SMED30006883
Overview
Neoblast Clusters
Zeng et. al., 2018
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 AppEmbryonic 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., 2020SMED30006883 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 15Note: Hover over icons to view figure legend
Alignments
SMED30006883 aligns in the following genomic locations:
Homology
BLAST of SMED30006883 vs. TrEMBL
Match: K1RVV6 (Uncharacterized protein OS=Crassostrea gigas OX=29159 GN=CGI_10026729 PE=4 SV=1) HSP 1 Score: 92.0485 bits (227), Expect = 1.885e-17 Identity = 39/79 (49.37%), Postives = 59/79 (74.68%), Query Frame = 2 Query: 482 IKREESIIYQTVHPDQDKEISIDNLESALQVVNRQLLSKNEFNYIYHILKLPHHPRINMQTFSCIAALSEKVTHLDASI 718 +R++S +Y+T+HPD D E++ + LE ALQ+VN LL++NEF+Y+YHIL L ++N + F IAALSE++TH+D I Sbjct: 483 FRRQQSFLYKTLHPDPDVEMNREELEGALQIVNHNLLTENEFSYMYHILNLTGRRKVNFKLFCVIAALSERITHMDPVI 561
BLAST of SMED30006883 vs. TrEMBL
Match: A0A1I8GZL3 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1) HSP 1 Score: 87.4261 bits (215), Expect = 7.308e-17 Identity = 46/98 (46.94%), Postives = 64/98 (65.31%), Query Frame = 2 Query: 425 ELLKSNQRKAAETNPVLMSIKREESIIYQTVHPDQDKEISIDNLESALQVVNRQLLSKNEFNYIYHILKLPHHPRINMQTFSCIAALSEKVTHLDASI 718 E L+ ++R+AA L RE+S++YQ +HP D E++ID +E ALQ +N L++K E Y+YHIL LP R+N + FS IAALSEKV L+ I Sbjct: 49 EQLEPSRRQAAGGADFL----REQSLLYQKLHPAIDLELNIDLVEEALQDINGHLITKKEMQYVYHILNLPARTRVNFRLFSVIAALSEKVVQLEPII 142
BLAST of SMED30006883 vs. TrEMBL
Match: V4BAS6 (Uncharacterized protein OS=Lottia gigantea OX=225164 GN=LOTGIDRAFT_235648 PE=4 SV=1) HSP 1 Score: 88.1965 bits (217), Expect = 4.989e-16 Identity = 42/91 (46.15%), Postives = 60/91 (65.93%), Query Frame = 2 Query: 446 RKAAETNPVLMSIKREESIIYQTVHPDQDKEISIDNLESALQVVNRQLLSKNEFNYIYHILKLPHHPRINMQTFSCIAALSEKVTHLDASI 718 R+ ET+P +R++S++Y T+ P D EI +DNL +LQ VN LL+ E +++YH+L LP +IN + FS +AALSEKVT LD I Sbjct: 1025 RQFTETHPA--DFRRQQSVLYNTLRPTPDYEIKLDNLRESLQQVNNHLLTDRECDFLYHVLDLPGREKINFRLFSVVAALSEKVTQLDPMI 1113
BLAST of SMED30006883 vs. TrEMBL
Match: A0A2R2MTE6 (uncharacterized protein LOC106167849 isoform X4 OS=Lingula unguis OX=7574 GN=LOC106167849 PE=4 SV=1) HSP 1 Score: 87.0409 bits (214), Expect = 1.141e-15 Identity = 50/151 (33.11%), Postives = 90/151 (59.60%), Query Frame = 2 Query: 260 ISNKEIVKKIDSLIRKKISKMNEFLPKWAELNQIRKTLNQITVKILNLKIKRQKLELLKSNQR-KAAETNPVLMSIKREESIIYQTVHPDQDKEISIDNLESALQVVNRQLLSKNEFNYIYHILKLPHHPRINMQTFSCIAALSEKVTHLD 709 ++ EI+ ++DS + IS M E A+L+ I K + ++ ++ +++++E+ + K N +R++S +YQ ++P D EI+++ +E+ALQ +N LL+ EF ++YH+L LP R+N++ FS +AALSEKV LD Sbjct: 970 LTADEIIGRLDSKMWSMISNMPEVTRTDAQLSIIEKKMAELEARMNITDEEKREMEIYTRDLFLKEQIENERTREFRRKQSPLYQQINPVPDVEINVEEVEAALQRINNNLLTDREFQFVYHVLDLPGRHRLNLKLFSAVAALSEKVKQLD 1120
BLAST of SMED30006883 vs. TrEMBL
