SMED30012026
Overview
Neoblast Clusters
Zeng et. al., 2018
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 AppEmbryonic 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., 2020SMED30012026 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 6
Alignments
SMED30012026 aligns in the following genomic locations:
Homology
BLAST of SMED30012026 vs. Planmine SMEST
Match: SMESG000043866.1 (SMESG000043866.1) HSP 1 Score: 83.1889 bits (204), Expect = 2.328e-22 Identity = 42/47 (89.36%), Postives = 43/47 (91.49%), Query Frame = 1 Query: 1 IGNLEEFNEKSLENMKSTKDENEQEENVGKKKCWMNCSGVKCVTRCT 141 I NLEEFNEKSLENMKS KDENEQEENVGKKKCW +CSG KCVTRCT Sbjct: 32 IENLEEFNEKSLENMKSAKDENEQEENVGKKKCWKHCSGGKCVTRCT 78
BLAST of SMED30012026 vs. Planmine SMEST
Match: SMESG000043866.1 (SMESG000043866.1) HSP 1 Score: 77.411 bits (189), Expect = 3.912e-20 Identity = 38/42 (90.48%), Postives = 39/42 (92.86%), Query Frame = 1 Query: 16 EFNEKSLENMKSTKDENEQEENVGKKKCWMNCSGVKCVTRCT 141 EFNEKSLENMKS KDENEQEENVGKKKCW +CSG KCVTRCT Sbjct: 35 EFNEKSLENMKSAKDENEQEENVGKKKCWKHCSGGKCVTRCT 76
BLAST of SMED30012026 vs. Planmine SMEST
Match: SMESG000043307.1 (SMESG000043307.1) HSP 1 Score: 76.6406 bits (187), Expect = 8.383e-20 Identity = 38/47 (80.85%), Postives = 41/47 (87.23%), Query Frame = 1 Query: 1 IGNLEEFNEKSLENMKSTKDENEQEENVGKKKCWMNCSGVKCVTRCT 141 + NLEEFNEKSLENMKS KDENEQEENV KKKCW +CSG +C TRCT Sbjct: 32 VENLEEFNEKSLENMKSAKDENEQEENVDKKKCWKHCSGRQCSTRCT 78
BLAST of SMED30012026 vs. Planmine SMEST
Match: SMESG000043307.1 (SMESG000043307.1) HSP 1 Score: 71.633 bits (174), Expect = 8.575e-18 Identity = 35/42 (83.33%), Postives = 37/42 (88.10%), Query Frame = 1 Query: 16 EFNEKSLENMKSTKDENEQEENVGKKKCWMNCSGVKCVTRCT 141 EFNEKSLENMKS KDENEQEENV KKKCW +CSG +C TRCT Sbjct: 35 EFNEKSLENMKSAKDENEQEENVDKKKCWKHCSGRQCSTRCT 76
BLAST of SMED30012026 vs. Planmine SMEST
Match: SMESG000043867.1 (SMESG000043867.1) HSP 1 Score: 70.0922 bits (170), Expect = 3.743e-17 Identity = 36/46 (78.26%), Postives = 39/46 (84.78%), Query Frame = 1 Query: 1 IGNLEEFNEKSLENMKSTKDENEQEENVGKKKCWMNCSGVKCVTRC 138 I NLEEFNEKSLENMKS KDE E EENVGKK+C+ +CS KCVTRC Sbjct: 32 IENLEEFNEKSLENMKSAKDEYELEENVGKKRCFKDCSRGKCVTRC 77 The following BLAST results are available for this feature:
BLAST of SMED30012026 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30012026 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30012026 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30012026 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30012026 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30012026 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30012026 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30012026 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30012026 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30012026 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30012026 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30012026 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30012026 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30012026 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 >SMED30012026 ID=SMED30012026|Name=SMED30012026|organism=Schmidtea mediterranea sexual|type=transcript|length=319bpback to top protein sequence of SMED30012026-orf-1 >SMED30012026-orf-1 ID=SMED30012026-orf-1|Name=SMED30012026-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=100bp NFGVTLINGDQNVQSEFYISIKLHFNEFLHLNAEIYFSFKNEQKNTKKKAback 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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