SMED30026973
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., 2020SMED30026973 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 1
Alignments
SMED30026973 aligns in the following genomic locations:
Homology
BLAST of SMED30026973 vs. Planmine SMEST
Match: SMESG000033974.1 (SMESG000033974.1) HSP 1 Score: 208.379 bits (529), Expect = 1.626e-69 Identity = 103/103 (100.00%), Postives = 103/103 (100.00%), Query Frame = 3 Query: 3 NSDLEIISPPRLMDFPQSAPIPFQFNISMENLSTDNATNAQIIISARSSPIREERHETSSGRSTPQIISVTEPPQVRNSINSTAGDTSRQNQTQFHRDLGKDT 311 NSDLEIISPPRLMDFPQSAPIPFQFNISMENLSTDNATNAQIIISARSSPIREERHETSSGRSTPQIISVTEPPQVRNSINSTAGDTSRQNQTQFHRDLGKDT Sbjct: 153 NSDLEIISPPRLMDFPQSAPIPFQFNISMENLSTDNATNAQIIISARSSPIREERHETSSGRSTPQIISVTEPPQVRNSINSTAGDTSRQNQTQFHRDLGKDT 255
BLAST of SMED30026973 vs. Planmine SMEST
Match: SMESG000068983.1 (SMESG000068983.1) HSP 1 Score: 114.775 bits (286), Expect = 2.840e-33 Identity = 60/90 (66.67%), Postives = 68/90 (75.56%), Query Frame = 3 Query: 3 NSDLEIISPPRLMDFPQSAPIPFQFNISMENLSTDNATNAQIIISARSSPIREERHETSSGRSTPQIISVTEPPQVRNSINSTAGDTSRQ 272 +SDLEII PRL+ F Q P+ QFNISMENL+T N N I IS RSSP+REE HE +SGRSTPQIISV EPPQVR S+NST + SRQ Sbjct: 96 DSDLEIIYAPRLVAFSQLDPVRSQFNISMENLTTGNPANVPITISTRSSPVREEGHEITSGRSTPQIISVIEPPQVRTSVNSTVENISRQ 185
BLAST of SMED30026973 vs. Planmine SMEST
Match: SMESG000046397.1 (SMESG000046397.1) HSP 1 Score: 103.99 bits (258), Expect = 3.176e-30 Identity = 57/88 (64.77%), Postives = 65/88 (73.86%), Query Frame = 3 Query: 9 DLEIISPPRLMDFPQSAPIPFQFNISMENLSTDNATNAQIIISARSSPIREERHETSSGRSTPQIISVTEPPQVRNSINSTAGDTSRQ 272 DLEII PRLMDF Q AP P QFNISM+NLS D TN QI+I SP+REE HE SSGRSTPQIISVTEPP +RN + T + ++Q Sbjct: 6 DLEIIYSPRLMDFSQPAPTPSQFNISMDNLSADTPTNVQIMI----SPVREEVHENSSGRSTPQIISVTEPP-IRNDFDLTVRNVAQQ 88
BLAST of SMED30026973 vs. Planmine SMEST
Match: SMESG000056168.1 (SMESG000056168.1) HSP 1 Score: 100.138 bits (248), Expect = 6.902e-26 Identity = 56/93 (60.22%), Postives = 61/93 (65.59%), Query Frame = 3 Query: 3 NSDLEIISPPRLMDFPQSAPIPFQFNISMENLSTDNATNAQIIISARSSPIREERHETSSGRSTPQIISVTEPPQVRNSINSTAGDTSRQNQT 281 NSDLEII P L+DF Q AP QFNI++ENL TDN + QI I RSSPIREERHE SS RST QIISV E PQ R I+ G Q T Sbjct: 71 NSDLEIIYGPLLVDFSQLAPTSSQFNIAIENLITDNPASVQITIFTRSSPIREERHEISSRRSTLQIISVIESPQKREVISFYIGQGGVQTGT 163
BLAST of SMED30026973 vs. Planmine SMEST
Match: SMESG000056168.1 (SMESG000056168.1) HSP 1 Score: 99.7525 bits (247), Expect = 9.897e-26 Identity = 56/93 (60.22%), Postives = 61/93 (65.59%), Query Frame = 3 Query: 3 NSDLEIISPPRLMDFPQSAPIPFQFNISMENLSTDNATNAQIIISARSSPIREERHETSSGRSTPQIISVTEPPQVRNSINSTAGDTSRQNQT 281 NSDLEII P L+DF Q AP QFNI++ENL TDN + QI I RSSPIREERHE SS RST QIISV E PQ R I+ G Q T Sbjct: 71 NSDLEIIYGPLLVDFSQLAPTSSQFNIAIENLITDNPASVQITIFTRSSPIREERHEISSRRSTLQIISVIESPQKREVISFYIGQGGVQTGT 163 The following BLAST results are available for this feature:
BLAST of SMED30026973 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30026973 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30026973 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30026973 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30026973 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30026973 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30026973 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30026973 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30026973 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30026973 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30026973 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30026973 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30026973 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30026973 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 >SMED30026973 ID=SMED30026973|Name=SMED30026973|organism=Schmidtea mediterranea sexual|type=transcript|length=311bpback to top protein sequence of SMED30026973-orf-1 >SMED30026973-orf-1 ID=SMED30026973-orf-1|Name=SMED30026973-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=103bp NSDLEIISPPRLMDFPQSAPIPFQFNISMENLSTDNATNAQIIISARSSPback to top Annotated Terms
The following terms have been associated with this transcript:
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