SMED30006083
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., 2020SMED30006083 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 9
Alignments
SMED30006083 aligns in the following genomic locations:
Homology
BLAST of SMED30006083 vs. Planmine SMEST
Match: SMESG000061797.1 (SMESG000061797.1) HSP 1 Score: 239.195 bits (609), Expect = 1.224e-81 Identity = 132/134 (98.51%), Postives = 132/134 (98.51%), Query Frame = 1 Query: 136 MKVXXXXXXXXXXXXVYSEKSALLEHCERILLLKIKRCDKLYKKVDQFCDNGYLETDLECGNEKKLACHMKYERSEKDCKSRMDLFWMNCDSVYGDYRKECVTPKELKDEQFEILLNEQDKLTEMEKRRIQKTN 537 MKVLILSMLFSLLILVYSEKSALLEHCERILLLKIKRCDKLYK VDQFCDNGYLETDLECGNEKKLACHMKYERSEKDCKSRMDLFWMNCD VYGDYRKECVTPKELKDEQFEILLNEQDKLTEMEKRRIQKTN Sbjct: 1 MKVLILSMLFSLLILVYSEKSALLEHCERILLLKIKRCDKLYKNVDQFCDNGYLETDLECGNEKKLACHMKYERSEKDCKSRMDLFWMNCDGVYGDYRKECVTPKELKDEQFEILLNEQDKLTEMEKRRIQKTN 134
BLAST of SMED30006083 vs. Planmine SMEST
Match: SMESG000061767.1 (SMESG000061767.1) HSP 1 Score: 85.5001 bits (210), Expect = 2.651e-21 Identity = 37/88 (42.05%), Postives = 57/88 (64.77%), Query Frame = 1 Query: 214 CERILLLKIKRCDKLYKKVDQFCDNGYLETDLECGNEKKLACHMKYERSEKDCKSRMDLFWMNCDSVYGDYRKECVTPKELKDEQFEI 477 C +IL +RCD+ YK+ D FC GY+ + +C ++ + C ++++ + DCK + D+FW CDSVY YR EC +PKE+K+E EI Sbjct: 28 CSKILTPAARRCDRKYKEADNFCSAGYVAINKDCKGKETIDCGKRFDQHDADCKEKQDIFWDLCDSVYTAYRNECASPKEIKEELQEI 115
BLAST of SMED30006083 vs. Planmine SMEST
Match: SMESG000022139.1 (SMESG000022139.1) HSP 1 Score: 76.6406 bits (187), Expect = 5.770e-18 Identity = 37/95 (38.95%), Postives = 55/95 (57.89%), Query Frame = 1 Query: 211 HCERILLLKIKRCDKLYKKVDQFCDNGYLETDLECGNEKKLACHMKYERSEKDCKSRMDLFWMNCDSVYGDYRKECVTPKELKDEQFEILLNEQD 495 C+ +L+ K+CDK YK+ D+FC+ G+ + + C + + C Y+ CK + D FW CD VY YRKEC TP+E+K+E EI +D Sbjct: 27 RCKNVLVPASKQCDKNYKETDEFCNGGFAKLNKVCYGKDTVECGDAYKAFTTLCKEKQDNFWDECDPVYTAYRKECATPEEIKEENQEIAEEAKD 121
BLAST of SMED30006083 vs. Planmine SMEST
Match: SMESG000061765.1 (SMESG000061765.1) HSP 1 Score: 75.485 bits (184), Expect = 1.500e-17 Identity = 35/96 (36.46%), Postives = 56/96 (58.33%), Query Frame = 1 Query: 190 EKSALLEHCERILLLKIKRCDKLYKKVDQFCDNGYLETDLECGNEKKLACHMKYERSEKDCKSRMDLFWMNCDSVYGDYRKECVTPKELKDEQFEI 477 E+ L +HC +L K CD+ Y D FC GY + + C ++ + C ++YE +K CK + FW +CD +Y +YR++C + KE+K+E EI Sbjct: 19 EEFQLSKHCIEVLTPLSKDCDRRYHVADTFCSQGYAKINKICTGKESVYCGLQYENHDKACKQVQNNFWNHCDDIYRNYRQQCASVKEIKEETLEI 114
BLAST of SMED30006083 vs. Planmine SMEST
Match: SMESG000061762.1 (SMESG000061762.1) HSP 1 Score: 75.485 bits (184), Expect = 1.500e-17 Identity = 35/96 (36.46%), Postives = 56/96 (58.33%), Query Frame = 1 Query: 190 EKSALLEHCERILLLKIKRCDKLYKKVDQFCDNGYLETDLECGNEKKLACHMKYERSEKDCKSRMDLFWMNCDSVYGDYRKECVTPKELKDEQFEI 477 E+ L +HC +L K CD+ Y D FC GY + + C ++ + C ++YE +K CK + FW +CD +Y +YR++C + KE+K+E EI Sbjct: 19 EEFQLSKHCIEVLTPLSKDCDRRYHVADTFCSQGYAKINKICTGKESVYCGLQYENHDKACKQVQNNFWNHCDDIYRNYRQQCASVKEIKEETLEI 114 The following BLAST results are available for this feature:
BLAST of SMED30006083 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30006083 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30006083 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30006083 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30006083 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30006083 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30006083 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30006083 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30006083 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30006083 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30006083 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30006083 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30006083 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30006083 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 >SMED30006083 ID=SMED30006083|Name=SMED30006083|organism=Schmidtea mediterranea sexual|type=transcript|length=617bpback to top protein sequence of SMED30006083-orf-1 >SMED30006083-orf-1 ID=SMED30006083-orf-1|Name=SMED30006083-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=135bp MKVLILSMLFSLLILVYSEKSALLEHCERILLLKIKRCDKLYKKVDQFCDback 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
|