SMED30031405
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., 2020SMED30031405 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 27Note: Hover over icons to view figure legend
Alignments
SMED30031405 aligns in the following genomic locations:
Homology
BLAST of SMED30031405 vs. Planmine SMEST
Match: SMESG000051904.1 (SMESG000051904.1) HSP 1 Score: 78.9518 bits (193), Expect = 9.532e-18 Identity = 38/42 (90.48%), Postives = 39/42 (92.86%), Query Frame = 2 Query: 98 MLLRFTTVFFVLAGCFNQMDCGVVGLAVGYSACQTVCNAGYV 223 MLLRFTTV FVLA CFNQMDCGVVGLAVGYSACQ+ CNAGYV Sbjct: 1 MLLRFTTVVFVLADCFNQMDCGVVGLAVGYSACQSACNAGYV 42
BLAST of SMED30031405 vs. Planmine SMEST
Match: SMESG000051918.1 (SMESG000051918.1) HSP 1 Score: 53.5286 bits (127), Expect = 8.545e-9 Identity = 23/41 (56.10%), Postives = 33/41 (80.49%), Query Frame = 2 Query: 101 LLRFTTVFFVLAGCFNQMDCGVVGLAVGYSACQTVCNAGYV 223 ++R VF +LA FNQ++CG++G+ +GY ACQ+VCNAGYV Sbjct: 1 MIRIAIVFIILASSFNQINCGILGI-LGYGACQSVCNAGYV 40
BLAST of SMED30031405 vs. Planmine SMEST
Match: SMESG000051914.1 (SMESG000051914.1) HSP 1 Score: 51.9878 bits (123), Expect = 2.291e-8 Identity = 22/41 (53.66%), Postives = 33/41 (80.49%), Query Frame = 2 Query: 101 LLRFTTVFFVLAGCFNQMDCGVVGLAVGYSACQTVCNAGYV 223 ++R VF ++A FNQ++CG++G+ +GY ACQ+VCNAGYV Sbjct: 1 MIRIAIVFIIVASSFNQINCGILGI-LGYGACQSVCNAGYV 40
BLAST of SMED30031405 vs. Planmine SMEST
Match: SMESG000051910.1 (SMESG000051910.1) HSP 1 Score: 49.6766 bits (117), Expect = 9.706e-8 Identity = 24/24 (100.00%), Postives = 24/24 (100.00%), Query Frame = 2 Query: 152 MDCGVVGLAVGYSACQTVCNAGYV 223 MDCGVVGLAVGYSACQTVCNAGYV Sbjct: 1 MDCGVVGLAVGYSACQTVCNAGYV 24
BLAST of SMED30031405 vs. Planmine SMEST
Match: SMESG000051904.1 (SMESG000051904.1) HSP 1 Score: 47.3654 bits (111), Expect = 8.212e-7 Identity = 22/24 (91.67%), Postives = 23/24 (95.83%), Query Frame = 2 Query: 152 MDCGVVGLAVGYSACQTVCNAGYV 223 MDCGVVGLAVGYSACQ+ CNAGYV Sbjct: 1 MDCGVVGLAVGYSACQSACNAGYV 24 The following BLAST results are available for this feature:
BLAST of SMED30031405 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30031405 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30031405 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30031405 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30031405 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30031405 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30031405 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30031405 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30031405 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30031405 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30031405 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30031405 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30031405 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30031405 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 >SMED30031405 ID=SMED30031405|Name=SMED30031405|organism=Schmidtea mediterranea sexual|type=transcript|length=1987bpback 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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