SMED30001667
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., 2020SMED30001667 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 3
Alignments
SMED30001667 aligns in the following genomic locations:
Homology
BLAST of SMED30001667 vs. Planmine SMEST
Match: SMESG000057219.1 (SMESG000057219.1) HSP 1 Score: 209.149 bits (531), Expect = 1.460e-67 Identity = 99/102 (97.06%), Postives = 100/102 (98.04%), Query Frame = -2 Query: 2 MQGTGEMMNPQHAIRCWLRVRRTARWPNSKTCRYIDKYLHGNSDKEFNSWQHSQAINLIRMLTINLARSFKYDKNIKLGNNFYKSSLIERKTDYLNKNYADI 307 MQGTGEMMNPQHAIRCWLRVRRTARWPNSKTCRYIDKYLHGNS+KE NSWQH QAINLIRMLTINLARSFKYDKNIKLGNNFYKSSLIERKTDYLNKNYADI Sbjct: 1 MQGTGEMMNPQHAIRCWLRVRRTARWPNSKTCRYIDKYLHGNSNKELNSWQHGQAINLIRMLTINLARSFKYDKNIKLGNNFYKSSLIERKTDYLNKNYADI 102
BLAST of SMED30001667 vs. Planmine SMEST
Match: SMESG000001175.1 (SMESG000001175.1) HSP 1 Score: 202.986 bits (515), Expect = 2.364e-64 Identity = 115/191 (60.21%), Postives = 145/191 (75.92%), Query Frame = -2 Query: 8 RFSDAQVLVAFLINFEGNRSNIWSIWNRLRTQLTPCELDSCYYPYSYIDGLLNGEKSNPWIHPGAIELGNCIXXXXXXXXXXXXXXXXXXLMQGTGEMMNPQHAIRCWLRVRRTARWPNSKTCRYIDKYLHGNSDKEFNSWQHSQAINLIRMLTINLARSFKYDKNIKLGNNFYKSSLIERKTDYLNKNYA 580 RFSD+QVL+ F+IN +G + +IWS WNRLRTQLTPC D Y YI L++GE + W HPGA +L ILTDATYRLALADLDTLA ++QG+ + +PQHA RCW RVRRTARWPNS+TCRYID +L GN + N W H QA++++RMLTI+LA+SFK DK++K+GN+ Y + LI RK DY+N YA Sbjct: 20 RFSDSQVLIDFIINKKGIKLDIWSSWNRLRTQLTPCASDPNYNIMKYISSLISGECIDNWWHPGAYKLATDILTDATYRLALADLDTLAKILQGSLSIWDPQHAARCWYRVRRTARWPNSRTCRYIDSFLKGNLAELPNKWLHGQALSMLRMLTISLAKSFKPDKDLKIGNDLYNAPLIYRKNDYINAQYA 210
BLAST of SMED30001667 vs. Planmine SMEST
Match: SMESG000011541.1 (SMESG000011541.1) HSP 1 Score: 205.682 bits (522), Expect = 1.877e-61 Identity = 112/191 (58.64%), Postives = 148/191 (77.49%), Query Frame = -2 Query: 8 RFSDAQVLVAFLINFEGNRSNIWSIWNRLRTQLTPCELDSCYYPYSYIDGLLNGEKSNPWIHPGAIELGNCIXXXXXXXXXXXXXXXXXXLMQGTGEMMNPQHAIRCWLRVRRTARWPNSKTCRYIDKYLHGNSDKEFNSWQHSQAINLIRMLTINLARSFKYDKNIKLGNNFYKSSLIERKTDYLNKNYA 580 R+SDAQVL+ F++N +G + +IWS WNRLRTQLTPC D Y +YI GL++G+ + W HPGA +L ILTDATYRLALADLD+LA ++QG+ + +PQHA RCW RVRRTARWPNS+TCRY+D +L GN D+ N W H QA++++RMLTI+LA+SFK DK++++GN+ Y + LI RK DY+N YA Sbjct: 29 RYSDAQVLIEFIMNEKGIKLDIWSSWNRLRTQLTPCASDPNYNIMNYISGLVSGDCVDNWRHPGAYKLATDILTDATYRLALADLDSLAKILQGSLSIWDPQHAARCWYRVRRTARWPNSRTCRYVDSFLKGNLDELPNKWLHGQALSMLRMLTISLAKSFKPDKDLRIGNDLYNAPLIYRKNDYMNAQYA 219
BLAST of SMED30001667 vs. Planmine SMEST
