SMED30008428
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., 2020SMED30008428 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 4
Alignments
SMED30008428 aligns in the following genomic locations:
Homology
BLAST of SMED30008428 vs. Planmine SMEST
Match: SMESG000007463.1 (SMESG000007463.1) HSP 1 Score: 270.781 bits (691), Expect = 7.272e-95 Identity = 132/133 (99.25%), Postives = 133/133 (100.00%), Query Frame = 2 Query: 29 MLFLAALLFVNSINCQHELASLVLENEAKCEFENGFCFAHDQCCGNLVCKVFNDFGQCSAVSANEIHKADVSCRSNTDCGSNMCCFSDTYGMGQREIRTCHNLIGETCVNHANLKNYKISNDWFTLKRKRNNF 427 MLFLAALLF+NSINCQHELASLVLENEAKCEFENGFCFAHDQCCGNLVCKVFNDFGQCSAVSANEIHKADVSCRSNTDCGSNMCCFSDTYGMGQREIRTCHNLIGETCVNHANLKNYKISNDWFTLKRKRNNF Sbjct: 1 MLFLAALLFMNSINCQHELASLVLENEAKCEFENGFCFAHDQCCGNLVCKVFNDFGQCSAVSANEIHKADVSCRSNTDCGSNMCCFSDTYGMGQREIRTCHNLIGETCVNHANLKNYKISNDWFTLKRKRNNF 133
BLAST of SMED30008428 vs. Planmine SMEST
Match: SMESG000007463.1 (SMESG000007463.1) HSP 1 Score: 252.292 bits (643), Expect = 9.510e-88 Identity = 123/124 (99.19%), Postives = 124/124 (100.00%), Query Frame = 2 Query: 56 VNSINCQHELASLVLENEAKCEFENGFCFAHDQCCGNLVCKVFNDFGQCSAVSANEIHKADVSCRSNTDCGSNMCCFSDTYGMGQREIRTCHNLIGETCVNHANLKNYKISNDWFTLKRKRNNF 427 +NSINCQHELASLVLENEAKCEFENGFCFAHDQCCGNLVCKVFNDFGQCSAVSANEIHKADVSCRSNTDCGSNMCCFSDTYGMGQREIRTCHNLIGETCVNHANLKNYKISNDWFTLKRKRNNF Sbjct: 1 MNSINCQHELASLVLENEAKCEFENGFCFAHDQCCGNLVCKVFNDFGQCSAVSANEIHKADVSCRSNTDCGSNMCCFSDTYGMGQREIRTCHNLIGETCVNHANLKNYKISNDWFTLKRKRNNF 124
BLAST of SMED30008428 vs. Planmine SMEST
Match: SMESG000035423.1 (SMESG000035423.1) HSP 1 Score: 53.1434 bits (126), Expect = 2.816e-9 Identity = 26/89 (29.21%), Postives = 43/89 (48.31%), Query Frame = 2 Query: 26 KMLFLAALLFVNSINCQHELASLVLENEAKCEFENGFCFAHDQCCGNLVCKVFNDFGQCSAVSANEIHKADVSCRSNTDCGSNMCCFSD 292 K+L L +V+S + + E +CE + FCF +QCC +LVC+ + G C N ++ C+ ++DC MCC + Sbjct: 2 KLLLLLINYYVHSKTFSYNIELKPYLQETQCEPRDSFCFKDNQCCSDLVCQFKDGIGSCVPFQWNSKFQSPRLCQKDSDCELEMCCVKE 90
BLAST of SMED30008428 vs. Planmine SMEST
Match: SMESG000035423.1 (SMESG000035423.1) HSP 1 Score: 52.7582 bits (125), Expect = 4.123e-9 Identity = 26/89 (29.21%), Postives = 43/89 (48.31%), Query Frame = 2 Query: 26 KMLFLAALLFVNSINCQHELASLVLENEAKCEFENGFCFAHDQCCGNLVCKVFNDFGQCSAVSANEIHKADVSCRSNTDCGSNMCCFSD 292 K+L L +V+S + + E +CE + FCF +QCC +LVC+ + G C N ++ C+ ++DC MCC + Sbjct: 10 KLLLLLINYYVHSKTFSYNIELKPYLQETQCEPRDSFCFKDNQCCSDLVCQFKDGIGSCVPFQWNSKFQSPRLCQKDSDCELEMCCVKE 98
BLAST of SMED30008428 vs. Planmine SMEST
Match: SMESG000006615.1 (SMESG000006615.1) HSP 1 Score: 51.2174 bits (121), Expect = 1.357e-8 Identity = 37/137 (27.01%), Postives = 60/137 (43.80%), Query Frame = 2 Query: 32 LFLAALLFVNSI---NCQHELASLVLENEAKCEFENGFCFAHDQCCGNLVCKVFNDFGQCSAVSANEIHKADVSCRSNTDCGSNMCC------FSDTYGMGQREIRTCHNLIGETCVNHANLKNYKISNDWFTLKRK 415 +FL L SI + LASL+ + +CE E G CF D CC L C + + G+C I + C+ N+DC +CC F ++I C + + ++N + +DW TL+++ Sbjct: 5 IFLITQLIRYSIEKDDLNPNLASLISNSNRQCEREQGLCFIDDNCCFGLHCVITSGLGRCVNSIYKLIQGDGLLCKKNSDCLPGLCCSVEFTKFLKGTFCRPKDIGDCLSTSDDLSNTNSN-NRINLQSDWITLRKR 140 The following BLAST results are available for this feature:
BLAST of SMED30008428 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30008428 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30008428 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30008428 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30008428 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30008428 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30008428 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30008428 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30008428 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30008428 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30008428 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30008428 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30008428 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30008428 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 >SMED30008428 ID=SMED30008428|Name=SMED30008428|organism=Schmidtea mediterranea sexual|type=transcript|length=478bpback to top protein sequence of SMED30008428-orf-1 >SMED30008428-orf-1 ID=SMED30008428-orf-1|Name=SMED30008428-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=134bp MLFLAALLFVNSINCQHELASLVLENEAKCEFENGFCFAHDQCCGNLVCKback to top InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
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