SMED30025552
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., 2020SMED30025552 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 7
Alignments
SMED30025552 aligns in the following genomic locations:
Homology
BLAST of SMED30025552 vs. Planmine SMEST
Match: SMESG000039545.1 (SMESG000039545.1) HSP 1 Score: 378.252 bits (970), Expect = 2.684e-120 Identity = 252/359 (70.19%), Postives = 262/359 (72.98%), Query Frame = 2 Query: 68 METPVQLNSSWISTFQYSNENFGNEYCREYLQNELLNLDDIVQSRHXXXXXXXXXXXXXXXXXXXXXXXDFNHNSNIASSENSHFRHSGVDIESQLPSRDSLFVTGEKDCNNAENNLKTTDSQSANSDLDQRLNPSSVDRQLSNGNPFNNNEYDFIKTKIDLQENESRFPNAELGNEIYFSGENEYLEGSFTNDSRNDLTSPAVDIELLDEDLYSNGEFGLNHAEANLQENGSQILNTNLDANELVEHKCI---------------------------------NVHGKTKS--------FP---FGN-----------EGIFTNDIRKDLTLPIVDTELLDEDLYSNGELCRNIEELN 979 METPVQLNSSWISTFQYSNENFGNEYCREYLQNELLNLDDIVQSRHSENNISNNNNIIINLENKSKNENDFNHN+NIASSENSHFR+SGVDIESQLPSRDSLFVTGEKDCNNAENNLKTTDSQSANSDLDQRLNPS VDRQLSNGNPFNNNEYDFIKTKIDLQENES FPNAELGNE F ENEYLEG FTNDS NDLT P VD +LLDEDLYSNGE N E NL++ SQILN ++D+ E +C N KTK+ FP GN EG FTND R DLT P VD ELLDEDLYSNGE N E N Sbjct: 1 METPVQLNSSWISTFQYSNENFGNEYCREYLQNELLNLDDIVQSRHSENNISNNNNIIINLENKSKNENDFNHNNNIASSENSHFRYSGVDIESQLPSRDSLFVTGEKDCNNAENNLKTTDSQSANSDLDQRLNPSRVDRQLSNGNPFNNNEYDFIKTKIDLQENESLFPNAELGNEKLFPLENEYLEGGFTNDSHNDLTPPVVDTKLLDEDLYSNGEPCSNIEEDNLEKVISQILNADVDSIEDFLTECGYFEQNLGSDNSNNDSILSMVDKQLAREDLFDNENDFIKTKTDLQENESRFPNAELGNEIYFPGENEYLEGSFTNDSRNDLTSPAVDIELLDEDLYSNGEFGLNHAEAN 359 HSP 2 Score: 321.242 bits (822), Expect = 1.772e-99 Identity = 175/230 (76.09%), Postives = 184/230 (80.00%), Query Frame = 2 Query: 371 LFVTGEKDCNNAENNLKTTDSQSANSDLD-------------QRLNP---------SSVDRQLSNGNPFNNNEYDFIKTKIDLQENESRFPNAELGNEIYFSGENEYLEGSFTNDSRNDLTSPAVDIELLDEDLYSNGEFGLNHAEANLQENGSQILNTNLDANELVEHKCINVHGKTKSFPFGNEGIFTNDIRKDLTLPIVDTELLDEDLYSNGELCRNIEELNENVEK 994 L+ GE N E+NL+ SQ N+D+D Q L S VD+QL+ + F+N E DFIKTK DLQENESRFPNAELGNEIYF GENEYLEGSFTNDSRNDLTSPAVDIELLDEDLYSNGEFGLNHAEANLQENGSQILNTNLDANELVEHKCINVHGKTKSFP GNEGIFTNDIRKDLTLPIVDTELLDEDLYSNGELCRNIEELNENVEK Sbjct: 213 LYSNGEPCSNIEEDNLEKVISQILNADVDSIEDFLTECGYFEQNLGSDNSNNDSILSMVDKQLAREDLFDN-ENDFIKTKTDLQENESRFPNAELGNEIYFPGENEYLEGSFTNDSRNDLTSPAVDIELLDEDLYSNGEFGLNHAEANLQENGSQILNTNLDANELVEHKCINVHGKTKSFPSGNEGIFTNDIRKDLTLPIVDTELLDEDLYSNGELCRNIEELNENVEK 441 HSP 3 Score: 87.8113 bits (216), Expect = 1.092e-18 Identity = 48/64 (75.00%), Postives = 50/64 (78.12%), Query Frame = 2 Query: 530 FIKTKIDLQENESRFPNAELGNEIYFSGENEYLEGSFTNDSRNDLTSPAVDIELLDEDLYSNGE 721 FIKTKIDLQEN+S PN ELG EI ENEY EGS TNDSRNDLT P VD +LLDEDL SNGE Sbjct: 452 FIKTKIDLQENKS--PNKELGIEICSPLENEYFEGSLTNDSRNDLTPPVVDTKLLDEDLCSNGE 513 The following BLAST results are available for this feature:
BLAST of SMED30025552 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30025552 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30025552 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30025552 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30025552 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30025552 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30025552 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30025552 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30025552 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30025552 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30025552 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30025552 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30025552 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30025552 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 1
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30025552 ID=SMED30025552|Name=SMED30025552|organism=Schmidtea mediterranea sexual|type=transcript|length=1019bpback to top protein sequence of SMED30025552-orf-1 >SMED30025552-orf-1 ID=SMED30025552-orf-1|Name=SMED30025552-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=317bp METPVQLNSSWISTFQYSNENFGNEYCREYLQNELLNLDDIVQSRHSENNback 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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