SMED30018334
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., 2020SMED30018334 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 4
Alignments
SMED30018334 aligns in the following genomic locations:
Homology
BLAST of SMED30018334 vs. Planmine SMEST
Match: SMESG000029410.1 (SMESG000029410.1) HSP 1 Score: 375.17 bits (962), Expect = 8.541e-130 Identity = 223/229 (97.38%), Postives = 225/229 (98.25%), Query Frame = 2 Query: 62 MYKLFSLLLFISGYIPEYMLLEVNSGNCLSNTVLTSLCKFSIKIYAPLETDLMCQLRFXXXXXXXXXXXXXGSILSSQIGNSCPSIQFIINNGANNEFSENCNKKIVFYNHSFTDFAFAKFIYSNYGVKDLTTNINMEIYLLGLRDCIKVPPAQSSSSKXXXXXXXXXXXXXXXXXXXXXXXDCMKKHPQKNANPQQLASTPTGDSKDEIKQEDKGQIPESRPMINETS 748 MYKLFSLLLFISGYIPEYMLLEVNSGNCLSNTVLTSLCKFSIKIYAPLETDLMCQLRFT TNVTTAVLVNNGSILSSQIGNSCPSIQFIINNGANNEFSENCNK+IVFYNHSFTDF FAKFIYSNYGVKDLTTNINMEIYLLGLRDCI+VPPAQSSSSKIIWIIIIICALILIVIIAIIIAIDCMKKHPQKNANPQQLASTPT DSKDEIKQEDK QIPESRPMINETS Sbjct: 1 MYKLFSLLLFISGYIPEYMLLEVNSGNCLSNTVLTSLCKFSIKIYAPLETDLMCQLRFTYTNVTTAVLVNNGSILSSQIGNSCPSIQFIINNGANNEFSENCNKRIVFYNHSFTDFTFAKFIYSNYGVKDLTTNINMEIYLLGLRDCIEVPPAQSSSSKIIWIIIIICALILIVIIAIIIAIDCMKKHPQKNANPQQLASTPTRDSKDEIKQEDKDQIPESRPMINETS 229
BLAST of SMED30018334 vs. Planmine SMEST
Match: SMESG000029410.1 (SMESG000029410.1) HSP 1 Score: 338.576 bits (867), Expect = 9.921e-116 Identity = 205/211 (97.16%), Postives = 207/211 (98.10%), Query Frame = 2 Query: 116 MLLEVNSGNCLSNTVLTSLCKFSIKIYAPLETDLMCQLRFXXXXXXXXXXXXXGSILSSQIGNSCPSIQFIINNGANNEFSENCNKKIVFYNHSFTDFAFAKFIYSNYGVKDLTTNINMEIYLLGLRDCIKVPPAQSSSSKXXXXXXXXXXXXXXXXXXXXXXXDCMKKHPQKNANPQQLASTPTGDSKDEIKQEDKGQIPESRPMINETS 748 MLLEVNSGNCLSNTVLTSLCKFSIKIYAPLETDLMCQLRFT TNVTTAVLVNNGSILSSQIGNSCPSIQFIINNGANNEFSENCNK+IVFYNHSFTDF FAKFIYSNYGVKDLTTNINMEIYLLGLRDCI+VPPAQSSSSKIIWIIIIICALILIVIIAIIIAIDCMKKHPQKNANPQQLASTPT DSKDEIKQEDK QIPESRPMINETS Sbjct: 1 MLLEVNSGNCLSNTVLTSLCKFSIKIYAPLETDLMCQLRFTYTNVTTAVLVNNGSILSSQIGNSCPSIQFIINNGANNEFSENCNKRIVFYNHSFTDFTFAKFIYSNYGVKDLTTNINMEIYLLGLRDCIEVPPAQSSSSKIIWIIIIICALILIVIIAIIIAIDCMKKHPQKNANPQQLASTPTRDSKDEIKQEDKDQIPESRPMINETS 211
BLAST of SMED30018334 vs. Planmine SMEST
Match: SMESG000029410.1 (SMESG000029410.1) HSP 1 Score: 271.552 bits (693), Expect = 5.445e-90 Identity = 171/177 (96.61%), Postives = 173/177 (97.74%), Query Frame = 2 Query: 218 MCQLRFXXXXXXXXXXXXXGSILSSQIGNSCPSIQFIINNGANNEFSENCNKKIVFYNHSFTDFAFAKFIYSNYGVKDLTTNINMEIYLLGLRDCIKVPPAQSSSSKXXXXXXXXXXXXXXXXXXXXXXXDCMKKHPQKNANPQQLASTPTGDSKDEIKQEDKGQIPESRPMINETS 748 MCQLRFT TNVTTAVLVNNGSILSSQIGNSCPSIQFIINNGANNEFSENCNK+IVFYNHSFTDF FAKFIYSNYGVKDLTTNINMEIYLLGLRDCI+VPPAQSSSSKIIWIIIIICALILIVIIAIIIAIDCMKKHPQKNANPQQLASTPT DSKDEIKQEDK QIPESRPMINETS Sbjct: 1 MCQLRFTYTNVTTAVLVNNGSILSSQIGNSCPSIQFIINNGANNEFSENCNKRIVFYNHSFTDFTFAKFIYSNYGVKDLTTNINMEIYLLGLRDCIEVPPAQSSSSKIIWIIIIICALILIVIIAIIIAIDCMKKHPQKNANPQQLASTPTRDSKDEIKQEDKDQIPESRPMINETS 177
