SMED30033006
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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., 2020SMED30033006 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 2
Alignments
SMED30033006 aligns in the following genomic locations: Homology
BLAST of SMED30033006 vs. Planmine SMEST
Match: SMESG000059904.1 (SMESG000059904.1) HSP 1 Score: 195.282 bits (495), Expect = 1.054e-58 Identity = 92/104 (88.46%), Postives = 97/104 (93.27%), Query Frame = 2
Query: 2 EEAAALVAEQHPEFVKEDDTTLTTKRSEEHMLPIQVKKTDEMQICLDISPVHNSTTTTKERSPALTSYWMDEFGEELCHTVPQVGTIPFQPLRNKRKFPVDIDE 313
EEAAALVAEQHPEFVK+DDTTLT KRS+EHMLPI VK+TDEMQICLDISP+ N +TTTKERSP L S WMDEFGEELCHTVPQVGTIPFQPLRNKRKFPVDIDE
Sbjct: 242 EEAAALVAEQHPEFVKKDDTTLTLKRSKEHMLPIHVKETDEMQICLDISPIENPSTTTKERSPTLASCWMDEFGEELCHTVPQVGTIPFQPLRNKRKFPVDIDE 345
BLAST of SMED30033006 vs. Planmine SMEST
Match: SMESG000007620.1 (SMESG000007620.1) HSP 1 Score: 192.2 bits (487), Expect = 9.044e-55 Identity = 91/104 (87.50%), Postives = 96/104 (92.31%), Query Frame = 2
Query: 2 EEAAALVAEQHPEFVKEDDTTLTTKRSEEHMLPIQVKKTDEMQICLDISPVHNSTTTTKERSPALTSYWMDEFGEELCHTVPQVGTIPFQPLRNKRKFPVDIDE 313
EEAAALVAEQHPEFVKEDDTTLT KRS+EH+L I VK+TDEMQICLDISPV+NSTTTTK RSP L SYWMDEFGEEL H+VPQVGT PFQPLRNKRKFPVDIDE
Sbjct: 553 EEAAALVAEQHPEFVKEDDTTLTPKRSKEHVLQIHVKETDEMQICLDISPVNNSTTTTKARSPTLASYWMDEFGEELHHSVPQVGTTPFQPLRNKRKFPVDIDE 656
BLAST of SMED30033006 vs. Planmine SMEST
Match: SMESG000042945.1 (SMESG000042945.1) HSP 1 Score: 177.563 bits (449), Expect = 1.136e-51 Identity = 85/104 (81.73%), Postives = 90/104 (86.54%), Query Frame = 2
Query: 2 EEAAALVAEQHPEFVKEDDTTLTTKRSEEHMLPIQVKKTDEMQICLDISPVHNSTTTTKERSPALTSYWMDEFGEELCHTVPQVGTIPFQPLRNKRKFPVDIDE 313
EEAAALVAEQHPEFVK+DD T KRS E +LPI VK+TDEMQ+CLDISPV NS TT +ERSP L S WMDEFGEELCHTVPQVGT PFQPLRNKRKFPVDIDE
Sbjct: 269 EEAAALVAEQHPEFVKDDDPAPTPKRSTEPVLPIHVKETDEMQMCLDISPVENSITTMRERSPTLASRWMDEFGEELCHTVPQVGTTPFQPLRNKRKFPVDIDE 372
BLAST of SMED30033006 vs. Planmine SMEST
Match: SMESG000039380.1 (SMESG000039380.1) HSP 1 Score: 169.088 bits (427), Expect = 9.887e-50 Identity = 83/104 (79.81%), Postives = 88/104 (84.62%), Query Frame = 2
Query: 2 EEAAALVAEQHPEFVKEDDTTLTTKRSEEHMLPIQVKKTDEMQICLDISPVHNSTTTTKERSPALTSYWMDEFGEELCHTVPQVGTIPFQPLRNKRKFPVDIDE 313
EEAAALV EQHPEFV ED K S E ++PIQVK+TDE+ ICLDISPV NSTTTTKERSP LTS WM+EFGEELCHTVPQVGT PFQPLRNKRKFPVDIDE
Sbjct: 161 EEAAALVTEQHPEFVTEDVPASNPKGSTELVMPIQVKETDEIPICLDISPVENSTTTTKERSPTLTSCWMNEFGEELCHTVPQVGTTPFQPLRNKRKFPVDIDE 264
BLAST of SMED30033006 vs. Planmine SMEST
Match: SMESG000072638.1 (SMESG000072638.1) HSP 1 Score: 172.555 bits (436), Expect = 4.969e-49 Identity = 84/104 (80.77%), Postives = 87/104 (83.65%), Query Frame = 2
Query: 2 EEAAALVAEQHPEFVKEDDTTLTTKRSEEHMLPIQVKKTDEMQICLDISPVHNSTTTTKERSPALTSYWMDEFGEELCHTVPQVGTIPFQPLRNKRKFPVDIDE 313
EEAAALVAEQHPEFV EDD K S E ++PIQVK+TDE QICL ISPV NSTTT KERSP L S WMDEFGEELCHTVPQVGT PFQPLRNKRKFPVDIDE
Sbjct: 350 EEAAALVAEQHPEFVTEDDPASNPKGSTELVIPIQVKETDERQICLGISPVENSTTTMKERSPTLASCWMDEFGEELCHTVPQVGTTPFQPLRNKRKFPVDIDE 453 The following BLAST results are available for this feature:
BLAST of SMED30033006 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30033006 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30033006 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30033006 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30033006 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30033006 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30033006 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30033006 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30033006 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30033006 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30033006 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30033006 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30033006 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30033006 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 >SMED30033006 ID=SMED30033006|Name=SMED30033006|organism=Schmidtea mediterranea sexual|type=transcript|length=1208bpback to top protein sequence of SMED30033006-orf-1 >SMED30033006-orf-1 ID=SMED30033006-orf-1|Name=SMED30033006-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=105bp EEAAALVAEQHPEFVKEDDTTLTTKRSEEHMLPIQVKKTDEMQICLDISPback to top |
