SMED30009437
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., 2020SMED30009437 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 3
Alignments
SMED30009437 aligns in the following genomic locations:
Homology
BLAST of SMED30009437 vs. Planmine SMEST
Match: SMESG000022786.1 (SMESG000022786.1) HSP 1 Score: 209.92 bits (533), Expect = 9.643e-72 Identity = 106/106 (100.00%), Postives = 106/106 (100.00%), Query Frame = 3 Query: 75 MSVFLYSVFSDKCSSRQFVYNPTHSNEICLNCNDFPRFSCIIGGTKQCNSCFGSNFICISRKSSNVCIQCIPQGSRCTVKDICCPNLSCKPGSFVSKNATNNLSIC 392 MSVFLYSVFSDKCSSRQFVYNPTHSNEICLNCNDFPRFSCIIGGTKQCNSCFGSNFICISRKSSNVCIQCIPQGSRCTVKDICCPNLSCKPGSFVSKNATNNLSIC Sbjct: 1 MSVFLYSVFSDKCSSRQFVYNPTHSNEICLNCNDFPRFSCIIGGTKQCNSCFGSNFICISRKSSNVCIQCIPQGSRCTVKDICCPNLSCKPGSFVSKNATNNLSIC 106
BLAST of SMED30009437 vs. Planmine SMEST
Match: SMESG000022784.1 (SMESG000022784.1) HSP 1 Score: 93.9745 bits (232), Expect = 8.144e-26 Identity = 42/83 (50.60%), Postives = 57/83 (68.67%), Query Frame = 3 Query: 144 HSNEICLNCNDFPRFSCIIGGTKQCNSCFGSNFICISRKSSNVCIQCIPQGSRCTVKDICCPNLSCKPGSFVSKNATNNLSIC 392 HS EICLNCNDFP++SC IGGT QC +C+G NFIC++ +S N C +C+ +G+RC D+CC L CK +N++ IC Sbjct: 32 HSTEICLNCNDFPQYSCFIGGTSQCTTCYGDNFICLALQSGNKCKECLSEGTRCGQSDLCCDGLKCKQNFVYPRNSSFAFQIC 114
BLAST of SMED30009437 vs. Planmine SMEST
Match: SMESG000000901.1 (SMESG000000901.1) HSP 1 Score: 51.6026 bits (122), Expect = 3.456e-9 Identity = 29/108 (26.85%), Postives = 49/108 (45.37%), Query Frame = 3 Query: 66 VLFMSVFLYSVFSDKCSSRQFVYNPTHSNEICLNCNDFPRFSCIIGGTKQCNSCFGSNFICISRKSSNVCIQCIPQGSRCTVKDICCPNLSCKPGSFVSKNATNNLSI 389 ++ + +F+ + +C ++ H+++ C C P G C +C G N+ CI + N C CIP+ C V +ICC L CKP + + + N I Sbjct: 6 LIILMLFIVNYSKAQCPPGYYLNTYPHNSQNCFPCPKDPAGQMCGDGDTVCQTCMGQNYKCIFLQQGNFCKPCIPRLGICGVINICCSGLVCKPTTTATDLPSRNRCI 113
BLAST of SMED30009437 vs. Planmine SMEST
Match: SMESG000000901.1 (SMESG000000901.1) HSP 1 Score: 49.2914 bits (116), Expect = 2.068e-8 Identity = 29/103 (28.16%), Postives = 46/103 (44.66%), Query Frame = 3 Query: 81 VFLYSVFSDKCSSRQFVYNPTHSNEICLNCNDFPRFSCIIGGTKQCNSCFGSNFICISRKSSNVCIQCIPQGSRCTVKDICCPNLSCKPGSFVSKNATNNLSI 389 +F+ + +C ++ H+++ C C P G C +C G N+ CI + N C CIP+ C V +ICC L CKP + + + N I Sbjct: 2 LFIVNYSKAQCPPGYYLNTYPHNSQNCFPCPKDPAGQMCGDGDTVCQTCMGQNYKCIFLQQGNFCKPCIPRLGICGVINICCSGLVCKPTTTATDLPSRNRCI 104 The following BLAST results are available for this feature:
BLAST of SMED30009437 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30009437 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30009437 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30009437 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30009437 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30009437 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30009437 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30009437 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30009437 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30009437 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30009437 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30009437 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30009437 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30009437 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 4
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30009437 ID=SMED30009437|Name=SMED30009437|organism=Schmidtea mediterranea sexual|type=transcript|length=393bpback to top protein sequence of SMED30009437-orf-1 >SMED30009437-orf-1 ID=SMED30009437-orf-1|Name=SMED30009437-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=130bp GKYFHQNSALRMFVKFYYSVIVLFMSVFLYSVFSDKCSSRQFVYNPTHSNback to top InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
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