1.E7.3

Overview
Name1.E7.3 (AHD24734.1)
Smed IDSMED30030602
Length (bp)777
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 1.E7.3 (SMED30030602) t-SNE clustered cells

Violin plots show distribution of expression levels for 1.E7.3 (SMED30030602) 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 1.E7.3 (SMED30030602) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for 1.E7.3 (SMED30030602) 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



SMED30030602

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
muscle cellSMED30030602h1SMcG0010108 dd_Smed_v4_15533_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30030602h1SMcG0010108 dd_Smed_v4_15533_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30030602h1SMcG0010108 dd_Smed_v4_15533_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of 1.E7.3 vs. TrEMBL
Match: V9XRT1 (1.E7.3 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 255.373 bits (651), Expect = 5.559e-83
Identity = 173/173 (100.00%), Postives = 173/173 (100.00%), Query Frame = 2 
Query:  146 MNFIGSNFRDKLCVQNSARMKFLYLFCVFMNSTEEIFNRTXXXXXXXXXIGLAFMALFASXXXXXXXXXXXXXXXWKYGVTYTKSVNLXXXXXXXXXXXXXXQNNVRNNYSTKVNQFSEVLSNIDRSNFNRRQNSEKIISRSNSFGEKVISNTLQKKLLSDLKDFQLIKDNNK 664
            MNFIGSNFRDKLCVQNSARMKFLYLFCVFMNSTEEIFNRTKENKNEENEIGLAFMALFASVILITLTLFVIIFVVWKYGVTYTKSVNLRYVSSSRRFSHSVVQNNVRNNYSTKVNQFSEVLSNIDRSNFNRRQNSEKIISRSNSFGEKVISNTLQKKLLSDLKDFQLIKDNNK
Sbjct:    1 MNFIGSNFRDKLCVQNSARMKFLYLFCVFMNSTEEIFNRTKENKNEENEIGLAFMALFASVILITLTLFVIIFVVWKYGVTYTKSVNLRYVSSSRRFSHSVVQNNVRNNYSTKVNQFSEVLSNIDRSNFNRRQNSEKIISRSNSFGEKVISNTLQKKLLSDLKDFQLIKDNNK 173
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BLAST of 1.E7.3 vs. Planmine SMEST
Match: SMESG000064601.1 (SMESG000064601.1)

HSP 1 Score: 255.373 bits (651), Expect = 1.546e-86
Identity = 173/173 (100.00%), Postives = 173/173 (100.00%), Query Frame = 2 
Query:  146 MNFIGSNFRDKLCVQNSARMKFLYLFCVFMNSTEEIFNRTXXXXXXXXXIGLAFMALFASXXXXXXXXXXXXXXXWKYGVTYTKSVNLXXXXXXXXXXXXXXQNNVRNNYSTKVNQFSEVLSNIDRSNFNRRQNSEKIISRSNSFGEKVISNTLQKKLLSDLKDFQLIKDNNK 664
            MNFIGSNFRDKLCVQNSARMKFLYLFCVFMNSTEEIFNRTKENKNEENEIGLAFMALFASVILITLTLFVIIFVVWKYGVTYTKSVNLRYVSSSRRFSHSVVQNNVRNNYSTKVNQFSEVLSNIDRSNFNRRQNSEKIISRSNSFGEKVISNTLQKKLLSDLKDFQLIKDNNK
Sbjct:    1 MNFIGSNFRDKLCVQNSARMKFLYLFCVFMNSTEEIFNRTKENKNEENEIGLAFMALFASVILITLTLFVIIFVVWKYGVTYTKSVNLRYVSSSRRFSHSVVQNNVRNNYSTKVNQFSEVLSNIDRSNFNRRQNSEKIISRSNSFGEKVISNTLQKKLLSDLKDFQLIKDNNK 173
The following BLAST results are available for this feature:
BLAST of 1.E7.3 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 1.E7.3 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 1.E7.3 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 1.E7.3 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 1.E7.3 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 1.E7.3 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 1.E7.3 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 1.E7.3 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
V9XRT15.559e-83100.001.E7.3 OS=Schmidtea mediterranea OX=79327 PE=2 SV=... [more]
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BLAST of 1.E7.3 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 1.E7.3 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 1.E7.3 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 1.E7.3 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 1.E7.3 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 1.E7.3 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000064601.11.546e-86100.00SMESG000064601.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30030602
GenBankAHD24734.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030602 ID=SMED30030602|Name=1.E7.3|organism=Schmidtea mediterranea sexual|type=transcript|length=777bp
CTCACCCATATAATTGAAGCATTAGACATTCTTTAATATAGACATTTTCT
TTGTAAAATCAGTAAACTGGTTTCCAGTTAAATCATCGATAAAGGTCTTG
TGAGTTCACGTCCAATCAATTTGAAATCTGCACACAAAGTTTGTAATGAA
TTTCATTGGTTCGAATTTCAGGGATAAATTGTGTGTGCAAAATTCTGCCA
GAATGAAATTTCTTTATTTATTCTGTGTATTTATGAACTCGACCGAAGAG
ATTTTCAATCGAACTAAAGAAAACAAAAATGAAGAAAATGAAATTGGTTT
GGCTTTTATGGCTTTGTTTGCGTCTGTGATTTTAATTACGTTAACTTTAT
TTGTAATAATATTTGTTGTATGGAAATATGGTGTAACGTACACGAAATCT
GTCAATCTCAGATATGTTAGCTCTTCTAGAAGGTTCAGTCATTCGGTAGT
TCAGAACAATGTGAGAAATAATTATTCAACCAAAGTGAATCAATTCAGTG
AAGTGTTGTCAAATATTGACCGATCTAATTTCAATCGTAGACAAAATTCA
GAAAAAATTATTTCAAGATCAAATTCTTTTGGAGAAAAAGTTATATCAAA
TACATTGCAGAAAAAACTGTTATCGGATCTAAAAGATTTTCAACTGATCA
AAGATAACAACAAATAATTATACTAATAAAAATCCCGAGTATTTTAAGAT
GGAGGAAATTGTCATTTATCAGAATTAAAGTATATTATGTAAATTTTTAA
ATTCGTTTTGTAAAATTTATTGTGAAT
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protein sequence of SMED30030602-orf-1

>SMED30030602-orf-1 ID=SMED30030602-orf-1|Name=SMED30030602-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=174bp
MNFIGSNFRDKLCVQNSARMKFLYLFCVFMNSTEEIFNRTKENKNEENEI
GLAFMALFASVILITLTLFVIIFVVWKYGVTYTKSVNLRYVSSSRRFSHS
VVQNNVRNNYSTKVNQFSEVLSNIDRSNFNRRQNSEKIISRSNSFGEKVI
SNTLQKKLLSDLKDFQLIKDNNK*
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Aliases
The feature '1.E7.3' has the following synonyms
Synonym
1.E7.3
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000101muscle cell
PLANA:0002056medial muscle cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 54..76