SMED30017833
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., 2020SMED30017833 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 3
Homology
BLAST of SMED30017833 vs. Planmine SMEST
Match: SMESG000002829.1 (SMESG000002829.1) HSP 1 Score: 60.4622 bits (145), Expect = 1.884e-16 Identity = 32/48 (66.67%), Postives = 35/48 (72.92%), Query Frame = 3 Query: 165 TWDKKINPILSKIGLTKPEIQSLAR-------IACYHIYREHVSCTKS 287 TWDKK N LSKIGLTK EI +LA+ IACYHIYREH+S TKS Sbjct: 2493 TWDKKNNATLSKIGLTKTEIIALAKIACSDAVIACYHIYREHISFTKS 2540 HSP 2 Score: 41.5874 bits (96), Expect = 1.884e-16 Identity = 23/36 (63.89%), Postives = 26/36 (72.22%), Query Frame = 2 Query: 50 SEENFVKARELN*VKYKDLALEIGKGFK*KTTISAL 157 S E F KARE N VKYKDLA++IGK F TISA+ Sbjct: 2451 SIEGFEKAREDNYVKYKDLAMQIGKAFNQTATISAV 2486
BLAST of SMED30017833 vs. Planmine SMEST
Match: SMESG000002829.1 (SMESG000002829.1) HSP 1 Score: 60.4622 bits (145), Expect = 1.884e-16 Identity = 32/48 (66.67%), Postives = 35/48 (72.92%), Query Frame = 3 Query: 165 TWDKKINPILSKIGLTKPEIQSLAR-------IACYHIYREHVSCTKS 287 TWDKK N LSKIGLTK EI +LA+ IACYHIYREH+S TKS Sbjct: 2464 TWDKKNNATLSKIGLTKTEIIALAKIACSDAVIACYHIYREHISFTKS 2511 HSP 2 Score: 41.5874 bits (96), Expect = 1.884e-16 Identity = 23/36 (63.89%), Postives = 26/36 (72.22%), Query Frame = 2 Query: 50 SEENFVKARELN*VKYKDLALEIGKGFK*KTTISAL 157 S E F KARE N VKYKDLA++IGK F TISA+ Sbjct: 2422 SIEGFEKAREDNYVKYKDLAMQIGKAFNQTATISAV 2457
BLAST of SMED30017833 vs. Planmine SMEST
Match: SMESG000002829.1 (SMESG000002829.1) HSP 1 Score: 60.4622 bits (145), Expect = 1.915e-16 Identity = 32/48 (66.67%), Postives = 35/48 (72.92%), Query Frame = 3 Query: 165 TWDKKINPILSKIGLTKPEIQSLAR-------IACYHIYREHVSCTKS 287 TWDKK N LSKIGLTK EI +LA+ IACYHIYREH+S TKS Sbjct: 2472 TWDKKNNATLSKIGLTKTEIIALAKIACSDAVIACYHIYREHISFTKS 2519 HSP 2 Score: 41.5874 bits (96), Expect = 1.915e-16 Identity = 23/36 (63.89%), Postives = 26/36 (72.22%), Query Frame = 2 Query: 50 SEENFVKARELN*VKYKDLALEIGKGFK*KTTISAL 157 S E F KARE N VKYKDLA++IGK F TISA+ Sbjct: 2430 SIEGFEKAREDNYVKYKDLAMQIGKAFNQTATISAV 2465
BLAST of SMED30017833 vs. Planmine SMEST
Match: SMESG000002829.1 (SMESG000002829.1) HSP 1 Score: 60.4622 bits (145), Expect = 1.979e-16 Identity = 32/48 (66.67%), Postives = 35/48 (72.92%), Query Frame = 3 Query: 165 TWDKKINPILSKIGLTKPEIQSLAR-------IACYHIYREHVSCTKS 287 TWDKK N LSKIGLTK EI +LA+ IACYHIYREH+S TKS Sbjct: 2485 TWDKKNNATLSKIGLTKTEIIALAKIACSDAVIACYHIYREHISFTKS 2532 HSP 2 Score: 41.5874 bits (96), Expect = 1.979e-16 Identity = 23/36 (63.89%), Postives = 26/36 (72.22%), Query Frame = 2 Query: 50 SEENFVKARELN*VKYKDLALEIGKGFK*KTTISAL 157 S E F KARE N VKYKDLA++IGK F TISA+ Sbjct: 2443 SIEGFEKAREDNYVKYKDLAMQIGKAFNQTATISAV 2478
BLAST of SMED30017833 vs. Planmine SMEST
Match: SMESG000002079.1 (SMESG000002079.1) HSP 1 Score: 55.8398 bits (133), Expect = 2.324e-16 Identity = 30/44 (68.18%), Postives = 31/44 (70.45%), Query Frame = 3 Query: 165 TWDKKINPILSKIGLTKPEIQSL-------ARIACYHIYREHVS 275 TWDKK N L+KIGL K EIQSL A IACYHIYREHVS Sbjct: 172 TWDKKNNAPLAKIGLNKAEIQSLAWIACPKAVIACYHIYREHVS 215 HSP 2 Score: 46.2098 bits (108), Expect = 2.324e-16 Identity = 24/36 (66.67%), Postives = 27/36 (75.00%), Query Frame = 2 Query: 50 SEENFVKARELN*VKYKDLALEIGKGFK*KTTISAL 157 S E F KARE N VKYKDLALEIG+ F K T+SA+ Sbjct: 130 SGEGFDKAREGNYVKYKDLALEIGQAFNEKATVSAI 165 The following BLAST results are available for this feature:
BLAST of SMED30017833 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30017833 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30017833 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30017833 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30017833 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30017833 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30017833 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30017833 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30017833 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30017833 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30017833 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30017833 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30017833 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30017833 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 >SMED30017833 ID=SMED30017833|Name=SMED30017833|organism=Schmidtea mediterranea sexual|type=transcript|length=452bpback to top Annotated Terms
The following terms have been associated with this transcript:
|