SMED30020849

Overview
NameSMED30020849
Smed IDSMED30020849
Length (bp)546
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 SMED30020849 (SMED30020849) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30020849 (SMED30020849) 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



SMED30020849

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



PAGE Curations: 28

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30020849SMESG000044682.1 Contig721newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30020849SMESG000044682.1 Contig721uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30020849SMESG000044682.1 Contig721newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30020849SMESG000044682.1 Contig721uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
gutSMED30020849SMESG000058940.1 Contig721newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30020849SMESG000058940.1 Contig721uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30020849SMESG000058940.1 Contig721newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30020849SMESG000058940.1 Contig721uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
head regionSMED30020849SMESG000044682.1 SmedASXL_004631SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30020849SMESG000044682.1 dd_Smed_v4_3494_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30020849SMESG000044682.1 dd_Smed_v4_3494_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30020849SMESG000044682.1 dd_Smed_v4_3494_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020849SMESG000044682.1 Contig721newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020849SMESG000044682.1 Contig721uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020849SMESG000044682.1 Contig50098newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020849SMESG000044682.1 SMESG000044677.1 Contig3899newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020849SMESG000044682.1 SMESG000044677.1 Contig3899uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020849SMESG000058940.1 Contig721newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020849SMESG000058940.1 Contig721uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020849SMESG000052764.1 SMESG000052762.1 SMESG000052759.1 SMESG000052750.1 SMESG000052741.1 SMESG000052739.1 Contig3899newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30020849SMESG000052764.1 SMESG000052762.1 SMESG000052759.1 SMESG000052750.1 SMESG000052741.1 SMESG000052739.1 Contig3899uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
epidermisSMED30020849SMESG000044682.1 dd_Smed_v4_3494_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30020849SMESG000044682.1 dd_Smed_v4_3494_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
ciliated epithelial cellSMED30020849SMESG000044682.1 dd_Smed_v4_3494_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
neoblastSMED30020849SMESG000044682.1 SMESG000044677.1 SMED_02677_V2_1rGPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30020849SMESG000044682.1 SMESG000044677.1 SMED_02677_V2_1rGPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30020849SMESG000044682.1 SMED_02677_V2_1rGPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30020849SMESG000044682.1 SMED_02677_V2_1rGPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30020849 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.038621:1291..1850 -2505
v31.007917:10385..10944 -2487
Homology
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BLAST of SMED30020849 vs. Planmine SMEST
Match: SMESG000044682.1 (SMESG000044682.1)

HSP 1 Score: 190.66 bits (483), Expect = 3.151e-57
Identity = 104/105 (99.05%), Postives = 104/105 (99.05%), Query Frame = 3 
Query:    3 IKPPFISTNYNPNSTKVFLFKNKKGETIIKDDLGYWKIEQLERQKRDXXXXXXXXXXXTTACICLIVFFVQRRHYKQKIGNSDCKPLINNEQFANYCSINNTEPV 317
            IKPPFISTNYNPNSTKVFLFKNKKGETIIKDDLGYWKIEQLERQKRDILIGSIIGSLLTTACICLIVFFVQRRHYKQKIGNSD KPLINNEQFANYCSINNTEPV
Sbjct:  578 IKPPFISTNYNPNSTKVFLFKNKKGETIIKDDLGYWKIEQLERQKRDILIGSIIGSLLTTACICLIVFFVQRRHYKQKIGNSDSKPLINNEQFANYCSINNTEPV 682
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BLAST of SMED30020849 vs. Planmine SMEST
Match: SMESG000044681.1 (SMESG000044681.1)

HSP 1 Score: 128.642 bits (322), Expect = 1.179e-34
Identity = 67/105 (63.81%), Postives = 84/105 (80.00%), Query Frame = 3 
Query:    3 IKPPFISTNYNPNSTKVFLFKNKKGETIIKDDLGYWKIEQLERQKRDXXXXXXXXXXXTTACICLIVFFVQRRHYKQKIGNSDCKPLINNEQFANYCSINNTEPV 317
            IKPPFIS +YNPNSTKV +F  K GET IKD++G WK+E ++R+KR++L+GSI+GS L  ACICL +FF+QRRHYK+ I   D KPL NNEQ A+Y SINNT+ V
Sbjct:  560 IKPPFISIDYNPNSTKVLIFTTKNGETFIKDNVGSWKLEDIQREKRNMLVGSIVGSFLMAACICLTIFFIQRRHYKRMIEKLDYKPLTNNEQLADYGSINNTDRV 664
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BLAST of SMED30020849 vs. Planmine SMEST
Match: SMESG000044672.1 (SMESG000044672.1)

