SMED30015362
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., 2020SMED30015362 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 16
Alignments
SMED30015362 aligns in the following genomic locations:
Homology
BLAST of SMED30015362 vs. Planmine SMEST
Match: SMESG000043289.1 (SMESG000043289.1) HSP 1 Score: 180.644 bits (457), Expect = 1.558e-60 Identity = 90/90 (100.00%), Postives = 90/90 (100.00%), Query Frame = -1 Query: 28 MKLAFIIFGLLFLNGVFCEEKLEEVKDVETKDNSELEVDLKVQEEKKWFLWKKCTTLYFRLCYGSCFNCKVHFFSYNKGVCSPEKKIECK 297 MKLAFIIFGLLFLNGVFCEEKLEEVKDVETKDNSELEVDLKVQEEKKWFLWKKCTTLYFRLCYGSCFNCKVHFFSYNKGVCSPEKKIECK Sbjct: 1 MKLAFIIFGLLFLNGVFCEEKLEEVKDVETKDNSELEVDLKVQEEKKWFLWKKCTTLYFRLCYGSCFNCKVHFFSYNKGVCSPEKKIECK 90
BLAST of SMED30015362 vs. Planmine SMEST
Match: SMESG000043280.1 (SMESG000043280.1) HSP 1 Score: 119.013 bits (297), Expect = 4.253e-36 Identity = 55/94 (58.51%), Postives = 73/94 (77.66%), Query Frame = -1 Query: 31 LKMKLAFIIFGLLFLNGVFCEEKLE---EVKDVETKDNSELEVDLKVQEEKKWFLWKKCTTLYFRLCYGSCFNCKVHFFSYNKGVCSPEKKIEC 303 +KMKL FIIFGLL LNG+FCEE L+ EV+D+ETK N E+ + ++Q +KKWFLW++CTT F+LCYG C+ C V ++SY KG CSP+KK+ C Sbjct: 1 MKMKLTFIIFGLLILNGIFCEENLDKKNEVEDLETKGNFEVTEEAEIQGDKKWFLWQRCTTQTFQLCYGRCWKCTVKYYSYKKGACSPDKKMHC 94
BLAST of SMED30015362 vs. Planmine SMEST
Match: SMESG000043280.1 (SMESG000043280.1) HSP 1 Score: 116.316 bits (290), Expect = 3.997e-35 Identity = 54/92 (58.70%), Postives = 71/92 (77.17%), Query Frame = -1 Query: 31 MKLAFIIFGLLFLNGVFCEEKLE---EVKDVETKDNSELEVDLKVQEEKKWFLWKKCTTLYFRLCYGSCFNCKVHFFSYNKGVCSPEKKIEC 297 MKL FIIFGLL LNG+FCEE L+ EV+D+ETK N E+ + ++Q +KKWFLW++CTT F+LCYG C+ C V ++SY KG CSP+KK+ C Sbjct: 1 MKLTFIIFGLLILNGIFCEENLDKKNEVEDLETKGNFEVTEEAEIQGDKKWFLWQRCTTQTFQLCYGRCWKCTVKYYSYKKGACSPDKKMHC 92
BLAST of SMED30015362 vs. Planmine SMEST
Match: SMESG000043277.1 (SMESG000043277.1) HSP 1 Score: 55.4546 bits (132), Expect = 3.423e-11 Identity = 33/92 (35.87%), Postives = 50/92 (54.35%), Query Frame = -1 Query: 28 MKLAFIIFGLLFLNGVFCEEKLEEVKDVETKDNSELEVDLKVQEEKKWFLWKKCTTLYFRLCYG--SCFNCKVHFFSYNKGVCSPEKKIECK 297 MK I ++L VFC L++ D ++K DL V+ KW++W+KC+ +C +CFNC V +SYN+ VC PE I+C+ Sbjct: 1 MKGFLFILISVYLIPVFCGTTLDK-PDTKSKGGLSSAYDLVVETVSKWWMWQKCSLTEVVICNTPKNCFNCTVTSWSYNRKVCKPE-GIKCR 90
BLAST of SMED30015362 vs. Planmine SMEST
Match: SMESG000043278.1 (SMESG000043278.1) HSP 1 Score: 46.595 bits (109), Expect = 7.559e-8 Identity = 25/87 (28.74%), Postives = 40/87 (45.98%), Query Frame = -1 Query: 46 LKMKLAFIIFGLLFLNGVFCEEKLEEVKDVETKDNSELEVDLKVQEEKKWFLWKKCTTLYFRLCYGS-CFNCKVHFFSYNKGVCSPE 303 ++ ++F I +F G + +V D + +E KWF W+KC+ + F +CY CF C+ F+SY K C P Sbjct: 1 MRFLVSFYIIICIFSTGFLSDSSTNLPSNVYGLDQTFME--------SKWFFWRKCSVVKFTICYEYFCFRCQATFWSYRKQSCQPR 79 The following BLAST results are available for this feature:
BLAST of SMED30015362 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30015362 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30015362 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30015362 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30015362 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30015362 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30015362 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30015362 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30015362 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30015362 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30015362 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30015362 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30015362 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30015362 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 >SMED30015362 ID=SMED30015362|Name=SMED30015362|organism=Schmidtea mediterranea sexual|type=transcript|length=348bpback to top protein sequence of SMED30015362-orf-1 >SMED30015362-orf-1 ID=SMED30015362-orf-1|Name=SMED30015362-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=108bp RILHALYNRNHCLVLLKMKLAFIIFGLLFLNGVFCEEKLEEVKDVETKDNback 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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