SMED30004033
Overview
Neoblast Clusters
Zeng et. al., 2018▻ Overview▻ Neoblast Population▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population
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 App
Neoblast Population
Sub-lethal Irradiated Surviving X1 and X2 Cell Population
Embryonic 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., 2020SMED30004033 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 1
Alignments
SMED30004033 aligns in the following genomic locations:
Homology
BLAST of SMED30004033 vs. Planmine SMEST
Match: SMESG000058576.1 (SMESG000058576.1) HSP 1 Score: 164.851 bits (416), Expect = 1.523e-50 Identity = 77/108 (71.30%), Postives = 90/108 (83.33%), Query Frame = 2 Query: 17 PSFAIKREPGRNPAREASQSAEFSLYRLEKLVRKFQWKVKMAQRRLDRINAVIKYEEVPSTDGYAPDYGVFFELKDPTLAQMRAPTNIILPAKLFNGPIRYRNRRDEH 340 PS AI + GRNPA EA Q AEFSLYRLE+LV KFQWKV+MA+RRL++INA I E+ STDGYAPDYG+ FELK+P L +M+A TNIILPAKLFNG +R+RNRRDEH Sbjct: 162 PSIAINHKLGRNPAEEARQHAEFSLYRLEELVLKFQWKVRMARRRLEQINAAIASGEILSTDGYAPDYGISFELKNPALTRMQALTNIILPAKLFNGSMRHRNRRDEH 269
BLAST of SMED30004033 vs. Planmine SMEST
Match: SMESG000026733.1 (SMESG000026733.1) HSP 1 Score: 139.428 bits (350), Expect = 3.203e-42 Identity = 69/101 (68.32%), Postives = 77/101 (76.24%), Query Frame = 2 Query: 20 SFAIKREPGRNPAREASQSAEFSLYRLEKLVRKFQWKVKMAQRRLDRINAVIKYEEVPSTDGYAPDYGVFFELKDPTLAQMRAPTNIILPAKLFNGPIRYR 322 S AIKREP RN ARE Q AEFSLYRLE+LVRKFQWKV+M QR L +INA I E+PSTDGYA DYG+ FEL DP L QM TN ILPA+LFN IR++ Sbjct: 57 SLAIKREPDRNLAREPCQRAEFSLYRLEELVRKFQWKVRMTQRHLKQINATIATGEIPSTDGYAQDYGLLFELNDPVLTQMH--TNAILPAQLFNERIRHQ 155
BLAST of SMED30004033 vs. Planmine SMEST
Match: SMESG000004883.1 (SMESG000004883.1) HSP 1 Score: 120.553 bits (301), Expect = 1.689e-33 Identity = 59/85 (69.41%), Postives = 71/85 (83.53%), Query Frame = 2 Query: 137 MAQRRLDRINAVIKYEEVPSTDGYAPDYGVFFELKDPTLAQMRAPTNIILPAKLFNGPIRYRNRRDEH-YQYQYTTKPEHDRYMR 388 MA+RRL+RINAVI E+PSTDGYAPDYGV FEL+DP A+M+APTNI+LP LFNGPIR+R+RRDEH YQ Q+ TK E ++Y R Sbjct: 1 MARRRLERINAVIASGEIPSTDGYAPDYGVSFELRDP--ARMKAPTNIVLPVNLFNGPIRHRDRRDEHSYQCQHPTKKERNQYRR 83 HSP 2 Score: 110.923 bits (276), Expect = 8.088e-30 Identity = 55/116 (47.41%), Postives = 76/116 (65.52%), Query Frame = 2 Query: 17 PSFAIKREPGRNPAREASQSAEFSLYRLEKLVRKFQWKVKMAQRRLDRINAVIKYEEVPSTDGYAPDYGVFFELKDPTLAQMRAPTNIILPAKLFNGPIRYRNRRDEHYQYQYTTK 364 PS AIKREPG NPAREA Q AE++ + E+L RK+Q K +A++RL ++N I +PSTDG+ P+YGV FEL DP L QM APT +++P KL +R R + + Y ++ Sbjct: 140 PSVAIKREPGHNPAREARQRAEYAAMKKEELERKYQRKAVLARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPEKLVRSTLRNRLGSSQTGDHTYASR 255
BLAST of SMED30004033 vs. Planmine SMEST
Match: SMESG000027782.1 (SMESG000027782.1) HSP 1 Score: 112.849 bits (281), Expect = 3.030e-31 Identity = 54/102 (52.94%), Postives = 71/102 (69.61%), Query Frame = 2 Query: 17 PSFAIKREPGRNPAREASQSAEFSLYRLEKLVRKFQWKVKMAQRRLDRINAVIKYEEVPSTDGYAPDYGVFFELKDPTLAQMRAPTNIILPAKLFNGPIRYR 322 PS AIKREPG NPAREA Q AE++ ++E+L RK+ K +A++RL ++N I +PSTDG+ P+YGV FEL DP L QM APT ++LP KL +R R Sbjct: 87 PSIAIKREPGHNPAREARQRAEYAAMKMEELERKYHRKAVLARQRLAQVNRDIASGAIPSTDGFPPEYGVSFELDDPRLMQMTAPTKLVLPEKLIQSTLRNR 188
BLAST of SMED30004033 vs. Planmine SMEST
Match: SMESG000057533.1 (SMESG000057533.1) HSP 1 Score: 117.857 bits (294), Expect = 1.203e-30 Identity = 59/131 (45.04%), Postives = 82/131 (62.60%), Query Frame = 2 Query: 17 PSFAIKREPGRNPAREASQSAEFSLYRLEKLVRKFQWKVKMAQRRLDRINAVIKYEEVPSTDGYAPDYGVFFELKDPTLAQMRAPTNIILPAKLFNGPIRYRNRRDEHYQYQYTTKPEHDRYMRPLQDRRS 409 PS AIKREPG NPAREA Q A+++ ++E+L RK+ K A++RL ++N I +PSTDG+ P+YGV FEL DP L QM APT +++P KL + RN+ H +T H ++ L +RRS Sbjct: 1697 PSIAIKREPGHNPAREARQRAKYAAMKMEELERKYHRKAVSARQRLAQVNRDIASGSIPSTDGFPPEYGVSFELDDPRLTQMTAPTKMVIPEKLVQSTL--RNQLGSHQTGDHTYASRHPQWNSKLNNRRS 1825 The following BLAST results are available for this feature:
BLAST of SMED30004033 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30004033 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30004033 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30004033 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30004033 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30004033 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30004033 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30004033 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30004033 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30004033 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30004033 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30004033 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30004033 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30004033 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 >SMED30004033 ID=SMED30004033|Name=SMED30004033|organism=Schmidtea mediterranea sexual|type=transcript|length=562bpback to top protein sequence of SMED30004033-orf-1 >SMED30004033-orf-1 ID=SMED30004033-orf-1|Name=SMED30004033-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=141bp RIPDKPSFAIKREPGRNPAREASQSAEFSLYRLEKLVRKFQWKVKMAQRRback to top Annotated Terms
The following terms have been associated with this transcript:
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