SMED30017058
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., 2020SMED30017058 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 2
Alignments
SMED30017058 aligns in the following genomic locations:
Homology
BLAST of SMED30017058 vs. Planmine SMEST
Match: SMESG000054252.1 (SMESG000054252.1) HSP 1 Score: 136.346 bits (342), Expect = 2.311e-42 Identity = 65/89 (73.03%), Postives = 71/89 (79.78%), Query Frame = 3 Query: 1602 GTQTRDLEDVDRTTMTVPTRFAGRYRQTLWDRGYTISTYGTPEWPSRNNNGSETDVELPSILIKREPGRNPAREIRQKTEVELHRFEQL 1868 GT + + +DVD TT+TVPT FAGRY Q LW+ GYTISTYGTP+WP R NG E D ELPSILIKREPGRNP REIRQK E ELHR EQL Sbjct: 13 GTHSGNWKDVDLTTLTVPTLFAGRYTQALWNLGYTISTYGTPKWPYRKTNGPEGDFELPSILIKREPGRNPTREIRQKAEGELHRLEQL 101 HSP 2 Score: 56.225 bits (134), Expect = 2.311e-42 Identity = 25/28 (89.29%), Postives = 26/28 (92.86%), Query Frame = 1 Query: 1867 YRFLAKRQREQLARINRDIASGRIPSSD 1950 YRFL KRQ+E LARINRDIASGRIPSSD Sbjct: 105 YRFLVKRQKEHLARINRDIASGRIPSSD 132
BLAST of SMED30017058 vs. Planmine SMEST
Match: SMESG000054252.1 (SMESG000054252.1) HSP 1 Score: 135.961 bits (341), Expect = 5.461e-42 Identity = 65/89 (73.03%), Postives = 71/89 (79.78%), Query Frame = 3 Query: 1602 GTQTRDLEDVDRTTMTVPTRFAGRYRQTLWDRGYTISTYGTPEWPSRNNNGSETDVELPSILIKREPGRNPAREIRQKTEVELHRFEQL 1868 GT + + +DVD TT+TVPT FAGRY Q LW+ GYTISTYGTP+WP R NG E D ELPSILIKREPGRNP REIRQK E ELHR EQL Sbjct: 13 GTHSGNWKDVDLTTLTVPTLFAGRYTQALWNLGYTISTYGTPKWPYRKTNGPEGDFELPSILIKREPGRNPTREIRQKAEGELHRLEQL 101 HSP 2 Score: 55.4546 bits (132), Expect = 5.461e-42 Identity = 25/28 (89.29%), Postives = 26/28 (92.86%), Query Frame = 1 Query: 1867 YRFLAKRQREQLARINRDIASGRIPSSD 1950 YRFL KRQ+E LARINRDIASGRIPSSD Sbjct: 105 YRFLVKRQKEHLARINRDIASGRIPSSD 132
BLAST of SMED30017058 vs. Planmine SMEST
Match: SMESG000008335.1 (SMESG000008335.1) HSP 1 Score: 131.339 bits (329), Expect = 1.367e-36 Identity = 58/81 (71.60%), Postives = 72/81 (88.89%), Query Frame = 3 Query: 1626 DVDRTTMTVPTRFAGRYRQTLWDRGYTISTYGTPEWPSRNNNGSETDVELPSILIKREPGRNPAREIRQKTEVELHRFEQL 1868 D++ TT+TVP+RFAGRYRQ LWD+GYTIST+GTPEWP+R +N + D ELPS++IKREPGRNPAREIRQ+TE L+R+EQL Sbjct: 95 DMESTTLTVPSRFAGRYRQALWDQGYTISTHGTPEWPNRRSNNCDEDTELPSLVIKREPGRNPAREIRQETEGLLYRYEQL 175 HSP 2 Score: 41.9726 bits (97), Expect = 1.367e-36 Identity = 18/28 (64.29%), Postives = 23/28 (82.14%), Query Frame = 1 Query: 1867 YRFLAKRQREQLARINRDIASGRIPSSD 1950 YR+LA ++R +LARIN DI +G IPSSD Sbjct: 179 YRYLANQKRRRLARINEDITNGHIPSSD 206
BLAST of SMED30017058 vs. Planmine SMEST
