SMED30016230
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., 2020SMED30016230 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 9
Alignments
SMED30016230 aligns in the following genomic locations:
Homology
BLAST of SMED30016230 vs. Planmine SMEST
Match: SMESG000017162.1 (SMESG000017162.1) HSP 1 Score: 397.127 bits (1019), Expect = 2.683e-141 Identity = 217/224 (96.88%), Postives = 219/224 (97.77%), Query Frame = 3 Query: 153 MIFYFLILDVFYFCQAKIFIDERNDISCNFGNCLVYAYQLYQNGNGXXXXXXXXXXXXXXXXXGCTIKSNWALIWKNGRYYMTRITSNCQAEKSKFINYMFPSPNSSFSDISCDFGKCTKYKYKISNKMFITSLIGPCENSNCKKCSDLSYWKIESVIIPSLVRSSSRCSAFDEILMEDFFIVPASSTESSFWNTSVIVAVIISCLSFVTLVIVLSICFCTKTK 824 MIFYFLILDVFYFCQAKIFIDERNDISCNFGNC VYAYQLYQNGNGSLLVSSFKSSCDSKSCDGCTIKSNWALIWKNGRYYMTRITSNCQAEKSKFINYMFPSP SSFSDISCDFGKC KYKYKISN FITSLIGPCENSNCKKC+DLSYW+IESVIIPSLVRSSSRCSAFDEILMEDFFIVPASSTESSFWNTSVIVAVIISCLSFVTLVIVLSICFCTKTK Sbjct: 1 MIFYFLILDVFYFCQAKIFIDERNDISCNFGNCSVYAYQLYQNGNGSLLVSSFKSSCDSKSCDGCTIKSNWALIWKNGRYYMTRITSNCQAEKSKFINYMFPSPKSSFSDISCDFGKCVKYKYKISNTRFITSLIGPCENSNCKKCNDLSYWEIESVIIPSLVRSSSRCSAFDEILMEDFFIVPASSTESSFWNTSVIVAVIISCLSFVTLVIVLSICFCTKTK 224
BLAST of SMED30016230 vs. Planmine SMEST
Match: SMESG000017134.1 (SMESG000017134.1) HSP 1 Score: 108.997 bits (271), Expect = 2.344e-28 Identity = 76/218 (34.86%), Postives = 114/218 (52.29%), Query Frame = 3 Query: 180 VFYFCQAKIFIDERNDISCNFGNCLVYAYQLYQNGNGXXXXXXXXXXXXXXXXXGCTIKSNWALIWKNGRYYMTRITSNCQAEKSKFINYMFPSPNSSFSDISCDFGKCTKYKYKISNKMFITSLIGPCENSNCKKCSDLSYWKIESVIIPS-LVRSSSRCSAFDEILMEDFFIVP-------ASSTESSFWNTSVIVAVIISCLSFVTLVIVLSICF 809 +F CQ I+ERND++C FG C YQL Q + + +F ++CDS+ C+ C+ KSNW++ N Y++ R TSNC AE + +FPS +SS D+ C C+K+ Y +N +F + +G C S C+ C + W ++S LVR + CS I MED+F++ S ++ W+ +AV ISCL L I I F Sbjct: 10 LFSICQGFQVINERNDVTCLFGYCQRIKYQLLQEISSYSIRPTFIANCDSRVCENCSYKSNWSMGMSNEGYFLVRSTSNCHAENERNSADIFPSNSSSVLDLVCVENTCSKFNYSFTNGVFFSENLGSCNISGCQNCVTSTKWNLKSFSSRLILVRQTESCSLPTFIKMEDYFVIQKFNSLTIQISIQNVRWDVVQTLAVTISCLLVFCLCITFVILF 227
BLAST of SMED30016230 vs. Planmine SMEST
Match: SMESG000017181.1 (SMESG000017181.1) HSP 1 Score: 107.457 bits (267), Expect = 8.909e-28 Identity = 74/227 (32.60%), Postives = 116/227 (51.10%), Query Frame = 3 Query: 153 MIFYFLILDVFYFCQAKIFIDERNDISCNFGNCLVYAYQLYQNGNGXXXXXXXXXXXX--XXXXXGCTIKSNWALIWKNGRYYMTRITSNCQAEKSKFINYMFPSPNS-SFSDISCDFGKCTKYKYKISNKMFITSLIGPCENSNCKKCSDLSYWK-IESVIIPSLVRSSSRCSAFDEILMEDFFI-VPASSTESSFWNTSVIVAVIISCLSFVTLVIVLSICFCTK 818 ++ + L+L C FI+ERNDI+C C Y+LY + + S +C+ C+ K NW L +G Y++ R T++C + + +FPS + + +DI+C C+KY Y + T +G C +C+ C L+ W+ + L R+ S C + I MEDFF + S FW+ I++VIISC+SFV L+I+LS+CFC K Sbjct: 4 LVIFLLLLRNALGCS---FINERNDITCANRTCNNVRYRLYYDDQSYHYYVNVAGESVCPSVNCNNCSYKGNWMLGKASGTYFLYRSTNSCSTDSIRNFTEIFPSSSPLNVTDIACSNYGCSKYNYLFESSKLYTKYLGNCSYPSCEGCKTLTPWQYVNGNSYNLLQRNVSSCPSITRINMEDFFRRLDQISFVKEFWDGGRILSVIISCVSFVALIIILSVCFCKK 227
BLAST of SMED30016230 vs. Planmine SMEST
