SMED30030959
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., 2020SMED30030959 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 2
Alignments
SMED30030959 aligns in the following genomic locations:
Homology
BLAST of SMED30030959 vs. Planmine SMEST
Match: SMESG000034723.1 (SMESG000034723.1) HSP 1 Score: 245.358 bits (625), Expect = 4.795e-83 Identity = 179/179 (100.00%), Postives = 179/179 (100.00%), Query Frame = 1 Query: 40 MNIIQKWLSFFNLKHVYRQTREFFLIDDLCALVGXXXXXXXXXXXXXXHINEKSRVTQHGYSYIDSEDFDYVVPSVTVDMLRPKVPIWVKVPXXXXXXXXXXXXXXXXXXXXFSYNKTANMPMXXXXXXXXXXXXXXXXXXXALYGEIEERYILHNVSEVEMYKEVVMWKVAEEVSYED 576 MNIIQKWLSFFNLKHVYRQTREFFLIDDLCALVGSNNSNRSRLNKNESHINEKSRVTQHGYSYIDSEDFDYVVPSVTVDMLRPKVPIWVKVPLICGIVICGIGVIVGILLLIFSYNKTANMPMLYYSLSIFIISSLFSYGLFALYGEIEERYILHNVSEVEMYKEVVMWKVAEEVSYED Sbjct: 1 MNIIQKWLSFFNLKHVYRQTREFFLIDDLCALVGSNNSNRSRLNKNESHINEKSRVTQHGYSYIDSEDFDYVVPSVTVDMLRPKVPIWVKVPLICGIVICGIGVIVGILLLIFSYNKTANMPMLYYSLSIFIISSLFSYGLFALYGEIEERYILHNVSEVEMYKEVVMWKVAEEVSYED 179
BLAST of SMED30030959 vs. Planmine SMEST
Match: SMESG000034740.1 (SMESG000034740.1) HSP 1 Score: 82.8037 bits (203), Expect = 1.394e-19 Identity = 77/182 (42.31%), Postives = 115/182 (63.19%), Query Frame = 1 Query: 40 MNIIQKWLSFFNLKHVYRQTREFFLIDDLCALVGXXXXXXXXXXXXXXHINEKSRVTQHGY---SYIDSEDFDYVVPSVTVDMLRPKVPIWVKVPXXXXXXXXXXXXXXXXXXXXFSYNKTANMPMXXXXXXXXXXXXXXXXXXXALYGEIEERYILHNVSEVEMYKEVVMWKVAEEVSYED 576 M +++K LS K Q + F D+L S N N N++ N SR+++ + +++D +DFD VP +T DML+P++ +W K ++ G VICG+G+I G++L+IF+YN+T N MLY SL + I+ S+ YGLF LYGE+EE I NV+EVEMYKE VM ++A + SY+D Sbjct: 1 MKVMRKLLSCLKSKRANSQANDLFEFDELNNSNKSRNLNEDSNEFNKNKSNRMSRMSRMSFVSQNFVDPDDFDNFVPPITDDMLKPELALWQKTLMVIGCVICGLGMIGGVILIIFAYNQTPNKGMLYSSLPLLIVCSMILYGLFVLYGEMEEESIEDNVAEVEMYKETVMTQLAAQQSYDD 182 The following BLAST results are available for this feature:
BLAST of SMED30030959 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30030959 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30030959 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30030959 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30030959 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30030959 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30030959 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30030959 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30030959 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30030959 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30030959 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30030959 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30030959 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30030959 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 2
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30030959 ID=SMED30030959|Name=SMED30030959|organism=Schmidtea mediterranea sexual|type=transcript|length=664bpback to top protein sequence of SMED30030959-orf-1 >SMED30030959-orf-1 ID=SMED30030959-orf-1|Name=SMED30030959-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=180bp MNIIQKWLSFFNLKHVYRQTREFFLIDDLCALVGSNNSNRSRLNKNESHIback 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
|