SMED30009885
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., 2020SMED30009885 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 6
Homology
BLAST of SMED30009885 vs. Planmine SMEST
Match: SMESG000065188.1 (SMESG000065188.1) HSP 1 Score: 59.3066 bits (142), Expect = 1.746e-17 Identity = 32/59 (54.24%), Postives = 41/59 (69.49%), Query Frame = 1 Query: 127 SKFERDGYTENSKDFSKTHGEIEDGYNVSKIYNTMKEDGKSISDFMNFIFYGESKQ*IV 303 SK + YTEN++DF TH EI + YNV + Y TM+EDGK+ISD M FI ES+Q I+ Sbjct: 188 SKSGKQDYTENNQDFRITHSEIGEIYNVPEKYTTMREDGKNISDSMGFISSVESRQYIM 246 HSP 2 Score: 46.9802 bits (110), Expect = 1.746e-17 Identity = 23/39 (58.97%), Postives = 27/39 (69.23%), Query Frame = 2 Query: 5 FPLSNKCLIGEKEGHKFRNCILLRKEVSRRYHRIAHVKK 121 FPL NK LI KE H F+NC L+KEV RY RIA ++K Sbjct: 147 FPLGNKSLICGKERHGFQNCFSLQKEVPGRYQRIACIEK 185
BLAST of SMED30009885 vs. Planmine SMEST
Match: SMESG000030673.1 (SMESG000030673.1) HSP 1 Score: 60.077 bits (144), Expect = 2.355e-12 Identity = 29/49 (59.18%), Postives = 36/49 (73.47%), Query Frame = 1 Query: 127 SKFERDGYTENSKDFSKTHGEIEDGYNVSKIYNTMKEDGKSISDFMNFI 273 SK + YTEN++DF TH E E+ YNV + Y TMKEDGK+I+DFM FI Sbjct: 36 SKSRKQDYTENNQDFRITHSETEERYNVPQKYTTMKEDGKNINDFMGFI 84
BLAST of SMED30009885 vs. Planmine SMEST
Match: SMESG000008586.1 (SMESG000008586.1) HSP 1 Score: 50.0618 bits (118), Expect = 1.599e-8 Identity = 25/49 (51.02%), Postives = 35/49 (71.43%), Query Frame = 1 Query: 127 SKFERDGYTENSKDFSKTHGEIEDGYNVSKIYNTMKEDGK-SISDFMNF 270 SKF + YTEN++DF TH +IE+ YNV + Y TMKED K S + +++F Sbjct: 33 SKFRKQDYTENNQDFRITHSKIEERYNVPEKYTTMKEDKKASATPWVSF 81
BLAST of SMED30009885 vs. Planmine SMEST
Match: SMESG000008586.1 (SMESG000008586.1) HSP 1 Score: 50.447 bits (119), Expect = 1.654e-8 Identity = 25/49 (51.02%), Postives = 35/49 (71.43%), Query Frame = 1 Query: 127 SKFERDGYTENSKDFSKTHGEIEDGYNVSKIYNTMKEDGK-SISDFMNF 270 SKF + YTEN++DF TH +IE+ YNV + Y TMKED K S + +++F Sbjct: 36 SKFRKQDYTENNQDFRITHSKIEERYNVPEKYTTMKEDKKASATPWVSF 84
BLAST of SMED30009885 vs. Planmine SMEST
Match: SMESG000009248.1 (SMESG000009248.1) HSP 1 Score: 47.7506 bits (112), Expect = 5.792e-7 Identity = 21/29 (72.41%), Postives = 25/29 (86.21%), Query Frame = 2 Query: 419 SKRLRSFLRFPTFYRRYIKNYTRIAEPLY 505 SK+LRSFL +YRR+IK+YTRIAEPLY Sbjct: 100 SKQLRSFLGLTNYYRRFIKDYTRIAEPLY 128 The following BLAST results are available for this feature:
BLAST of SMED30009885 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30009885 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30009885 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30009885 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30009885 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30009885 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30009885 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30009885 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30009885 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30009885 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30009885 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30009885 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30009885 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30009885 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 5
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30009885 ID=SMED30009885|Name=SMED30009885|organism=Schmidtea mediterranea sexual|type=transcript|length=520bpback to top Annotated Terms
The following terms have been associated with this transcript:
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
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