SMED30031993

Overview
NameSMED30031993
Smed IDSMED30031993
Length (bp)3410
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 SMED30031993 (SMED30031993) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30031993 (SMED30031993) 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 SMED30031993 (SMED30031993) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30031993 (SMED30031993) 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



SMED30031993

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30031993h1SMcG0019460 dd_Smed_v4_8073_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30031993h1SMcG0019460 dd_Smed_v4_8073_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30031993h1SMcG0019460 dd_Smed_v4_8073_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30031993h1SMcG0019460 dd_Smed_v4_8073_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30031993h1SMcG0019460 dd_Smed_v4_8073_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30031993h1SMcG0019460 dd_Smed_v4_8073_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30031993h1SMcG0019460 dd_Smed_v4_8073_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30031993h1SMcG0019460 dd_Smed_v4_8073_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Category 4 cellSMED30031993h1SMcG0019460 dd_Smed_v4_8073_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
Alignments
SMED30031993 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000851:2954..5965 -13935
Homology
[Close]
BLAST of SMED30031993 vs. Planmine SMEST
Match: SMESG000020288.1 (SMESG000020288.1)

HSP 1 Score: 97.4413 bits (241), Expect = 3.397e-24
Identity = 47/59 (79.66%), Postives = 53/59 (89.83%), Query Frame = 1 
Query:  172 EPMSGNVDINEKYEIARLFQIYKKRYQLINIAHRTAIILSEITELVEINTKESNKDFKT 348
            E MSG VDIN+KYEIA LFQ YK+ YQLI+IAHRT IILSEITE+VE+NTKESNKDF+T
Sbjct:   15 ESMSGYVDINDKYEIAGLFQFYKRCYQLIDIAHRTEIILSEITEIVEVNTKESNKDFET 73
[Close]
BLAST of SMED30031993 vs. Planmine SMEST
Match: SMESG000050479.1 (SMESG000050479.1)

HSP 1 Score: 50.0618 bits (118), Expect = 1.854e-18
Identity = 28/60 (46.67%), Postives = 36/60 (60.00%), Query Frame = 3 
Query: 1962 PYSEDFENLKFSVTKSFCNSNVFKILSKSLK*INMFSYKSQTPIAFVSDQVFTFSCNSYN 2141
            PYSE F N K  ++K   N   +KI+S S K  NMF  KS+TP+   SD V+ F+CN  N
Sbjct: 1841 PYSEGFTNYKRKLSKQMGNLE-YKIVSNSCKVRNMFINKSKTPVGLCSDLVYHFTCNGCN 1899

HSP 2 Score: 49.2914 bits (116), Expect = 1.854e-18
Identity = 21/30 (70.00%), Postives = 25/30 (83.33%), Query Frame = 1 
Query: 1612 LPFLDFLIERTAKSFESEIYRKPTDTGLYT 1701
            + FLD LI+R  K +E+EIYRKPTDTGLYT
Sbjct: 1703 IAFLDLLIQRKDKQYETEIYRKPTDTGLYT 1732

HSP 3 Score: 33.4982 bits (75), Expect = 1.854e-18
Identity = 17/33 (51.52%), Postives = 23/33 (69.70%), Query Frame = 2 
Query: 1796 KLVSLLNKNGYSKVFVIPLIK*TIGHLLIGPDE 1894
            KLV LL KNGYSK F++ +IK T+  L+  P +
Sbjct: 1770 KLVELLIKNGYSKSFLLLMIKETVDKLIKNPKD 1802
[Close]
BLAST of SMED30031993 vs. Planmine SMEST
Match: SMESG000050479.1 (SMESG000050479.1)

HSP 1 Score: 50.0618 bits (118), Expect = 2.024e-18
Identity = 28/60 (46.67%), Postives = 36/60 (60.00%), Query Frame = 3 
Query: 1962 PYSEDFENLKFSVTKSFCNSNVFKILSKSLK*INMFSYKSQTPIAFVSDQVFTFSCNSYN 2141
            PYSE F N K  ++K   N   +KI+S S K  NMF  KS+TP+   SD V+ F+CN  N
Sbjct: 1907 PYSEGFTNYKRKLSKQMGNLE-YKIVSNSCKVRNMFINKSKTPVGLCSDLVYHFTCNGCN 1965