Match: SMESG000037845.1 (SMESG000037845.1) HSP 1 Score: 201.06 bits (510), Expect = 2.050e-59 Identity = 113/190 (59.47%), Postives = 144/190 (75.79%), Query Frame = -2 Query: 8 FSDAQVLVAFLINFEGNRSNIWSIWNRLRTQLTPCELDSCYYPYSYIDGLLNGEKSNPWIHPGAIELGNCIXXXXXXXXXXXXXXXXXXLMQGTGEMMNPQHAIRCWLRVRRTARWPNSKTCRYIDKYLHGNSDKEFNSWQHSQAINLIRMLTINLARSFKYDKNIKLGNNFYKSSLIERKTDYLNKNYA 577 FSDAQVL+ F++N +G + +IWS WNRLRTQLTPC DS Y YI L++GE + W HPGA +L ILTDATYRLALADLD+LA ++QG+ + +P HA RCW RVRRTARWPNS+TCRYID +L GN + N W H QA++++RMLTI+LA+SFK DK++K+GN+ Y + LI RK DY+N YA Sbjct: 552 FSDAQVLIDFIMNKKGIKLDIWSSWNRLRTQLTPCASDSNYIIIKYISSLISGECIDNWRHPGAYKLATDILTDATYRLALADLDSLAKILQGSLSIWDPHHAARCWYRVRRTARWPNSRTCRYIDSFLKGNLAELPNKWLHGQALSMLRMLTISLAKSFKPDKDLKIGNDLYNAPLIYRKNDYINAQYA 741
BLAST of SMED30001667 vs. Planmine SMEST
Match: SMESG000037845.1 (SMESG000037845.1) HSP 1 Score: 200.675 bits (509), Expect = 2.524e-59 Identity = 113/190 (59.47%), Postives = 144/190 (75.79%), Query Frame = -2 Query: 8 FSDAQVLVAFLINFEGNRSNIWSIWNRLRTQLTPCELDSCYYPYSYIDGLLNGEKSNPWIHPGAIELGNCIXXXXXXXXXXXXXXXXXXLMQGTGEMMNPQHAIRCWLRVRRTARWPNSKTCRYIDKYLHGNSDKEFNSWQHSQAINLIRMLTINLARSFKYDKNIKLGNNFYKSSLIERKTDYLNKNYA 577 FSDAQVL+ F++N +G + +IWS WNRLRTQLTPC DS Y YI L++GE + W HPGA +L ILTDATYRLALADLD+LA ++QG+ + +P HA RCW RVRRTARWPNS+TCRYID +L GN + N W H QA++++RMLTI+LA+SFK DK++K+GN+ Y + LI RK DY+N YA Sbjct: 552 FSDAQVLIDFIMNKKGIKLDIWSSWNRLRTQLTPCASDSNYIIIKYISSLISGECIDNWRHPGAYKLATDILTDATYRLALADLDSLAKILQGSLSIWDPHHAARCWYRVRRTARWPNSRTCRYIDSFLKGNLAELPNKWLHGQALSMLRMLTISLAKSFKPDKDLKIGNDLYNAPLIYRKNDYINAQYA 741 The following BLAST results are available for this feature:
BLAST of SMED30001667 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30001667 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30001667 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30001667 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30001667 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30001667 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30001667 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30001667 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30001667 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30001667 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30001667 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30001667 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30001667 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30001667 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 >SMED30001667 ID=SMED30001667|Name=SMED30001667|organism=Schmidtea mediterranea sexual|type=transcript|length=602bpback to top protein sequence of SMED30001667-orf-1 >SMED30001667-orf-1 ID=SMED30001667-orf-1|Name=SMED30001667-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=200bp KKKKKKKRFSDAQVLVAFLINFEGNRSNIWSIWNRLRTQLTPCELDSCYYback to top Annotated Terms
The following terms have been associated with this transcript:
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