SMED30031952
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., 2020SMED30031952 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 9
Alignments
SMED30031952 aligns in the following genomic locations:
Homology
BLAST of SMED30031952 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: 45.0542 bits (105), Expect = 4.351e-7 Identity = 29/86 (33.72%), Postives = 45/86 (52.33%), Query Frame = -1 Query: 111 SLYLFHKTLKMKVIVK-FGDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGG 365 ++ L H + V VK ++ EV SV LK+++ QK GIA L + + L DD+ L+ Y IQ +S + M +L+GG Sbjct: 66 TVNLLHVDNAVDVFVKTLANKTLTIEVKLSNSVLSLKQKVHQKAGIAVNQQILTFGSHTLEDDQKLESYGIQQHSTITMQGRLRGG 151
BLAST of SMED30031952 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: 45.0542 bits (105), Expect = 1.142e-6 Identity = 29/83 (34.94%), Postives = 43/83 (51.81%), Query Frame = -1 Query: 111 LFHKTLKMKVIVK-FGDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGG 356 L H + V VK ++ EV SV LK+++ QK GIA L + + L DD+ L+ Y IQ +S + M +L+GG Sbjct: 145 LLHVDNAVDVFVKTLANKTLTIEVKLSNSVLSLKQKVHQKAGIAVNQQILTFGSHTLEDDQKLESYGIQQHSTITMQGRLRGG 227 HSP 2 Score: 45.0542 bits (105), Expect = 1.142e-6 Identity = 29/83 (34.94%), Postives = 43/83 (51.81%), Query Frame = -1 Query: 111 LFHKTLKMKVIVK-FGDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGG 356 L H + V VK ++ EV SV LK+++ QK GIA L + + L DD+ L+ Y IQ +S + M +L+GG Sbjct: 296 LLHVDNAVDVFVKTLANKTLTIEVKLSNSVLSLKQKVHQKAGIAVNQQILTFGSHTLEDDQKLESYGIQQHSTITMQGRLRGG 378
BLAST of SMED30031952 vs. Planmine SMEST
Match: SMESG000003398.1 (SMESG000003398.1) HSP 1 Score: 154.836 bits (390), Expect = 2.845e-50 Identity = 77/77 (100.00%), Postives = 77/77 (100.00%), Query Frame = -1 Query: 105 MKVIVKFGDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGGCV 335 MKVIVKFGDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGGCV Sbjct: 1 MKVIVKFGDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGGCV 77
BLAST of SMED30031952 vs. Planmine SMEST
Match: SMESG000014648.1 (SMESG000014648.1) HSP 1 Score: 114.005 bits (284), Expect = 3.843e-34 Identity = 54/77 (70.13%), Postives = 63/77 (81.82%), Query Frame = -1 Query: 105 MKVIVKFGDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGGCV 335 MKV VKF +QNF FEVT +T GDLK QI QKTG+AS I L YN +YLLDDKPL+KYDIQSN+N+VMIS+L+GG V Sbjct: 1 MKVFVKFKNQNFTFEVTGETLTGDLKNQIAQKTGMASDQIELMYNVVYLLDDKPLRKYDIQSNANIVMISRLRGGRV 77
BLAST of SMED30031952 vs. Planmine SMEST
Match: SMESG000014651.1 (SMESG000014651.1) HSP 1 Score: 95.5153 bits (236), Expect = 8.435e-27 Identity = 47/77 (61.04%), Postives = 61/77 (79.22%), Query Frame = -1 Query: 105 MKVIVKFGDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGGCV 335 MKV V + Q F FEVTS+T VGDLKKQI QKTG+A ++ L +N +YLL+DK L+KY+IQ+N+NLV+ISK+ GG V Sbjct: 1 MKVFVTYNSQIFTFEVTSETLVGDLKKQIVQKTGMAIENLELLFNQVYLLNDKELKKYNIQNNANLVVISKVIGGRV 77
BLAST of SMED30031952 vs. Planmine SMEST
Match: SMESG000063621.1 (SMESG000063621.1) HSP 1 Score: 46.2098 bits (108), Expect = 1.722e-6 Identity = 24/86 (27.91%), Postives = 47/86 (54.65%), Query Frame = -1 Query: 108 SLYLFHKTLKMKVIVKFGDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGGC 365 ++ +F KT+ D+ AFEV ++ D+KK+I +K G+A + L Y L D++ +++Y I S + ++++L+ G Sbjct: 573 AMQMFAKTV--------NDKTVAFEVQKSDTIRDVKKKIQEKIGLAPDEQKLVYQGEILEDERTVEEYQIAEKSVINIVARLRWGM 650 HSP 2 Score: 45.8246 bits (107), Expect = 2.785e-6 Identity = 24/85 (28.24%), Postives = 46/85 (54.12%), Query Frame = -1 Query: 108 LYLFHKTLKMKVIVKFGDQNFAFEVTSDTSVGDLKKQITQKTGIASGDINLQYNAIYLLDDKPLQKYDIQSNSNLVMISKLQGGC 362 + +F KT+ D+ AFEV ++ D+KK+I +K G+A + L Y L D++ +++Y I S + ++++L+ G Sbjct: 650 MQMFAKTV--------NDKTVAFEVQKSDTIRDVKKKIQEKIGLAPDEQKLVYQGEILEDERTVEEYQIAEKSVINIVARLRWGM 726 The following BLAST results are available for this feature:
BLAST of SMED30031952 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30031952 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30031952 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30031952 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30031952 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30031952 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30031952 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30031952 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30031952 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30031952 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 2
BLAST of SMED30031952 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30031952 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30031952 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30031952 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 >SMED30031952 ID=SMED30031952|Name=SMED30031952|organism=Schmidtea mediterranea sexual|type=transcript|length=401bpback 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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