SMED30016068
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., 2020SMED30016068 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 5
Homology
BLAST of SMED30016068 vs. Planmine SMEST
Match: SMESG000024705.1 (SMESG000024705.1) HSP 1 Score: 189.504 bits (480), Expect = 2.347e-56 Identity = 90/91 (98.90%), Postives = 90/91 (98.90%), Query Frame = -1 Query: 2 YARTLAISKPSLEDAINLCELEVYGYPFTKTMSMTFKYFGALSIYDSLGNFGTFPVQSNLDCAMICLLEAKCLSFSVQLGVKCFIYFHTGG 274 YARTLAISKPSLEDAINLCELEVYGYPFTKTMSMTFKYFGALSIYDSLGNFGTFPVQSNLDCAMICLLEAKCLSFSVQ GVKCFIYFHTGG Sbjct: 145 YARTLAISKPSLEDAINLCELEVYGYPFTKTMSMTFKYFGALSIYDSLGNFGTFPVQSNLDCAMICLLEAKCLSFSVQFGVKCFIYFHTGG 235
BLAST of SMED30016068 vs. Planmine SMEST
Match: SMESG000024705.1 (SMESG000024705.1) HSP 1 Score: 190.274 bits (482), Expect = 3.407e-56 Identity = 90/91 (98.90%), Postives = 90/91 (98.90%), Query Frame = -1 Query: 2 YARTLAISKPSLEDAINLCELEVYGYPFTKTMSMTFKYFGALSIYDSLGNFGTFPVQSNLDCAMICLLEAKCLSFSVQLGVKCFIYFHTGG 274 YARTLAISKPSLEDAINLCELEVYGYPFTKTMSMTFKYFGALSIYDSLGNFGTFPVQSNLDCAMICLLEAKCLSFSVQ GVKCFIYFHTGG Sbjct: 184 YARTLAISKPSLEDAINLCELEVYGYPFTKTMSMTFKYFGALSIYDSLGNFGTFPVQSNLDCAMICLLEAKCLSFSVQFGVKCFIYFHTGG 274
BLAST of SMED30016068 vs. Planmine SMEST
Match: SMESG000046835.1 (SMESG000046835.1) HSP 1 Score: 150.599 bits (379), Expect = 9.059e-42 Identity = 71/91 (78.02%), Postives = 76/91 (83.52%), Query Frame = -1 Query: 2 YARTLAISKPSLEDAINLCELEVYGYPFTKTMSMTFKYFGALSIYDSLGNFGTFPVQSNLDCAMICLLEAKCLSFSVQLGVKCFIYFHTGG 274 Y RTLAISKP E A+N+CELEVYGY F K MSM FKYFG S+YDSLGNFGTFPVQSN+DCA+ICL EAKCLSFSVQ GV CFIY H GG Sbjct: 314 YMRTLAISKPFGEQALNICELEVYGYTFIKKMSMIFKYFGRQSLYDSLGNFGTFPVQSNIDCAIICLQEAKCLSFSVQFGVSCFIYAHIGG 404 HSP 2 Score: 39.6614 bits (91), Expect = 9.059e-42 Identity = 16/21 (76.19%), Postives = 18/21 (85.71%), Query Frame = -3 Query: 276 NHYAGPPPPGEIITTLNFKRL 338 ++Y GPPPPGE ITTLNF RL Sbjct: 293 SYYVGPPPPGEFITTLNFTRL 313
BLAST of SMED30016068 vs. Planmine SMEST
Match: SMESG000046841.1 (SMESG000046841.1) HSP 1 Score: 150.214 bits (378), Expect = 1.087e-41 Identity = 73/91 (80.22%), Postives = 74/91 (81.32%), Query Frame = -1 Query: 2 YARTLAISKPSLEDAINLCELEVYGYPFTKTMSMTFKYFGALSIYDSLGNFGTFPVQSNLDCAMICLLEAKCLSFSVQLGVKCFIYFHTGG 274 YARTLAISKP E NLCELEVYGYPF KTM MTFKY ALSIYDSLGN GTFPV SNLD AMICL EAKC+SFSVQ VKCFIY H GG Sbjct: 148 YARTLAISKPFAEQPFNLCELEVYGYPFIKTMPMTFKYLRALSIYDSLGNIGTFPVLSNLDSAMICLQEAKCISFSVQFSVKCFIYAHIGG 238
BLAST of SMED30016068 vs. Planmine SMEST
Match: SMESG000046835.1 (SMESG000046835.1) HSP 1 Score: 151.754 bits (382), Expect = 1.377e-40 Identity = 71/92 (77.17%), Postives = 77/92 (83.70%), Query Frame = -1 Query: 2 WYARTLAISKPSLEDAINLCELEVYGYPFTKTMSMTFKYFGALSIYDSLGNFGTFPVQSNLDCAMICLLEAKCLSFSVQLGVKCFIYFHTGG 277 +Y RTLAISKP E A+N+CELEVYGY F K MSM FKYFG S+YDSLGNFGTFPVQSN+DCA+ICL EAKCLSFSVQ GV CFIY H GG Sbjct: 295 YYMRTLAISKPFGEQALNICELEVYGYTFIKKMSMIFKYFGRQSLYDSLGNFGTFPVQSNIDCAIICLQEAKCLSFSVQFGVSCFIYAHIGG 386 The following BLAST results are available for this feature:
BLAST of SMED30016068 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30016068 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30016068 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30016068 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30016068 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30016068 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30016068 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30016068 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30016068 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30016068 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30016068 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30016068 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30016068 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30016068 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 >SMED30016068 ID=SMED30016068|Name=SMED30016068|organism=Schmidtea mediterranea sexual|type=transcript|length=1630bpback to top protein sequence of SMED30016068-orf-1 >SMED30016068-orf-1 ID=SMED30016068-orf-1|Name=SMED30016068-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=113bp MASSKDGLDIARVLAYQSFEIQRRNNFTRWRRPRVMIIKRIQDEIHPLPFback to top Annotated Terms
The following terms have been associated with this transcript:
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