SMED30026685

Overview
NameSMED30026685
Smed IDSMED30026685
Length (bp)1155
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 SMED30026685 (SMED30026685) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30026685 (SMED30026685) 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 SMED30026685 (SMED30026685) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30026685 (SMED30026685) 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




SMED30026685

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermisSMED30026685h1SMcG0007431 dd_Smed_v4_11448_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
SMED30026685 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004471:7558..10018 -4371
Homology
BLAST of SMED30026685 vs. Planmine SMEST
Match: SMESG000071514.1 (SMESG000071514.1)

HSP 1 Score: 418.698 bits (1075), Expect = 3.424e-148
Identity = 225/225 (100.00%), Postives = 225/225 (100.00%), Query Frame = 2
Query:  461 MLVEFLFKATFAFADFSLAYFRREKNFGMVNRAALLRSIYRQGDFRRLCKCPGGFCAGNRDIIQTLRNLNGHYYMMWKLPDVIGKAICNSMTKWKYEEFHESVLLTRSRNSKFQKLFEEKLFRKWKIVGYPYSYVKHIYPINEHERKETLIEMKKMFSNEGIKINISLPCWIXXXXXXXXXXXXXXXXXXXXXXIMRKPTIELHLPAQMTINDIDFFVKFIENNF 1135
            MLVEFLFKATFAFADFSLAYFRREKNFGMVNRAALLRSIYRQGDFRRLCKCPGGFCAGNRDIIQTLRNLNGHYYMMWKLPDVIGKAICNSMTKWKYEEFHESVLLTRSRNSKFQKLFEEKLFRKWKIVGYPYSYVKHIYPINEHERKETLIEMKKMFSNEGIKINISLPCWISASSSTEVSSTDVSSTNASSTDIMRKPTIELHLPAQMTINDIDFFVKFIENNF
Sbjct:    1 MLVEFLFKATFAFADFSLAYFRREKNFGMVNRAALLRSIYRQGDFRRLCKCPGGFCAGNRDIIQTLRNLNGHYYMMWKLPDVIGKAICNSMTKWKYEEFHESVLLTRSRNSKFQKLFEEKLFRKWKIVGYPYSYVKHIYPINEHERKETLIEMKKMFSNEGIKINISLPCWISASSSTEVSSTDVSSTNASSTDIMRKPTIELHLPAQMTINDIDFFVKFIENNF 225          
BLAST of SMED30026685 vs. Planmine SMEST
Match: SMESG000071514.1 (SMESG000071514.1)

HSP 1 Score: 335.495 bits (859), Expect = 2.097e-114
Identity = 183/183 (100.00%), Postives = 183/183 (100.00%), Query Frame = 2
Query:  587 GDFRRLCKCPGGFCAGNRDIIQTLRNLNGHYYMMWKLPDVIGKAICNSMTKWKYEEFHESVLLTRSRNSKFQKLFEEKLFRKWKIVGYPYSYVKHIYPINEHERKETLIEMKKMFSNEGIKINISLPCWIXXXXXXXXXXXXXXXXXXXXXXIMRKPTIELHLPAQMTINDIDFFVKFIENNF 1135
            GDFRRLCKCPGGFCAGNRDIIQTLRNLNGHYYMMWKLPDVIGKAICNSMTKWKYEEFHESVLLTRSRNSKFQKLFEEKLFRKWKIVGYPYSYVKHIYPINEHERKETLIEMKKMFSNEGIKINISLPCWISASSSTEVSSTDVSSTNASSTDIMRKPTIELHLPAQMTINDIDFFVKFIENNF
Sbjct:  108 GDFRRLCKCPGGFCAGNRDIIQTLRNLNGHYYMMWKLPDVIGKAICNSMTKWKYEEFHESVLLTRSRNSKFQKLFEEKLFRKWKIVGYPYSYVKHIYPINEHERKETLIEMKKMFSNEGIKINISLPCWISASSSTEVSSTDVSSTNASSTDIMRKPTIELHLPAQMTINDIDFFVKFIENNF 290          
BLAST of SMED30026685 vs. Planmine SMEST
Match: SMESG000071514.1 (SMESG000071514.1)

