SMED30012217
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., 2020SMED30012217 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 18
Alignments
SMED30012217 aligns in the following genomic locations:
Homology
BLAST of SMED30012217 vs. Planmine SMEST
Match: SMESG000079382.1 (SMESG000079382.1) HSP 1 Score: 526.554 bits (1355), Expect = 0.000e+0 Identity = 265/265 (100.00%), Postives = 265/265 (100.00%), Query Frame = 2 Query: 173 MTKIYHCIKDKNMEDFRNKDPANGYAYHVTNIDCCGRTKLNMKKINWIRNRVDERVESIKSILSGESXXXXXXXXXXXDMTGLADQLAAINLNEDLELRPFEIRKSNYHPAVEGVEGVFMNTTLYDGHLPDWTVYPFGKPQCQVDHYYQRISIKFDKISEKYPQCKFWCIKDKQRHYICYKSESKIKNFNKTKSATAGIKFSEDFQDSELEVMGIKKEGATKDILPYLQNDYKKEEYFNNLVLLGGIEILGDAIIDIAHKFNCKS 967 MTKIYHCIKDKNMEDFRNKDPANGYAYHVTNIDCCGRTKLNMKKINWIRNRVDERVESIKSILSGESQPNQPNQPNQQDMTGLADQLAAINLNEDLELRPFEIRKSNYHPAVEGVEGVFMNTTLYDGHLPDWTVYPFGKPQCQVDHYYQRISIKFDKISEKYPQCKFWCIKDKQRHYICYKSESKIKNFNKTKSATAGIKFSEDFQDSELEVMGIKKEGATKDILPYLQNDYKKEEYFNNLVLLGGIEILGDAIIDIAHKFNCKS Sbjct: 1 MTKIYHCIKDKNMEDFRNKDPANGYAYHVTNIDCCGRTKLNMKKINWIRNRVDERVESIKSILSGESQPNQPNQPNQQDMTGLADQLAAINLNEDLELRPFEIRKSNYHPAVEGVEGVFMNTTLYDGHLPDWTVYPFGKPQCQVDHYYQRISIKFDKISEKYPQCKFWCIKDKQRHYICYKSESKIKNFNKTKSATAGIKFSEDFQDSELEVMGIKKEGATKDILPYLQNDYKKEEYFNNLVLLGGIEILGDAIIDIAHKFNCKS 265
BLAST of SMED30012217 vs. Planmine SMEST
Match: SMESG000079382.1 (SMESG000079382.1) HSP 1 Score: 501.901 bits (1291), Expect = 0.000e+0 Identity = 253/253 (100.00%), Postives = 253/253 (100.00%), Query Frame = 2 Query: 209 MEDFRNKDPANGYAYHVTNIDCCGRTKLNMKKINWIRNRVDERVESIKSILSGESXXXXXXXXXXXDMTGLADQLAAINLNEDLELRPFEIRKSNYHPAVEGVEGVFMNTTLYDGHLPDWTVYPFGKPQCQVDHYYQRISIKFDKISEKYPQCKFWCIKDKQRHYICYKSESKIKNFNKTKSATAGIKFSEDFQDSELEVMGIKKEGATKDILPYLQNDYKKEEYFNNLVLLGGIEILGDAIIDIAHKFNCKS 967 MEDFRNKDPANGYAYHVTNIDCCGRTKLNMKKINWIRNRVDERVESIKSILSGESQPNQPNQPNQQDMTGLADQLAAINLNEDLELRPFEIRKSNYHPAVEGVEGVFMNTTLYDGHLPDWTVYPFGKPQCQVDHYYQRISIKFDKISEKYPQCKFWCIKDKQRHYICYKSESKIKNFNKTKSATAGIKFSEDFQDSELEVMGIKKEGATKDILPYLQNDYKKEEYFNNLVLLGGIEILGDAIIDIAHKFNCKS Sbjct: 1 MEDFRNKDPANGYAYHVTNIDCCGRTKLNMKKINWIRNRVDERVESIKSILSGESQPNQPNQPNQQDMTGLADQLAAINLNEDLELRPFEIRKSNYHPAVEGVEGVFMNTTLYDGHLPDWTVYPFGKPQCQVDHYYQRISIKFDKISEKYPQCKFWCIKDKQRHYICYKSESKIKNFNKTKSATAGIKFSEDFQDSELEVMGIKKEGATKDILPYLQNDYKKEEYFNNLVLLGGIEILGDAIIDIAHKFNCKS 253
BLAST of SMED30012217 vs. Planmine SMEST
Match: SMESG000079668.1 (SMESG000079668.1) HSP 1 Score: 395.201 bits (1014), Expect = 1.849e-138 Identity = 206/266 (77.44%), Postives = 218/266 (81.95%), Query Frame = 2 Query: 224 NKDPANGYAYHVTNIDCCGRTKLNMKKINWIRNRVD------------------ERVESIKSILSGESXXXXXXXXXXXDMTGLADQLAAINLNEDLELRPFEIRKSNYHPAVEGVEGVFMNTTLYDGHLPDWTVYPFGKPQCQVDHYYQRISIKFDKISEKYPQCKFWCIKDKQRHYICYKSESKIKNFNKTKSATAGIKFSEDFQDSELEVMGIKKEGATKDILPYLQNDYKKEEYFNNLVLLGGIEILGDAIIDIAHKFNCKS 967 N+DPANGYAYHVT+ DCCGRT +M +INWIRNRVD E ++ SILSGESQPNQ + + D+T IN EL+ F IR+S YHP VEGVEGVFM+TTLYDGHLPDWTVYPFGKPQCQVDHYYQRISIKFDKISEKYPQCKFWCIKDKQRHYICYKSESKIKNFNKTKSATAGIKFSEDFQDSELEVMGIKKEGATKDILPYLQNDYKKEEYFNNLVLLGGIEILGDAIIDIAHKFNCKS Sbjct: 12 NEDPANGYAYHVTSTDCCGRTDNDMLQINWIRNRVDGKKIFVFIKFFYILFGVKECLDHNSSILSGESQPNQQEEDEK-DLTYPFKMKTEINC----ELKAFRIRESYYHPTVEGVEGVFMSTTLYDGHLPDWTVYPFGKPQCQVDHYYQRISIKFDKISEKYPQCKFWCIKDKQRHYICYKSESKIKNFNKTKSATAGIKFSEDFQDSELEVMGIKKEGATKDILPYLQNDYKKEEYFNNLVLLGGIEILGDAIIDIAHKFNCKS 272
