SMED30004349
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., 2020SMED30004349 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 8
Homology
BLAST of SMED30004349 vs. Planmine SMEST
Match: SMESG000075378.1 (SMESG000075378.1) HSP 1 Score: 92.8189 bits (229), Expect = 1.187e-24 Identity = 42/84 (50.00%), Postives = 61/84 (72.62%), Query Frame = 1 Query: 169 KLILEENSINAISLSRNLPVMYLQYSMEYLKFPIIYSFREPTTLKQSLYNMKVGEIGEIDRKNITELLRAINKDISFNEQFTFM 420 +++LEENS I ++ N PV YLQYSM YLKFPI Y+F+E LK YN+++G I + DRKNI ++L +NKD+ FN++F+ + Sbjct: 6 EVLLEENSTAVIGMTCNSPVQYLQYSMNYLKFPITYTFKEAVDLKAYEYNIQIGNIEDEDRKNIADILHLMNKDMVFNDRFSLI 89
BLAST of SMED30004349 vs. Planmine SMEST
Match: SMESG000012310.1 (SMESG000012310.1) HSP 1 Score: 89.7373 bits (221), Expect = 4.954e-23 Identity = 43/95 (45.26%), Postives = 63/95 (66.32%), Query Frame = 1 Query: 136 FIETSVRKEAIKLILEENSINAISLSRNLPVMYLQYSMEYLKFPIIYSFREPTTLKQSLYNMKVGEIGEIDRKNITELLRAINKDISFNEQFTFM 420 F E + + +++LEENS I ++ PV YLQYSM YL FPI Y+F+E LK YN+ +G I E DRKNI+++L +N ++ FNE+F+F+ Sbjct: 17 FDEKATMSKVYEILLEENSTAVIGMTFKPPVQYLQYSMNYLNFPITYTFKESVDLKAYDYNIMIGNIEEEDRKNISDILHLLNNEMVFNEKFSFI 111
BLAST of SMED30004349 vs. Planmine SMEST
Match: SMESG000038231.1 (SMESG000038231.1) HSP 1 Score: 87.0409 bits (214), Expect = 2.040e-22 Identity = 41/84 (48.81%), Postives = 59/84 (70.24%), Query Frame = 1 Query: 169 KLILEENSINAISLSRNLPVMYLQYSMEYLKFPIIYSFREPTTLKQSLYNMKVGEIGEIDRKNITELLRAINKDISFNEQFTFM 420 +++LEENS I ++ PV YLQYSM YL FPI Y+F+E LK YN+ +G I E DRKNI+++L +N ++ FNE+F+F+ Sbjct: 6 EILLEENSTAVIGMTFKPPVQYLQYSMNYLNFPITYTFKESVDLKAYDYNIMIGNIEEEDRKNISDILHLLNNEMVFNEKFSFI 89
BLAST of SMED30004349 vs. Planmine SMEST
Match: SMESG000024996.1 (SMESG000024996.1) HSP 1 Score: 83.5741 bits (205), Expect = 3.014e-21 Identity = 38/71 (53.52%), Postives = 53/71 (74.65%), Query Frame = 1 Query: 208 LSRNLPVMYLQYSMEYLKFPIIYSFREPTTLKQSLYNMKVGEIGEIDRKNITELLRAINKDISFNEQFTFM 420 +S PV YLQYSM YLKFPI Y+F+E LK YN+++G I + DRKNIT++L +NKD+ FN++F+F+ Sbjct: 1 MSCKPPVQYLQYSMNYLKFPITYTFKEAVDLKAYEYNIQIGNIEDEDRKNITDILHLMNKDMVFNDRFSFI 71
BLAST of SMED30004349 vs. Planmine SMEST
Match: SMESG000050479.1 (SMESG000050479.1) HSP 1 Score: 68.5514 bits (166), Expect = 1.924e-13 Identity = 33/76 (43.42%), Postives = 50/76 (65.79%), Query Frame = 1 Query: 169 KLILEENSINAISLSRNLPVMYLQYSMEYLKFPIIYSFREPTTLKQSLYNMKVGEIGEIDRKNITELLRAINKDIS 396 +++ +ENS I ++ PV YLQYSM+YLKFPI Y+F++ LK YN+++ I + D KNI ++L +NK S Sbjct: 1413 EVLFKENSTAVIEMTCKPPVQYLQYSMKYLKFPITYTFKDAVDLKAYEYNIQIKNIEDDDGKNIADILHLMNKSRS 1488 The following BLAST results are available for this feature:
BLAST of SMED30004349 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30004349 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30004349 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30004349 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30004349 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30004349 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30004349 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30004349 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30004349 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30004349 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30004349 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30004349 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30004349 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30004349 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 >SMED30004349 ID=SMED30004349|Name=SMED30004349|organism=Schmidtea mediterranea sexual|type=transcript|length=584bpback to top protein sequence of SMED30004349-orf-1 >SMED30004349-orf-1 ID=SMED30004349-orf-1|Name=SMED30004349-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=110bp MYLQYSMEYLKFPIIYSFREPTTLKQSLYNMKVGEIGEIDRKNITELLRAback to top Annotated Terms
The following terms have been associated with this transcript:
|