SMED30031918
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., 2020SMED30031918 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 20Note: Hover over icons to view figure legend
Alignments
SMED30031918 aligns in the following genomic locations:
Homology
BLAST of SMED30031918 vs. Planmine SMEST
Match: SMESG000043420.1 (SMESG000043420.1) HSP 1 Score: 116.316 bits (290), Expect = 8.635e-35 Identity = 55/55 (100.00%), Postives = 55/55 (100.00%), Query Frame = 1 Query: 265 MKFIVLFATIVISPIIFDNFVKTTASMDHVLKVNAVRHHENTRPNRIFCGYRTAT 429 MKFIVLFATIVISPIIFDNFVKTTASMDHVLKVNAVRHHENTRPNRIFCGYRTAT Sbjct: 1 MKFIVLFATIVISPIIFDNFVKTTASMDHVLKVNAVRHHENTRPNRIFCGYRTAT 55
BLAST of SMED30031918 vs. Planmine SMEST
Match: SMESG000037491.1 (SMESG000037491.1) HSP 1 Score: 106.686 bits (265), Expect = 1.305e-27 Identity = 47/54 (87.04%), Postives = 51/54 (94.44%), Query Frame = 1 Query: 40 VSWIWDGLKSRLEIGTLNALLTIQFNCDLDCNQFYSFIKNDIEFLDKVHSSENS 201 ++WIWD LKSRLEIGTLN LLTIQFNCDLDCNQFY+FIKNDIEFLDKVHSSE + Sbjct: 228 MNWIWDDLKSRLEIGTLNTLLTIQFNCDLDCNQFYNFIKNDIEFLDKVHSSEKT 281
BLAST of SMED30031918 vs. Planmine SMEST
Match: SMESG000074722.1 (SMESG000074722.1) HSP 1 Score: 105.531 bits (262), Expect = 4.161e-27 Identity = 47/52 (90.38%), Postives = 50/52 (96.15%), Query Frame = 1 Query: 40 VSWIWDGLKSRLEIGTLNALLTIQFNCDLDCNQFYSFIKNDIEFLDKVHSSE 195 ++WIWD LKSRLEIGTLNALLTIQFNCDLDCNQFYSFIKNDIEFL +VHSSE Sbjct: 663 MNWIWDDLKSRLEIGTLNALLTIQFNCDLDCNQFYSFIKNDIEFLIRVHSSE 714
BLAST of SMED30031918 vs. Planmine SMEST
Match: SMESG000074722.1 (SMESG000074722.1) HSP 1 Score: 105.531 bits (262), Expect = 4.195e-27 Identity = 47/52 (90.38%), Postives = 50/52 (96.15%), Query Frame = 1 Query: 40 VSWIWDGLKSRLEIGTLNALLTIQFNCDLDCNQFYSFIKNDIEFLDKVHSSE 195 ++WIWD LKSRLEIGTLNALLTIQFNCDLDCNQFYSFIKNDIEFL +VHSSE Sbjct: 658 MNWIWDDLKSRLEIGTLNALLTIQFNCDLDCNQFYSFIKNDIEFLIRVHSSE 709
BLAST of SMED30031918 vs. Planmine SMEST
Match: SMESG000006546.1 (SMESG000006546.1) HSP 1 Score: 83.5741 bits (205), Expect = 1.372e-21 Identity = 40/67 (59.70%), Postives = 50/67 (74.63%), Query Frame = 1 Query: 7 ARDGSTSQLGKV----SWIWDGLKSRLEIGTLNALLTIQFNCDLDCNQFYSFIKNDIEFLDKVHSSE 195 A G+++ + ++ +WI D LK +LEIG LNA TIQFNCDLDCN FYSFIKNDI+ LDK+H SE Sbjct: 37 ALSGTSTDVERIFSLMNWICDDLKIQLEIGILNARFTIQFNCDLDCNHFYSFIKNDIDCLDKIHPSE 103 The following BLAST results are available for this feature:
BLAST of SMED30031918 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30031918 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30031918 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30031918 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30031918 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30031918 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30031918 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30031918 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30031918 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30031918 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30031918 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30031918 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30031918 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30031918 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 >SMED30031918 ID=SMED30031918|Name=SMED30031918|organism=Schmidtea mediterranea sexual|type=transcript|length=429bpback to top protein sequence of SMED30031918-orf-1 >SMED30031918-orf-1 ID=SMED30031918-orf-1|Name=SMED30031918-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=143bp MAARDGSTSQLGKVSWIWDGLKSRLEIGTLNALLTIQFNCDLDCNQFYSFback 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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