SMED30003317
Overview
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 progeniesWe 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
Sub-lethal Irradiated Surviving X1 and X2 Cell Population
Embryonic Expression
Davies et. al., 2017
Hover the mouse over a column in the graph to view average RPKM values per sample. Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult. back to top Anatomical Expression
PAGE et. al., 2020SMED30003317 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 2
Alignments
SMED30003317 aligns in the following genomic locations:
Homology
BLAST of SMED30003317 vs. Planmine SMEST
Match: SMESG000069846.1 (SMESG000069846.1) HSP 1 Score: 128.642 bits (322), Expect = 9.179e-39 Identity = 69/125 (55.20%), Postives = 83/125 (66.40%), Query Frame = 1 Query: 70 PRTCQLTGAANLKSKLSQ*EKATSFQMPTRSREA*ITHFYKYPIPGEDHHYFIKNMSNRSRTKNYDVNIHETDRRKERGNYSTNSRPNENRMENCVKNFQESRATKKE*LCSGDYASGEAVYFII 444 PRTC +TG ANL+SK SQ ATSFQ RSR A IT YKY +PG RTKNYD+N+HE++ RKE +YS N +P+ NRM+ C NFQES +TKKE CS DYASGE V+F+I Sbjct: 13 PRTCHITGEANLESKRSQSVTATSFQCLPRSRGALITQSYKYLVPG--------------RTKNYDINVHESNLRKEERDYSANIKPSMNRMKKCDINFQESSSTKKEETCSEDYASGETVHFLI 123
BLAST of SMED30003317 vs. Planmine SMEST
Match: SMESG000010307.1 (SMESG000010307.1) HSP 1 Score: 66.2402 bits (160), Expect = 3.048e-13 Identity = 36/72 (50.00%), Postives = 44/72 (61.11%), Query Frame = 1 Query: 235 MSNRSRTKNYDVNIHETDRRKERGNYSTNSRPNENRMENCVKNFQESRATKKE*LCSG-DYASGEAVYFIIP 447 M N+SRTKNYD+N+HE++ RKE G+YS N RP+ NRM C NFQES SG + E IIP Sbjct: 1 MPNQSRTKNYDINVHESNLRKEEGDYSANIRPSMNRMIKCDINFQESEGYPSVIGNSGTQWKDDERTTLIIP 72
BLAST of SMED30003317 vs. Planmine SMEST
Match: SMESG000010307.1 (SMESG000010307.1) HSP 1 Score: 65.4698 bits (158), Expect = 4.991e-13 Identity = 30/47 (63.83%), Postives = 37/47 (78.72%), Query Frame = 1 Query: 235 MSNRSRTKNYDVNIHETDRRKERGNYSTNSRPNENRMENCVKNFQES 375 M N+SRTKNYD+N+HE++ RKE G+YS N RP+ NRM C NFQES Sbjct: 1 MPNQSRTKNYDINVHESNLRKEEGDYSANIRPSMNRMIKCDINFQES 47 The following BLAST results are available for this feature:
BLAST of SMED30003317 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30003317 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30003317 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30003317 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30003317 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30003317 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30003317 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30003317 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30003317 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30003317 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30003317 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30003317 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30003317 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30003317 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 3
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30003317 ID=SMED30003317|Name=SMED30003317|organism=Schmidtea mediterranea sexual|type=transcript|length=494bpback to top Annotated Terms
The following terms have been associated with this transcript:
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