SMED30012712

Overview
NameSMED30012712
Smed IDSMED30012712
Length (bp)614
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 SMED30012712 (SMED30012712) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30012712 (SMED30012712) 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



SMED30012712

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
cephalic gangliaSMED30012712SMESG000055206.1 SMESG000055195.1 dd_Smed_v4_8451_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30012712SMESG000055206.1 SMESG000055195.1 dd_Smed_v4_8451_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30012712SMESG000055206.1 SMESG000055195.1 dd_Smed_v4_8451_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
SMED30012712 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.011020:9161..9773 +3044
Homology
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BLAST of SMED30012712 vs. Planmine SMEST
Match: SMESG000055195.1 (SMESG000055195.1)

HSP 1 Score: 232.646 bits (592), Expect = 2.076e-74
Identity = 110/110 (100.00%), Postives = 110/110 (100.00%), Query Frame = 2 
Query:   23 DSFENYPVPNNYSRIANKTYFWIGNVGPYTGMNGIKYEALRDAIFGCIHFLYIDFKKIQIINNSKNFSKSCTNSYRETICVKDNCSVQNKSENFLDCSFSGLNTNRMCYK 352
            DSFENYPVPNNYSRIANKTYFWIGNVGPYTGMNGIKYEALRDAIFGCIHFLYIDFKKIQIINNSKNFSKSCTNSYRETICVKDNCSVQNKSENFLDCSFSGLNTNRMCYK
Sbjct:  129 DSFENYPVPNNYSRIANKTYFWIGNVGPYTGMNGIKYEALRDAIFGCIHFLYIDFKKIQIINNSKNFSKSCTNSYRETICVKDNCSVQNKSENFLDCSFSGLNTNRMCYK 238
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BLAST of SMED30012712 vs. Planmine SMEST
Match: SMESG000055195.1 (SMESG000055195.1)

HSP 1 Score: 232.646 bits (592), Expect = 2.389e-74
Identity = 110/110 (100.00%), Postives = 110/110 (100.00%), Query Frame = 2 
Query:   23 DSFENYPVPNNYSRIANKTYFWIGNVGPYTGMNGIKYEALRDAIFGCIHFLYIDFKKIQIINNSKNFSKSCTNSYRETICVKDNCSVQNKSENFLDCSFSGLNTNRMCYK 352
            DSFENYPVPNNYSRIANKTYFWIGNVGPYTGMNGIKYEALRDAIFGCIHFLYIDFKKIQIINNSKNFSKSCTNSYRETICVKDNCSVQNKSENFLDCSFSGLNTNRMCYK
Sbjct:  136 DSFENYPVPNNYSRIANKTYFWIGNVGPYTGMNGIKYEALRDAIFGCIHFLYIDFKKIQIINNSKNFSKSCTNSYRETICVKDNCSVQNKSENFLDCSFSGLNTNRMCYK 245
[Close]
BLAST of SMED30012712 vs. Planmine SMEST
Match: SMESG000055206.1 (SMESG000055206.1)

HSP 1 Score: 124.02 bits (310), Expect = 1.619e-33
Identity = 54/110 (49.09%), Postives = 73/110 (66.36%), Query Frame = 2 
Query:   23 DSFENYPVPNNYSRIANKTYFWIGNVGPYTGMNGIKYEALRDAIFGCIHFLYIDFKKIQIINNSKNFSKSCTNSYRETICVKDNCSVQNKSENFLDCSFSGLNTNRMCYK 352
            D+F NYPVP +++ + NK YFWIGN+G Y G  G  YE      FGC++ LY+D   ++ I  ++ FS++C +   E +CVKDNCS+    ENFLDCSF  +NT RMCYK
Sbjct:   95 DAFRNYPVPKDFTNLKNKVYFWIGNIGRYVGFEGRIYEPFTTPTFGCLNSLYVDDYSLEFIKEAEYFSRTCLHLVDEHLCVKDNCSLIKTKENFLDCSFPSVNTKRMCYK 204
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BLAST of SMED30012712 vs. Planmine SMEST
Match: SMESG000050299.1 (SMESG000050299.1)

