SMED30013474
Overview
Neoblast Clusters
Zeng et. al., 2018▻ Overview▻ Neoblast 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
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., 2020SMED30013474 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 8
Alignments
SMED30013474 aligns in the following genomic locations:
Homology
BLAST of SMED30013474 vs. Planmine SMEST
Match: SMESG000044971.1 (SMESG000044971.1) HSP 1 Score: 73.1738 bits (178), Expect = 2.282e-17 Identity = 32/50 (64.00%), Postives = 40/50 (80.00%), Query Frame = -3 Query: 106 VSFELDDPRLMNMNTPTKLILPDRLVQSMLLSQPEQRQLGDHTYARQHPQ 255 VSFELDDPRLM M PTK+++P++LVQS L ++ RQ GDHTYA +HPQ Sbjct: 1256 VSFELDDPRLMQMTAPTKMVIPEKLVQSTLRNRLGSRQTGDHTYASRHPQ 1305 HSP 2 Score: 31.187 bits (69), Expect = 2.282e-17 Identity = 14/22 (63.64%), Postives = 15/22 (68.18%), Query Frame = -1 Query: 267 QWNADIASGLIPITDDFTSKYG 332 Q N DIASG IP TD F +YG Sbjct: 1234 QVNRDIASGAIPSTDGFPPEYG 1255
BLAST of SMED30013474 vs. Planmine SMEST
Match: SMESG000031842.1 (SMESG000031842.1) HSP 1 Score: 72.7886 bits (177), Expect = 3.193e-17 Identity = 32/51 (62.75%), Postives = 40/51 (78.43%), Query Frame = -3 Query: 103 VSFELDDPRLMNMNTPTKLILPDRLVQSMLLSQPEQRQLGDHTYARQHPQL 255 VSFELDDPRLM M PTK+++P++LVQS L ++ RQ GDHTYA +HPQ Sbjct: 820 VSFELDDPRLMQMTAPTKMVIPEKLVQSTLRNRLGSRQTGDHTYASRHPQW 870 HSP 2 Score: 31.187 bits (69), Expect = 3.193e-17 Identity = 14/22 (63.64%), Postives = 15/22 (68.18%), Query Frame = -1 Query: 267 QWNADIASGLIPITDDFTSKYG 332 Q N DIASG IP TD F +YG Sbjct: 798 QVNRDIASGAIPSTDGFPPEYG 819
BLAST of SMED30013474 vs. Planmine SMEST
Match: SMESG000031842.1 (SMESG000031842.1) HSP 1 Score: 73.1738 bits (178), Expect = 3.604e-17 Identity = 32/51 (62.75%), Postives = 40/51 (78.43%), Query Frame = -3 Query: 103 VSFELDDPRLMNMNTPTKLILPDRLVQSMLLSQPEQRQLGDHTYARQHPQL 255 VSFELDDPRLM M PTK+++P++LVQS L ++ RQ GDHTYA +HPQ Sbjct: 894 VSFELDDPRLMQMTAPTKMVIPEKLVQSTLRNRLGSRQTGDHTYASRHPQW 944 HSP 2 Score: 30.8018 bits (68), Expect = 3.604e-17 Identity = 14/22 (63.64%), Postives = 15/22 (68.18%), Query Frame = -1 Query: 267 QWNADIASGLIPITDDFTSKYG 332 Q N DIASG IP TD F +YG Sbjct: 872 QVNRDIASGAIPSTDGFPPEYG 893
BLAST of SMED30013474 vs. Planmine SMEST
Match: SMESG000027782.1 (SMESG000027782.1) HSP 1 Score: 71.633 bits (174), Expect = 6.797e-17 Identity = 32/49 (65.31%), Postives = 39/49 (79.59%), Query Frame = -3 Query: 109 VSFELDDPRLMNMNTPTKLILPDRLVQSMLLSQPEQRQLGDHTYARQHP 255 VSFELDDPRLM M PTKL+LP++L+QS L ++ RQ GDHTYA +HP Sbjct: 156 VSFELDDPRLMQMTAPTKLVLPEKLIQSTLRNRLGSRQTGDHTYASRHP 204 HSP 2 Score: 31.187 bits (69), Expect = 6.797e-17 Identity = 14/22 (63.64%), Postives = 15/22 (68.18%), Query Frame = -1 Query: 267 QWNADIASGLIPITDDFTSKYG 332 Q N DIASG IP TD F +YG Sbjct: 134 QVNRDIASGAIPSTDGFPPEYG 155
BLAST of SMED30013474 vs. Planmine SMEST
Match: SMESG000042475.1 (SMESG000042475.1) HSP 1 Score: 72.0182 bits (175), Expect = 7.458e-17 Identity = 32/49 (65.31%), Postives = 39/49 (79.59%), Query Frame = -3 Query: 109 VSFELDDPRLMNMNTPTKLILPDRLVQSMLLSQPEQRQLGDHTYARQHP 255 VSFELDDPRLM M PTKL+LP++L+QS L ++ RQ GDHTYA +HP Sbjct: 1451 VSFELDDPRLMQMTAPTKLVLPEKLIQSTLRNRLGSRQTGDHTYASRHP 1499 HSP 2 Score: 30.4166 bits (67), Expect = 7.458e-17 Identity = 14/22 (63.64%), Postives = 15/22 (68.18%), Query Frame = -1 Query: 267 QWNADIASGLIPITDDFTSKYG 332 Q N DIASG IP TD F +YG Sbjct: 1429 QVNRDIASGAIPSTDGFPQEYG 1450 The following BLAST results are available for this feature:
BLAST of SMED30013474 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30013474 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30013474 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30013474 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30013474 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30013474 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30013474 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30013474 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30013474 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30013474 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30013474 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30013474 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30013474 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30013474 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 >SMED30013474 ID=SMED30013474|Name=SMED30013474|organism=Schmidtea mediterranea sexual|type=transcript|length=356bpback to top protein sequence of SMED30013474-orf-1 >SMED30013474-orf-1 ID=SMED30013474-orf-1|Name=SMED30013474-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=101bp LHVAIHWYHNSSLAFRFIVDSRTDYFGEDGPYVSIVGVVEHMCDLRAAVVback 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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