HSP 2 Score: 48.9062 bits (115), Expect = 2.024e-18
Identity = 21/30 (70.00%), Postives = 25/30 (83.33%), Query Frame = 1 
Query: 1612 LPFLDFLIERTAKSFESEIYRKPTDTGLYT 1701
            + FLD LI+R  K +E+EIYRKPTDTGLYT
Sbjct: 1769 IAFLDLLIQRKDKQYETEIYRKPTDTGLYT 1798

HSP 3 Score: 33.4982 bits (75), Expect = 2.024e-18
Identity = 17/33 (51.52%), Postives = 23/33 (69.70%), Query Frame = 2 
Query: 1796 KLVSLLNKNGYSKVFVIPLIK*TIGHLLIGPDE 1894
            KLV LL KNGYSK F++ +IK T+  L+  P +
Sbjct: 1836 KLVELLIKNGYSKSFLLLMIKETVDKLIKNPKD 1868
[Close]
BLAST of SMED30031993 vs. Planmine SMEST
Match: SMESG000007021.1 (SMESG000007021.1)

HSP 1 Score: 49.2914 bits (116), Expect = 2.283e-18
Identity = 28/60 (46.67%), Postives = 35/60 (58.33%), Query Frame = 3 
Query: 1962 PYSEDFENLKFSVTKSFCNSNVFKILSKSLK*INMFSYKSQTPIAFVSDQVFTFSCNSYN 2141
            PYSE F N K  + K   N   +KI+S S K  NMF  KS+TP+   SD V+ F+CN  N
Sbjct:  285 PYSEGFTNYKRKLGKLIGNLE-YKIVSNSCKVRNMFINKSKTPVGLCSDLVYQFTCNGCN 343

HSP 2 Score: 48.9062 bits (115), Expect = 2.283e-18
Identity = 21/30 (70.00%), Postives = 25/30 (83.33%), Query Frame = 1 
Query: 1612 LPFLDFLIERTAKSFESEIYRKPTDTGLYT 1701
            + FLD LI+R  K +E+EIYRKPTDTGLYT
Sbjct:  147 IAFLDLLIQRKDKQYETEIYRKPTDTGLYT 176

HSP 3 Score: 34.2686 bits (77), Expect = 2.283e-18
Identity = 19/42 (45.24%), Postives = 25/42 (59.52%), Query Frame = 2 
Query: 1796 KLVSLLNKNGYSKVFVIPLIK*TIGHLLIGPDENNGNYSSLN 1921
            KLV LL KNGYSK F++ +IK T+  L+  P +     S  N
Sbjct:  214 KLVELLIKNGYSKSFLLLMIKETVDKLIKNPKDPCCGKSECN 255
[Close]
BLAST of SMED30031993 vs. Planmine SMEST
Match: SMESG000018320.1 (SMESG000018320.1)

HSP 1 Score: 49.6766 bits (117), Expect = 2.366e-18
Identity = 21/30 (70.00%), Postives = 25/30 (83.33%), Query Frame = 1 
Query: 1612 LPFLDFLIERTAKSFESEIYRKPTDTGLYT 1701
            + FLD LI+R  K +E+EIYRKPTDTGLYT
Sbjct:   57 IAFLDLLIQRKDKQYETEIYRKPTDTGLYT 86

HSP 2 Score: 48.521 bits (114), Expect = 2.366e-18
Identity = 28/60 (46.67%), Postives = 35/60 (58.33%), Query Frame = 3 
Query: 1962 PYSEDFENLKFSVTKSFCNSNVFKILSKSLK*INMFSYKSQTPIAFVSDQVFTFSCNSYN 2141
            PYSE F N K  + K   N   +KI+S S K  NMF  KS+TP+   SD V+ F+CN  N
Sbjct:  195 PYSEGFTNYKRKLGKLIGNLE-YKIVSNSCKVRNMFINKSKTPVGLCSDLVYQFTCNGCN 253

