SMED30008491
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., 2020SMED30008491 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 2
Alignments
SMED30008491 aligns in the following genomic locations:
Homology
BLAST of SMED30008491 vs. Planmine SMEST
Match: SMESG000014051.1 (SMESG000014051.1) HSP 1 Score: 73.1738 bits (178), Expect = 2.028e-14 Identity = 41/85 (48.24%), Postives = 54/85 (63.53%), Query Frame = -1 Query: 292 DVVRYHEDALEQSKRAESLVPNFRHQEPTWISPEVARKLQQQIKMSKNQYNEELDTPMALKVKIREQFRQVARMKA*SHTKSDLN 546 DV +YHE+A+ QS+RAESLV R E TWI + A+KL QQI K Y EEL +LKVKIR+Q R +A ++ ++DL Sbjct: 236 DVAKYHEEAMSQSQRAESLVWRCRRMEETWIRLDEAKKLHQQIAQIKKLYEEELTRSRSLKVKIRQQARTIAALETKLQIRTDLT 320
BLAST of SMED30008491 vs. Planmine SMEST
Match: SMESG000000582.1 (SMESG000000582.1) HSP 1 Score: 67.781 bits (164), Expect = 2.196e-14 Identity = 35/76 (46.05%), Postives = 45/76 (59.21%), Query Frame = -1 Query: 319 DVVRYHEDALEQSKRAESLVPNFRHQEPTWISPEVARKLQQQIKMSKNQYNEELDTPMALKVKIREQFRQVARMKA 546 DV +YHE+A+ QS+R ESLV R + TWI A+KL QQI Y EEL LK+KIR+Q +A +A Sbjct: 26 DVAKYHEEAMNQSQRTESLVQRCRRMKETWICSNEAKKLHQQIAQMTCLYEEELTLSRGLKIKIRQQACAIATFEA 101
BLAST of SMED30008491 vs. Planmine SMEST
Match: SMESG000034649.1 (SMESG000034649.1) HSP 1 Score: 62.3882 bits (150), Expect = 1.111e-12 Identity = 30/54 (55.56%), Postives = 39/54 (72.22%), Query Frame = -1 Query: 385 DVVRYHEDALEQSKRAESLVPNFRHQEPTWISPEVARKLQQQIKMSKNQYNEEL 546 D+V+YHE+A+ QS+RAESLV R E TWI P+ A+KL +QI K +Y EEL Sbjct: 14 DLVKYHEEAMNQSQRAESLVRRCRRMEETWIRPDEAKKLHEQITQLKRRYEEEL 67
BLAST of SMED30008491 vs. Planmine SMEST
Match: SMESG000012193.1 (SMESG000012193.1) HSP 1 Score: 63.1586 bits (152), Expect = 6.945e-12 Identity = 40/85 (47.06%), Postives = 50/85 (58.82%), Query Frame = -1 Query: 292 DVVRYHEDALEQSKRAESLVPNFRHQEPTWISPEVARKLQQQIKMSKNQYNEELDTPMALKVKIREQFRQVARMKA*SHTKSDLN 546 DV +YHE+A+ QSK AESLV + R E TWI P+ A+KL QQI K Y EEL ALKV I +Q +A ++ DL Sbjct: 55 DVSKYHEEAINQSKSAESLVWHCRRMEETWIHPDEAKKLHQQIAQMKRLY-EELTLSRALKVNIWQQACTIATLETKLQIHHDLT 138
BLAST of SMED30008491 vs. Planmine SMEST
Match: SMESG000022058.1 (SMESG000022058.1) HSP 1 Score: 59.3066 bits (142), Expect = 5.302e-11 Identity = 34/85 (40.00%), Postives = 49/85 (57.65%), Query Frame = -1 Query: 292 DVVRYHEDALEQSKRAESLVPNFRHQEPTWISPEVARKLQQQIKMSKNQYNEELDTPMALKVKIREQFRQVARMKA*SHTKSDLN 546 D+ + E+++ Q + AESLV R E TWI P+ A+KL QQI K Y +EL +LKVKIR+Q +A ++ + DL Sbjct: 14 DIAKSLEESMSQPQLAESLVRRCRRMEETWIRPDEAKKLHQQIAQIKKLYEKELSLSRSLKVKIRQQACTIAALETKLQIRIDLT 98 The following BLAST results are available for this feature:
BLAST of SMED30008491 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30008491 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30008491 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30008491 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30008491 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30008491 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30008491 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30008491 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30008491 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30008491 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30008491 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30008491 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30008491 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30008491 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 >SMED30008491 ID=SMED30008491|Name=SMED30008491|organism=Schmidtea mediterranea sexual|type=transcript|length=813bpback to top Annotated Terms
The following terms have been associated with this transcript:
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