SMED30016848
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., 2020SMED30016848 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 11
Alignments
SMED30016848 aligns in the following genomic locations:
Homology
BLAST of SMED30016848 vs. Planmine SMEST
Match: SMESG000079496.1 (SMESG000079496.1) HSP 1 Score: 334.339 bits (856), Expect = 5.138e-118 Identity = 161/181 (88.95%), Postives = 170/181 (93.92%), Query Frame = 1 Query: 145 MVKANCCCQIVSFSDSTNWVYSCKNDKYTHLYADANGSDLRLRSLTEDSCENYTNYDFREYHYRGNDCCVPVSVIQHKVSKKAIFYDDTTKRFVLKSVPGNIKKITDPNSNFLLFVGGGSTVACFSNRRTTTTLACVGKNLTTYVNTTYPPWKYSPAALQNSTKDFTWIRSAKINASHCKN 687 M+KANCCCQ VSFSDSTNWVYSCKND+Y +L ADANGSDL+L ++ EDSCENYTNY+FREYHYR NDC VPVSVIQHKVSKKAIFYD TT+RFVLKSVP NI+KITDPNSNFLLFVGGGSTVACFSNRRTT TLACVGKNLTTYVNTTYPPWKYSPAALQNSTKDFTWIRSA INASHCKN Sbjct: 1 MMKANCCCQKVSFSDSTNWVYSCKNDEYKYLKADANGSDLKLWTMVEDSCENYTNYEFREYHYRCNDCNVPVSVIQHKVSKKAIFYDGTTERFVLKSVPENIEKITDPNSNFLLFVGGGSTVACFSNRRTTRTLACVGKNLTTYVNTTYPPWKYSPAALQNSTKDFTWIRSANINASHCKN 181
BLAST of SMED30016848 vs. Planmine SMEST
Match: SMESG000079496.1 (SMESG000079496.1) HSP 1 Score: 331.257 bits (848), Expect = 7.683e-117 Identity = 160/180 (88.89%), Postives = 169/180 (93.89%), Query Frame = 1 Query: 148 VKANCCCQIVSFSDSTNWVYSCKNDKYTHLYADANGSDLRLRSLTEDSCENYTNYDFREYHYRGNDCCVPVSVIQHKVSKKAIFYDDTTKRFVLKSVPGNIKKITDPNSNFLLFVGGGSTVACFSNRRTTTTLACVGKNLTTYVNTTYPPWKYSPAALQNSTKDFTWIRSAKINASHCKN 687 +KANCCCQ VSFSDSTNWVYSCKND+Y +L ADANGSDL+L ++ EDSCENYTNY+FREYHYR NDC VPVSVIQHKVSKKAIFYD TT+RFVLKSVP NI+KITDPNSNFLLFVGGGSTVACFSNRRTT TLACVGKNLTTYVNTTYPPWKYSPAALQNSTKDFTWIRSA INASHCKN Sbjct: 1 MKANCCCQKVSFSDSTNWVYSCKNDEYKYLKADANGSDLKLWTMVEDSCENYTNYEFREYHYRCNDCNVPVSVIQHKVSKKAIFYDGTTERFVLKSVPENIEKITDPNSNFLLFVGGGSTVACFSNRRTTRTLACVGKNLTTYVNTTYPPWKYSPAALQNSTKDFTWIRSANINASHCKN 180
BLAST of SMED30016848 vs. Planmine SMEST
Match: SMESG000079498.1 (SMESG000079498.1) HSP 1 Score: 168.318 bits (425), Expect = 1.268e-52 Identity = 87/158 (55.06%), Postives = 106/158 (67.09%), Query Frame = 1 Query: 184 SDSTNWVYSCKNDKYTHLYADANGSDLRLRSLTEDSCENYTNYDFREYHYRGNDCCVPVSVIQHKVSKKAIFYDDTTKRFVLKSVPGNIKKITDPNSNFLLFVGGGSTVACFSNRRTTTTLACVGKNLTTYVNTTYPPWKYSPAALQNSTKDFTWIRS 657 D T Y C NDKY L A+ +GSDLRL + ++ + F+E HY D +P+SVIQH+VS KA+FYDD K F LKS N+ ITDPNSNFLL+VGGGSTV CFSN++TT TLA VG NL TY NTT PPW S L++S DF+WIR+ Sbjct: 10 GDFTECTYCCYNDKYYWLTANTDGSDLRLLNTKTEAGHVIEPFMFKELHYHSEDG-IPISVIQHEVSGKALFYDDENKTFELKSSEDNLDNITDPNSNFLLYVGGGSTVTCFSNKKTTGTLAYVGLNLITYENTTSPPWTLSQDTLEDSRNDFSWIRN 166
BLAST of SMED30016848 vs. Planmine SMEST
