SMED30006642

Overview
NameSMED30006642
Smed IDSMED30006642
Length (bp)531
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30006642 (SMED30006642) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30006642 (SMED30006642) in cells (dots) of each of the 12 neoblast clusters.

 

back to top

 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020



SMED30006642

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30006642h1SMcG0019784 SmedASXL_007078SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
gutSMED30006642h1SMcG0019784 dd_Smed_v4_1488_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30006642h1SMcG0019784 dd_Smed_v6_1488_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30006642h1SMcG0019784 OX_Smed_1.0.16331ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
reproductive organSMED30006642h1SMcG0012614 Contig1293GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30006642h1SMcG0019783 Contig1293GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30006642h1SMcG0019784 Contig1293GPL15192PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30006642 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.011785:8339..14399 +2419
Homology
[Close]
BLAST of SMED30006642 vs. Planmine SMEST
Match: SMESG000014240.1 (SMESG000014240.1)

HSP 1 Score: 279.256 bits (713), Expect = 2.010e-96
Identity = 153/155 (98.71%), Postives = 154/155 (99.35%), Query Frame = -2 
Query:   66 RELLTALKSDEKKKIANFLLQIFDVEXXXXXXXXXXREYLDLRSRILGNHAKGNQFLLTFITSDGFFEVMKGLNNQEKSEIYKLINEINQSTQTKQTRSEYSQQFLDLRKWILSSFHKGNLGLFIRRPVTVDLIKNLNKSEQKEIYELIENLLAV 530
            RELLTALKSDEKKKIANFLLQIFDVEKSKSKRSSFSREYLDLRSRILGNHAKGNQFLL FITSDGFFEVMKGLNNQEKSEIY+LINEINQSTQTKQTRSEYSQQFLDLRKWILSSFHKGNLGLFIRRPVTVDLIKNLNKSEQKEIYELIENLLAV
Sbjct:   78 RELLTALKSDEKKKIANFLLQIFDVEKSKSKRSSFSREYLDLRSRILGNHAKGNQFLLPFITSDGFFEVMKGLNNQEKSEIYELINEINQSTQTKQTRSEYSQQFLDLRKWILSSFHKGNLGLFIRRPVTVDLIKNLNKSEQKEIYELIENLLAV 232

HSP 2 Score: 58.9214 bits (141), Expect = 7.513e-11
Identity = 44/114 (38.60%), Postives = 66/114 (57.89%), Query Frame = -2 
Query:   84 EYLDLRSRILGNHAKGNQFLLTFITSDGFFEVMKGLNNQEKSEIYKLINEINQSTQTKQTRSEYSQQFLDLRKWILSSFHKGN--LGLFIRRPVTVDLIKNLNKSEQKEIYELI 419
            EY DLR+RIL +   G    +TF+ +  F E++  L + EK +I   + +I    ++K  RS +S+++LDLR  IL +  KGN  L  FI      +++K LN  E+ EIYELI
Sbjct:   49 EYTDLRNRILESRVGGYPSFVTFVNTQEFRELLTALKSDEKKKIANFLLQIFDVEKSKSKRSSFSREYLDLRSRILGNHAKGNQFLLPFITSDGFFEVMKGLNNQEKSEIYELI 162
[Close]
BLAST of SMED30006642 vs. Planmine SMEST
Match: SMESG000014240.1 (SMESG000014240.1)

HSP 1 Score: 276.559 bits (706), Expect = 2.781e-95
Identity = 152/154 (98.70%), Postives = 153/154 (99.35%), Query Frame = -2 
Query:   69 RELLTALKSDEKKKIANFLLQIFDVEXXXXXXXXXXREYLDLRSRILGNHAKGNQFLLTFITSDGFFEVMKGLNNQEKSEIYKLINEINQSTQTKQTRSEYSQQFLDLRKWILSSFHKGNLGLFIRRPVTVDLIKNLNKSEQKEIYELIENLLA 530
            RELLTALKSDEKKKIANFLLQIFDVEKSKSKRSSFSREYLDLRSRILGNHAKGNQFLL FITSDGFFEVMKGLNNQEKSEIY+LINEINQSTQTKQTRSEYSQQFLDLRKWILSSFHKGNLGLFIRRPVTVDLIKNLNKSEQKEIYELIENLLA
Sbjct:   78 RELLTALKSDEKKKIANFLLQIFDVEKSKSKRSSFSREYLDLRSRILGNHAKGNQFLLPFITSDGFFEVMKGLNNQEKSEIYELINEINQSTQTKQTRSEYSQQFLDLRKWILSSFHKGNLGLFIRRPVTVDLIKNLNKSEQKEIYELIENLLA 231