BLAST of SMED30018334 vs. Planmine SMEST
Match: SMESG000029374.1 (SMESG000029374.1) HSP 1 Score: 51.6026 bits (122), Expect = 2.556e-7 Identity = 38/119 (31.93%), Postives = 59/119 (49.58%), Query Frame = 2 Query: 125 EVNSGNCLSNTVLTSLCKFSIKIYAPLETDLMCQLRFXXXXXXXXXXXXXGSILSSQIGNSCPSIQFIINNGANNE-FSENCNKKIVFYNHSFTDFAFAKFIYSNYGVKDLTTNINMEI 478 ++ + NCL+ +T+ C F+I+I + L+C L F + N + V N +I + Q+GN CP I F + N E S C K N +F F+ A Y N G+ D T + + I Sbjct: 27 KITTLNCLNGAKITTSCIFAIEIKPVITAPLICNLLFDSNNAKVLLTVTNITI-TGQVGNKCPKINFAVFFSGNPEQISTTCGKSTPLINKTFDGFSRAIIYYDNKGLNDTNTVVFITI 144
BLAST of SMED30018334 vs. Planmine SMEST
Match: SMESG000079509.1 (SMESG000079509.1) HSP 1 Score: 47.7506 bits (112), Expect = 5.344e-6 Identity = 41/141 (29.08%), Postives = 63/141 (44.68%), Query Frame = 2 Query: 128 VNSGNCLSNTVLTSLCKFSIKIYAPLETDLMCQLRFXXXXXXXXXXXXXGSILSSQIGNSCPSIQFIINNGAN--NEFSENCNKKIVFYNHSFTDFAFAKFIYSNYGVKDLTTNINMEIYLLGLRD-----CIKVPPAQSS 529 VN C +N +L ++C+F I I ++ C L+F T I++ G +CP +II G N S +C I YN ++ DF A+F+Y + T++I M LL + D C V P +S Sbjct: 25 VNQYTCKNNEILKAVCEFRIAITGTVDHSFQCVLKFNTTKYLIVEYYLKRLIIAQAKGPNCPD-AYIILFGHNLSQPVSGSCGCNIEQYNRTWPDFKKAEFVYRHENFVQNTSDILM---LLKVNDTKEKRCPSVTPQSTS 161 The following BLAST results are available for this feature:
BLAST of SMED30018334 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30018334 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30018334 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30018334 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30018334 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30018334 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30018334 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30018334 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30018334 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30018334 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30018334 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30018334 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30018334 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30018334 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 >SMED30018334 ID=SMED30018334|Name=SMED30018334|organism=Schmidtea mediterranea sexual|type=transcript|length=1365bpback to top protein sequence of SMED30018334-orf-1 >SMED30018334-orf-1 ID=SMED30018334-orf-1|Name=SMED30018334-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=231bp MYKLFSLLLFISGYIPEYMLLEVNSGNCLSNTVLTSLCKFSIKIYAPLETback 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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