SMED30002839
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., 2020SMED30002839 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 12
Alignments
SMED30002839 aligns in the following genomic locations:
Homology
BLAST of SMED30002839 vs. Planmine SMEST
Match: SMESG000079498.1 (SMESG000079498.1) HSP 1 Score: 360.533 bits (924), Expect = 1.646e-128 Identity = 174/174 (100.00%), Postives = 174/174 (100.00%), Query Frame = 3 Query: 93 MDVNTVYYTGDFTECTYCCYNDKYYWLTANTDGSDLRLLNTKTEAGHVIEPFMFKELHYHSEDGIPISVIQHEVSGKALFYDDENKTFELKSSEDNLDNITDPNSNFLLYVGGGSTVTCFSNKKTTGTLAYVGLNLITYENTTSPPWTLSQDTLEDSRNDFSWIRNTSDFTNKG 614 MDVNTVYYTGDFTECTYCCYNDKYYWLTANTDGSDLRLLNTKTEAGHVIEPFMFKELHYHSEDGIPISVIQHEVSGKALFYDDENKTFELKSSEDNLDNITDPNSNFLLYVGGGSTVTCFSNKKTTGTLAYVGLNLITYENTTSPPWTLSQDTLEDSRNDFSWIRNTSDFTNKG Sbjct: 1 MDVNTVYYTGDFTECTYCCYNDKYYWLTANTDGSDLRLLNTKTEAGHVIEPFMFKELHYHSEDGIPISVIQHEVSGKALFYDDENKTFELKSSEDNLDNITDPNSNFLLYVGGGSTVTCFSNKKTTGTLAYVGLNLITYENTTSPPWTLSQDTLEDSRNDFSWIRNTSDFTNKG 174
BLAST of SMED30002839 vs. Planmine SMEST
Match: SMESG000079496.1 (SMESG000079496.1) HSP 1 Score: 166.007 bits (419), Expect = 1.061e-51 Identity = 83/157 (52.87%), Postives = 106/157 (67.52%), Query Frame = 3 Query: 120 GDFTECTYCCYNDKYYWLTANTDGSDLRLLNTKTEAGHVIEPFMFKELHYHSED-GIPISVIQHEVSGKALFYDDENKTFELKSSEDNLDNITDPNSNFLLYVGGGSTVTCFSNKKTTGTLAYVGLNLITYENTTSPPWTLSQDTLEDSRNDFSWIR 587 D T Y C ND+Y +L A+ +GSDL+L ++ + F+E HY D +P+SVIQH+VS KA+FYD + F LKS +N++ ITDPNSNFLL+VGGGSTV CFSN++TT TLA VG NL TY NTT PPW S L++S DF+WIR Sbjct: 14 SDSTNWVYSCKNDEYKYLKADANGSDLKLWTMVEDSCENYTNYEFREYHYRCNDCNVPVSVIQHKVSKKAIFYDGTTERFVLKSVPENIEKITDPNSNFLLFVGGGSTVACFSNRRTTRTLACVGKNLTTYVNTTYPPWKYSPAALQNSTKDFTWIR 170
BLAST of SMED30002839 vs. Planmine SMEST
Match: SMESG000079496.1 (SMESG000079496.1) HSP 1 Score: 166.007 bits (419), Expect = 1.185e-51 Identity = 83/157 (52.87%), Postives = 106/157 (67.52%), Query Frame = 3 Query: 120 GDFTECTYCCYNDKYYWLTANTDGSDLRLLNTKTEAGHVIEPFMFKELHYHSED-GIPISVIQHEVSGKALFYDDENKTFELKSSEDNLDNITDPNSNFLLYVGGGSTVTCFSNKKTTGTLAYVGLNLITYENTTSPPWTLSQDTLEDSRNDFSWIR 587 D T Y C ND+Y +L A+ +GSDL+L ++ + F+E HY D +P+SVIQH+VS KA+FYD + F LKS +N++ ITDPNSNFLL+VGGGSTV CFSN++TT TLA VG NL TY NTT PPW S L++S DF+WIR Sbjct: 13 SDSTNWVYSCKNDEYKYLKADANGSDLKLWTMVEDSCENYTNYEFREYHYRCNDCNVPVSVIQHKVSKKAIFYDGTTERFVLKSVPENIEKITDPNSNFLLFVGGGSTVACFSNRRTTRTLACVGKNLTTYVNTTYPPWKYSPAALQNSTKDFTWIR 169
BLAST of SMED30002839 vs. Planmine SMEST