HSP 1 Score: 337.806 bits (865), Expect = 8.693e-114
Identity = 183/183 (100.00%), Postives = 183/183 (100.00%), Query Frame = 2
Query:  587 GDFRRLCKCPGGFCAGNRDIIQTLRNLNGHYYMMWKLPDVIGKAICNSMTKWKYEEFHESVLLTRSRNSKFQKLFEEKLFRKWKIVGYPYSYVKHIYPINEHERKETLIEMKKMFSNEGIKINISLPCWIXXXXXXXXXXXXXXXXXXXXXXIMRKPTIELHLPAQMTINDIDFFVKFIENNF 1135
            GDFRRLCKCPGGFCAGNRDIIQTLRNLNGHYYMMWKLPDVIGKAICNSMTKWKYEEFHESVLLTRSRNSKFQKLFEEKLFRKWKIVGYPYSYVKHIYPINEHERKETLIEMKKMFSNEGIKINISLPCWISASSSTEVSSTDVSSTNASSTDIMRKPTIELHLPAQMTINDIDFFVKFIENNF
Sbjct:  216 GDFRRLCKCPGGFCAGNRDIIQTLRNLNGHYYMMWKLPDVIGKAICNSMTKWKYEEFHESVLLTRSRNSKFQKLFEEKLFRKWKIVGYPYSYVKHIYPINEHERKETLIEMKKMFSNEGIKINISLPCWISASSSTEVSSTDVSSTNASSTDIMRKPTIELHLPAQMTINDIDFFVKFIENNF 398          
BLAST of SMED30026685 vs. Planmine SMEST
Match: SMESG000000888.1 (SMESG000000888.1)

HSP 1 Score: 52.7582 bits (125), Expect = 7.332e-10
Identity = 24/30 (80.00%), Postives = 25/30 (83.33%), Query Frame = 2
Query:  107 KIFTMCDHVISNQEFPAEMLYDKSEYLAAL 196
            +I  MCDHVISNQEFP EMLY KS YLAAL
Sbjct:  138 QIIAMCDHVISNQEFPDEMLYGKSGYLAAL 167          

HSP 2 Score: 29.261 bits (64), Expect = 7.332e-10
Identity = 14/21 (66.67%), Postives = 16/21 (76.19%), Query Frame = 3
Query:  201 ILHTYDKAVDIPLIKKPTKVV 263
            ILH YDKAVDI +IKK  K +
Sbjct:  169 ILHKYDKAVDIQIIKKVFKAI 189          
BLAST of SMED30026685 vs. Planmine SMEST
Match: SMESG000000888.1 (SMESG000000888.1)

HSP 1 Score: 52.7582 bits (125), Expect = 7.571e-10
Identity = 24/30 (80.00%), Postives = 25/30 (83.33%), Query Frame = 2
Query:  107 KIFTMCDHVISNQEFPAEMLYDKSEYLAAL 196
            +I  MCDHVISNQEFP EMLY KS YLAAL
Sbjct:  138 QIIAMCDHVISNQEFPDEMLYGKSGYLAAL 167          

