SMED30031307
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., 2020SMED30031307 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 6
Homology
BLAST of SMED30031307 vs. Planmine SMEST
Match: SMESG000057533.1 (SMESG000057533.1) HSP 1 Score: 86.6557 bits (213), Expect = 3.560e-24 Identity = 42/99 (42.42%), Postives = 61/99 (61.62%), Query Frame = 3 Query: 1149 ARNRQALLDHGYVILAMGDLDWPMRQAYRNGDV*MLSIAIKKEPVRNPE*KARHRIEFELFQLEAAGKRMKWKVSAAR*RLARVNVDVTLGLIPSTDEY 1445 AR RQ L D+GY++ GD WP R Y+ ++ + SIAIK+EP NP +AR R ++ ++E ++ K +AR RLA+VN D+ G IPSTD + Sbjct: 1662 ARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREPGHNPAREARQRAKYAAMKMEELERKYHRKAVSARQRLAQVNRDIASGSIPSTDGF 1760 HSP 2 Score: 45.0542 bits (105), Expect = 3.560e-24 Identity = 22/61 (36.07%), Postives = 38/61 (62.30%), Query Frame = 2 Query: 1448 YGVS*RMGDPVLRKMTAPTSIVVPQRILPLSVKKHFGERSYRVDHSYSNGN--WNRQSLNR 1624 YGVS + DP L +MTAPT +V+P++++ +++ G DH+Y++ + WN + NR Sbjct: 1764 YGVSFELDDPRLTQMTAPTKMVIPEKLVQSTLRNQLGSHQTG-DHTYASRHPQWNSKLNNR 1823
BLAST of SMED30031307 vs. Planmine SMEST
Match: SMESG000035366.1 (SMESG000035366.1) HSP 1 Score: 83.5741 bits (205), Expect = 1.835e-23 Identity = 45/99 (45.45%), Postives = 60/99 (60.61%), Query Frame = 3 Query: 1149 ARNRQALLDHGYVILAMGDLDWPMRQAYRNGDV*MLSIAIKKEPVRNPE*KARHRIEFELFQLEAAGKRMKWKVSAAR*RLARVNVDVTLGLIPSTDEY 1445 AR RQ L D+GY++ GD WP R Y+ +V + SIAIK EP +NP +AR R EF ++E ++ K AR RLA+VN D+ G IPSTD + Sbjct: 683 ARYRQVLWDNGYLLSIYGDSSWPRRSEYQAEEVELPSIAIKCEPGKNPAREARQRAEFSAMKMEQMEQKYHRKAVLARQRLAQVNWDIASGAIPSTDGF 781 HSP 2 Score: 45.8246 bits (107), Expect = 1.835e-23 Identity = 25/61 (40.98%), Postives = 38/61 (62.30%), Query Frame = 2 Query: 1448 YGVS*RMGDPVLRKMTAPTSIVVPQRILPLSVKKHFGERSYRVDHSYSNGN--WNRQSLNR 1624 YGVS + DP L +M+APT +V+P+RI+ +++ G R DH Y++ + WN S NR Sbjct: 785 YGVSFELDDPRLLQMSAPTKLVLPERIIQSTLRNRLGSRQ-TGDHMYTSRHPRWNFNSNNR 844
BLAST of SMED30031307 vs. Planmine SMEST
Match: SMESG000035366.1 (SMESG000035366.1) HSP 1 Score: 83.5741 bits (205), Expect = 1.881e-23 Identity = 45/99 (45.45%), Postives = 60/99 (60.61%), Query Frame = 3 Query: 1149 ARNRQALLDHGYVILAMGDLDWPMRQAYRNGDV*MLSIAIKKEPVRNPE*KARHRIEFELFQLEAAGKRMKWKVSAAR*RLARVNVDVTLGLIPSTDEY 1445 AR RQ L D+GY++ GD WP R Y+ +V + SIAIK EP +NP +AR R EF ++E ++ K AR RLA+VN D+ G IPSTD + Sbjct: 684 ARYRQVLWDNGYLLSIYGDSSWPRRSEYQAEEVELPSIAIKCEPGKNPAREARQRAEFSAMKMEQMEQKYHRKAVLARQRLAQVNWDIASGAIPSTDGF 782 HSP 2 Score: 45.8246 bits (107), Expect = 1.881e-23 Identity = 25/61 (40.98%), Postives = 38/61 (62.30%), Query Frame = 2 Query: 1448 YGVS*RMGDPVLRKMTAPTSIVVPQRILPLSVKKHFGERSYRVDHSYSNGN--WNRQSLNR 1624 YGVS + DP L +M+APT +V+P+RI+ +++ G R DH Y++ + WN S NR Sbjct: 786 YGVSFELDDPRLLQMSAPTKLVLPERIIQSTLRNRLGSRQ-TGDHMYTSRHPRWNFNSNNR 845
BLAST of SMED30031307 vs. Planmine SMEST
