SMED30023889
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., 2020SMED30023889 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 19
Alignments
SMED30023889 aligns in the following genomic locations:
Homology
BLAST of SMED30023889 vs. TrEMBL
Match: V9XTG6 (X1.D.A5.1 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1) HSP 1 Score: 60.8474 bits (146), Expect = 1.932e-9 Identity = 33/93 (35.48%), Postives = 53/93 (56.99%), Query Frame = 2 Query: 44 IALCAIFCTTFVHSSVSFGNGYF-KDGKPFVKISETEYPADESLEVEVGEGDNCNLCSISPPTSTDTNPTFECQGPSPAEIDGETIYLPVCKE 319 +A+C + ++ +S + +G G+ KDG+ V+I + ++ A + EVEV C C I P S + P FEC+GPS +D + IYL C+E Sbjct: 10 LAMCLM---SYTNSELVYGRGFVDKDGRQIVEIFDQQFDASKQKEVEVNFVKKCYKCLIEPAVSGE-QPLFECEGPSLVRVDEKDIYLDPCQE 98
BLAST of SMED30023889 vs. Planmine SMEST
Match: SMESG000055805.1 (SMESG000055805.1) HSP 1 Score: 195.667 bits (496), Expect = 4.639e-66 Identity = 96/97 (98.97%), Postives = 96/97 (98.97%), Query Frame = 2 Query: 32 MKVIIALCAIFCTTFVHSSVSFGNGYFKDGKPFVKISETEYPADESLEVEVGEGDNCNLCSISPPTSTDTNPTFECQGPSPAEIDGETIYLPVCKEK 322 MKVIIALCAIFCT FVHSSVSFGNGYFKDGKPFVKISETEYPADESLEVEVGEGDNCNLCSISPPTSTDTNPTFECQGPSPAEIDGETIYLPVCKEK Sbjct: 1 MKVIIALCAIFCTKFVHSSVSFGNGYFKDGKPFVKISETEYPADESLEVEVGEGDNCNLCSISPPTSTDTNPTFECQGPSPAEIDGETIYLPVCKEK 97
BLAST of SMED30023889 vs. Planmine SMEST
Match: SMESG000020860.1 (SMESG000020860.1) HSP 1 Score: 90.5077 bits (223), Expect = 1.294e-24 Identity = 44/96 (45.83%), Postives = 60/96 (62.50%), Query Frame = 2 Query: 32 MKVIIALCAIFCTTFVHSSVSFGNGYFKDGKPFVKISETEYPADESLEVEVGEGDNCNLCSISPPTSTDTNPTFECQGPSPAEIDGETIYLPVCKE 319 MKVI+ + ++ T ++SVSFG GYF+DGK +VKI+ EY A+E E++ GEGD C +C+ PT+ C GPSP IDG+ Y CKE Sbjct: 1 MKVILLVLSVL--TVAYASVSFGRGYFRDGKGYVKINGVEYLAEEDGEIQYGEGDRCVVCNYFASKDKVKPPTYSCYGPSPMMIDGKLTYRSQCKE 94
BLAST of SMED30023889 vs. Planmine SMEST
Match: SMESG000062897.1 (SMESG000062897.1) HSP 1 Score: 77.0258 bits (188), Expect = 3.259e-19 Identity = 34/83 (40.96%), Postives = 50/83 (60.24%), Query Frame = 2 Query: 65 CTTFVHSSVSFGNGYFKDGKPFVKISETEYPADESLEVEVGEGDNCNLCSISPPTSTDTNPTFECQGPSPAEIDGETIYLPVC 313 C S+S G GY+++GKP VKI+ +PAD++ ++G GD C C I+ P + D P F+C GPSP +DG+ Y+ C Sbjct: 23 CILNSKGSLSRGIGYYENGKPVVKINNQVFPADKNSVQQIGSGDRCLKCFINAPANNDEKPKFQCHGPSPVYMDGKMAYISEC 105
BLAST of SMED30023889 vs. Planmine SMEST
Match: SMESG000062896.1 (SMESG000062896.1) HSP 1 Score: 75.8702 bits (185), Expect = 7.493e-19 Identity = 36/97 (37.11%), Postives = 55/97 (56.70%), Query Frame = 2 Query: 32 MKVIIALCAI-FCTTFVHSSVSFGNGYFKDGKPFVKISETEYPADESLEVEVGEGDNCNLCSISPPTSTDTNPTFECQGPSPAEIDGETIYLPVCKE 319 MK +IAL + C +VH + +GY++DG+P VKI + YPAD + ++G G C C I+ P+ NP FEC SPA + + +Y+ C + Sbjct: 1 MKYLIALFLVSVCILYVHGGMFGASGYYEDGRPVVKIEDQVYPADTNNVQQIGTGQGCKKCYINAPSEKGQNPDFECHTASPAIENNKVVYVSPCDQ 97
BLAST of SMED30023889 vs. Planmine SMEST
Match: SMESG000054105.1 (SMESG000054105.1) HSP 1 Score: 70.0922 bits (170), Expect = 1.314e-16 Identity = 37/96 (38.54%), Postives = 50/96 (52.08%), Query Frame = 2 Query: 32 MKVIIALCAIFCTTFVHSSVSFGNGYFKDGKPFVKISETEYPADESLEVEVGEGDNCNLCSISPPTSTDTNPTFECQGPSPAE-IDGETIYLPVCK 316 M I+ L I + SS + G G+++ GK +V ++ TEY AD V +G GD C CSI+P S + N TF CQ P + I G Y CK Sbjct: 1 MNSILLLTVILFSILSCSSDTNGRGFWRKGKQYVVLNGTEYSADLKASVNIGTGDKCIYCSITPSKSANQNSTFYCQDPMTTKTITGYVTYYSFCK 96 The following BLAST results are available for this feature:
BLAST of SMED30023889 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30023889 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30023889 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30023889 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30023889 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30023889 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30023889 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30023889 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 1
BLAST of SMED30023889 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30023889 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30023889 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30023889 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30023889 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30023889 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 >SMED30023889 ID=SMED30023889|Name=SMED30023889|organism=Schmidtea mediterranea sexual|type=transcript|length=397bpback 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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