SMED30004361
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., 2020SMED30004361 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 3
Alignments
SMED30004361 aligns in the following genomic locations:
Homology
BLAST of SMED30004361 vs. Planmine SMEST
Match: SMESG000033504.1 (SMESG000033504.1) HSP 1 Score: 244.202 bits (622), Expect = 1.422e-79 Identity = 117/117 (100.00%), Postives = 117/117 (100.00%), Query Frame = 3 Query: 1110 MVYESATLIYFGNTWHIITGVFAFLSSFPLTILLDLMARRYISRPGMGSWAEKICPLFPIMNLNLSLIFIEVLNHYKDKSDNPLILYNYFKMNSMSSYLQRFFTVVYCLKVINLIYH 1460 MVYESATLIYFGNTWHIITGVFAFLSSFPLTILLDLMARRYISRPGMGSWAEKICPLFPIMNLNLSLIFIEVLNHYKDKSDNPLILYNYFKMNSMSSYLQRFFTVVYCLKVINLIYH Sbjct: 1 MVYESATLIYFGNTWHIITGVFAFLSSFPLTILLDLMARRYISRPGMGSWAEKICPLFPIMNLNLSLIFIEVLNHYKDKSDNPLILYNYFKMNSMSSYLQRFFTVVYCLKVINLIYH 117
BLAST of SMED30004361 vs. Planmine SMEST
Match: SMESG000062786.1 (SMESG000062786.1) HSP 1 Score: 54.6842 bits (130), Expect = 1.132e-7 Identity = 52/208 (25.00%), Postives = 87/208 (41.83%), Query Frame = 3 Query: 825 NKTIQNHGHENEQVVVLNRKNKTTT--------IPSWITVVSILFTTFSTV---------------LVKKYIFI-FKCVAHIFIFIFSVIQILEVKQWKS-LNHSNLGIEKLFVWLG---------------FVSMVYESATLIYFG-NTWHIITGVFAFLSSFPLTILLDLMARRYISRPGMGSWAEKICPLFPIMNLNLSLIFIEV 1325 N ++ G E++Q++V+ KN + +PS V+ I+F + S + L+ IF F + S++ I EV++W L IEK +W+G F S++ ++ T I N I + +F TIL+ L R RP + SWAE +CP +M LN+ L+ + + Sbjct: 290 NISMSQEGDEDDQLLVVVEKNPLISTPQNPSFRLPSAALVLCIIFLSLSFLSFIIMLSLNNNTHLQLIGGLIFTTFPIFVYALGSGLSIVHINEVERWPIFLERHGKVIEKCLIWIGAAGQLSISMATVAISFESLIVKNGTEIEMARNILLIPNNILIVFQTFLQTILISLAIDRKWIRPEINSWAELLCPAVGMMGLNIGLLLLSI 497
BLAST of SMED30004361 vs. Planmine SMEST
Match: SMESG000040922.1 (SMESG000040922.1) HSP 1 Score: 50.0618 bits (118), Expect = 3.360e-6 Identity = 30/127 (23.62%), Postives = 60/127 (47.24%), Query Frame = 3 Query: 1008 IFSVIQILEVKQWKSLNHSNLGIEKLFVWLGFVSMVYESATLIYFG------NTWHIITGVFAFL--SSFPLTILLDLMARRYISRPGMGSWAEKICPLFPIMNLNLSLIFIEVLNHYKDKSDNPLI 1364 I IQI E+ +WK ++ + ++K+ +W+G + ++ N +I + L F T+ L++ R RP + SW EK+ P +++LN+ +FI +LN + + + + Sbjct: 337 ILLAIQINEIMEWKKISTNEFTVDKMMLWIGAAGQLVICFAKLFMEFIERTENFSALIIAKYGLLLVQIFIQTVALNMALNRKWLRPKLKSWQEKLFPPISLLSLNMGFLFISMLNDFNRNTSHSTV 463
BLAST of SMED30004361 vs. Planmine SMEST
Match: SMESG000020517.1 (SMESG000020517.1) HSP 1 Score: 49.2914 bits (116), Expect = 6.209e-6 Identity = 33/135 (24.44%), Postives = 60/135 (44.44%), Query Frame = 3 Query: 975 IFKCVAHIFIFIFSVIQILEVKQWKSLNHSNLGIEKLFVWLGFVSMVYESATLIYFGN--------TWHIITGVFAFLSSFPLTILLDLMARRYISRPGMGSWAEKICPLFPIMNLNLSLIFIEVLNHYKDKSDN 1355 IF ++F +IQ+ ++ +W+ L I+++ +W+G V E I + W I F + T+++ L R S+P + SW E +CP +++LNLS + + + KS N Sbjct: 331 IFPIPIYLFSIFLLIIQMNDICRWEKLGTDKYLIDRMILWVGATGQVVEIVAQISMNSYQYYPKLSGWIIAEYAILFFQTMFQTLVISLALDRKWSQPKLESWHEYLCPPVGMLSLNLSFMIFSLFDIINTKSLN 465 The following BLAST results are available for this feature:
BLAST of SMED30004361 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30004361 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30004361 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30004361 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30004361 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30004361 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30004361 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30004361 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30004361 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30004361 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30004361 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30004361 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30004361 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30004361 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 4
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30004361 ID=SMED30004361|Name=SMED30004361|organism=Schmidtea mediterranea sexual|type=transcript|length=1516bpback to top protein sequence of SMED30004361-orf-1 >SMED30004361-orf-1 ID=SMED30004361-orf-1|Name=SMED30004361-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=440bp MTSDFKEDLWKYSVDIFSILLFVFKFSALFCGICFNYGKYYNSFLKIDKYback 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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