SMED30007633

Overview
NameSMED30007633
Smed IDSMED30007633
Length (bp)1089
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 SMED30007633 (SMED30007633) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30007633 (SMED30007633) 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



SMED30007633

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



PAGE Curations: 14

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymal cellSMED30007633h1SMcG0020738 dd_Smed_v4_8426_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30007633h1SMcG0020738 dd_Smed_v4_5368_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30007633h1SMcG0020738 dd_Smed_v4_5368_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30007633h1SMcG0020738 dd_Smed_v4_5368_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30007633h1SMcG0020738 dd_Smed_v4_5368_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30007633h1SMcG0020738 dd_Smed_v4_5368_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007633h1SMcG0006181 Contig4376uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007633h1SMcG0006181 Contig4376newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007633h1SMcG0020738 Contig4376uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007633h1SMcG0020738 Contig4376newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007633h1SMcG0020738 Contig9511uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007633h1SMcG0020738 Contig9511newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007633h1SMcG0020738 Contig20040uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007633h1SMcG0020738 Contig20040newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30007633 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006212:13233..14421 -5398
Homology
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BLAST of SMED30007633 vs. Planmine SMEST
Match: SMESG000017211.1 (SMESG000017211.1)

HSP 1 Score: 439.884 bits (1130), Expect = 4.042e-150
Identity = 212/212 (100.00%), Postives = 212/212 (100.00%), Query Frame = -1 
Query:  394 MRIVIINGVEGGRKEEIYISQYMEVRDIKSNLDAKYGGQGVLVKYYYRFIHGNLILYENVCIKHYRIAANDEIWFGKIENFLKSDDVIVEIFLLGFIPTSVFMIMKTFDSISEIRSKLSRIYPMISNIWNARGRLMRDDQMITDSDEEGHYKLIICYCDIESCEMNYSFEECCDLHDRSWVEQFLIWDQVRDENNNDSRRMMLIKRLDKVRL 1029
            MRIVIINGVEGGRKEEIYISQYMEVRDIKSNLDAKYGGQGVLVKYYYRFIHGNLILYENVCIKHYRIAANDEIWFGKIENFLKSDDVIVEIFLLGFIPTSVFMIMKTFDSISEIRSKLSRIYPMISNIWNARGRLMRDDQMITDSDEEGHYKLIICYCDIESCEMNYSFEECCDLHDRSWVEQFLIWDQVRDENNNDSRRMMLIKRLDKVRL
Sbjct:    1 MRIVIINGVEGGRKEEIYISQYMEVRDIKSNLDAKYGGQGVLVKYYYRFIHGNLILYENVCIKHYRIAANDEIWFGKIENFLKSDDVIVEIFLLGFIPTSVFMIMKTFDSISEIRSKLSRIYPMISNIWNARGRLMRDDQMITDSDEEGHYKLIICYCDIESCEMNYSFEECCDLHDRSWVEQFLIWDQVRDENNNDSRRMMLIKRLDKVRL 212
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BLAST of SMED30007633 vs. Planmine SMEST
Match: SMESG000017211.1 (SMESG000017211.1)

HSP 1 Score: 396.741 bits (1018), Expect = 1.376e-133
Identity = 190/190 (100.00%), Postives = 190/190 (100.00%), Query Frame = -1 
Query:  394 MEVRDIKSNLDAKYGGQGVLVKYYYRFIHGNLILYENVCIKHYRIAANDEIWFGKIENFLKSDDVIVEIFLLGFIPTSVFMIMKTFDSISEIRSKLSRIYPMISNIWNARGRLMRDDQMITDSDEEGHYKLIICYCDIESCEMNYSFEECCDLHDRSWVEQFLIWDQVRDENNNDSRRMMLIKRLDKVRL 963
            MEVRDIKSNLDAKYGGQGVLVKYYYRFIHGNLILYENVCIKHYRIAANDEIWFGKIENFLKSDDVIVEIFLLGFIPTSVFMIMKTFDSISEIRSKLSRIYPMISNIWNARGRLMRDDQMITDSDEEGHYKLIICYCDIESCEMNYSFEECCDLHDRSWVEQFLIWDQVRDENNNDSRRMMLIKRLDKVRL
Sbjct:    1 MEVRDIKSNLDAKYGGQGVLVKYYYRFIHGNLILYENVCIKHYRIAANDEIWFGKIENFLKSDDVIVEIFLLGFIPTSVFMIMKTFDSISEIRSKLSRIYPMISNIWNARGRLMRDDQMITDSDEEGHYKLIICYCDIESCEMNYSFEECCDLHDRSWVEQFLIWDQVRDENNNDSRRMMLIKRLDKVRL 190
[Close]
BLAST of SMED30007633 vs. Planmine SMEST
Match: SMESG000017211.1 (SMESG000017211.1)

