SMED30001095
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., 2020SMED30001095 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 9
Alignments
SMED30001095 aligns in the following genomic locations:
Homology
BLAST of SMED30001095 vs. Ensembl Sea Lamprey
Match: ENSPMAT00000006261.1 (pep scaffold:Pmarinus_7.0:GL477433:28222:29567:1 gene:ENSPMAG00000005664.1 transcript:ENSPMAT00000006261.1 gene_biotype:protein_coding transcript_biotype:protein_coding) HSP 1 Score: 43.8986 bits (102), Expect = 1.411e-6 Identity = 24/68 (35.29%), Postives = 37/68 (54.41%), Query Frame = -1 Query: 108 GDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGG 311 ++ EV SV LK+++ QK GIA L + + L DD+ L+ Y IQ +S + M +L+GG Sbjct: 84 ANKTLTIEVKLSNSVLSLKQKVHQKAGIAVNQQILTFGSHTLEDDQKLESYGIQQHSTITMQGRLRGG 151
BLAST of SMED30001095 vs. Ensembl Sea Lamprey
Match: ENSPMAT00000006254.1 (pep scaffold:Pmarinus_7.0:GL477433:3744:20801:-1 gene:ENSPMAG00000005642.1 transcript:ENSPMAT00000006254.1 gene_biotype:protein_coding transcript_biotype:protein_coding) HSP 1 Score: 43.8986 bits (102), Expect = 2.819e-6 Identity = 24/68 (35.29%), Postives = 37/68 (54.41%), Query Frame = -1 Query: 108 GDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGG 311 ++ EV SV LK+++ QK GIA L + + L DD+ L+ Y IQ +S + M +L+GG Sbjct: 160 ANKTLTIEVKLSNSVLSLKQKVHQKAGIAVNQQILTFGSHTLEDDQKLESYGIQQHSTITMQGRLRGG 227 HSP 2 Score: 43.8986 bits (102), Expect = 2.819e-6 Identity = 24/68 (35.29%), Postives = 37/68 (54.41%), Query Frame = -1 Query: 108 GDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGG 311 ++ EV SV LK+++ QK GIA L + + L DD+ L+ Y IQ +S + M +L+GG Sbjct: 311 ANKTLTIEVKLSNSVLSLKQKVHQKAGIAVNQQILTFGSHTLEDDQKLESYGIQQHSTITMQGRLRGG 378
BLAST of SMED30001095 vs. Planmine SMEST
Match: SMESG000003398.1 (SMESG000003398.1) HSP 1 Score: 141.354 bits (355), Expect = 7.781e-45 Identity = 70/70 (100.00%), Postives = 70/70 (100.00%), Query Frame = -1 Query: 102 GDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGGCV 311 GDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGGCV Sbjct: 8 GDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGGCV 77
BLAST of SMED30001095 vs. Planmine SMEST
Match: SMESG000014648.1 (SMESG000014648.1) HSP 1 Score: 103.219 bits (256), Expect = 8.727e-30 Identity = 48/69 (69.57%), Postives = 57/69 (82.61%), Query Frame = -1 Query: 102 DQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGGCV 308 +QNF FEVT +T GDLK QI QKTG+AS I L YN +YLLDDKPL+KYDIQSN+N+VMIS+L+GG V Sbjct: 9 NQNFTFEVTGETLTGDLKNQIAQKTGMASDQIELMYNVVYLLDDKPLRKYDIQSNANIVMISRLRGGRV 77
BLAST of SMED30001095 vs. Planmine SMEST
Match: SMESG000014651.1 (SMESG000014651.1) HSP 1 Score: 88.9669 bits (219), Expect = 4.070e-24 Identity = 43/68 (63.24%), Postives = 56/68 (82.35%), Query Frame = -1 Query: 102 QNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGGCV 305 Q F FEVTS+T VGDLKKQI QKTG+A ++ L +N +YLL+DK L+KY+IQ+N+NLV+ISK+ GG V Sbjct: 10 QIFTFEVTSETLVGDLKKQIVQKTGMAIENLELLFNQVYLLNDKELKKYNIQNNANLVVISKVIGGRV 77
BLAST of SMED30001095 vs. Planmine SMEST
Match: SMESG000063621.1 (SMESG000063621.1) HSP 1 Score: 45.0542 bits (105), Expect = 5.599e-6 Identity = 21/68 (30.88%), Postives = 40/68 (58.82%), Query Frame = -1 Query: 105 DQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGGC 308 D+ AFEV ++ D+KK+I +K G+A + L Y L D++ +++Y I S + ++++L+ G Sbjct: 583 DKTVAFEVQKSDTIRDVKKKIQEKIGLAPDEQKLVYQGEILEDERTVEEYQIAEKSVINIVARLRWGM 650 HSP 2 Score: 45.0542 bits (105), Expect = 5.599e-6 Identity = 21/68 (30.88%), Postives = 40/68 (58.82%), Query Frame = -1 Query: 105 DQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGGC 308 D+ AFEV ++ D+KK+I +K G+A + L Y L D++ +++Y I S + ++++L+ G Sbjct: 659 DKTVAFEVQKSDTIRDVKKKIQEKIGLAPDEQKLVYQGEILEDERTVEEYQIAEKSVINIVARLRWGM 726 The following BLAST results are available for this feature:
BLAST of SMED30001095 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30001095 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30001095 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30001095 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30001095 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30001095 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30001095 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30001095 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30001095 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30001095 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 2
BLAST of SMED30001095 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30001095 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30001095 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30001095 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 4
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30001095 ID=SMED30001095|Name=SMED30001095|organism=Schmidtea mediterranea sexual|type=transcript|length=422bpback 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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