SMED30025582
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., 2020SMED30025582 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 4
Alignments
SMED30025582 aligns in the following genomic locations:
Homology
BLAST of SMED30025582 vs. Planmine SMEST
Match: SMESG000057502.1 (SMESG000057502.1) HSP 1 Score: 286.189 bits (731), Expect = 6.195e-99 Identity = 156/156 (100.00%), Postives = 156/156 (100.00%), Query Frame = 3 Query: 78 MPIITVTVVIIDYCKRELQKFIENIDPMAPIGNLKTVISNKYQIEIQYLNCKGQILALEKNCKYYDIKDGSTIICGKQEDFIKLKVEMNSKDPVQEPFYINVKRFISTEQLLXXXXXXXXXXXXFPIVHFQGKPLRHGVSLSDQFIRNGDIINIVQ 545 MPIITVTVVIIDYCKRELQKFIENIDPMAPIGNLKTVISNKYQIEIQYLNCKGQILALEKNCKYYDIKDGSTIICGKQEDFIKLKVEMNSKDPVQEPFYINVKRFISTEQLLNEIINNINCNIEFPIVHFQGKPLRHGVSLSDQFIRNGDIINIVQ Sbjct: 1 MPIITVTVVIIDYCKRELQKFIENIDPMAPIGNLKTVISNKYQIEIQYLNCKGQILALEKNCKYYDIKDGSTIICGKQEDFIKLKVEMNSKDPVQEPFYINVKRFISTEQLLNEIINNINCNIEFPIVHFQGKPLRHGVSLSDQFIRNGDIINIVQ 156
BLAST of SMED30025582 vs. Planmine SMEST
Match: SMESG000016779.1 (SMESG000016779.1) HSP 1 Score: 88.5817 bits (218), Expect = 1.584e-21 Identity = 56/154 (36.36%), Postives = 86/154 (55.84%), Query Frame = 3 Query: 78 MPIITVTVVIIDYCKRELQKFIENIDPMAPIGNLKTVISNKYQIEIQYLNCKGQILALEKNCKYYDIKDGST--IICGKQEDFIKLKVEMNSKDPVQEPFYINVKRFISTEQLLXXXXXXXXXXXXFPIVHFQGKPLRHGVSLSDQFIRNGDII 533 M +IT T+ +D R+ ++ N+DP P+ L+T + IQ + K + L E NC+YY+I+ GS IIC ++ I LKV++ SK +PF I V +TEQL++ I N I P + ++G+ L HG SL +Q +RN D+I Sbjct: 1 MSMITTTIKFLDSNGRQFRQLDSNVDPQKPLRILRTNLEQTTGEYIQCIKFKDEELNDENNCRYYNIRSGSELLIICKRESLEITLKVDVASKSSNLKPFTIEVDPNKTTEQLVDLITNKIPFKTSSPDLSWKGRRLTHGESLVNQGVRNNDLI 154
BLAST of SMED30025582 vs. Planmine SMEST
Match: SMESG000016781.1 (SMESG000016781.1) HSP 1 Score: 86.2705 bits (212), Expect = 1.089e-20 Identity = 55/152 (36.18%), Postives = 85/152 (55.92%), Query Frame = 3 Query: 84 IITVTVVIIDYCKRELQKFIENIDPMAPIGNLKTVISNKYQIEIQYLNCKGQILALEKNCKYYDIKDGST--IICGKQEDFIKLKVEMNSKDPVQEPFYINVKRFISTEQLLXXXXXXXXXXXXFPIVHFQGKPLRHGVSLSDQFIRNGDII 533 +IT T+ +D R+ ++ N+DP P+ L+T + IQ + K + L E NC+YY+I+ GS IIC ++ I LKV++ SK +PF I V +TEQL++ I I N P + ++G+ L HG SL +Q +RN D+I Sbjct: 1 MITTTIKFLDSNGRQFRQLDSNVDPQKPLRILRTNLEQTTGEYIQCIKFKDEELNDENNCRYYNIRSGSELLIICKRESLEITLKVDVASKSSNLKPFTIEVDPNKTTEQLVDLITKKIPFNTSSPDLSWKGRRLTHGESLVNQGVRNNDLI 152
BLAST of SMED30025582 vs. Planmine SMEST
Match: SMESG000016779.1 (SMESG000016779.1) HSP 1 Score: 86.2705 bits (212), Expect = 1.089e-20 Identity = 55/152 (36.18%), Postives = 85/152 (55.92%), Query Frame = 3 Query: 84 IITVTVVIIDYCKRELQKFIENIDPMAPIGNLKTVISNKYQIEIQYLNCKGQILALEKNCKYYDIKDGST--IICGKQEDFIKLKVEMNSKDPVQEPFYINVKRFISTEQLLXXXXXXXXXXXXFPIVHFQGKPLRHGVSLSDQFIRNGDII 533 +IT T+ +D R+ ++ N+DP P+ L+T + IQ + K + L E NC+YY+I+ GS IIC ++ I LKV++ SK +PF I V +TEQL++ I N I P + ++G+ L HG SL +Q +RN D+I Sbjct: 1 MITTTIKFLDSNGRQFRQLDSNVDPQKPLRILRTNLEQTTGEYIQCIKFKDEELNDENNCRYYNIRSGSELLIICKRESLEITLKVDVASKSSNLKPFTIEVDPNKTTEQLVDLITNKIPFKTSSPDLSWKGRRLTHGESLVNQGVRNNDLI 152
BLAST of SMED30025582 vs. Planmine SMEST
Match: SMESG000016789.1 (SMESG000016789.1) HSP 1 Score: 86.2705 bits (212), Expect = 1.230e-20 Identity = 58/157 (36.94%), Postives = 88/157 (56.05%), Query Frame = 3 Query: 78 MPIITVTVVIIDYCKRELQKFIENIDPMAPIGNLKTVISNKYQIEIQYLNCKGQILALEKNCKYYDIKDGST--IICGKQEDFIKLKVEMNSKDPVQEPFYINVKRFISTEQLLXXXXXXXXXXXXFPIVHFQGKPLRHGVSLSDQFIRNGDIINIV 542 M I + + I + + L++ N +P I LK S+KY ++IQ + GQ L+ +KNC +Y+I+DGST +I K + I L VE+ S +P Q P + V I TE L+N I NI N + + G+ LR GVSL DQ ++N D+I ++ Sbjct: 1 MSNIKLNLQITNSNRELLKRDQVNANPSMSISVLKGNWSDKYGVDIQSVRFNGQTLSDDKNCNFYNIRDGSTLELISSKSDSEINLIVEVQSINPGQRPIQVRVNPSIKTEDLMNVIKENIYFNFDSAYLTHHGETLREGVSLRDQCVKNNDMIQVL 157 The following BLAST results are available for this feature:
BLAST of SMED30025582 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30025582 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30025582 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30025582 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30025582 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30025582 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30025582 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30025582 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30025582 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30025582 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30025582 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30025582 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30025582 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30025582 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 >SMED30025582 ID=SMED30025582|Name=SMED30025582|organism=Schmidtea mediterranea sexual|type=transcript|length=790bpback to top protein sequence of SMED30025582-orf-1 >SMED30025582-orf-1 ID=SMED30025582-orf-1|Name=SMED30025582-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=172bp MNIFIIIRIRVNKAEMPIITVTVVIIDYCKRELQKFIENIDPMAPIGNLKback to top Annotated Terms
The following terms have been associated with this transcript:
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
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