Match: SMESG000025939.1 (SMESG000025939.1) HSP 1 Score: 68.5514 bits (166), Expect = 3.460e-14 Identity = 49/159 (30.82%), Postives = 81/159 (50.94%), Query Frame = 1 Query: 190 STNWVYSCKNDKYTHLYADANGSDLRLRSLTEDSCENYTNYDFREYHYRGNDCCVPVSVIQHKVSKKAIFYDDTTKRFVLKSVPGNIKKITDPNSNFLLFVGGGSTVACFSNRRTTTTLACVGKNLTTYVNTTYPPWKYSPAAL-QNSTKDFTWIRSAK 663 S +V+ C ++ +L AD++ L+L + + ++ N F++Y+ ++ V +SVI+HK S K I+YD+ +K F+LK P +SNF+L GG S + C SN T TLA T ++ PW YS L + K W + ++ Sbjct: 18 SNEYVFCCYLNENAYLVADSDMVHLQLTNFS--MLQSTHNVIFQQYYLDSDN--VHLSVIKHKRSGKFIYYDEDSKDFILKENPE--VHFDKFDSNFILARGGNSNIFCLSNLETNATLAYNNGQFQT-LHIPEKPWLYSSEDLIDDKMKHIAWKKKSE 169
BLAST of SMED30016848 vs. Planmine SMEST
Match: SMESG000025939.1 (SMESG000025939.1) HSP 1 Score: 68.9366 bits (167), Expect = 3.989e-14 Identity = 49/159 (30.82%), Postives = 81/159 (50.94%), Query Frame = 1 Query: 190 STNWVYSCKNDKYTHLYADANGSDLRLRSLTEDSCENYTNYDFREYHYRGNDCCVPVSVIQHKVSKKAIFYDDTTKRFVLKSVPGNIKKITDPNSNFLLFVGGGSTVACFSNRRTTTTLACVGKNLTTYVNTTYPPWKYSPAAL-QNSTKDFTWIRSAK 663 S +V+ C ++ +L AD++ L+L + + ++ N F++Y+ ++ V +SVI+HK S K I+YD+ +K F+LK P +SNF+L GG S + C SN T TLA T ++ PW YS L + K W + ++ Sbjct: 38 SNEYVFCCYLNENAYLVADSDMVHLQLTNFS--MLQSTHNVIFQQYYLDSDN--VHLSVIKHKRSGKFIYYDEDSKDFILKENPE--VHFDKFDSNFILARGGNSNIFCLSNLETNATLAYNNGQFQT-LHIPEKPWLYSSEDLIDDKMKHIAWKKKSE 189 The following BLAST results are available for this feature:
BLAST of SMED30016848 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30016848 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30016848 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30016848 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30016848 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30016848 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30016848 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30016848 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30016848 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30016848 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30016848 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30016848 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30016848 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30016848 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 >SMED30016848 ID=SMED30016848|Name=SMED30016848|organism=Schmidtea mediterranea sexual|type=transcript|length=712bpback to top protein sequence of SMED30016848-orf-1 >SMED30016848-orf-1 ID=SMED30016848-orf-1|Name=SMED30016848-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=182bp MVKANCCCQIVSFSDSTNWVYSCKNDKYTHLYADANGSDLRLRSLTEDSCback to top Annotated Terms
The following terms have been associated with this transcript:
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