identity = 82/97 (84.54%), Postives = 83/97 (85.57%), Query Frame = 3 
Query:  102 MKLTYCXXXXXXXXXXXXVAEYHIRESHGDSYLYTEINYINGANYQIELKFSLNKIEGSLLYFFDKYDNQLIISLSDDLEERMKIEFRGEEYHSTLS 392
            MKLTY              +EYHIRESHGDSYLYTEINYINGANYQIELKFSLNKIEGSLLYFFDKYDNQLIISLSDDLEERMKIEFRGEEYHSTLS
Sbjct:    1 MKLTY--------------SEYHIRESHGDSYLYTEINYINGANYQIELKFSLNKIEGSLLYFFDKYDNQLIISLSDDLEERMKIEFRGEEYHSTLS 83
The following BLAST results are available for this feature:
BLAST of SMED30018547 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 SMED30018547 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 SMED30018547 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 SMED30018547 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 SMED30018547 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 SMED30018547 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 SMED30018547 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 SMED30018547 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 SMED30018547 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 SMED30018547 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 SMED30018547 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 SMED30018547 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 SMED30018547 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 SMED30018547 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000060548.11.668e-6186.73SMESG000060548.1[more]
SMESG000060548.13.050e-6186.73SMESG000060548.1[more]
SMESG000060548.12.009e-6086.73SMESG000060548.1[more]
SMESG000060548.13.049e-4884.54SMESG000060548.1[more]
SMESG000060548.11.907e-4784.54SMESG000060548.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018547 ID=SMED30018547|Name=SMED30018547|organism=Schmidtea mediterranea sexual|type=transcript|length=393bp
AAATTGAATCAATTTTTTCTTTTTTGTTATTTTTGAAAAGACAGTATTTC
TTTATGAGCCTATATTTTTGGGAAGGAGTTGCCTGGGTATTTATTCTTTA
TATGAAGTTAACATACTGTATTTGTATTATCATTACGATCGGAATAATTT
TGATTGTAGCCGAATACCACATCAGGGAGAGTCACGGTGACAGCTACTTA
TACACTGAGATTAATTATATCAACGGAGCAAATTATCAAATTGAATTAAA
ATTTAGTTTGAATAAAATAGAAGGAAGTTTATTATATTTCTTTGATAAAT
ATGACAATCAATTGATAATTTCCCTTTCTGATGATCTGGAAGAGAGAATG
AAAATAGAATTCAGGGGTGAAGAATATCATTCAACTCTATCTG
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protein sequence of SMED30018547-orf-1

>SMED30018547-orf-1 ID=SMED30018547-orf-1|Name=SMED30018547-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=130bp
IESIFSFLLFLKRQYFFMSLYFWEGVAWVFILYMKLTYCICIIITIGIIL
IVAEYHIRESHGDSYLYTEINYINGANYQIELKFSLNKIEGSLLYFFDKY
DNQLIISLSDDLEERMKIEFRGEEYHSTLS
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InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 13..35