SMED30022646
Overview
Neoblast Clusters
Zeng et. al., 2018
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 AppEmbryonic 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., 2020SMED30022646 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 2
Homology
BLAST of SMED30022646 vs. Planmine SMEST
Match: SMESG000031752.1 (SMESG000031752.1) HSP 1 Score: 123.635 bits (309), Expect = 1.372e-34 Identity = 62/111 (55.86%), Postives = 80/111 (72.07%), Query Frame = 1 Query: 331 ESGYSIFPVNGSSWNKFSIRHDEVELPYVAIKREPGRNSAREARQKAELKLAQLMEHQQQTQVQIVTAHHHLNQVNTDIAAGRIPSTDSYAPSYGISYKLDDQTLEEMEAP 663 ++GYSI V S + S RHDEVEL YVA+KREP RN AREARQ+AE L +L H++QT Q++ A +++V DIAAGRIPSTD + YG+SY+LDD L+EM+AP Sbjct: 23 DAGYSISTVKESREHHLS-RHDEVELAYVAMKREPVRNLAREARQRAEFTLIRLEIHKRQTNWQVLVARRRMDRVKADIAAGRIPSTDGHTSEYGVSYELDDLALKEMDAP 132
BLAST of SMED30022646 vs. Planmine SMEST
Match: SMESG000036641.1 (SMESG000036641.1) HSP 1 Score: 126.331 bits (316), Expect = 1.616e-34 Identity = 64/111 (57.66%), Postives = 80/111 (72.07%), Query Frame = 1 Query: 331 ESGYSIFPVNGSSWNKFSIRHDEVELPYVAIKREPGRNSAREARQKAELKLAQLMEHQQQTQVQIVTAHHHLNQVNTDIAAGRIPSTDSYAPSYGISYKLDDQTLEEMEAP 663 ++GYSI PV S ++ +DEVELPYVAIK+EPGRN AREARQ+AE L L HQ+QT Q+ A L++VN DIAAG+IPSTD YAP G+S++LDD L EM+ P Sbjct: 3 DAGYSISPVRESRESRH-FNNDEVELPYVAIKQEPGRNPAREARQRAESTLDCLEIHQKQTNWQVAMARQWLDKVNADIAAGKIPSTDGYAPECGVSFELDDPALMEMDTP 112
BLAST of SMED30022646 vs. Planmine SMEST
Match: SMESG000008360.1 (SMESG000008360.1) HSP 1 Score: 123.635 bits (309), Expect = 5.621e-34 Identity = 61/111 (54.95%), Postives = 79/111 (71.17%), Query Frame = 1 Query: 331 ESGYSIFPVNGSSWNKFSIRHDEVELPYVAIKREPGRNSAREARQKAELKLAQLMEHQQQTQVQIVTAHHHLNQVNTDIAAGRIPSTDSYAPSYGISYKLDDQTLEEMEAP 663 ++G+SI PV S + + + E +LPYVAIK+EPGRN ARE RQ+AE LA+L HQ+QT Q+V A L+++N +IAAGRIP TD YAPSYG+SY+LDD L E P Sbjct: 3 DAGFSISPVRESREGRLN-DYKEADLPYVAIKKEPGRNPARETRQRAEFTLARLELHQRQTNSQVVMARRRLSRINAEIAAGRIPITDGYAPSYGVSYELDDPALVESTIP 112
BLAST of SMED30022646 vs. Planmine SMEST
Match: SMESG000038777.1 (SMESG000038777.1) HSP 1 Score: 118.627 bits (296), Expect = 3.408e-31 Identity = 56/90 (62.22%), Postives = 68/90 (75.56%), Query Frame = 1 Query: 391 HDEVELPYVAIKREPGRNSAREARQKAELKLAQLMEHQQQTQVQIVTAHHHLNQVNTDIAAGRIPSTDSYAPSYGISYKLDDQTLEEMEA 660 HDE ELPY+AIKREPGRN A EARQ+ E +A+L HQ+QT Q+ A L++VN DIA GRIPSTD YAP+YG+SY+LDD L EM+ Sbjct: 54 HDEGELPYMAIKREPGRNLALEARQRTEFTIARLEMHQKQTNWQVAMARRRLDRVNADIATGRIPSTDVYAPNYGVSYELDDPALVEMDT 143
BLAST of SMED30022646 vs. Planmine SMEST
Match: SMESG000038895.1 (SMESG000038895.1) HSP 1 Score: 113.62 bits (283), Expect = 4.111e-31 Identity = 60/111 (54.05%), Postives = 77/111 (69.37%), Query Frame = 1 Query: 331 ESGYSIFPVNGSSWNKFSIRHDEVELPYVAIKREPGRNSAREARQKAELKLAQLMEHQQQTQVQIVTAHHHLNQVNTDIAAGRIPSTDSYAPSYGISYKLDDQTLEEMEAP 663 ++GYSI V S ++ S R+DEVEL YVAIKREP RN EA Q+AE LA+L HQ+QT Q+ + ++VN +IA GRIPSTD Y P Y +SY+L+D LEEM+AP Sbjct: 7 DAGYSISSVRESMDHRLS-RNDEVELSYVAIKREPWRNPVIEAGQRAEFTLARLDIHQRQTNWQVAMVRNRSDRVNAEIATGRIPSTDGYIPGYRVSYELNDPALEEMDAP 116 The following BLAST results are available for this feature:
BLAST of SMED30022646 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30022646 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30022646 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30022646 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30022646 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30022646 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30022646 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30022646 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30022646 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30022646 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30022646 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30022646 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30022646 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30022646 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 >SMED30022646 ID=SMED30022646|Name=SMED30022646|organism=Schmidtea mediterranea sexual|type=transcript|length=799bpback to top protein sequence of SMED30022646-orf-1 >SMED30022646-orf-1 ID=SMED30022646-orf-1|Name=SMED30022646-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=152bp MSTSDVESGYSIFPVNGSSWNKFSIRHDEVELPYVAIKREPGRNSAREARback to top Annotated Terms
The following terms have been associated with this transcript:
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