HSP 3 Score: 33.8834 bits (76), Expect = 2.366e-18
Identity = 17/33 (51.52%), Postives = 23/33 (69.70%), Query Frame = 2 
Query: 1796 KLVSLLNKNGYSKVFVIPLIK*TIGHLLIGPDE 1894
            KLV LL KNGYSK F++ +IK T+  L+  P +
Sbjct:  124 KLVELLIKNGYSKSFLLLMIKETVDKLIKNPKD 156
The following BLAST results are available for this feature:
BLAST of SMED30031993 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 SMED30031993 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 SMED30031993 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 SMED30031993 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 SMED30031993 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 SMED30031993 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 SMED30031993 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 SMED30031993 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 SMED30031993 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 SMED30031993 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 SMED30031993 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 SMED30031993 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 SMED30031993 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 SMED30031993 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000020288.13.397e-2479.66SMESG000020288.1[more]
SMESG000050479.11.854e-1846.67SMESG000050479.1[more]
SMESG000050479.12.024e-1846.67SMESG000050479.1[more]
SMESG000007021.12.283e-1846.67SMESG000007021.1[more]
SMESG000018320.12.366e-1870.00SMESG000018320.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031993 ID=SMED30031993|Name=SMED30031993|organism=Schmidtea mediterranea sexual|type=transcript|length=3410bp
ATGAAACAAGAAACCGATTCTTGGAAATATTTGTTAAGTCGTCCTTGTCG
AGTGGAAAATTCGAATGAAGTTCAAAACAAAATTCGGGGAGCTTCTTATC
AGACTAATATGACCAAAATCAAACTCAATTCAACTCATTATTCCGCTTTA
AATAATAATATCGAAGTTTATGAACCAATGTCGGGAAATGTAGACATTAA
TGAGAAATATGAAATCGCCAGATTGTTTCAGATATATAAAAAACGCTACC
AACTGATTAACATTGCTCACAGAACTGCGATTATTTTGTCGGAAATTACA
GAATTAGTTGAAATCAACACGAAAGAATCAAACAAAGATTTCAAAACAGA
GTCAGTTGAGCTCCGAGAGAACTGTGGAGAAGTTGATACGATTTGAAGAC
AACCCGAACTAAAATTATCAATGCATTGTTTATGAAAAATGAACGAGGAA
TTTGATTTAGGACCTCTGTCGGGATTATATAAGTCACGTCTTTAGCCTCA
GTTAGATGCCTCATTCCTTTGTTGACTGTCAATTTGTCCAGACCATTTGC
ACTGGACTAGGACGCAAGTCGACATCGAAGATCTTCTATCACTTTTCTTT
TATACACCTTACTGATCGAGAAGAAGACCGATGAAAACTAAGCGAATGCA
TAAAATCACCTTGCTGAGAATTTTCTCAGTATAGCTCAGTCAATTTGTGA
CTAGTGACTAAATAAATAGGCTCCATAACACAGGTAAGCTCATGTGATTC
CATCACCGATGTTACTCATATTCTTGAGAATAGATTGAGAAAGGCAAAGG
CGAGGGTTCGAGTATTTGACATAATAAAGATAAAAGATAAGTTCAAATAA
AATAAAATAATGGAGTGTTAGATGAATTGTTAGAACCTGGCATGTTAATA
ATGTTTGCTTCCGTTTTATACAGTGTATAATCACATAATGCGAACCTTTT
TTATATTGTCGAGTTTTCTTCAGCTGGAAGATCGCTTTTTGCCATCCTAA
AGAATAAAGTTCCCGATAGGTATACCACAATCGAGAGCTAAAAAGTTAAA