Match: SMESG000025939.1 (SMESG000025939.1) HSP 1 Score: 75.8702 bits (185), Expect = 5.943e-17 Identity = 50/158 (31.65%), Postives = 87/158 (55.06%), Query Frame = 3 Query: 132 ECTYCCYNDKYYWLTANTDGSDLRLLN-TKTEAGHVIEPFMFKELHYHSEDGIPISVIQHEVSGKALFYDDENKTFELKSS-EDNLDNITDPNSNFLLYVGGGSTVTCFSNKKTTGTLAYVGLNLITYENTTSPPWTLSQDTLEDSRNDFSWIRNTSD 599 E +CCY ++ +L A++D L+L N + ++ H + +F++ +Y D + +SVI+H+ SGK ++YD+++K F LK + E + D +SNF+L GG S + C SN +T TLAY T P S+D ++D +W + + + Sbjct: 20 EYVFCCYLNENAYLVADSDMVHLQLTNFSMLQSTHNV---IFQQ-YYLDSDNVHLSVIKHKRSGKFIYYDEDSKDFILKENPEVHFDKF---DSNFILARGGNSNIFCLSNLETNATLAYNNGQFQTLHIPEKPWLYSSEDLIDDKMKHIAWKKKSEN 170
BLAST of SMED30002839 vs. Planmine SMEST
Match: SMESG000025939.1 (SMESG000025939.1) HSP 1 Score: 76.2554 bits (186), Expect = 6.260e-17 Identity = 50/158 (31.65%), Postives = 87/158 (55.06%), Query Frame = 3 Query: 132 ECTYCCYNDKYYWLTANTDGSDLRLLN-TKTEAGHVIEPFMFKELHYHSEDGIPISVIQHEVSGKALFYDDENKTFELKSS-EDNLDNITDPNSNFLLYVGGGSTVTCFSNKKTTGTLAYVGLNLITYENTTSPPWTLSQDTLEDSRNDFSWIRNTSD 599 E +CCY ++ +L A++D L+L N + ++ H + +F++ +Y D + +SVI+H+ SGK ++YD+++K F LK + E + D +SNF+L GG S + C SN +T TLAY T P S+D ++D +W + + + Sbjct: 40 EYVFCCYLNENAYLVADSDMVHLQLTNFSMLQSTHNV---IFQQ-YYLDSDNVHLSVIKHKRSGKFIYYDEDSKDFILKENPEVHFDKF---DSNFILARGGNSNIFCLSNLETNATLAYNNGQFQTLHIPEKPWLYSSEDLIDDKMKHIAWKKKSEN 190 The following BLAST results are available for this feature:
BLAST of SMED30002839 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30002839 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30002839 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30002839 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30002839 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30002839 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30002839 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30002839 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30002839 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30002839 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30002839 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30002839 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30002839 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30002839 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 >SMED30002839 ID=SMED30002839|Name=SMED30002839|organism=Schmidtea mediterranea sexual|type=transcript|length=697bpback to top protein sequence of SMED30002839-orf-1 >SMED30002839-orf-1 ID=SMED30002839-orf-1|Name=SMED30002839-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=175bp MDVNTVYYTGDFTECTYCCYNDKYYWLTANTDGSDLRLLNTKTEAGHVIEback to top Annotated Terms
The following terms have been associated with this transcript:
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