HSP 2 Score: 58.9214 bits (141), Expect = 8.719e-11
Identity = 44/114 (38.60%), Postives = 66/114 (57.89%), Query Frame = -2 
Query:   84 EYLDLRSRILGNHAKGNQFLLTFITSDGFFEVMKGLNNQEKSEIYKLINEINQSTQTKQTRSEYSQQFLDLRKWILSSFHKGN--LGLFIRRPVTVDLIKNLNKSEQKEIYELI 419
            EY DLR+RIL +   G    +TF+ +  F E++  L + EK +I   + +I    ++K  RS +S+++LDLR  IL +  KGN  L  FI      +++K LN  E+ EIYELI
Sbjct:   49 EYTDLRNRILESRVGGYPSFVTFVNTQEFRELLTALKSDEKKKIANFLLQIFDVEKSKSKRSSFSREYLDLRSRILGNHAKGNQFLLPFITSDGFFEVMKGLNNQEKSEIYELI 162
[Close]
BLAST of SMED30006642 vs. Planmine SMEST
Match: SMESG000014240.1 (SMESG000014240.1)

HSP 1 Score: 266.159 bits (679), Expect = 5.769e-92
Identity = 146/149 (97.99%), Postives = 148/149 (99.33%), Query Frame = -2 
Query:   69 ALKSDEKKKIANFLLQIFDVEXXXXXXXXXXREYLDLRSRILGNHAKGNQFLLTFITSDGFFEVMKGLNNQEKSEIYKLINEINQSTQTKQTRSEYSQQFLDLRKWILSSFHKGNLGLFIRRPVTVDLIKNLNKSEQKEIYELIENLLA 515
            +LKSDEKKKIANFLLQIFDVEKSKSKRSSFSREYLDLRSRILGNHAKGNQFLL FITSDGFFEVMKGLNNQEKSEIY+LINEINQSTQTKQTRSEYSQQFLDLRKWILSSFHKGNLGLFIRRPVTVDLIKNLNKSEQKEIYELIENLLA
Sbjct:   28 SLKSDEKKKIANFLLQIFDVEKSKSKRSSFSREYLDLRSRILGNHAKGNQFLLPFITSDGFFEVMKGLNNQEKSEIYELINEINQSTQTKQTRSEYSQQFLDLRKWILSSFHKGNLGLFIRRPVTVDLIKNLNKSEQKEIYELIENLLA 176
[Close]
BLAST of SMED30006642 vs. Planmine SMEST
Match: SMESG000014241.1 (SMESG000014241.1)

HSP 1 Score: 98.2117 bits (243), Expect = 1.081e-26
Identity = 58/90 (64.44%), Postives = 70/90 (77.78%), Query Frame = -2 
Query:  261 RELLTALKSDEKKKIANFLLQIFDVEXXXXXXXXXXREYLDLRSRILGNHAKGNQFLLTFITSDGFFEVMKGLNNQEKSEIYKLINEINQ 530
            RELLTAL SDEK KI NF+  IFDVE SK KRSS+SREYLDLRSRIL  HAKG+ +L  F++S GF  V++GLN  EK EI +L+++I Q
Sbjct:   34 RELLTALNSDEKTKIGNFVSHIFDVEISKVKRSSYSREYLDLRSRILAQHAKGDSYLSKFLSSQGFINVLEGLNENEKDEIEELVSQIIQ 123

HSP 2 Score: 64.6994 bits (156), Expect = 9.916e-14
Identity = 38/114 (33.33%), Postives = 68/114 (59.65%), Query Frame = -2 
Query:   72 LRSRILGNHAKGNQFLLTFITSDGFFEVMKGLNNQEKSEIYKLINEINQSTQTKQTRSEYSQQFLDLRKWILSSFHKGN--LGLFIRRPVTVDLIKNLNKSEQKEIYELIENLL 407
            LR+RIL +   G    +TF+ +  F E++  LN+ EK++I   ++ I     +K  RS YS+++LDLR  IL+   KG+  L  F+     +++++ LN++E+ EI EL+  ++
Sbjct:    9 LRNRILESRVGGYPSFVTFVNTQEFRELLTALNSDEKTKIGNFVSHIFDVEISKVKRSSYSREYLDLRSRILAQHAKGDSYLSKFLSSQGFINVLEGLNENEKDEIEELVSQII 122
[Close]
BLAST of SMED30006642 vs. Planmine SMEST
Match: SMESG000014241.1 (SMESG000014241.1)