Match: SMESG000044971.1 (SMESG000044971.1) HSP 1 Score: 81.6481 bits (200), Expect = 1.883e-23 Identity = 43/99 (43.43%), Postives = 60/99 (60.61%), Query Frame = 3 Query: 1149 ARNRQALLDHGYVILAMGDLDWPMRQAYRNGDV*MLSIAIKKEPVRNPE*KARHRIEFELFQLEAAGKRMKWKVSAAR*RLARVNVDVTLGLIPSTDEY 1445 AR RQ L D+GY++ GD WP R Y+ ++ + SIAIK+EP NP +AR R E+ ++E ++ K AR RLA+VN D+ G IPSTD + Sbjct: 1152 ARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREPGHNPAREARQRAEYVAMKMEELERKYHRKAVLARQRLAQVNRDIASGAIPSTDGF 1250 HSP 2 Score: 47.7506 bits (112), Expect = 1.883e-23 Identity = 23/61 (37.70%), Postives = 39/61 (63.93%), Query Frame = 2 Query: 1448 YGVS*RMGDPVLRKMTAPTSIVVPQRILPLSVKKHFGERSYRVDHSYSNGN--WNRQSLNR 1624 YGVS + DP L +MTAPT +V+P++++ +++ G R DH+Y++ + WN + NR Sbjct: 1254 YGVSFELDDPRLMQMTAPTKMVIPEKLVQSTLRNRLGSRQTG-DHTYASRHPQWNPKRNNR 1313
BLAST of SMED30031307 vs. Planmine SMEST
Match: SMESG000077847.1 (SMESG000077847.1) HSP 1 Score: 82.4185 bits (202), Expect = 6.245e-23 Identity = 43/99 (43.43%), Postives = 60/99 (60.61%), Query Frame = 3 Query: 1149 ARNRQALLDHGYVILAMGDLDWPMRQAYRNGDV*MLSIAIKKEPVRNPE*KARHRIEFELFQLEAAGKRMKWKVSAAR*RLARVNVDVTLGLIPSTDEY 1445 AR RQ L D+GY++ GD WP R Y+ ++ + SIAIK+EP NP +AR R E+ ++E ++ K AR RLA+VN D+ G IPSTD + Sbjct: 695 ARYRQVLWDNGYLLSTYGDSSWPRRSEYQAEEIELPSIAIKREPGHNPAREARQRAEYAAMKMEELERKYHRKAVLARQRLAQVNRDIASGAIPSTDGF 793 HSP 2 Score: 45.0542 bits (105), Expect = 6.245e-23 Identity = 23/61 (37.70%), Postives = 38/61 (62.30%), Query Frame = 2 Query: 1448 YGVS*RMGDPVLRKMTAPTSIVVPQRILPLSVKKHFGERSYRVDHSYSNGN--WNRQSLNR 1624 YGVS + DP L +MTAPT +V+P+ ++ +++ G R DH+Y++ + WN + NR Sbjct: 797 YGVSFELDDPRLTQMTAPTKMVIPENLVQSTLRNRLGSRQTG-DHTYASRHPQWNSKHNNR 856 The following BLAST results are available for this feature:
BLAST of SMED30031307 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30031307 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30031307 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30031307 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30031307 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30031307 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30031307 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30031307 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30031307 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30031307 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30031307 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30031307 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30031307 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30031307 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 >SMED30031307 ID=SMED30031307|Name=SMED30031307|organism=Schmidtea mediterranea sexual|type=transcript|length=2169bpback to top Annotated Terms
The following terms have been associated with this transcript:
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