Match: SMESG000048698.1 (SMESG000048698.1) HSP 1 Score: 101.679 bits (252), Expect = 1.193e-25 Identity = 66/203 (32.51%), Postives = 107/203 (52.71%), Query Frame = 3 Query: 210 IDERNDISCNFGNCLVYAYQLYQNGNGXXXXXXXXXXXXXXXXXGCTIKSNWALIWKNGRYYMTRITSNCQAEKSKFINYMFPSPNSSFSDISCDFGKCTKYKYKISNKMFITSLIGPCENSNCKKCSDLSYWKIESVIIPSLVRSSSRCSAFDEILMEDFFIVPASSTESSFWNTSVIVAVIISCLSFVTLVIVLSICFCTK 818 I+ER DI+C G+C V +Y L + + FKS+C ++ C+ C K +W++ +G YM R + C + +F + + SD +C KC+KY Y + M S IG C++S C C W S++ L R++ C D+I +ED+F++P + +F+ +A+ ISC SF+ LVI+L +CF K Sbjct: 27 INERADITCETGSCSVLSYTLQIDDQIYKVKKGFKSACSTRLCENCAHKGDWSMRLIDGNKYMVRQVNKCLTNNILAVEQLFTNLYTPVSDFTCSLHKCSKYNYSYNGNMISFSYIGVCDHSYCDSCRYSDNW---SLLTGYLQRTTISCYVVDKIRLEDYFLIPEFT--ETFYTLIRKLAITISCASFLCLVIILLVCFAKK 224
BLAST of SMED30016230 vs. Planmine SMEST
Match: SMESG000057635.1 (SMESG000057635.1) HSP 1 Score: 100.523 bits (249), Expect = 4.601e-25 Identity = 69/211 (32.70%), Postives = 112/211 (53.08%), Query Frame = 3 Query: 189 FCQAKIFIDERNDISCNFGNCLVYAYQLYQNGNGXXXXXXXXXXXXXXXXXGCTIKSNWALIWKNGRYYMTRITSNCQAEKSKFINYMFPSPNSSFSDISCDFGKCTKYKYKIS-NKMFITSLIG--PCENSNCKKCSDLSYWKIESVIIPSL--VRSSSRCSAFDEILMEDFFIVPAS----STESSFWNTSVIVAVIISCLSFVTLVIV 794 F +FIDERND++C G C V Y+LY L S+ + C S SC GC +K +W+L +G+Y+++R T NC E K ++ MFP +S S+I C C K Y++ NK+ SL G C C+ CS L W + + + +L RS++ C+A + I MED+F + + + + W S+++ + ++ ++ L V Sbjct: 14 FVTESLFIDERNDVTCLNGKCSVIRYKLYFQNQTYSLRSAREFPCVSLSCSGCAVKGHWSLSEISGKYFLSRFTKNCSIENEKHLSEMFPFYDSKVSEIQCYGFTCRKTIYRMQHNKIIFYSLTGNYSCNKIACRSCSYLGRWVLNNTLGRNLTITRSTNYCAAPNMIAMEDYFSLGGTKAVKAKKEIMWK-SIVIGITLTLVAVFGLTFV 223 The following BLAST results are available for this feature:
BLAST of SMED30016230 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30016230 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30016230 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30016230 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30016230 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30016230 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30016230 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30016230 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30016230 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30016230 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30016230 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30016230 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30016230 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30016230 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 >SMED30016230 ID=SMED30016230|Name=SMED30016230|organism=Schmidtea mediterranea sexual|type=transcript|length=854bpback to top protein sequence of SMED30016230-orf-1 >SMED30016230-orf-1 ID=SMED30016230-orf-1|Name=SMED30016230-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=225bp MIFYFLILDVFYFCQAKIFIDERNDISCNFGNCLVYAYQLYQNGNGSLLVback 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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