SMED30029293
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., 2020SMED30029293 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 4
Alignments
SMED30029293 aligns in the following genomic locations:
Homology
BLAST of SMED30029293 vs. TrEMBL
Match: A0A0L8GI73 (Uncharacterized protein OS=Octopus bimaculoides OX=37653 GN=OCBIM_22033073mg PE=4 SV=1) HSP 1 Score: 54.299 bits (129), Expect = 4.989e-6 Identity = 28/90 (31.11%), Postives = 51/90 (56.67%), Query Frame = 3 Query: 36 HYFPFELKSELNKIDLKTYFLSCVRKNENNKGITYFGSFRGRPLSGCVVKPVPSYSGMIISPEN--LSRQNVTKYQVNEVFPQYTHWNLG 299 HY P +K + + + YF + ++++++ K +T SFRGRPL+G ++ P Y MI+ + LS + ++ + PQ+T+WNL Sbjct: 20 HYMPCIIKYS-GETNAEKYFETTIQEDDDKKELT--ASFRGRPLNGKILTPPQGYESMIVKEKKVPLSEEEDRQFSIVARVPQFTYWNLD 106
BLAST of SMED30029293 vs. Ensembl Nematostella
Match: EDO28923 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7T538]) HSP 1 Score: 45.4394 bits (106), Expect = 6.606e-7 Identity = 33/108 (30.56%), Postives = 54/108 (50.00%), Query Frame = 3 Query: 78 DLKTYFLSCVRKNENNKGITYFGSFRGRPLSGCVVKPVPSYSGMIISPENLSRQNVTKYQ-----VNEVFPQYTHWNL-----GLDINEKEHKFFEEWIEISTILNSE 371 ++ +F +RKNE + SFRGR L G V++P YSG I+ + RQ T+ Q V + F ++ +WNL G D K +WI ++++L+ + Sbjct: 12 NVANFFDPTIRKNEGTEQ-DISASFRGRKLRGAVMQPPAGYSGFILRED---RQPTTEEQDHHLKVTKKFNKFHYWNLETPPSGNDAVAKAM----QWITLASVLHGQ 111
BLAST of SMED30029293 vs. Ensembl Nematostella
Match: EDO27966 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7T7T3]) HSP 1 Score: 44.2838 bits (103), Expect = 1.175e-6 Identity = 29/92 (31.52%), Postives = 47/92 (51.09%), Query Frame = 3 Query: 36 HYFPFELKSELNKIDLKTYFLSCVRKNENNKGITYFGSFRGRPLSGCVVKPVPSYSGMIISPENLSRQNVTKYQ-----VNEVFPQYTHWNL 296 H+ P ++ + ++ +F +RKNE + SFRGR L G V++P YSG I+ + RQ T+ Q V + F ++ +WNL Sbjct: 3 HWMPCQI-THNGDANVANFFDPTIRKNEGTEQ-DISASFRGRKLRGAVMQPPAGYSGFILRED---RQPTTEEQDHHLKVTKKFNKFHYWNL 89
BLAST of SMED30029293 vs. Planmine SMEST
Match: SMESG000064498.1 (SMESG000064498.1) HSP 1 Score: 239.58 bits (610), Expect = 1.306e-82 Identity = 114/115 (99.13%), Postives = 115/115 (100.00%), Query Frame = 3 Query: 27 MDAHYFPFELKSELNKIDLKTYFLSCVRKNENNKGITYFGSFRGRPLSGCVVKPVPSYSGMIISPENLSRQNVTKYQVNEVFPQYTHWNLGLDINEKEHKFFEEWIEISTILNSE 371 MDAHYFPFELKSELNKIDLKTYFLSCVRKNENNKGITYFGSFRGRPLSGCVVKPVPSYSGMIISPENLSRQNVTKYQVNE+FPQYTHWNLGLDINEKEHKFFEEWIEISTILNSE Sbjct: 1 MDAHYFPFELKSELNKIDLKTYFLSCVRKNENNKGITYFGSFRGRPLSGCVVKPVPSYSGMIISPENLSRQNVTKYQVNEIFPQYTHWNLGLDINEKEHKFFEEWIEISTILNSE 115 The following BLAST results are available for this feature:
BLAST of SMED30029293 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30029293 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30029293 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30029293 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30029293 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30029293 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30029293 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30029293 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 1
BLAST of SMED30029293 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30029293 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30029293 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30029293 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 2
BLAST of SMED30029293 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30029293 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 >SMED30029293 ID=SMED30029293|Name=SMED30029293|organism=Schmidtea mediterranea sexual|type=transcript|length=507bpback to top protein sequence of SMED30029293-orf-1 >SMED30029293-orf-1 ID=SMED30029293-orf-1|Name=SMED30029293-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=116bp MDAHYFPFELKSELNKIDLKTYFLSCVRKNENNKGITYFGSFRGRPLSGCback 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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