SMED30023206
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., 2020SMED30023206 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 3
Homology
BLAST of SMED30023206 vs. Planmine SMEST
Match: SMESG000030608.1 (SMESG000030608.1) HSP 1 Score: 175.637 bits (444), Expect = 9.876e-55 Identity = 90/110 (81.82%), Postives = 94/110 (85.45%), Query Frame = -2 Query: 254 QFEHAYETLKRAKNELYDDIIYLNKTIGTIKNELRKSVLELKENRKLNEKMMNQVQYSIKFYSNKTTDQFNRIVKEVQQPVNKLKEVQHPVNSGNKSSLSFPLYIFTYFL 583 +FEH YETLKRAKNELYDDIIYLNKTIG IKNELRKS+LELKEN KLNEKMMNQVQYSIKFYSNKTTDQFNRI+K +Q PVN VNS NK SL FPLYIFTYFL Sbjct: 141 RFEHTYETLKRAKNELYDDIIYLNKTIGIIKNELRKSILELKENHKLNEKMMNQVQYSIKFYSNKTTDQFNRIMK-LQPPVNSGGNSLKEVNSANKPSLPFPLYIFTYFL 249
BLAST of SMED30023206 vs. Planmine SMEST
Match: SMESG000036590.1 (SMESG000036590.1) HSP 1 Score: 180.644 bits (457), Expect = 5.182e-53 Identity = 91/110 (82.73%), Postives = 95/110 (86.36%), Query Frame = -2 Query: 254 QFEHAYETLKRAKNELYDDIIYLNKTIGTIKNELRKSVLELKENRKLNEKMMNQVQYSIKFYSNKTTDQFNRIVKEVQQPVNKLKEVQHPVNSGNKSSLSFPLYIFTYFL 583 +FEH YETLKRAKNELYDDIIYLNKTIGTIKNELRKS+LELKEN KLNEKMMNQVQYSIKFYSNKTT+QFNRI+K Q PVN VNS NKSSL FPLYIFTYFL Sbjct: 548 RFEHTYETLKRAKNELYDDIIYLNKTIGTIKNELRKSILELKENHKLNEKMMNQVQYSIKFYSNKTTEQFNRIMKLQQHPVNSGGNSLKEVNSANKSSLPFPLYIFTYFL 657
BLAST of SMED30023206 vs. Planmine SMEST
Match: SMESG000036590.1 (SMESG000036590.1) HSP 1 Score: 180.644 bits (457), Expect = 6.720e-53 Identity = 91/110 (82.73%), Postives = 95/110 (86.36%), Query Frame = -2 Query: 254 QFEHAYETLKRAKNELYDDIIYLNKTIGTIKNELRKSVLELKENRKLNEKMMNQVQYSIKFYSNKTTDQFNRIVKEVQQPVNKLKEVQHPVNSGNKSSLSFPLYIFTYFL 583 +FEH YETLKRAKNELYDDIIYLNKTIGTIKNELRKS+LELKEN KLNEKMMNQVQYSIKFYSNKTT+QFNRI+K Q PVN VNS NKSSL FPLYIFTYFL Sbjct: 567 RFEHTYETLKRAKNELYDDIIYLNKTIGTIKNELRKSILELKENHKLNEKMMNQVQYSIKFYSNKTTEQFNRIMKLQQHPVNSGGNSLKEVNSANKSSLPFPLYIFTYFL 676
BLAST of SMED30023206 vs. Planmine SMEST
Match: SMESG000039142.1 (SMESG000039142.1) HSP 1 Score: 166.777 bits (421), Expect = 1.007e-52 Identity = 86/111 (77.48%), Postives = 95/111 (85.59%), Query Frame = -2 Query: 251 QFEHAYETLKRAKNELYDDIIYLNKTIGTIKNELRKSVLELKENRKLNEKMMNQVQYSIKFYSNKTTDQFNRIVKEVQQPVNKLKEVQHPVNSGNKSSLSFPLYIFTYFLK 583 +FE YETLKRA+N +YDDI+YLN+TIG IKNELRKS+ EL ENR LNEKM+NQVQYSI+FYSNK TDQFNRI+KEV KLKEV VNSGNKSSLSFPLYIFTYFLK Sbjct: 28 RFELTYETLKRARNAIYDDILYLNRTIGIIKNELRKSIFELNENRNLNEKMVNQVQYSIQFYSNKITDQFNRIMKEVNSG-KKLKEVN--VNSGNKSSLSFPLYIFTYFLK 135
BLAST of SMED30023206 vs. Planmine SMEST
Match: SMESG000081267.1 (SMESG000081267.1) HSP 1 Score: 173.711 bits (439), Expect = 3.260e-50 Identity = 91/114 (79.82%), Postives = 99/114 (86.84%), Query Frame = -2 Query: 254 QFEHAYETLKRAKNELYDDIIYLNKTIGTIKNELRKSVLELKENRKLNEKMMNQVQYSIKFYSNKTTDQFNRIVKEVQQPV----NKLKEVQHPVNSGNKSSLSFPLYIFTYFL 583 +FEH YE LKRAKNELYDDIIYLNKTIG IKNELRKS+ +LKENRKLNEKM+NQVQYSIKFYSNKTTDQFNRI+K +QQP+ NKLKEV+ S NKSSL FPLYIFTYFL Sbjct: 55 RFEHIYEILKRAKNELYDDIIYLNKTIGIIKNELRKSIFKLKENRKLNEKMLNQVQYSIKFYSNKTTDQFNRIMK-LQQPINSGDNKLKEVK----SANKSSLPFPLYIFTYFL 163 The following BLAST results are available for this feature:
BLAST of SMED30023206 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30023206 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30023206 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30023206 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30023206 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30023206 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30023206 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30023206 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30023206 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30023206 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30023206 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30023206 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30023206 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30023206 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 >SMED30023206 ID=SMED30023206|Name=SMED30023206|organism=Schmidtea mediterranea sexual|type=transcript|length=665bpback to top protein sequence of SMED30023206-orf-1 >SMED30023206-orf-1 ID=SMED30023206-orf-1|Name=SMED30023206-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=114bp MRQFEHAYETLKRAKNELYDDIIYLNKTIGTIKNELRKSVLELKENRKLNback to top Annotated Terms
The following terms have been associated with this transcript:
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