HSP 1 Score: 233.032 bits (593), Expect = 3.377e-71
Identity = 110/110 (100.00%), Postives = 110/110 (100.00%), Query Frame = -1 
Query:  394 MIMKTFDSISEIRSKLSRIYPMISNIWNARGRLMRDDQMITDSDEEGHYKLIICYCDIESCEMNYSFEECCDLHDRSWVEQFLIWDQVRDENNNDSRRMMLIKRLDKVRL 723
            MIMKTFDSISEIRSKLSRIYPMISNIWNARGRLMRDDQMITDSDEEGHYKLIICYCDIESCEMNYSFEECCDLHDRSWVEQFLIWDQVRDENNNDSRRMMLIKRLDKVRL
Sbjct:    1 MIMKTFDSISEIRSKLSRIYPMISNIWNARGRLMRDDQMITDSDEEGHYKLIICYCDIESCEMNYSFEECCDLHDRSWVEQFLIWDQVRDENNNDSRRMMLIKRLDKVRL 110
[Close]
BLAST of SMED30007633 vs. Planmine SMEST
Match: SMESG000017211.1 (SMESG000017211.1)

HSP 1 Score: 229.565 bits (584), Expect = 6.766e-70
Identity = 108/108 (100.00%), Postives = 108/108 (100.00%), Query Frame = -1 
Query:  394 MKTFDSISEIRSKLSRIYPMISNIWNARGRLMRDDQMITDSDEEGHYKLIICYCDIESCEMNYSFEECCDLHDRSWVEQFLIWDQVRDENNNDSRRMMLIKRLDKVRL 717
            MKTFDSISEIRSKLSRIYPMISNIWNARGRLMRDDQMITDSDEEGHYKLIICYCDIESCEMNYSFEECCDLHDRSWVEQFLIWDQVRDENNNDSRRMMLIKRLDKVRL
Sbjct:    1 MKTFDSISEIRSKLSRIYPMISNIWNARGRLMRDDQMITDSDEEGHYKLIICYCDIESCEMNYSFEECCDLHDRSWVEQFLIWDQVRDENNNDSRRMMLIKRLDKVRL 108
[Close]
BLAST of SMED30007633 vs. Planmine SMEST
Match: SMESG000071997.1 (SMESG000071997.1)

