SMED30008401
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., 2020SMED30008401 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 1
Alignments
SMED30008401 aligns in the following genomic locations:
Homology
BLAST of SMED30008401 vs. Planmine SMEST
Match: SMESG000077490.1 (SMESG000077490.1) HSP 1 Score: 43.8986 bits (102), Expect = 9.296e-7 Identity = 32/86 (37.21%), Postives = 50/86 (58.14%), Query Frame = -3 Query: 382 CRDLLIAETRVQKLVISNQSAAFMKIFSXXXXXXXXXXRCVTEQAKVIPSNDISTPDVRTT*TNPSIFIKSNPCRNKRRRMQR*AD 639 CR+ LIAE R Q++VI++QSA + F+E EL +RL R + + +IP+ND+ + P K NP +N+ R +R A+ Sbjct: 70 CREDLIAENRAQRIVINDQSAVLIASFTETELTKRLASRDLAVKLNLIPANDLPERNQIGPAQTPKTSKKHNPSKNRSGRERRRAE 155 HSP 2 Score: 27.335 bits (59), Expect = 9.296e-7 Identity = 10/24 (41.67%), Postives = 15/24 (62.50%), Query Frame = -2 Query: 644 EKIKGAWFQPAVLKELKQMIYQLV 715 E+ G WF P V+K L + I++L Sbjct: 45 ERTLGTWFAPEVVKALHKQIHRLT 68
BLAST of SMED30008401 vs. Planmine SMEST
Match: SMESG000036854.1 (SMESG000036854.1) HSP 1 Score: 41.9726 bits (97), Expect = 8.525e-6 Identity = 29/77 (37.66%), Postives = 45/77 (58.44%), Query Frame = -3 Query: 412 QCRDLLIAETRVQKLVISNQSAAFMKIFSXXXXXXXXXXRCVTEQAKVIPSNDISTPDVRTT*TNPSIFIKSNPCRN 642 +CR+ LIAE+R Q+++I+NQSA + F+E EL +RL R + + +IP+N I+ P K NP +N Sbjct: 187 RCREDLIAESRAQRIIINNQSAVLVASFNEDELTKRLASRDLAIKLNLIPANHITGKGTTGPPQTPKTNKKHNPSKN 263 HSP 2 Score: 25.7942 bits (55), Expect = 8.525e-6 Identity = 9/24 (37.50%), Postives = 13/24 (54.17%), Query Frame = -2 Query: 644 EKIKGAWFQPAVLKELKQMIYQLV 715 E+ G WF P +K L I++L Sbjct: 163 ERTLGTWFAPEAVKALHNQIHRLT 186 The following BLAST results are available for this feature:
BLAST of SMED30008401 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30008401 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30008401 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30008401 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30008401 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30008401 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30008401 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30008401 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30008401 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30008401 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30008401 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30008401 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30008401 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30008401 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 2
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30008401 ID=SMED30008401|Name=SMED30008401|organism=Schmidtea mediterranea sexual|type=transcript|length=890bpback to top Annotated Terms
The following terms have been associated with this transcript:
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