AATTGAGTAAAAATAAGCTATAAAGTAAAAGGCGCAACTCATTTCAGGTT
AATGGCCTTCGTAAGAAGATTTTTTGATTAGGTAATTATAGAGTCGTGTC
CAGTGATGAAAGTAAAGCTCTTATAAACATATACACAGAAAGAAAGCTGA
AGTGCAGAATGAAAAATCTAGAGTTGGAGAATCAATCAAATGTCATACCA
CCACATAATCTCCGCCATAGGCAAATAATGAGATGAATACATAAGCATTA
ATATAAAATCGTTTGGGCCTCAGAAAAATACATTCAAAGAATTCAACCTA
ATTAAAAATAAGCAATTAATTAATTAGATAATAAAACCGACCAGCAGATG
GAAAAATAATAAGATCCACTTTTCCTCCAAAGGTCAATAAAGCGATTAGG
TTTTCATAGAGAGGCGAGAGGTCGCCTACCAAATTAGTTTGTTGAAAACA
AAATGTTAATAAACTAATCATTTCGTTGTAGGTTTATTTTTATTATTTGT
TACCATACTTCGCAAGGTTTCACTAAAATATTAAGTTCACAGTGGAAGAA
GTTATTATTTTCTTCCCTTTTTAGATTTTTTAATAGAAAGAACGGCTAAG
AGTTTTGAATCAGAAATATATAGAAAACCAACAGATACAGGTCTATATAC
ACTACGTCTTATAGCATTTGTGACTTTCAAAATATGAATAACGCTTCGAT
TTTTAGATATTGGTCTTGATCTTCTACGTCTCAAAAATCTAACAAAAGTT
AGTTTCTCTTTTGAATAAAAATGGATATTCTAAGGTTTTTGTAATTCCAC
TAATAAAGTAAACCATTGGTCATCTTTTGATTGGTCCTGATGAAAACAAT
GGAAATTATAGTTCACTTAATGCTGATGAACCTATAAAAACTCATGTTTT
AGTGATATTCGCCATATTCGGAAGATTTTGAAAATTTGAAGTTTTCGGTT
ACAAAATCATTCTGCAATTCTAATGTATTTAAAATATTGTCAAAATCTTT
AAAATGAATAAACATGTTTAGTTATAAATCTCAAACTCCAATAGCTTTTG
TGTCTGATCAAGTGTTTACGTTTTCATGTAATAGTTATAATTATCCAGTT
CTTGATTACAATTCCTGTGTAAATGGTAAATATCAATACAACGTTTTATT
TTAGCTTTCACAAAGTTATTTCCAACTACCGAAAATACTCGACTGCGAAA
ATTAGAGCGGCATAAAATCCGACGCCGCTCGAATTAACTCGAGCGTGTAC
GATAAAGATTAATCGTCAACGAAAGTCTACCGAAAAATGTAAATTAAATT
CCTTTGAATTGAGAAAAAGACAAATGCTTATAAAATTTCAAAGACATCGT
TCACAAATTTAGCATTTCAATAAGATATTTTGTCAGCGGGGGGTCTAAAA
AATATTTATTTTAAGTAAAATCAATAATTAAATTAATTTTATTAATAATA
CTATTTTTGTAATTTTAGATATTTCCTTCAGTGCAAACATGGGCAAACAA
ACAAACAAACACACACATACATGCATACATACACTCAAAGTATGGAACAC
GCAAACACACACACACACACACAACGACTCGTCTTGCATTCATTAGCGGA
TTTCTCTATAGCTGTTGCTGGGTAACCTTATCTTCCATTGTTACGGAATA
AGTCTACTAGAAAAAAAATAATAGTTTTTTCCCTTGATTTTGCTGTCAGT
GAATTTTTTGGACTTTCAAATCGAATTTGCAAATTATGACAATTCTCTAT
TTGGATGATGTAACGAGACGCACAGAGATCGGCTGTATTTTTCGGTTGCT
GAAAAGGTGAGTTGACATTTGCACTAGTTTTATTGATTAAAATGCGCTGA
TAATCGATCAGGTTGTTTTTTTTGTCAATGACTCAATAATTGACCGACTG
TGCATTTGTCATTGATGGCTACAATAGAAGCTTTTTTATTCTCATATTTT
AAATTGACGTAGCCGTTACGTGTCTCATTGAATATCAGCTTCGATGCAGC
ACACAATTGTCAGTGGATGCGCACGCTAACACGAGCGTTGACTTATACGC
ACACACTCACGCACACGCACTTACGTGAATGCACATGAGCGTTGACTTAT
ACGCACACACCCACGCACTTACGCGAATGCACGCTAGCGTACACGCGTGA
AAGCATGCGTGCAAACAATTGATAAAATATTTCAACTCAATTGTTTAGTT
TTTTGAAAAATTATTATTATTATTATTATCATTTTCTGCTATGGCGGATT
GATTTAGTTTTTGTTTTGTAGTGCTAGCAATGATCGTTATTTGGTCTGTA
CAATCATTTTATGAACAGATTTTATATGGGAATATATACTGACTTGATTT
CAAAAAAAAA
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protein sequence of SMED30031993-orf-1

>SMED30031993-orf-1 ID=SMED30031993-orf-1|Name=SMED30031993-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=132bp
MKQETDSWKYLLSRPCRVENSNEVQNKIRGASYQTNMTKIKLNSTHYSAL
NNNIEVYEPMSGNVDINEKYEIARLFQIYKKRYQLINIAHRTAIILSEIT
ELVEINTKESNKDFKTESVELRENCGEVDTI*
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