SMED30001176
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., 2020SMED30001176 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 2
Alignments
SMED30001176 aligns in the following genomic locations:
Homology
BLAST of SMED30001176 vs. UniProt/SwissProt
Match: sp|O94323|YGK5_SCHPO (Uncharacterized pyrophosphatase/phosphodiesterase C725.05c OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) OX=284812 GN=SPBC725.05c PE=3 SV=1) HSP 1 Score: 54.299 bits (129), Expect = 1.914e-6 Identity = 35/98 (35.71%), Postives = 50/98 (51.02%), Query Frame = 2 Query: 251 KCEPIWVNNQRNNLESAIIDWPNQLVYNETIWPTFSFGCNSNDISLNLKLNRFINWMERP-KTSLGIMYITSPENNDFLTNFISIVDKWNLIIITFDI 541 K EPIWVN +RNN+ SA+ WP V N PT+S G N D +L K +R + W++ P K ++ +P + F + N+II DI Sbjct: 166 KGEPIWVNAERNNVRSAVHMWPGNEVENHGYRPTYSDGFNF-DTTLREKKDRILEWLDLPDKDRPQLLLAYAPHVDMVGHAFGPDSPELNIIIQEVDI 262
BLAST of SMED30001176 vs. Planmine SMEST
Match: SMESG000020646.1 (SMESG000020646.1) HSP 1 Score: 579.711 bits (1493), Expect = 0.000e+0 Identity = 315/317 (99.37%), Postives = 316/317 (99.68%), Query Frame = 2 Query: 50 FYATFVYCHGDHGDKPKLXXXXXXXXXXXXXFNTTKSKFPFISLPFKVTDMKSIFNSILNGCYNNKTKCEPIWVNNQRNNLESAIIDWPNQLVYNETIWPTFSFGCNSNDISLNLKLNRFINWMERPKTSLGIMYITSPENNDFLTNFISIVDKWNLIIITFDINNNKYEFLALGSKFVKPNNTLSVSEVXXXXXXXXXXXXXTSHNDDLQSLSDGNAGLVKMLTSSTAHGNKLGFLKFVYISSIIGSAVIMACAFIIVAIKSSCVTKQKVNHQYNLGLNDISINTGYPENAYLLNASDDDELFSDAVPHIQTTMVK 1000 FYATFVYCHGDHGDKPKLILISVISNSSIISFNTTKSKFPFISLPFKVTDMKSIFNSILNGCYNNKTKCEPIWVNNQRNNLESAIIDWPNQLVYNETIWPTFSFGCNSNDISL+LKLNRFINWMERPKTSLGIMYIT PENNDFLTNFISIVDKWNLIIITFDINNNKYEFLALGSKFVKPNNTLSVSEVDIKLLIEKILDLKTSHNDDLQSLSDGNAGLVKMLTSSTAHGNKLGFLKFVYISSIIGSAVIMACAFIIVAIKSSCVTKQKVNHQYNLGLNDISINTGYPENAYLLNASDDDELFSDAVPHIQTTMVK Sbjct: 9 FYATFVYCHGDHGDKPKLILISVISNSSIISFNTTKSKFPFISLPFKVTDMKSIFNSILNGCYNNKTKCEPIWVNNQRNNLESAIIDWPNQLVYNETIWPTFSFGCNSNDISLDLKLNRFINWMERPKTSLGIMYITYPENNDFLTNFISIVDKWNLIIITFDINNNKYEFLALGSKFVKPNNTLSVSEVDIKLLIEKILDLKTSHNDDLQSLSDGNAGLVKMLTSSTAHGNKLGFLKFVYISSIIGSAVIMACAFIIVAIKSSCVTKQKVNHQYNLGLNDISINTGYPENAYLLNASDDDELFSDAVPHIQTTMVK 325
BLAST of SMED30001176 vs. Planmine SMEST
Match: SMESG000005655.1 (SMESG000005655.1) HSP 1 Score: 65.4698 bits (158), Expect = 4.868e-11 Identity = 30/80 (37.50%), Postives = 46/80 (57.50%), Query Frame = 2 Query: 248 TKCEPIWVNNQRNNLESAIIDWPNQLV-YNETIWPTFSFGCNSNDISLNLKLNRFINWMERPKTSLGIMYITSPENNDFL 484 + CEPIW +N N +S + WP Q+ Y TI+P+ SFG S+++SL K++ I+W+ T L I+Y P+ L Sbjct: 125 SDCEPIWASNIINGYQSGVFYWPGQMASYKNTIFPSHSFGLFSSNVSLEYKIDVIISWLLHKSTKLAILYHHEPDRTGHL 204 The following BLAST results are available for this feature:
BLAST of SMED30001176 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30001176 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30001176 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30001176 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30001176 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30001176 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30001176 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 1
BLAST of SMED30001176 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30001176 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30001176 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30001176 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30001176 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30001176 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30001176 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 2
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30001176 ID=SMED30001176|Name=SMED30001176|organism=Schmidtea mediterranea sexual|type=transcript|length=1566bpback to top protein sequence of SMED30001176-orf-1 >SMED30001176-orf-1 ID=SMED30001176-orf-1|Name=SMED30001176-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=330bp MNLLMILLCILNFYATFVYCHGDHGDKPKLILISVISNSSIISFNTTKSKback 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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