SMED30016976
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., 2020SMED30016976 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 1
Alignments
SMED30016976 aligns in the following genomic locations:
Homology
BLAST of SMED30016976 vs. Planmine SMEST
Match: SMESG000054106.1 (SMESG000054106.1) HSP 1 Score: 71.2478 bits (173), Expect = 3.448e-17 Identity = 36/75 (48.00%), Postives = 45/75 (60.00%), Query Frame = 3 Query: 78 FMGTGYYTNGIPYVNIRGQEYSATTQKRIQIGTGDQCIVCYIYPAANSKSKPYYNCNEPMPFSGDDGQISYISSC 302 F+G G NG YV I G EYSA +Q+ I IGTGD+C +C I P N K+ P YNC EP+ G++ Y S C Sbjct: 21 FIGVGVVRNGKQYVTITGVEYSADSQRNILIGTGDKCNLCKIVPGKN-KTNPTYNCLEPIKVISASGKVMYKSQC 94
BLAST of SMED30016976 vs. Planmine SMEST
Match: SMESG000062897.1 (SMESG000062897.1) HSP 1 Score: 64.6994 bits (156), Expect = 1.479e-14 Identity = 32/73 (43.84%), Postives = 43/73 (58.90%), Query Frame = 3 Query: 84 GTGYYTNGIPYVNIRGQEYSATTQKRIQIGTGDQCIVCYIYPAANSKSKPYYNCNEPMPFSGDDGQISYISSC 302 G GYY NG P V I Q + A QIG+GD+C+ C+I AN+ KP + C+ P P DG+++YIS C Sbjct: 34 GIGYYENGKPVVKINNQVFPADKNSVQQIGSGDRCLKCFINAPANNDEKPKFQCHGPSPVYM-DGKMAYISEC 105
BLAST of SMED30016976 vs. Planmine SMEST
Match: SMESG000020860.1 (SMESG000020860.1) HSP 1 Score: 62.003 bits (149), Expect = 1.227e-13 Identity = 32/92 (34.78%), Postives = 48/92 (52.17%), Query Frame = 3 Query: 27 NVFVLLIFVMNPLLCNAFMGTGYYTNGIPYVNIRGQEYSATTQKRIQIGTGDQCIVCYIYPAANSKSKPYYNCNEPMPFSGDDGQISYISSC 302 V +L++ V+ + G GY+ +G YV I G EY A IQ G GD+C+VC + + + P Y+C P P DG+++Y S C Sbjct: 2 KVILLVLSVLTVAYASVSFGRGYFRDGKGYVKINGVEYLAEEDGEIQYGEGDRCVVCNYFASKDKVKPPTYSCYGPSPMM-IDGKLTYRSQC 92
BLAST of SMED30016976 vs. Planmine SMEST
Match: SMESG000054105.1 (SMESG000054105.1) HSP 1 Score: 61.2326 bits (147), Expect = 2.664e-13 Identity = 30/93 (32.26%), Postives = 51/93 (54.84%), Query Frame = 3 Query: 27 NVFVLLIFVMNPLLCNAFM-GTGYYTNGIPYVNIRGQEYSATTQKRIQIGTGDQCIVCYIYPAANSKSKPYYNCNEPMPFSGDDGQISYISSC 302 ++ +L + + + L C++ G G++ G YV + G EYSA + + IGTGD+CI C I P+ ++ + C +PM G ++Y S C Sbjct: 3 SILLLTVILFSILSCSSDTNGRGFWRKGKQYVVLNGTEYSADLKASVNIGTGDKCIYCSITPSKSANQNSTFYCQDPMTTKTITGYVTYYSFC 95
BLAST of SMED30016976 vs. Planmine SMEST
Match: SMESG000055805.1 (SMESG000055805.1) HSP 1 Score: 58.5362 bits (140), Expect = 3.526e-12 Identity = 28/93 (30.11%), Postives = 46/93 (49.46%), Query Frame = 3 Query: 42 LIFVMNPLLCNAFM------GTGYYTNGIPYVNIRGQEYSATTQKRIQIGTGDQCIVCYIYPAANSKSKPYYNCNEPMPFSGDDGQISYISSC 302 +I + + C F+ G GY+ +G P+V I EY A +++G GD C +C I P ++ + P + C P P + DG+ Y+ C Sbjct: 3 VIIALCAIFCTKFVHSSVSFGNGYFKDGKPFVKISETEYPADESLEVEVGEGDNCNLCSISPPTSTDTNPTFECQGPSP-AEIDGETIYLPVC 94 The following BLAST results are available for this feature:
BLAST of SMED30016976 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30016976 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30016976 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30016976 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30016976 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30016976 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30016976 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30016976 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30016976 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30016976 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30016976 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30016976 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30016976 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30016976 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 >SMED30016976 ID=SMED30016976|Name=SMED30016976|organism=Schmidtea mediterranea sexual|type=transcript|length=367bpback to top protein sequence of SMED30016976-orf-1 >SMED30016976-orf-1 ID=SMED30016976-orf-1|Name=SMED30016976-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=102bp HSAKKMKPNVFVLLIFVMNPLLCNAFMGTGYYTNGIPYVNIRGQEYSATTback to top InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
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