SMED30025741
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., 2020SMED30025741 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 25Note: Hover over icons to view figure legend
Alignments
SMED30025741 aligns in the following genomic locations:
Homology
BLAST of SMED30025741 vs. Planmine SMEST
Match: SMESG000024991.1 (SMESG000024991.1) HSP 1 Score: 187.193 bits (474), Expect = 1.849e-61 Identity = 93/96 (96.88%), Postives = 93/96 (96.88%), Query Frame = 3 Query: 207 MRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYGQEKAKEAKFYQDNFKKCINEIPMTQECRKGITQISIRYGEEIQKINNACENEYR 494 MRLDKIQKREMSAEC GELQKLRD F KATDELDKKCESQYGQEKAKEAKFYQDNFKKCINEIPMTQECRKGITQISIRYGEEIQKINNACENEYR Sbjct: 1 MRLDKIQKREMSAECLGELQKLRDDFAKATDELDKKCESQYGQEKAKEAKFYQDNFKKCINEIPMTQECRKGITQISIRYGEEIQKINNACENEYR 96
BLAST of SMED30025741 vs. Planmine SMEST
Match: SMESG000054781.1 (SMESG000054781.1) HSP 1 Score: 120.553 bits (301), Expect = 2.649e-35 Identity = 63/97 (64.95%), Postives = 73/97 (75.26%), Query Frame = 3 Query: 207 MRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYGQEKAKEAKFYQDNFKKCINEI-PMTQECRKGITQISIRYGEEIQKINNACENEYR 494 MRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQY + + K Y N +KC + I ++ECR G + + + EE +KINNACENE R Sbjct: 1 MRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYNELRKKAETAYMANLRKCGDNIKDFSKECRDGHVKHTKWFSEEDEKINNACENESR 97
BLAST of SMED30025741 vs. Planmine SMEST
Match: SMESG000025013.1 (SMESG000025013.1) HSP 1 Score: 120.553 bits (301), Expect = 2.649e-35 Identity = 63/97 (64.95%), Postives = 73/97 (75.26%), Query Frame = 3 Query: 207 MRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYGQEKAKEAKFYQDNFKKCINEI-PMTQECRKGITQISIRYGEEIQKINNACENEYR 494 MRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQY + + K Y N +KC + I ++ECR G + + + EE +KINNACENE R Sbjct: 1 MRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYNELRKKAETAYMANLRKCGDNIKDFSKECRDGHVKHTKWFSEEDEKINNACENESR 97
BLAST of SMED30025741 vs. Planmine SMEST
Match: SMESG000025003.1 (SMESG000025003.1) HSP 1 Score: 115.931 bits (289), Expect = 2.175e-33 Identity = 60/95 (63.16%), Postives = 72/95 (75.79%), Query Frame = 3 Query: 213 LDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYGQEKAKEAKFYQDNFKKCINEI-PMTQECRKGITQISIRYGEEIQKINNACENEYR 494 LDKIQKREMSAECQGELQKLRDGFDKATDELDKKC+SQY + + K Y N +KC + I ++ECR G+ + + + EE +KINNACENE R Sbjct: 9 LDKIQKREMSAECQGELQKLRDGFDKATDELDKKCKSQYNELRKKAETAYMANLRKCGDNIKDFSKECRDGLVKHTKWFSEEDEKINNACENESR 103
BLAST of SMED30025741 vs. Planmine SMEST
Match: SMESG000025000.1 (SMESG000025000.1) HSP 1 Score: 77.411 bits (189), Expect = 2.870e-18 Identity = 43/118 (36.44%), Postives = 71/118 (60.17%), Query Frame = 3 Query: 141 MAKLIFIVLAVLFVYGECRRFKMRLDKIQKREMSAECQGELQKLRDGFDKATDELDKKCESQYGQEKAKEAKFYQDNFKKC-INEIPMTQECRKGITQISIRYGEEIQKINNACENEY 491 M K++ + + FV ECR F++RLDKI KREMS+EC+ EL+KL D F A +++D C++ Y + K Y +KC ++ MT++C+ + ++ + E K++ C+NEY Sbjct: 1 MNKILLLTFVIFFVSVECR-FRLRLDKIAKREMSSECKAELKKLDDQFTAAANKIDDDCDAVYVKWSKKYLPEYVALKEKCGLDTSKMTKDCKTELKRLFNLFAEGNYKVDLECDNEY 117 The following BLAST results are available for this feature:
BLAST of SMED30025741 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30025741 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30025741 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30025741 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30025741 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30025741 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30025741 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30025741 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30025741 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30025741 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30025741 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30025741 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30025741 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30025741 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 >SMED30025741 ID=SMED30025741|Name=SMED30025741|organism=Schmidtea mediterranea sexual|type=transcript|length=592bpback to top protein sequence of SMED30025741-orf-1 >SMED30025741-orf-1 ID=SMED30025741-orf-1|Name=SMED30025741-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=160bp MSLLFVSSNYKYLRKMFFFNYFIMAKLIFIVLAVLFVYGECRRFKMRLDKback to top Aliases
The feature 'SMED30025741' has the following synonyms
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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