Match: A0A2R2MSZ1 (uncharacterized protein LOC106167849 isoform X1 OS=Lingula unguis OX=7574 GN=LOC106167849 PE=4 SV=1) HSP 1 Score: 87.0409 bits (214), Expect = 1.252e-15 Identity = 50/151 (33.11%), Postives = 90/151 (59.60%), Query Frame = 2 Query: 260 ISNKEIVKKIDSLIRKKISKMNEFLPKWAELNQIRKTLNQITVKILNLKIKRQKLELLKSNQR-KAAETNPVLMSIKREESIIYQTVHPDQDKEISIDNLESALQVVNRQLLSKNEFNYIYHILKLPHHPRINMQTFSCIAALSEKVTHLD 709 ++ EI+ ++DS + IS M E A+L+ I K + ++ ++ +++++E+ + K N +R++S +YQ ++P D EI+++ +E+ALQ +N LL+ EF ++YH+L LP R+N++ FS +AALSEKV LD Sbjct: 1334 LTADEIIGRLDSKMWSMISNMPEVTRTDAQLSIIEKKMAELEARMNITDEEKREMEIYTRDLFLKEQIENERTREFRRKQSPLYQQINPVPDVEINVEEVEAALQRINNNLLTDREFQFVYHVLDLPGRHRLNLKLFSAVAALSEKVKQLD 1484
BLAST of SMED30006883 vs. Planmine SMEST
Match: SMESG000063750.1 (SMESG000063750.1) HSP 1 Score: 357.066 bits (915), Expect = 2.790e-116 Identity = 180/181 (99.45%), Postives = 181/181 (100.00%), Query Frame = 2 Query: 167 DSLENEIAMKIKEKYPKVVEKLKYSKSEESAISNKEIVKKIDSLIRKKISKMNEFLPKWAELNQIRKTLNQITVKILNLKIKRQKLELLKSNQRKAAETNPVLMSIKREESIIYQTVHPDQDKEISIDNLESALQVVNRQLLSKNEFNYIYHILKLPHHPRINMQTFSCIAALSEKVTHLD 709 DSLENEIAMKIKEKYPKVVEKLKYSKSEESAISNKEIVKKIDSLIRKKISKMNEFLPKWAELNQIRKTLNQITVKILNLKIKRQKLELLKSNQRKAAETNPVLMSIKREESIIYQTVHPDQDKEISIDNLESALQVVNRQLLSKNEFNYIYHILKLPHHPRINMQTFSCIAALSEKVTHL+ Sbjct: 763 DSLENEIAMKIKEKYPKVVEKLKYSKSEESAISNKEIVKKIDSLIRKKISKMNEFLPKWAELNQIRKTLNQITVKILNLKIKRQKLELLKSNQRKAAETNPVLMSIKREESIIYQTVHPDQDKEISIDNLESALQVVNRQLLSKNEFNYIYHILKLPHHPRINMQTFSCIAALSEKVTHLE 943 The following BLAST results are available for this feature:
BLAST of SMED30006883 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30006883 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30006883 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30006883 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30006883 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30006883 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30006883 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30006883 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 5
BLAST of SMED30006883 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30006883 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30006883 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30006883 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30006883 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30006883 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 >SMED30006883 ID=SMED30006883|Name=SMED30006883|organism=Schmidtea mediterranea sexual|type=transcript|length=759bpback to top protein sequence of SMED30006883-orf-1 >SMED30006883-orf-1 ID=SMED30006883-orf-1|Name=SMED30006883-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=187bp MKIKEKYPKVVEKLKYSKSEESAISNKEIVKKIDSLIRKKISKMNEFLPKback 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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