SMED30018580
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., 2020SMED30018580 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 7
Alignments
SMED30018580 aligns in the following genomic locations:
Homology
BLAST of SMED30018580 vs. Planmine SMEST
Match: SMESG000018267.1 (SMESG000018267.1) HSP 1 Score: 171.785 bits (434), Expect = 7.224e-55 Identity = 125/127 (98.43%), Postives = 126/127 (99.21%), Query Frame = 3 Query: 111 MVKISPTRXXXXXXXXXXXXXXXXXSTQYEVLYASDRLKAYGSXXXXXXXXXXXXXXXXXXXNFVQSLSENKFIQILSVAFMVLAGVSLIISCSIYGDGNMSYGWTVASCTLIMEGILIFLVIRFCS 491 MVKISPT+ILLIIFALSLICAIIAISTQYEVLYASDRLKAYGSFIII IIFLALVLFFEILLNFVQSLSENKFIQILSVAFMVLAGVSLIISCSIYGDGNMSYGWTVASCTLIMEGILIFLVIRFCS Sbjct: 1 MVKISPTKILLIIFALSLICAIIAISTQYEVLYASDRLKAYGSFIIIGIIFLALVLFFEILLNFVQSLSENKFIQILSVAFMVLAGVSLIISCSIYGDGNMSYGWTVASCTLIMEGILIFLVIRFCS 127
BLAST of SMED30018580 vs. Planmine SMEST
Match: SMESG000015329.1 (SMESG000015329.1) HSP 1 Score: 127.102 bits (318), Expect = 2.493e-37 Identity = 95/127 (74.80%), Postives = 110/127 (86.61%), Query Frame = 3 Query: 111 MVKISPTRXXXXXXXXXXXXXXXXXSTQYEVLYASDRLKAYGSXXXXXXXXXXXXXXXXXXXNFVQSLSENKFIQILSVAFMVLAGVSLIISCSIYGDGNMSYGWTVASCTLIMEGILIFLVIRFCS 491 MVKI+P +I+LIIFA+SL+CAIIAI+T + SDR KAYGSF+IIAII L +VLF E+LLNFV SLSEN+ +QILS+AFMVLAGVSLIISCSIY +M YGWTVASCTLIMEGILIFLV+RFCS Sbjct: 1 MVKIAPPKIMLIIFAMSLVCAIIAIATDSSLFSYSDRNKAYGSFLIIAIISLGIVLFIELLLNFVGSLSENRIMQILSIAFMVLAGVSLIISCSIYSTSHMPYGWTVASCTLIMEGILIFLVLRFCS 127
BLAST of SMED30018580 vs. Planmine SMEST
Match: SMESG000015390.1 (SMESG000015390.1) HSP 1 Score: 94.3597 bits (233), Expect = 1.679e-24 Identity = 56/93 (60.22%), Postives = 74/93 (79.57%), Query Frame = 3 Query: 213 SDRLKAYGSXXXXXXXXXXXXXXXXXXXNFVQSLSENKFIQILSVAFMVLAGVSLIISCSIYGDGNMSYGWTVASCTLIMEGILIFLVIRFCS 491 SDR KAYG+F+II II L +V+ EILLNF+ S ++N+ IQILS++FMV+ GV+LII+C+I + YGWTVASCTL+ME I IF+ +RFCS Sbjct: 36 SDRDKAYGAFLIIGIISLGIVVVMEILLNFIHSFTDNRIIQILSLSFMVIGGVALIIACAICFPMHFPYGWTVASCTLLMEAIFIFIFLRFCS 128
BLAST of SMED30018580 vs. Planmine SMEST
Match: SMESG000045656.1 (SMESG000045656.1) HSP 1 Score: 79.7221 bits (195), Expect = 6.274e-19 Identity = 46/85 (54.12%), Postives = 64/85 (75.29%), Query Frame = 3 Query: 213 SDRLKAYGSXXXXXXXXXXXXXXXXXXXNFVQSLSENKFIQILSVAFMVLAGVSLIISCSIYGDGNMSYGWTVASCTLIMEGILI 467 SDR K Y +F++I+II L V+ EIL +F++S N+ ++ILSVA MVL GVSLIISC++ + N YGWTVA+CTL+ME ++I Sbjct: 38 SDRRKTYAAFLVISIIALVFVIVMEILTSFIESFKTNRILKILSVAAMVLTGVSLIISCAVVSERNNPYGWTVAACTLVMEALVI 122
BLAST of SMED30018580 vs. Planmine SMEST
Match: SMESG000045652.1 (SMESG000045652.1) HSP 1 Score: 73.1738 bits (178), Expect = 1.055e-16 Identity = 31/62 (50.00%), Postives = 45/62 (72.58%), Query Frame = 3 Query: 300 FVQSLSENKFIQILSVAFMVLAGVSLIISCSIYGDGNMSYGWTVASCTLIMEGILIFLVIRF 485 F+ S+ N IQI+ + MV+A V LII+C++Y DGN+ YGWTVA CTL++E ++I L+ F Sbjct: 42 FISSVRSNGSIQIVGIVAMVIAAVCLIIACAVYNDGNVPYGWTVAGCTLVIEAVVIILITHF 103 The following BLAST results are available for this feature:
BLAST of SMED30018580 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30018580 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30018580 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30018580 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30018580 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30018580 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30018580 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30018580 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30018580 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30018580 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30018580 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30018580 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30018580 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30018580 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 >SMED30018580 ID=SMED30018580|Name=SMED30018580|organism=Schmidtea mediterranea sexual|type=transcript|length=673bpback to top protein sequence of SMED30018580-orf-1 >SMED30018580-orf-1 ID=SMED30018580-orf-1|Name=SMED30018580-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=128bp MVKISPTRILLIIFALSLICAIIAISTQYEVLYASDRLKAYGSFIIIAIIback to top Annotated Terms
The following terms have been associated with this transcript:
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