SMED30017376
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., 2020SMED30017376 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 2
Alignments
SMED30017376 aligns in the following genomic locations:
Homology
BLAST of SMED30017376 vs. Planmine SMEST
Match: SMESG000057359.1 (SMESG000057359.1) HSP 1 Score: 83.9593 bits (206), Expect = 1.630e-21 Identity = 41/60 (68.33%), Postives = 50/60 (83.33%), Query Frame = 1 Query: 193 AAMDAIKDIG*ELKKLRRENDSLQQQCIQLSCELQQVKATCVEPS*VKRLYQKITAAQKG 372 +AM+ IK+IG ELKKLR EN +L QQC+QLSCE Q++ T +EPS VKRLYQKI+AAQKG Sbjct: 11 SAMNTIKNIGRELKKLRTENANLHQQCVQLSCEQQRINDTWIEPSRVKRLYQKISAAQKG 70
BLAST of SMED30017376 vs. Planmine SMEST
Match: SMESG000053804.1 (SMESG000053804.1) HSP 1 Score: 83.1889 bits (204), Expect = 1.985e-21 Identity = 43/59 (72.88%), Postives = 47/59 (79.66%), Query Frame = 1 Query: 199 MDAIKDIG*ELKKLRRENDSLQQQCIQLSCELQQVKATCVEPS*VKRLYQKITAAQKGW 375 MDAI+ IG ELKKLRREND L QQC+QLS ELQ +KAT EPS VK LY+K AAQKGW Sbjct: 1 MDAIQGIGVELKKLRRENDCLHQQCLQLSRELQWIKATWSEPSRVKLLYEKNDAAQKGW 59
BLAST of SMED30017376 vs. Planmine SMEST
Match: SMESG000022029.1 (SMESG000022029.1) HSP 1 Score: 81.6481 bits (200), Expect = 1.375e-20 Identity = 39/59 (66.10%), Postives = 49/59 (83.05%), Query Frame = 1 Query: 199 MDAIKDIG*ELKKLRRENDSLQQQCIQLSCELQQVKATCVEPS*VKRLYQKITAAQKGW 375 MD+IK+IG E KKLRR+N L QQC+QLS ELQ+ KAT +E S VKR+YQ++TAAQ+GW Sbjct: 1 MDSIKEIGLERKKLRRKNIDLHQQCVQLSHELQRTKATWIETSGVKRIYQRLTAAQRGW 59
BLAST of SMED30017376 vs. Planmine SMEST
Match: SMESG000077887.1 (SMESG000077887.1) HSP 1 Score: 75.485 bits (184), Expect = 1.823e-18 Identity = 38/58 (65.52%), Postives = 47/58 (81.03%), Query Frame = 1 Query: 199 MDAIKDIG*ELKKLRRENDSLQQQCIQLSCELQQVKATCVEPS*VKRLYQKITAAQKG 372 MDA++ IG ELK LR+EN +L QQC+QLS ELQ++KAT +P+ VKRLYQKI AQKG Sbjct: 1 MDAMQKIGKELKDLRKENANLHQQCLQLSRELQRIKATWSDPTRVKRLYQKIDTAQKG 58
BLAST of SMED30017376 vs. Planmine SMEST
Match: SMESG000006907.1 (SMESG000006907.1) HSP 1 Score: 78.9518 bits (193), Expect = 4.696e-18 Identity = 37/50 (74.00%), Postives = 44/50 (88.00%), Query Frame = 1 Query: 226 ELKKLRRENDSLQQQCIQLSCELQQVKATCVEPS*VKRLYQKITAAQKGW 375 ELKKL +ENDS+ QQC+QLSCELQ+VKAT EPS VKRLYQ+I AA++GW Sbjct: 574 ELKKLHQENDSIHQQCLQLSCELQRVKATWSEPSKVKRLYQRIDAAKRGW 623 The following BLAST results are available for this feature:
BLAST of SMED30017376 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30017376 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30017376 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30017376 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30017376 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30017376 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30017376 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30017376 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30017376 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30017376 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30017376 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30017376 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30017376 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30017376 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 >SMED30017376 ID=SMED30017376|Name=SMED30017376|organism=Schmidtea mediterranea sexual|type=transcript|length=376bpback to top Annotated Terms
The following terms have been associated with this transcript:
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