HSP 1 Score: 131.724 bits (330), Expect = 1.579e-33
Identity = 87/244 (35.66%), Postives = 133/244 (54.51%), Query Frame = -1 
Query:  319 MRIVIINGVEGGRKEEIYISQYMEVRDIKSNLDAKYGGQGVLVKYYYRFIHGNLILYENVCIKHYRIAANDEIWFGKIENFLKSDDVIVEIFLLGFIPTSVFMIMKTFDSISEIRSKLSRIYPMISNIWNARGRLMRDDQMITDSDEEGHYKLIICYCDIESCEMNYSFEECCDLHD------RSWVEQFLIWDQVRDENNNDSRRMMLIKRLDKVR-LVSFLVIFP*RLSSKGKSFTDLMFVI 1029
            M+I ++NG  GG K  I I     V +IK  L  +       V Y++     N +L +N  +  Y ++ NDEIW G +ENF+K DDVIVEIFL G+ P   ++++K   S+SEIR+ L RI P I NI+N  G+LM D+Q++TD D +G+Y+LII  C      MN +F+EC   +       +      L + Q   E   +  R  LI ++ ++R ++S   +   RL+   K+ +D +F I
Sbjct:    1 MKIFVVNGENGGEKTAIEIEGLTFVSEIKLRLPEE-----CRVNYFWLINSNNFLLNDNDHLSRYNLSDNDEIWHGSLENFIKKDDVIVEIFLSGWTPFISWLVVKVNQSMSEIRAALVRIEPDIINIFNGDGQLMEDNQLVTDIDRDGYYRLIIS-CG-RGANMNLAFDECYKFYKLHILRFKYSKSHLLYYAQFYSEGIQEQTRYQLIYQMIRIREIMSSNDVIDTRLN---KNLSDFLFFI 234
The following BLAST results are available for this feature:
BLAST of SMED30007633 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 SMED30007633 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 SMED30007633 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 SMED30007633 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 SMED30007633 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 SMED30007633 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 SMED30007633 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 SMED30007633 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 SMED30007633 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 SMED30007633 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 SMED30007633 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 SMED30007633 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 SMED30007633 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 SMED30007633 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000017211.14.042e-150100.00SMESG000017211.1[more]
SMESG000017211.11.376e-133100.00SMESG000017211.1[more]
SMESG000017211.13.377e-71100.00SMESG000017211.1[more]
SMESG000017211.16.766e-70100.00SMESG000017211.1[more]
SMESG000071997.11.579e-3335.66SMESG000071997.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007633 ID=SMED30007633|Name=SMED30007633|organism=Schmidtea mediterranea sexual|type=transcript|length=1089bp
GTGTCCTTCCCCATCAGTAGGGTTACCTTTGATGTACATGTATTTTGGCT
ACCGCTTTTATTACAGAATCATTTCAAACAAATTGAATGTCTTAAAGCTC
TTCCAAGTTCTCAATTTCTCAACATCACCTTAACTGTACTATACATTGTC
CTTCCTTCCTCCTCGTTTACGTGTTTACGTAATTTACATTTGCCTGCCAT
GCTGGAACAAGTGCATAGTGACAATGGATAAAATATGTGGATAAAGCATT
ATATTGTTATTGCCCAAGCAACTCACCATAAAAACCTATAAGATGATAAT
CCAATCTCCTAGTCTAATGATAACAAACATCAAATCTGTAAAAGATTTCC
CCTTTGAACTAAGTCGTCAAGGAAATATCACCAAAAATGAAACTAACCGG
ACTTTATCAAGCCTTTTAATTAGCATCATTCTCCTTGAGTCATTATTGTT
TTCGTCACGAACTTGATCCCAGATCAGGAACTGCTCAACCCAGGACCGAT
CGTGAAGGTCACAGCACTCCTCGAATGAATAATTCATTTCACAGCTCTCA
ATGTCACAGTAACAAATTATCAATTTGTAATGGCCCTCCTCATCAGAATC
CGTGATCATTTGATCGTCCCTCATCAGGCGCCCCCTCGCATTCCAAATAT
TCGATATCATCGGATATATTCGACTGAGTTTTGATCTGATCTCAGAGATC
GAATCAAACGTTTTCATAATCATAAAGACAGAGGTGGGAATAAACCCCAA
TAAAAAAATCTCTACAATGACGTCATCGCTTTTCAAAAAATTTTCAATTT
TCCCGAACCAAATCTCGTCATTGGCAGCAATTCTGTAATGCTTGATGCAA
ACATTCTCGTAGAGAATGAGATTCCCATGAATAAATCGATAATAATATTT
CACCAGGACCCCCTGGCCCCCATATTTGGCATCCAAATTTGATTTGATAT
CCCTCACTTCCATATATTGGCTAATATATATTTCCTCTTTCCTTCCCCCC
TCCACCCCATTTATGATCACTATTCTCATTTAATACTTAAATATATGATT
AATTATTTTTAATTTTGTTTTAATTGACAACTGATAAAT
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protein sequence of SMED30007633-orf-1

>SMED30007633-orf-1 ID=SMED30007633-orf-1|Name=SMED30007633-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=221bp
MRIVIINGVEGGRKEEIYISQYMEVRDIKSNLDAKYGGQGVLVKYYYRFI
HGNLILYENVCIKHYRIAANDEIWFGKIENFLKSDDVIVEIFLLGFIPTS
VFMIMKTFDSISEIRSKLSRIYPMISNIWNARGRLMRDDQMITDSDEEGH
YKLIICYCDIESCEMNYSFEECCDLHDRSWVEQFLIWDQVRDENNNDSRR
MMLIKRLDKVRLVSFLVIFP*
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