HSP 1 Score: 102.449 bits (254), Expect = 6.457e-28
Identity = 56/105 (53.33%), Postives = 74/105 (70.48%), Query Frame = 3 
Query:    3 IKPPFISTNYNPNSTKVFLFKNKKGETIIKDDLGYWKIEQLERQKRDXXXXXXXXXXXTTACICLIVFFVQRRHYKQKIGNSDCKPLINNEQFANYCSINNTEPV 317
            IKPPFIS NYNPNST V LFK ++G+  IK+DLG WK+E LER+++ IL+G+I+GSL+   C CL +FFVQ+RHY +K+   +     N    A+Y SIN T  V
Sbjct:   46 IKPPFISINYNPNSTVVLLFKTEEGKRFIKNDLGSWKLEDLERERKIILVGTIVGSLVMATCACLFIFFVQKRHYNRKMERMNYHAFANENILASYGSINTTNRV 150
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BLAST of SMED30020849 vs. Planmine SMEST
Match: SMESG000044678.1 (SMESG000044678.1)

HSP 1 Score: 107.842 bits (268), Expect = 1.656e-27
Identity = 58/103 (56.31%), Postives = 77/103 (74.76%), Query Frame = 3 
Query:    3 IKPPFISTNYNPNSTKVFLFKNKKGETIIKDDLGYWKIEQLERQKRDXXXXXXXXXXXTTACICLIVFFVQRRHYKQKIGNSDCKPLINNEQFANYCSINNTE 311
            IKPPFIS NYNPNSTKV +F N KGET+IKD+ G WK+++L++Q RD+LIG+I+GSLL  ACIC ++F++QRR+Y  +    + K   + E   NY SIN TE
Sbjct:  399 IKPPFISINYNPNSTKVLVFSNLKGETLIKDNFGTWKVDELKKQNRDLLIGTIVGSLLLAACICFVIFYIQRRYYINRYKLINRKKFTDEESMTNYGSINGTE 501
[Close]
BLAST of SMED30020849 vs. Planmine SMEST
Match: SMESG000044678.1 (SMESG000044678.1)

HSP 1 Score: 107.457 bits (267), Expect = 2.106e-27
Identity = 58/103 (56.31%), Postives = 77/103 (74.76%), Query Frame = 3 
Query:    3 IKPPFISTNYNPNSTKVFLFKNKKGETIIKDDLGYWKIEQLERQKRDXXXXXXXXXXXTTACICLIVFFVQRRHYKQKIGNSDCKPLINNEQFANYCSINNTE 311
            IKPPFIS NYNPNSTKV +F N KGET+IKD+ G WK+++L++Q RD+LIG+I+GSLL  ACIC ++F++QRR+Y  +    + K   + E   NY SIN TE
Sbjct:  415 IKPPFISINYNPNSTKVLVFSNLKGETLIKDNFGTWKVDELKKQNRDLLIGTIVGSLLLAACICFVIFYIQRRYYINRYKLINRKKFTDEESMTNYGSINGTE 517
The following BLAST results are available for this feature:
BLAST of SMED30020849 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 SMED30020849 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 SMED30020849 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 SMED30020849 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 SMED30020849 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 SMED30020849 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 SMED30020849 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 SMED30020849 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 SMED30020849 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 SMED30020849 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 SMED30020849 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 SMED30020849 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 SMED30020849 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 SMED30020849 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000044682.13.151e-5799.05SMESG000044682.1[more]
SMESG000044681.11.179e-3463.81SMESG000044681.1[more]
SMESG000044672.16.457e-2853.33SMESG000044672.1[more]
SMESG000044678.11.656e-2756.31SMESG000044678.1[more]
SMESG000044678.12.106e-2756.31SMESG000044678.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020849 ID=SMED30020849|Name=SMED30020849|organism=Schmidtea mediterranea sexual|type=transcript|length=546bp
TAATTAAACCTCCATTTATTTCAACAAATTATAATCCAAACAGCACAAAG
GTTTTTCTATTTAAAAACAAGAAAGGTGAAACGATTATAAAAGATGATTT
GGGATATTGGAAAATAGAACAATTGGAAAGACAAAAAAGAGATATTTTAA
TTGGATCTATTATTGGAAGTTTGTTAACGACTGCCTGCATATGTTTGATT
GTTTTCTTCGTCCAAAGAAGGCATTATAAACAAAAAATTGGAAATTCAGA
TTGCAAACCCTTAATCAACAATGAACAATTTGCGAACTACTGCTCAATAA
ATAATACGGAACCAGTTTAATTAAAACAACAAAATGATTTATTTCTCAAA
CAGTTTATGTTATCTCAAGTGTCATTTTAAATCCTTTTCTCTTCAAAAAA
ATTTTACATCTTTCATAATTGATAATTTATTTCCTTTTTATATAAATTAT
TATAATTGCTTTTAATCTCATAAAATGATAGTATTATGTTTATTTACAAA
TATATTGCTCCTGCAGTCGCCAATAACCTGGAAGCACAGTGTGAAC
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protein sequence of SMED30020849-orf-1

>SMED30020849-orf-1 ID=SMED30020849-orf-1|Name=SMED30020849-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=106bp
IKPPFISTNYNPNSTKVFLFKNKKGETIIKDDLGYWKIEQLERQKRDILI
GSIIGSLLTTACICLIVFFVQRRHYKQKIGNSDCKPLINNEQFANYCSIN
NTEPV*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000026gut
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0000070intestinal phagocyte
PLANA:0000106ciliated epithelial cell
PLANA:0000418head
PLANA:0000429neoblast
PLANA:0002032epidermal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 48..70