SMED30010150

Overview
NameSMED30010150
Smed IDSMED30010150
Length (bp)489
Neoblast Clusters

Zeng et. al., 2018




▻ Overview

▻ 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




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 SMED30010150 (SMED30010150) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30010150 (SMED30010150) 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.
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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




SMED30010150

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30010150h1SMcG0019306 Contig50645uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30010150h1SMcG0019306 Contig50645newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
protonephridiaSMED30010150h1SMcG0019306 dd_Smed_v4_11060_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30010150h1SMcG0019306 dd_Smed_v4_11060_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30010150h1SMcG0019306 dd_Smed_v4_11060_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30010150h1SMcG0019306 dd_Smed_v4_11060_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
SMED30010150 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007259:9712..10200 -2445
Homology
BLAST of SMED30010150 vs. Planmine SMEST
Match: SMESG000067313.1 (SMESG000067313.1)

HSP 1 Score: 288.115 bits (736), Expect = 1.810e-101
Identity = 145/145 (100.00%), Postives = 145/145 (100.00%), Query Frame = 1
Query:   55 MEVHKIGKDLKDLCFGISFLSCGSIQTYFAVGVILLSHRGLGDLFSGVFLAIVGALIIFAYNSKTKRIFKVILVFECLSCALNVIHPIVFNAYFIYKIKDHLHYSIIFFIVQHTLFYFLLVALLCYHSVLLYRQMKPQVNVSVNY 489
            MEVHKIGKDLKDLCFGISFLSCGSIQTYFAVGVILLSHRGLGDLFSGVFLAIVGALIIFAYNSKTKRIFKVILVFECLSCALNVIHPIVFNAYFIYKIKDHLHYSIIFFIVQHTLFYFLLVALLCYHSVLLYRQMKPQVNVSVNY
Sbjct:    1 MEVHKIGKDLKDLCFGISFLSCGSIQTYFAVGVILLSHRGLGDLFSGVFLAIVGALIIFAYNSKTKRIFKVILVFECLSCALNVIHPIVFNAYFIYKIKDHLHYSIIFFIVQHTLFYFLLVALLCYHSVLLYRQMKPQVNVSVNY 145          
BLAST of SMED30010150 vs. Planmine SMEST
Match: SMESG000067312.1 (SMESG000067312.1)

HSP 1 Score: 97.8265 bits (242), Expect = 1.894e-26
Identity = 54/137 (39.42%), Postives = 85/137 (62.04%), Query Frame = 1
Query:   55 MEVHKIGKDLKDLCFGISFLSCGSIQTYFAVGVILLSHRGLGDLFSGVFLAIVGALIIFAYNSKTKRIFKVILVFECLSCALNVIHPIVFNAYFIYKIKDHLHYSI-IFFIVQHTLFYFLLVALLCYHSVLLYRQMK 462
            M+ ++IG DLK+L FG+ FL+CG IQTYF+  +++  H     L  G+FL   GA+ I ++  +TKRI  +  +FEC+S   +++  IV+     Y +  H  YS+ +F  +QH L+Y ++ ++L  HS LLY QMK
Sbjct:   10 MDENRIGIDLKNLIFGVMFLTCGLIQTYFSFAILIGLHEEWITLILGLFLTTSGAMSILSFKQRTKRILLITFIFECISSLFHMMFTIVY-----YNLNFHNPYSLHLFQDIQHLLYYIIMASILFGHSFLLYWQMK 141          
BLAST of SMED30010150 vs. Planmine SMEST
Match: SMESG000067307.1 (SMESG000067307.1)

HSP 1 Score: 95.1301 bits (235), Expect = 2.267e-25
Identity = 53/137 (38.69%), Postives = 84/137 (61.31%), Query Frame = 1
Query:   55 MEVHKIGKDLKDLCFGISFLSCGSIQTYFAVGVILLSHRGLGDLFSGVFLAIVGALIIFAYNSKTKRIFKVILVFECLSCALNVIHPIVFNAYFIYKIKDHLHYSIIFFI-VQHTLFYFLLVALLCYHSVLLYRQMK 462
            M+ ++IG DLK+L FG+ FL+CG IQTYF+  +++  H     L  G+FL   GA+ I ++  +TKRI  +  +FEC+S   +++  IV+     Y +     YS+ F+  +QH L+Y ++ ++L  HS LLY QMK
Sbjct:   10 MDENRIGIDLKNLIFGVMFLTCGLIQTYFSFAILIGLHEEWITLILGLFLTTSGAMSILSFKQRTKRILLITFIFECISSLFHMMFTIVY-----YNLNFQNLYSLHFYPDIQHLLYYIIMASILFGHSFLLYWQMK 141          
The following BLAST results are available for this feature:
BLAST of SMED30010150 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 SMED30010150 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 SMED30010150 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 SMED30010150 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 SMED30010150 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 SMED30010150 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 SMED30010150 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 SMED30010150 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 SMED30010150 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 SMED30010150 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 SMED30010150 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 SMED30010150 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 SMED30010150 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 SMED30010150 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000067313.11.810e-101100.00SMESG000067313.1[more]
SMESG000067312.11.894e-2639.42SMESG000067312.1[more]
SMESG000067307.12.267e-2538.69SMESG000067307.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30010150 ID=SMED30010150|Name=SMED30010150|organism=Schmidtea mediterranea sexual|type=transcript|length=489bp
ATAATAATCTGATCAAATTGACAAACATTTCAATCGGAGTTTCCGCCTAA
ATAAATGGAAGTTCACAAAATTGGAAAAGATTTAAAAGATTTATGCTTTG
GAATAAGTTTTTTGTCGTGCGGATCTATTCAAACCTATTTCGCAGTCGGG
GTAATTCTCCTCAGCCATCGAGGATTGGGAGATCTATTTTCGGGTGTCTT
CTTGGCCATCGTAGGTGCGTTGATCATTTTCGCTTACAACAGTAAAACGA
AGCGGATTTTCAAAGTGATTTTGGTGTTTGAATGTCTATCCTGCGCATTA
AATGTGATTCATCCGATAGTTTTCAATGCTTACTTTATCTATAAAATTAA
AGATCATTTGCATTACTCAATTATTTTTTTCATTGTTCAACACACTCTGT
TTTATTTCCTTCTTGTAGCTTTGCTCTGCTATCATTCGGTTCTGCTCTAC
CGTCAAATGAAGCCACAGGTGAATGTATCAGTTAATTAC
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protein sequence of SMED30010150-orf-1

>SMED30010150-orf-1 ID=SMED30010150-orf-1|Name=SMED30010150-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=145bp
MEVHKIGKDLKDLCFGISFLSCGSIQTYFAVGVILLSHRGLGDLFSGVFL
AIVGALIIFAYNSKTKRIFKVILVFECLSCALNVIHPIVFNAYFIYKIKD
HLHYSIIFFIVQHTLFYFLLVALLCYHSVLLYRQMKPQVNVSVNY
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 68..90
NoneNo IPR availableTMHMMTMhelixcoord: 39..61
NoneNo IPR availableTMHMMTMhelixcoord: 13..35
NoneNo IPR availableTMHMMTMhelixcoord: 105..127