SMED30020042
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., 2020SMED30020042 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 3
Alignments
SMED30020042 aligns in the following genomic locations:
Homology
BLAST of SMED30020042 vs. Planmine SMEST
Match: SMESG000014768.1 (SMESG000014768.1) HSP 1 Score: 186.808 bits (473), Expect = 2.106e-61 Identity = 91/93 (97.85%), Postives = 91/93 (97.85%), Query Frame = 3 Query: 165 MKCFYIFYIFPLLAFTGATEQSEFDEIFYDELKQDACGRINDFGPRKVRRSFFDLCLASKKNEKSCTELTKNVKLELQIQQLRDQCKIGKYSP 443 MK FYIFYIFPLLAFTGATEQSEFDEI YDELKQDACGRINDFGPRKVRRSFFDLCLASKKNEKSCTELTKNVKLELQIQQLRDQCKIGKYSP Sbjct: 1 MKWFYIFYIFPLLAFTGATEQSEFDEILYDELKQDACGRINDFGPRKVRRSFFDLCLASKKNEKSCTELTKNVKLELQIQQLRDQCKIGKYSP 93
BLAST of SMED30020042 vs. Planmine SMEST
Match: SMESG000014769.1 (SMESG000014769.1) HSP 1 Score: 78.9518 bits (193), Expect = 4.215e-19 Identity = 38/92 (41.30%), Postives = 56/92 (60.87%), Query Frame = 3 Query: 165 MKCFYIFYIFPLLAFTGATEQSEFDEIFYDELKQDACGRINDFGPRKVRRSFFDLCLASKKNEKSCTELTKNVKLELQIQQLRDQCKIGKYS 440 MK IF + L+ ++ F+E +E K CG++N+FGPRKVR++F D CL ++KN K+CTE K VKL+ Q + L C+ G+ S Sbjct: 1 MKLIVIFIVLSLVTLMKCQDEQYFEEFTDEEFKNAKCGKVNEFGPRKVRKAFRDACLKNEKNSKTCTEKVKTVKLDEQRRHLYYLCQTGRLS 92 The following BLAST results are available for this feature:
BLAST of SMED30020042 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30020042 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30020042 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30020042 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30020042 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30020042 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30020042 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30020042 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30020042 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30020042 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30020042 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30020042 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30020042 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30020042 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 2
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30020042 ID=SMED30020042|Name=SMED30020042|organism=Schmidtea mediterranea sexual|type=transcript|length=646bpback 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
|