SMED30031259
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., 2020SMED30031259 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 4
Alignments
SMED30031259 aligns in the following genomic locations:
Homology
BLAST of SMED30031259 vs. Ensembl Human
Match: SH3BGRL3 (SH3 domain binding glutamate rich protein like 3 [Source:HGNC Symbol;Acc:HGNC:15568]) HSP 1 Score: 46.9802 bits (110), Expect = 8.276e-7 Identity = 26/76 (34.21%), Postives = 44/76 (57.89%), Query Frame = -1 Query: 343 RVXXXXFSGSSKIKAEXTYVNDLLVKMKVTFQXIDISVETEKRDIMKEIVLAAGAKAFTPPRVLKDGKYIGGYDEF 570 RV+ +GS +IK++ + V +L ++ +Q +DIS + RD M+ LA KA TPP+++ +Y G Y+ F Sbjct: 5 RVYSTSVTGSREIKSQQSEVTRILDGKRIQYQLVDISQDNALRDEMR--ALAGNPKA-TPPQIVNGDQYCGDYELF 77
BLAST of SMED30031259 vs. Ensembl Mouse
Match: Sh3bgrl3 (SH3 domain binding glutamic acid-rich protein-like 3 [Source:MGI Symbol;Acc:MGI:1920973]) HSP 1 Score: 46.9802 bits (110), Expect = 5.182e-7 Identity = 26/76 (34.21%), Postives = 43/76 (56.58%), Query Frame = -1 Query: 343 RVXXXXFSGSSKIKAEXTYVNDLLVKMKVTFQXIDISVETEKRDIMKEIVLAAGAKAFTPPRVLKDGKYIGGYDEF 570 RV+ +GS +IK++ + V +L ++ +Q +DIS + RD M+ LA KA TPP+++ Y G Y+ F Sbjct: 5 RVYSTSVTGSREIKSQQSEVTRILDGKRIQYQLVDISQDNALRDEMR--TLAGNPKA-TPPQIVNGNHYCGDYELF 77
BLAST of SMED30031259 vs. UniProt/SwissProt
Match: sp|Q91VW3|SH3L3_MOUSE (SH3 domain-binding glutamic acid-rich-like protein 3 OS=Mus musculus OX=10090 GN=Sh3bgrl3 PE=1 SV=1) HSP 1 Score: 46.9802 bits (110), Expect = 3.625e-6 Identity = 26/76 (34.21%), Postives = 43/76 (56.58%), Query Frame = -1 Query: 343 RVXXXXFSGSSKIKAEXTYVNDLLVKMKVTFQXIDISVETEKRDIMKEIVLAAGAKAFTPPRVLKDGKYIGGYDEF 570 RV+ +GS +IK++ + V +L ++ +Q +DIS + RD M+ LA KA TPP+++ Y G Y+ F Sbjct: 5 RVYSTSVTGSREIKSQQSEVTRILDGKRIQYQLVDISQDNALRDEMR--TLAGNPKA-TPPQIVNGNHYCGDYELF 77
BLAST of SMED30031259 vs. UniProt/SwissProt
Match: sp|Q5RC61|SH3L3_PONAB (SH3 domain-binding glutamic acid-rich-like protein 3 OS=Pongo abelii OX=9601 GN=SH3BGRL3 PE=3 SV=1) HSP 1 Score: 46.9802 bits (110), Expect = 3.975e-6 Identity = 26/76 (34.21%), Postives = 44/76 (57.89%), Query Frame = -1 Query: 343 RVXXXXFSGSSKIKAEXTYVNDLLVKMKVTFQXIDISVETEKRDIMKEIVLAAGAKAFTPPRVLKDGKYIGGYDEF 570 RV+ +GS +IK++ + V +L ++ +Q +DIS + RD M+ LA KA TPP+++ +Y G Y+ F Sbjct: 5 RVYSTSVTGSREIKSQQSEVTRILDGKRIQYQLVDISQDNALRDEMR--ALAGNPKA-TPPQIVNGDQYCGDYELF 77
BLAST of SMED30031259 vs. UniProt/SwissProt
Match: sp|Q9H299|SH3L3_HUMAN (SH3 domain-binding glutamic acid-rich-like protein 3 OS=Homo sapiens OX=9606 GN=SH3BGRL3 PE=1 SV=1) HSP 1 Score: 46.9802 bits (110), Expect = 3.975e-6 Identity = 26/76 (34.21%), Postives = 44/76 (57.89%), Query Frame = -1 Query: 343 RVXXXXFSGSSKIKAEXTYVNDLLVKMKVTFQXIDISVETEKRDIMKEIVLAAGAKAFTPPRVLKDGKYIGGYDEF 570 RV+ +GS +IK++ + V +L ++ +Q +DIS + RD M+ LA KA TPP+++ +Y G Y+ F Sbjct: 5 RVYSTSVTGSREIKSQQSEVTRILDGKRIQYQLVDISQDNALRDEMR--ALAGNPKA-TPPQIVNGDQYCGDYELF 77
BLAST of SMED30031259 vs. UniProt/SwissProt
Match: sp|Q3ZCL8|SH3L3_BOVIN (SH3 domain-binding glutamic acid-rich-like protein 3 OS=Bos taurus OX=9913 GN=SH3BGRL3 PE=3 SV=1) HSP 1 Score: 46.9802 bits (110), Expect = 3.975e-6 Identity = 26/76 (34.21%), Postives = 44/76 (57.89%), Query Frame = -1 Query: 343 RVXXXXFSGSSKIKAEXTYVNDLLVKMKVTFQXIDISVETEKRDIMKEIVLAAGAKAFTPPRVLKDGKYIGGYDEF 570 RV+ +GS +IK++ + V +L ++ +Q +DIS + RD M+ LA KA TPP+++ +Y G Y+ F Sbjct: 5 RVYSTSVTGSREIKSQQSEVTRILDGKRIQYQLVDISQDNALRDEMR--ALAGNPKA-TPPQIVNGDQYCGDYELF 77
BLAST of SMED30031259 vs. Planmine SMEST
Match: SMESG000007873.1 (SMESG000007873.1) HSP 1 Score: 144.05 bits (362), Expect = 6.664e-45 Identity = 80/83 (96.39%), Postives = 80/83 (96.39%), Query Frame = -1 Query: 301 SGSSKIKAEXTYVNDLLVKMKVTFQXIDISVETEKRDIMKEIVLAAGAKAFTPPRVLKDGKYIGGYDEFYXXXXXXXXESILQ 549 SGSSKIKAE TYVNDLLVKMKVTFQ IDISVETEKRDIMKEIVLAAGAKAFTPPRVLKDGKYIGGYDEFYEAAEAEN ESILQ Sbjct: 11 SGSSKIKAEQTYVNDLLVKMKVTFQTIDISVETEKRDIMKEIVLAAGAKAFTPPRVLKDGKYIGGYDEFYEAAEAENLESILQ 93 The following BLAST results are available for this feature:
BLAST of SMED30031259 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 1
BLAST of SMED30031259 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30031259 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30031259 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30031259 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30031259 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 1
BLAST of SMED30031259 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 4
BLAST of SMED30031259 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30031259 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30031259 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30031259 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30031259 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30031259 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30031259 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 1
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30031259 ID=SMED30031259|Name=SMED30031259|organism=Schmidtea mediterranea sexual|type=transcript|length=570bpback 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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