HSP 1 Score: 80.8777 bits (198), Expect = 1.152e-17
Identity = 43/110 (39.09%), Postives = 63/110 (57.27%), Query Frame = 2 
Query:   23 DSFENYPVPNNYSRIANKTYFWIGNVGPYTGMNGIKYEALRDAIFGCIHFLYIDFKKIQIINNSKNFSKSCTNSYRETICVKDNCSVQNKSENFLDCSFSGLNTNRMCYK 352
            D F+NYPVPN Y+R    TY ++GN+GPY G N ++Y  L + + GC+   Y + K I++ +NS  F   C   Y ET+  ++  +    S +  DCS S LNT R C +
Sbjct:  136 DQFDNYPVPNMYNREKKVTYIFMGNIGPYKGPNYMEYLPLYNQLIGCLDKFYFNGKLIRVTSNSTKFKSFCLTEYIETVHSENFTTKFTVSYDIPDCSISSLNT-RYCIR 244
[Close]
BLAST of SMED30012712 vs. Planmine SMEST
Match: SMESG000050303.1 (SMESG000050303.1)

HSP 1 Score: 80.4925 bits (197), Expect = 1.157e-17
Identity = 46/117 (39.32%), Postives = 64/117 (54.70%), Query Frame = 2 
Query:   14 IILDSFEN------YPVPNNYSRIANKTYFWIGNVGPYTGMNGIKYEALRDAIFGCIHFLYIDFKKIQIINNSKNFSKSCTNSYRETICVKDNCSVQNKSENFLDCSFSGLNTNRMC 346
            I ++S EN      YP+P NY  I N+T+  IGN+GP+ G  GI Y  LR+ + GC++ LYI+  +I   +    F+ SC   Y ETIC    C+  + +    DCS S LN  R C
Sbjct:   24 ITVESRENANKILAYPLPKNYDTIRNQTFIMIGNIGPFEGNTGIVYNPLRNQLVGCLYKLYINGSRILFNSKGSIFNSSCFTDYTETICGPRYCNESSVTYKITDCSISVLN-RRYC 139
The following BLAST results are available for this feature:
BLAST of SMED30012712 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 SMED30012712 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 SMED30012712 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 SMED30012712 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 SMED30012712 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 SMED30012712 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 SMED30012712 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 SMED30012712 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 SMED30012712 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 SMED30012712 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 SMED30012712 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 SMED30012712 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 SMED30012712 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 SMED30012712 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000055195.12.076e-74100.00SMESG000055195.1[more]
SMESG000055195.12.389e-74100.00SMESG000055195.1[more]
SMESG000055206.11.619e-3349.09SMESG000055206.1[more]
SMESG000050299.11.152e-1739.09SMESG000050299.1[more]
SMESG000050303.11.157e-1739.32SMESG000050303.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30012712 ID=SMED30012712|Name=SMED30012712|organism=Schmidtea mediterranea sexual|type=transcript|length=614bp
AATGAACAGCTACATTATTTTAGATTCCTTTGAAAACTACCCTGTACCTA
ATAATTACTCGAGAATCGCTAATAAAACCTATTTCTGGATCGGGAATGTT
GGTCCGTATACTGGAATGAATGGAATAAAGTATGAAGCTTTAAGAGATGC
AATATTTGGTTGCATACATTTCTTGTACATTGACTTTAAAAAAATCCAAA
TAATAAATAATTCGAAAAATTTCTCAAAGTCCTGCACAAATTCCTACAGA
GAAACTATTTGTGTCAAAGATAATTGCTCAGTGCAAAACAAAAGTGAAAA
CTTTCTGGATTGCTCATTTTCTGGTCTAAATACGAATAGGATGTGCTACA
AAGGTGAGGTCTTAATGTTTCCATGAAGGTGTCAAATATTGGTCCGCTCA
TAAAATATGATATTTTAATTACGTTGGAAATGTTTTAACCATATTTGGTT
TTTATTTTGACTAAATGTTGAATTCATAAAAAAAAATATAGTTTAGCTTT
TTCTTTGAAGTGAAAATAATTGCAAGGTAACAAGGTCAGAAAGTGACAAA
ATCTGGCCGATTATGGCTGGACAAATTATCAAAAATAGAAATGCAAAATA
TAATTAAGATCTTT
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protein sequence of SMED30012712-orf-1

>SMED30012712-orf-1 ID=SMED30012712-orf-1|Name=SMED30012712-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=125bp
MNSYIILDSFENYPVPNNYSRIANKTYFWIGNVGPYTGMNGIKYEALRDA
IFGCIHFLYIDFKKIQIINNSKNFSKSCTNSYRETICVKDNCSVQNKSEN
FLDCSFSGLNTNRMCYKGEVLMFP*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003116parenchymal cell