SMED30028359
Overview
Neoblast Clusters
Zeng et. al., 2018
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 AppEmbryonic 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., 2020SMED30028359 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 3
Alignments
SMED30028359 aligns in the following genomic locations:
Homology
BLAST of SMED30028359 vs. Planmine SMEST
Match: SMESG000005062.1 (SMESG000005062.1) HSP 1 Score: 52.7582 bits (125), Expect = 1.050e-9 Identity = 31/73 (42.47%), Postives = 46/73 (63.01%), Query Frame = 3 Query: 9 LNSYISNESNNKQVGISIT--NSTYERI*HFQKTIKRTQNIEFLYIALKTASPTSTNSERIFSVSGNFYTKLH 221 +N+ ++N S K+VG+ T NS E ++KT+KRT+ ++ L+ A+ T PT T SER+FS S NF KL Sbjct: 1 MNACLNNAS--KEVGVQETPYNSLKEEFVIYKKTVKRTETLQQLFDAVLTVGPTYTESERVFSFSANFTRKLR 71
BLAST of SMED30028359 vs. Planmine SMEST
Match: SMESG000061313.1 (SMESG000061313.1) HSP 1 Score: 46.2098 bits (108), Expect = 5.912e-7 Identity = 20/43 (46.51%), Postives = 32/43 (74.42%), Query Frame = 3 Query: 93 FQKTIKRTQNIEFLYIALKTASPTSTNSERIFSVSGNFYTKLH 221 F T ++++ ++ L+ L + PTST+SER+FS++GNF TKLH Sbjct: 525 FGVTKQKSKTVQNLFNVLASIQPTSTDSERVFSIAGNFCTKLH 567
BLAST of SMED30028359 vs. Planmine SMEST
Match: SMESG000060816.1 (SMESG000060816.1) HSP 1 Score: 45.4394 bits (106), Expect = 1.070e-6 Identity = 28/66 (42.42%), Postives = 38/66 (57.58%), Query Frame = 3 Query: 9 LNSYISNESNNKQVGISITNSTYERI*HFQKTIKRTQNIEFLYIALKTASPTSTNSERIFSVSGNF 206 +N+ I+N S V + S E ++KT KRTQ ++ LY A+ T P T SER+FSVS NF Sbjct: 234 MNACINNASKEGGVKETPYKSLKEEFAIYKKTGKRTQTLQQLYDAVLTVRPKFTESERVFSVSTNF 299
BLAST of SMED30028359 vs. Planmine SMEST
Match: SMESG000022344.1 (SMESG000022344.1) HSP 1 Score: 44.669 bits (104), Expect = 1.978e-6 Identity = 22/49 (44.90%), Postives = 34/49 (69.39%), Query Frame = 3 Query: 93 FQKTIK-------RTQNIEFLYIALKTASPTSTNSERIFSVSGNFYTKL 218 FQK +K +++ ++ L+ AL + PTST+SER+FS++GNF TKL Sbjct: 522 FQKELKMFGVTKQKSKTVQNLFNALASIQPTSTDSERVFSIAGNFCTKL 570 The following BLAST results are available for this feature:
BLAST of SMED30028359 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30028359 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30028359 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30028359 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30028359 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30028359 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30028359 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30028359 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30028359 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30028359 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30028359 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30028359 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30028359 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30028359 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 4
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30028359 ID=SMED30028359|Name=SMED30028359|organism=Schmidtea mediterranea sexual|type=transcript|length=311bpback to top Annotated Terms
The following terms have been associated with this transcript:
|