SMED30025261

Overview
NameSMED30025261
Smed IDSMED30025261
Length (bp)358
Neoblast Clusters

Zeng et. al., 2018




 



 

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




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




SMED30025261

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30025261SMESG000072141.1 SmedASXL_058121SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
neoblastSMED30025261SMESG000072141.1 dd_Smed_v4_16626_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
prepharyngeal regionSMED30025261SMESG000072141.1 dd_Smed_v6_16626_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
head regionSMED30025261SMESG000072141.1 OX_Smed_1.0.10969ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30025261 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006346:14689..16767 +1629
Homology
BLAST of SMED30025261 vs. TrEMBL
Match: A0A5K4F5G3 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 PE=4 SV=1)

HSP 1 Score: 57.7658 bits (138), Expect = 1.995e-8
Identity = 24/45 (53.33%), Postives = 30/45 (66.67%), Query Frame = 1
Query:  136 RKWVHNTAINCTPKFSCFHNLHCFARYKSNKYYCANIYPCGTSCA 270
            R WV++   NC   +SCF+   C  RY S  Y+CANIYPCG+SCA
Sbjct:   41 RSWVYSDTYNCEKIYSCFNTRQCRQRYNSPNYFCANIYPCGSSCA 85          
BLAST of SMED30025261 vs. TrEMBL
Match: A0A4Z2DHT6 (Uncharacterized protein OS=Schistosoma japonicum OX=6182 GN=EWB00_000804 PE=4 SV=1)

HSP 1 Score: 56.225 bits (134), Expect = 8.023e-8
Identity = 23/45 (51.11%), Postives = 30/45 (66.67%), Query Frame = 1
Query:  136 RKWVHNTAINCTPKFSCFHNLHCFARYKSNKYYCANIYPCGTSCA 270
            R WV++   NC   +SCF+   C  RY S  Y+CAN+YPCG+SCA
Sbjct:   37 RTWVYSDTYNCEKIYSCFNTRQCRLRYNSPNYFCANMYPCGSSCA 81          
BLAST of SMED30025261 vs. Planmine SMEST
Match: SMESG000072141.1 (SMESG000072141.1)

HSP 1 Score: 182.57 bits (462), Expect = 5.343e-61
Identity = 88/92 (95.65%), Postives = 89/92 (96.74%), Query Frame = 1
Query:    7 ESPIYFQIMNSISVKILVVITFVLILSKHQCSPQIDNILGSRVRKWVHNTAINCTPKFSCFHNLHCFARYKSNKYYCANIYPCGTSCAIRNG 282
            ES   FQIMNSISVKILVVITFVLILSKHQCSPQIDNILGSRVR+WVHNTAINCTPKFSCFHNLHCFARYKSNKYYCANIYPCGTSCAIRNG
Sbjct:   24 ESLSVFQIMNSISVKILVVITFVLILSKHQCSPQIDNILGSRVRRWVHNTAINCTPKFSCFHNLHCFARYKSNKYYCANIYPCGTSCAIRNG 115          
BLAST of SMED30025261 vs. Planmine SMEST
Match: SMESG000077009.1 (SMESG000077009.1)

HSP 1 Score: 58.151 bits (139), Expect = 3.852e-12
Identity = 21/45 (46.67%), Postives = 31/45 (68.89%), Query Frame = 1
Query:  136 RKWVHNTAINCTPKFSCFHNLHCFARYKSNKYYCANIYPCGTSCA 270
            ++WVH  ++ C   +SCF +  C  RYK +  YCA++YPCG+SCA
Sbjct:   27 KRWVHFHSVGCDEAYSCFKDDSCRDRYKRDDLYCADMYPCGSSCA 71          
BLAST of SMED30025261 vs. Planmine SMEST
Match: SMESG000077009.1 (SMESG000077009.1)

HSP 1 Score: 56.9954 bits (136), Expect = 5.369e-12
Identity = 21/45 (46.67%), Postives = 31/45 (68.89%), Query Frame = 1
Query:  136 RKWVHNTAINCTPKFSCFHNLHCFARYKSNKYYCANIYPCGTSCA 270
            ++WVH  ++ C   +SCF +  C  RYK +  YCA++YPCG+SCA
Sbjct:    9 KRWVHFHSVGCDEAYSCFKDDSCRDRYKRDDLYCADMYPCGSSCA 53          
The following BLAST results are available for this feature:
BLAST of SMED30025261 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 SMED30025261 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 SMED30025261 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 SMED30025261 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 SMED30025261 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 SMED30025261 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 SMED30025261 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 SMED30025261 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
A0A5K4F5G31.995e-853.33Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
A0A4Z2DHT68.023e-851.11Uncharacterized protein OS=Schistosoma japonicum O... [more]
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BLAST of SMED30025261 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 SMED30025261 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 SMED30025261 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 SMED30025261 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 SMED30025261 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 SMED30025261 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000072141.15.343e-6195.65SMESG000072141.1[more]
SMESG000077009.13.852e-1246.67SMESG000077009.1[more]
SMESG000077009.15.369e-1246.67SMESG000077009.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30025261 ID=SMED30025261|Name=SMED30025261|organism=Schmidtea mediterranea sexual|type=transcript|length=358bp
TTACTCGAGAGCCCAATATATTTTCAAATAATGAATTCTATATCGGTGAA
AATTTTGGTAGTCATAACGTTCGTCTTGATCTTGTCCAAACACCAATGTA
GTCCTCAAATTGATAATATATTGGGCTCTCGAGTAAGGAAATGGGTCCAC
AATACGGCTATAAATTGCACTCCAAAATTCAGTTGCTTCCACAACTTGCA
CTGCTTTGCAAGGTACAAATCAAACAAATATTACTGTGCAAACATCTACC
CTTGTGGAACGTCATGTGCCATCAGAAATGGCTGAGATGATAAAAAAAAT
CGGACGTGATTAGCTTGGGACTGGCAGTAATTGTATGAAATAAATGTTCC
CATTCTCA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0000419prepharyngeal region
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..26
score: 0.627