HSP 1 Score: 98.2117 bits (243), Expect = 1.260e-26
Identity = 58/90 (64.44%), Postives = 70/90 (77.78%), Query Frame = -2 
Query:  261 RELLTALKSDEKKKIANFLLQIFDVEXXXXXXXXXXREYLDLRSRILGNHAKGNQFLLTFITSDGFFEVMKGLNNQEKSEIYKLINEINQ 530
            RELLTAL SDEK KI NF+  IFDVE SK KRSS+SREYLDLRSRIL  HAKG+ +L  F++S GF  V++GLN  EK EI +L+++I Q
Sbjct:   45 RELLTALNSDEKTKIGNFVSHIFDVEISKVKRSSYSREYLDLRSRILAQHAKGDSYLSKFLSSQGFINVLEGLNENEKDEIEELVSQIIQ 134

HSP 2 Score: 71.2478 bits (173), Expect = 4.618e-16
Identity = 41/118 (34.75%), Postives = 71/118 (60.17%), Query Frame = -2 
Query:   72 EYLDLRSRILGNHAKGNQFLLTFITSDGFFEVMKGLNNQEKSEIYKLINEINQSTQTKQTRSEYSQQFLDLRKWILSSFHKGN--LGLFIRRPVTVDLIKNLNKSEQKEIYELIENLL 419
            EY DLR+RIL +   G    +TF+ +  F E++  LN+ EK++I   ++ I     +K  RS YS+++LDLR  IL+   KG+  L  F+     +++++ LN++E+ EI EL+  ++
Sbjct:   16 EYTDLRNRILESRVGGYPSFVTFVNTQEFRELLTALNSDEKTKIGNFVSHIFDVEISKVKRSSYSREYLDLRSRILAQHAKGDSYLSKFLSSQGFINVLEGLNENEKDEIEELVSQII 133
The following BLAST results are available for this feature:
BLAST of SMED30006642 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30006642 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30006642 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30006642 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30006642 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30006642 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30006642 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30006642 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30006642 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30006642 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30006642 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30006642 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30006642 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30006642 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000014240.12.010e-9698.71SMESG000014240.1[more]
SMESG000014240.12.781e-9598.70SMESG000014240.1[more]
SMESG000014240.15.769e-9297.99SMESG000014240.1[more]
SMESG000014241.11.081e-2664.44SMESG000014241.1[more]
SMESG000014241.11.260e-2664.44SMESG000014241.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006642 ID=SMED30006642|Name=SMED30006642|organism=Schmidtea mediterranea sexual|type=transcript|length=531bp
TTTTTTTTAAATAATTAAAATGAAATTGTATTAAATGAAAATAAATTTGT
TGAATTTCATCGTCAAACGGCCAGCAAATTTTCAATAAGCTCATAAATTT
CTTTTTGTTCTGATTTGTTTAAATTTTTTATCAAATCAACAGTTACTGGT
CGACGAATAAACAAGCCTAAATTTCCTTTGTGAAAGCTAGATAAAATCCA
TTTTCTTAAGTCAAGAAATTGCTGAGAATATTCGGATCTTGTTTGTTTAG
TTTGAGTTGATTGATTAATTTCGTTTATTAATTTATATATTTCACTTTTT
TCTTGATTGTTTAATCCTTTCATCACTTCAAAAAATCCGTCACTTGTAAT
AAATGTGAGTAAAAACTGATTTCCTTTGGCATGATTACCTAGAATTCGGC
TTCTTAAATCTAAATACTCTCTTGAAAATGAAGATCGTTTTGATTTAGAT
TTTTCTACATCAAATATCTGTAATAAAAAATTTGCGATTTTCTTCTTTTC
ATCGCTTTTCAAAGCGGTTAATAATTCACGA
back to top

protein sequence of SMED30006642-orf-1

>SMED30006642-orf-1 ID=SMED30006642-orf-1|Name=SMED30006642-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=156bp
RELLTALKSDEKKKIANFLLQIFDVEKSKSKRSSFSREYLDLRSRILGNH
AKGNQFLLTFITSDGFFEVMKGLNNQEKSEIYKLINEINQSTQTKQTRSE
YSQQFLDLRKWILSSFHKGNLGLFIRRPVTVDLIKNLNKSEQKEIYELIE
NLLAV*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0000419prepharyngeal region
PLANA:0000420parapharyngeal region