HSP 2 Score: 29.261 bits (64), Expect = 7.571e-10
Identity = 14/21 (66.67%), Postives = 16/21 (76.19%), Query Frame = 3
Query:  201 ILHTYDKAVDIPLIKKPTKVV 263
            ILH YDKAVDI +IKK  K +
Sbjct:  169 ILHKYDKAVDIQIIKKVFKAI 189          
The following BLAST results are available for this feature:
BLAST of SMED30026685 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 SMED30026685 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 SMED30026685 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 SMED30026685 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 SMED30026685 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 SMED30026685 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 SMED30026685 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 SMED30026685 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 SMED30026685 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 SMED30026685 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 SMED30026685 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 SMED30026685 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 SMED30026685 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 SMED30026685 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000071514.13.424e-148100.00SMESG000071514.1[more]
SMESG000071514.12.097e-114100.00SMESG000071514.1[more]
SMESG000071514.18.693e-114100.00SMESG000071514.1[more]
SMESG000000888.17.332e-1080.00SMESG000000888.1[more]
SMESG000000888.17.571e-1080.00SMESG000000888.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026685 ID=SMED30026685|Name=SMED30026685|organism=Schmidtea mediterranea sexual|type=transcript|length=1155bp
TGAAACTATGTGAGATAATGCAGTTTATAATATTACAATCTTAACAGTTC
TTTATATTTATTACAGTTTGGTAAGGTTAGGGATTTATATTACTTTATAT
AATTGTAAAATATTTACAATGTGTGATCATGTTATATCCAATCAGGAGTT
TCCAGCTGAAATGCTTTATGACAAAAGTGAATATTTGGCAGCTTTATAAA
ATATTGCATACATATGATAAAGCAGTTGACATTCCACTTATTAAAAAACC
TACGAAAGTTGTATACCGATCGATGCAACTGTTAGACGATTTTTGTATAA
TGACGGCTTATTAGACCGTGAATAAATTATTATGTATCTGTGCGTTTGGA
TCTCTCTTTTTATTTCACGATTTCCATTTGCTCGCCCTACTGGATGTGGA
TTTTCTAAATCATTCTCCGAGTCACCTGCCTGTATTCGCGGTGGATGTCT
TAGCTATAAGATGTTGGTGGAGTTCTTATTCAAAGCGACATTTGCGTTCG
CGGATTTTTCTTTAGCCTATTTTCGGAGAGAAAAAAATTTCGGAATGGTC
AATCGTGCTGCTCTCCTGCGGAGCATTTATCGGCAAGGTGACTTTCGACG
GTTATGCAAATGTCCCGGTGGGTTTTGTGCGGGAAATCGAGACATTATAC
AAACGTTAAGAAATCTGAATGGACATTACTATATGATGTGGAAACTTCCA
GATGTTATTGGTAAGGCAATTTGTAACTCCATGACCAAATGGAAATATGA
GGAATTCCACGAGTCAGTCCTGCTCACGAGATCTAGAAATTCAAAATTTC
AGAAATTGTTTGAGGAAAAATTATTTCGGAAATGGAAAATAGTAGGATAT
CCGTATTCATATGTCAAGCATATTTATCCAATTAATGAACATGAAAGAAA
AGAAACTTTGATAGAAATGAAAAAAATGTTTTCAAATGAAGGGATAAAAA
TAAATATTTCACTACCGTGCTGGATCAGTGCATCAAGCAGCACTGAAGTG
AGCAGCACTGACGTGAGCAGCACTAACGCAAGCAGCACTGATATCATGCG
GAAACCAACCATAGAATTGCATTTGCCGGCACAAATGACAATCAACGATA
TAGATTTTTTTGTTAAATTCATTGAAAATAATTTTTAGAAATGCAGATCG
GAAGA
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protein sequence of SMED30026685-orf-1

>SMED30026685-orf-1 ID=SMED30026685-orf-1|Name=SMED30026685-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=269bp
MYLCVWISLFISRFPFARPTGCGFSKSFSESPACIRGGCLSYKMLVEFLF
KATFAFADFSLAYFRREKNFGMVNRAALLRSIYRQGDFRRLCKCPGGFCA
GNRDIIQTLRNLNGHYYMMWKLPDVIGKAICNSMTKWKYEEFHESVLLTR
SRNSKFQKLFEEKLFRKWKIVGYPYSYVKHIYPINEHERKETLIEMKKMF
SNEGIKINISLPCWISASSSTEVSSTDVSSTNASSTDIMRKPTIELHLPA
QMTINDIDFFVKFIENNF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: INTERPRO
TermDefinition
IPR015424PyrdxlP-dep_Trfase
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR015424Pyridoxal phosphate-dependent transferaseSUPERFAMILYSSF53383PLP-dependent transferasescoord: 51..223