Match: SMESG000060519.1 (SMESG000060519.1) HSP 1 Score: 127.102 bits (318), Expect = 9.251e-34 Identity = 58/81 (71.60%), Postives = 63/81 (77.78%), Query Frame = 3 Query: 1626 DVDRTTMTVPTRFAGRYRQTLWDRGYTISTYGTPEWPSRNNNGSETDVELPSILIKREPGRNPAREIRQKTEVELHRFEQL 1868 DV+RTT+TV RFAGRY Q LWD GY+ISTYGT EWP RN + D ELP ILIKREPGRNPAREIRQK E LH FE+L Sbjct: 857 DVERTTLTVQNRFAGRYHQALWDPGYSISTYGTLEWPCRNPESRDKDTELPCILIKREPGRNPAREIRQKAEGALHHFEKL 937 HSP 2 Score: 36.5798 bits (83), Expect = 9.251e-34 Identity = 18/28 (64.29%), Postives = 20/28 (71.43%), Query Frame = 1 Query: 1867 YRFLAKRQREQLARINRDIASGRIPSSD 1950 YR L +QRE LARI DIAS RIP+ D Sbjct: 941 YRPLTNQQREHLARIIMDIASWRIPNLD 968
BLAST of SMED30017058 vs. Planmine SMEST
Match: SMESG000057450.1 (SMESG000057450.1) HSP 1 Score: 102.834 bits (255), Expect = 2.821e-32 Identity = 48/70 (68.57%), Postives = 54/70 (77.14%), Query Frame = 3 Query: 1659 RFAGRYRQTLWDRGYTISTYGTPEWPSRNNNGSETDVELPSILIKREPGRNPAREIRQKTEVELHRFEQL 1868 + R RQ LWDRGYTISTYGTPEWP R + D+ELPS+LIKRE G+NPAREIRQ+ E ELHR EQL Sbjct: 45 QVCSRCRQALWDRGYTISTYGTPEWPKRKTDELRDDIELPSVLIKRELGQNPAREIRQEAERELHRLEQL 114 HSP 2 Score: 46.2098 bits (108), Expect = 2.821e-32 Identity = 21/28 (75.00%), Postives = 24/28 (85.71%), Query Frame = 1 Query: 1867 YRFLAKRQREQLARINRDIASGRIPSSD 1950 YRFLA+RQ+E LAR+NRDI SG IPS D Sbjct: 118 YRFLARRQKEYLARVNRDIRSGHIPSLD 145 HSP 3 Score: 30.0314 bits (66), Expect = 2.821e-32 Identity = 10/15 (66.67%), Postives = 12/15 (80.00%), Query Frame = 2 Query: 1619 FGRCRPYHDDGTDKI 1663 GRCRPYH DG D++ Sbjct: 32 LGRCRPYHSDGADQV 46 The following BLAST results are available for this feature:
BLAST of SMED30017058 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30017058 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30017058 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30017058 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30017058 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30017058 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30017058 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30017058 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30017058 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30017058 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30017058 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30017058 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30017058 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30017058 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 >SMED30017058 ID=SMED30017058|Name=SMED30017058|organism=Schmidtea mediterranea sexual|type=transcript|length=1950bpback to top protein sequence of SMED30017058-orf-1 >SMED30017058-orf-1 ID=SMED30017058-orf-1|Name=SMED30017058-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=100bp MTVPTRFAGRYRQTLWDRGYTISTYGTPEWPSRNNNGSETDVELPSILIKback to top Annotated Terms
The following terms have been associated with this transcript:
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