SMED30000902

Overview
NameSMED30000902
Smed IDSMED30000902
Length (bp)333
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 SMED30000902 (SMED30000902) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30000902 (SMED30000902) 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



SMED30000902

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
epidermisSMED30000902SMESG000043277.1 dd_Smed_v4_647_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30000902SMESG000043277.1 dd_Smed_v4_647_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30000902SMESG000043277.1 Contig47006newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30000902SMESG000043277.1 Contig47006uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
parenchymaSMED30000902SMESG000043277.1 SMED30000902smed_20140614PMID:26457503
Tu et al., 2015		whole organism asexual adult colorimetric in situ hybridization evidence
Category 3 cellSMED30000902SMESG000043277.1 dd_Smed_v6_647_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30000902 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.023721:7480..7877 -1640
Homology
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BLAST of SMED30000902 vs. Planmine SMEST
Match: SMESG000043277.1 (SMESG000043277.1)

HSP 1 Score: 187.963 bits (476), Expect = 1.713e-63
Identity = 91/91 (100.00%), Postives = 91/91 (100.00%), Query Frame = 1 
Query:   40 MKGFLFILISVYLIPVFCGTTLDKPDTKSKGGLSSAYDLVVETVSKWWMWQKCSLTEVVICNTPKNCFNCTVTSWSYNRKVCKPEGIKCRT 312
            MKGFLFILISVYLIPVFCGTTLDKPDTKSKGGLSSAYDLVVETVSKWWMWQKCSLTEVVICNTPKNCFNCTVTSWSYNRKVCKPEGIKCRT
Sbjct:    1 MKGFLFILISVYLIPVFCGTTLDKPDTKSKGGLSSAYDLVVETVSKWWMWQKCSLTEVVICNTPKNCFNCTVTSWSYNRKVCKPEGIKCRT 91
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BLAST of SMED30000902 vs. Planmine SMEST
Match: SMESG000043289.1 (SMESG000043289.1)

HSP 1 Score: 55.4546 bits (132), Expect = 3.416e-11
Identity = 33/92 (35.87%), Postives = 50/92 (54.35%), Query Frame = 1 
Query:   40 MKGFLFILISVYLIPVFCGTTLDK-PDTKSKGGLSSAYDLVVETVSKWWMWQKCSLTEVVICNTPKNCFNCTVTSWSYNRKVCKPE-GIKCR 309
            MK    I   ++L  VFC   L++  D ++K       DL V+   KW++W+KC+     +C    +CFNC V  +SYN+ VC PE  I+C+
Sbjct:    1 MKLAFIIFGLLFLNGVFCEEKLEEVKDVETKDNSELEVDLKVQEEKKWFLWKKCTTLYFRLCYG--SCFNCKVHFFSYNKGVCSPEKKIECK 90
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BLAST of SMED30000902 vs. Planmine SMEST
Match: SMESG000043278.1 (SMESG000043278.1)

HSP 1 Score: 48.521 bits (114), Expect = 1.172e-8
Identity = 27/84 (32.14%), Postives = 40/84 (47.62%), Query Frame = 1 
Query:   58 ILISVYLIP-VFCGTTLDKPDTKSKGGLSSAYDLVVETVSKWWMWQKCSLTEVVICNTPKNCFNCTVTSWSYNRKVCKPEGIKC 306
             L+S Y+I  +F    L    T     +       +E  SKW+ W+KCS+ +  IC     CF C  T WSY ++ C+P   +C
Sbjct:    3 FLVSFYIIICIFSTGFLSDSSTNLPSNVYGLDQTFME--SKWFFWRKCSVVKFTIC-YEYFCFRCQATFWSYRKQSCQPRNFRC 83
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BLAST of SMED30000902 vs. Planmine SMEST
Match: SMESG000043280.1 (SMESG000043280.1)

HSP 1 Score: 48.521 bits (114), Expect = 1.696e-8
Identity = 26/91 (28.57%), Postives = 43/91 (47.25%), Query Frame = 1 
Query:   34 VSMKGFLFILISVYLIPVFCGTTLDK----PDTKSKGGLSSAYDLVVETVSKWWMWQKCSLTEVVICNTPKNCFNCTVTSWSYNRKVCKPE 294
            + MK    I   + L  +FC   LDK     D ++KG      +  ++   KW++WQ+C+     +C     C+ CTV  +SY +  C P+
Sbjct:    1 MKMKLTFIIFGLLILNGIFCEENLDKKNEVEDLETKGNFEVTEEAEIQGDKKWFLWQRCTTQTFQLCYG--RCWKCTVKYYSYKKGACSPD 89
[Close]
BLAST of SMED30000902 vs. Planmine SMEST
Match: SMESG000043280.1 (SMESG000043280.1)

HSP 1 Score: 48.1358 bits (113), Expect = 2.147e-8
Identity = 24/85 (28.24%), Postives = 43/85 (50.59%), Query Frame = 1 
Query:   55 FILISVYLI-PVFCGTTLDK----PDTKSKGGLSSAYDLVVETVSKWWMWQKCSLTEVVICNTPKNCFNCTVTSWSYNRKVCKPE 294
            FI+  + ++  +FC   LDK     D ++KG      +  ++   KW++WQ+C+     +C     C+ CTV  +SY +  C P+
Sbjct:    5 FIIFGLLILNGIFCEENLDKKNEVEDLETKGNFEVTEEAEIQGDKKWFLWQRCTTQTFQLCYG--RCWKCTVKYYSYKKGACSPD 87
The following BLAST results are available for this feature:
BLAST of SMED30000902 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 SMED30000902 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 SMED30000902 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 SMED30000902 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 SMED30000902 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 SMED30000902 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 SMED30000902 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 SMED30000902 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 SMED30000902 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 SMED30000902 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 SMED30000902 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 SMED30000902 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 SMED30000902 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 SMED30000902 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000043277.11.713e-63100.00SMESG000043277.1[more]
SMESG000043289.13.416e-1135.87SMESG000043289.1[more]
SMESG000043278.11.172e-832.14SMESG000043278.1[more]
SMESG000043280.11.696e-828.57SMESG000043280.1[more]
SMESG000043280.12.147e-828.24SMESG000043280.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000902 ID=SMED30000902|Name=SMED30000902|organism=Schmidtea mediterranea sexual|type=transcript|length=333bp
ATTAATGAAAAAAAAGTTTCAACGACTCATAAAGTATCAATGAAAGGTTT
TCTGTTTATCTTAATTTCAGTTTATCTTATACCGGTTTTCTGCGGAACTA
CACTAGACAAACCCGACACAAAATCCAAAGGAGGATTAAGCAGTGCATAT
GATTTAGTTGTTGAAACCGTGAGTAAATGGTGGATGTGGCAGAAATGCTC
TTTGACCGAAGTGGTAATATGCAATACACCGAAGAATTGCTTCAATTGCA
CCGTCACGTCTTGGTCTTATAATAGAAAAGTTTGCAAGCCTGAAGGAATC
AAGTGCCGAACATAAATTTAATTTCAATTTAGC
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protein sequence of SMED30000902-orf-1

>SMED30000902-orf-1 ID=SMED30000902-orf-1|Name=SMED30000902-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=105bp
INEKKVSTTHKVSMKGFLFILISVYLIPVFCGTTLDKPDTKSKGGLSSAY
DLVVETVSKWWMWQKCSLTEVVICNTPKNCFNCTVTSWSYNRKVCKPEGI
KCRT*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell
PLANA:0002032epidermal cell
PLANA:0002142parenchyma
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 13..35