BLAST of SMED30012217 vs. Planmine SMEST
Match: SMESG000079644.1 (SMESG000079644.1) HSP 1 Score: 148.673 bits (374), Expect = 5.166e-42 Identity = 98/275 (35.64%), Postives = 146/275 (53.09%), Query Frame = 2 Query: 218 FRNKDPANGYAYHVTNIDCCGRTKLNMKKINWIRNRVDERVESIKSILSGESXXXXXXXXXXXDMTGLADQLAAINLNEDLELRPFEIRKSNYHPAVEGVEGVFMNTTLYDGHLPDWT-VYPFGK---------PQCQVD----HYYQRISIKFDKISEKYPQCKFWCI-KD---------------KQRHYICYKS---------ESKIKNFNK--TKSATAGIKFSEDFQDSELEVMGIKKEGATKDILPYLQNDYKKEEYFNNLVLLGGIEI 919 FR GYAYHVT+IDCCG+T M+ I+W N + L E + + +D+ + I N+++ L+ FEI+K YHP+ EGV+ VF+N TL++ LP+ T VYP + P +++ H+YQRISIKF +IS++YP+CKFWC+ KD KQ YICY E+K + ++ ++ + I F +D E + I K+GATK+IL +QN+Y K Y+ ++VLLG I+I Sbjct: 5 FRTTHSMRGYAYHVTSIDCCGKTDNTMRIIDWDHNPPRDGFH----YLDAEESQTSNEENSVEDLIDQMGKKVHIKDNKNI-LKAFEIKKCKYHPSAEGVKAVFLNLTLFNNSLPNSTKVYPHARQIFSEDYCIPSRRLEYPYGHFYQRISIKFKRISKRYPKCKFWCLMKDEDKGRSEKFTNSSCVKQISYICYNEEEEIENITFENKYEEYDVEIVRNRSDEILFYDDIDQYERCKLKIIKDGATKNILNLIQNNYYKNTYYTSIVLLGDIDI 274
BLAST of SMED30012217 vs. Planmine SMEST
Match: SMESG000079644.1 (SMESG000079644.1) HSP 1 Score: 144.821 bits (364), Expect = 9.736e-41 Identity = 96/267 (35.96%), Postives = 144/267 (53.93%), Query Frame = 2 Query: 242 GYAYHVTNIDCCGRTKLNMKKINWIRNRVDERVESIKSILSGESXXXXXXXXXXXDMTGLADQLAAINLNEDLELRPFEIRKSNYHPAVEGVEGVFMNTTLYDGHLPDWT-VYPFGK---------PQCQVD----HYYQRISIKFDKISEKYPQCKFWCI-KD---------------KQRHYICYKS---------ESKIKNFNK--TKSATAGIKFSEDFQDSELEVMGIKKEGATKDILPYLQNDYKKEEYFNNLVLLGGIEI 919 GYAYHVT+IDCCG+T M+ I+W N + L E + + +D+ + I N+++ L+ FEI+K YHP+ EGV+ VF+N TL++ LP+ T VYP + P +++ H+YQRISIKF +IS++YP+CKFWC+ KD KQ YICY E+K + ++ ++ + I F +D E + I K+GATK+IL +QN+Y K Y+ ++VLLG I+I Sbjct: 3 GYAYHVTSIDCCGKTDNTMRIIDWDHNPPRDGFH----YLDAEESQTSNEENSVEDLIDQMGKKVHIKDNKNI-LKAFEIKKCKYHPSAEGVKAVFLNLTLFNNSLPNSTKVYPHARQIFSEDYCIPSRRLEYPYGHFYQRISIKFKRISKRYPKCKFWCLMKDEDKGRSEKFTNSSCVKQISYICYNEEEEIENITFENKYEEYDVEIVRNRSDEILFYDDIDQYERCKLKIIKDGATKNILNLIQNNYYKNTYYTSIVLLGDIDI 264 The following BLAST results are available for this feature:
BLAST of SMED30012217 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30012217 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30012217 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30012217 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30012217 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30012217 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30012217 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30012217 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30012217 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30012217 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30012217 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30012217 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30012217 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30012217 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 >SMED30012217 ID=SMED30012217|Name=SMED30012217|organism=Schmidtea mediterranea sexual|type=transcript|length=1109bpback to top protein sequence of SMED30012217-orf-1 >SMED30012217-orf-1 ID=SMED30012217-orf-1|Name=SMED30012217-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=266bp MTKIYHCIKDKNMEDFRNKDPANGYAYHVTNIDCCGRTKLNMKKINWIRNback to top |