SMED30009699

Overview
NameSMED30009699
Smed IDSMED30009699
Length (bp)545
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 SMED30009699 (SMED30009699) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30009699 (SMED30009699) 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



SMED30009699

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30009699SMESG000051012.1 dd_Smed_v4_1787_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30009699SMESG000051012.1 dd_Smed_v4_1787_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30009699SMESG000051012.1 dd_Smed_v4_1787_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30009699SMESG000051012.1 dd_Smed_v4_1787_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30009699SMESG000051012.1 DN299744ncbi_smed_estsPMID:30399335
Ross et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
neuronSMED30009699SMESG000051012.1 DN299744ncbi_smed_estsPMID:30399335
Ross et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
enteric muscle cellSMED30009699SMESG000051012.1 dd_Smed_v4_1787_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30009699 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004464:35097..36438 -2690
Homology
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BLAST of SMED30009699 vs. Planmine SMEST
Match: SMESG000051012.1 (SMESG000051012.1)

HSP 1 Score: 245.743 bits (626), Expect = 8.472e-85
Identity = 119/119 (100.00%), Postives = 119/119 (100.00%), Query Frame = 3 
Query:   51 MEILIGIIYSNGKITVEISKGTGFPCNIDYCVELSLNYNSPLWYKPRNQILGKYSGTTPYFRKSFTFNMTEAALSTAILSIIVHGEELYKVLNLKLGSMDLLSTNDGCHFQKFNIYRLS 407
            MEILIGIIYSNGKITVEISKGTGFPCNIDYCVELSLNYNSPLWYKPRNQILGKYSGTTPYFRKSFTFNMTEAALSTAILSIIVHGEELYKVLNLKLGSMDLLSTNDGCHFQKFNIYRLS
Sbjct:    1 MEILIGIIYSNGKITVEISKGTGFPCNIDYCVELSLNYNSPLWYKPRNQILGKYSGTTPYFRKSFTFNMTEAALSTAILSIIVHGEELYKVLNLKLGSMDLLSTNDGCHFQKFNIYRLS 119
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BLAST of SMED30009699 vs. Planmine SMEST
Match: SMESG000051013.1 (SMESG000051013.1)

HSP 1 Score: 88.9669 bits (219), Expect = 6.307e-23
Identity = 51/102 (50.00%), Postives = 61/102 (59.80%), Query Frame = 3 
Query:   84 GKITVEISKGTGFPCNIDYCVELSLNYNSPLWYKPRNQILGKYSGTTPYFRKSFTFNMTEAALSTAILSIIVHGEELYKVLNLKLGSMDLLSTNDGCHFQKF 389
            GK+TVEI KGTGF  N++YCVELSLNYNS L  KP+NQ  GK  G     RKSF FNM + AL+ A LS+I+ G    K LN   G           H+ +F
Sbjct:   14 GKLTVEIVKGTGFSSNMEYCVELSLNYNSQLLSKPQNQRTGKIFGDKFNVRKSFIFNMVDDALNKATLSVILMGGGPSK-LNKSNGGFKPSGKGTQAHWNQF 114
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BLAST of SMED30009699 vs. Planmine SMEST
Match: SMESG000051015.1 (SMESG000051015.1)

HSP 1 Score: 74.7146 bits (182), Expect = 2.134e-17
Identity = 40/85 (47.06%), Postives = 54/85 (63.53%), Query Frame = 3 
Query:   54 EILIGIIYSNGKITVEISKGTGFPCNIDYCVELSLNYNSPLWYKPRNQILGKYSGTTPYFRKSFTFNMTEAALSTAILSIIVHGE 308
            EI+  + Y+ GK+TVEI+KGTGFP N    V+  +N +S L YK + Q +  +SG T + RKS  FN+   ALSTA LS+ V  E
Sbjct:    4 EIVSKLSYNRGKLTVEINKGTGFPSNTKRSVKSLMNDDSKLAYKRKEQKICTFSGKTDHIRKSVIFNVPPKALSTASLSLNVTEE 88
The following BLAST results are available for this feature:
BLAST of SMED30009699 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 SMED30009699 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 SMED30009699 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 SMED30009699 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 SMED30009699 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 SMED30009699 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 SMED30009699 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 SMED30009699 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 SMED30009699 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 SMED30009699 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 SMED30009699 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 SMED30009699 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 SMED30009699 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 SMED30009699 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000051012.18.472e-85100.00SMESG000051012.1[more]
SMESG000051013.16.307e-2350.00SMESG000051013.1[more]
SMESG000051015.12.134e-1747.06SMESG000051015.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009699 ID=SMED30009699|Name=SMED30009699|organism=Schmidtea mediterranea sexual|type=transcript|length=545bp
AGCTACTATATATAAGGGGCTAGGTTGTATATAGATCAATAAATGATTTT
ATGGAAATTTTGATAGGGATAATTTATAGTAATGGCAAAATTACAGTAGA
AATATCAAAAGGAACTGGATTTCCCTGCAATATAGATTATTGTGTTGAAC
TGTCATTAAATTATAACTCTCCACTTTGGTACAAACCACGAAATCAAATA
TTGGGCAAATATTCTGGAACTACACCTTATTTCAGGAAATCTTTCACTTT
TAATATGACAGAAGCAGCCCTAAGCACTGCTATTTTATCAATAATTGTCC
ACGGAGAAGAACTCTATAAAGTATTAAACTTAAAACTTGGTTCGATGGAT
TTGTTGTCAACAAATGATGGATGTCATTTTCAGAAGTTTAACATTTACAG
ACTTTCGTAAAAAAAATTTGTTGATTTTACATTATTCTGGATCCTAAATG
TAATTTCTATTTATATATTTAATCACTGCTTTTTCATCCTAATTTCCAAG
AATGTGATTTTGAGAATTTATATTTTTTACATTAAATAAATATTA
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protein sequence of SMED30009699-orf-1

>SMED30009699-orf-1 ID=SMED30009699-orf-1|Name=SMED30009699-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=120bp
MEILIGIIYSNGKITVEISKGTGFPCNIDYCVELSLNYNSPLWYKPRNQI
LGKYSGTTPYFRKSFTFNMTEAALSTAILSIIVHGEELYKVLNLKLGSMD
LLSTNDGCHFQKFNIYRLS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0003104enteric muscle cell
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR000008C2_dom
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSUPERFAMILYSSF49562C2 domain (Calcium/lipid-binding domain, CaLB)coord: 5..88