SMED30014713
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., 2020SMED30014713 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 8
Alignments
SMED30014713 aligns in the following genomic locations:
Homology
BLAST of SMED30014713 vs. Planmine SMEST
Match: SMESG000061767.1 (SMESG000061767.1) HSP 1 Score: 280.026 bits (715), Expect = 7.404e-98 Identity = 135/136 (99.26%), Postives = 136/136 (100.00%), Query Frame = 1 Query: 124 MKNLSIFLCFLSVAVVFSTKWVPPSNRCSKILTPAARRCDRKYKEADNFCSAGYVAINKDCKGKETIDCGKRFDQHDADCKEKQDIFWDLCDSVYTAYRNECASPKEIKEELQEIAEDSKESKKHYKWTPSNIYED 531 MKNLSIFLCFLSVAVVFSTKWVPPSNRCSKILTPAARRCDRKYKEADNFCSAGYVAINKDCKGKETIDCGKRFDQHDADCKEKQDIFWDLCDSVYTAYRNECASPKEIKEELQEIA+DSKESKKHYKWTPSNIYED Sbjct: 1 MKNLSIFLCFLSVAVVFSTKWVPPSNRCSKILTPAARRCDRKYKEADNFCSAGYVAINKDCKGKETIDCGKRFDQHDADCKEKQDIFWDLCDSVYTAYRNECASPKEIKEELQEIADDSKESKKHYKWTPSNIYED 136
BLAST of SMED30014713 vs. Planmine SMEST
Match: SMESG000022139.1 (SMESG000022139.1) HSP 1 Score: 141.354 bits (355), Expect = 3.449e-43 Identity = 64/123 (52.03%), Postives = 86/123 (69.92%), Query Frame = 1 Query: 124 MKNLSIFLCFLSVAVVFSTKWVPPSNRCSKILTPAARRCDRKYKEADNFCSAGYVAINKDCKGKETIDCGKRFDQHDADCKEKQDIFWDLCDSVYTAYRNECASPKEIKEELQEIAEDSKESK 492 MK SI + V + + W+PPS RC +L PA+++CD+ YKE D FC+ G+ +NK C GK+T++CG + CKEKQD FWD CD VYTAYR ECA+P+EIKEE QEIAE++K++K Sbjct: 1 MKKFSIIAFSIFVTLAVADVWIPPSARCKNVLVPASKQCDKNYKETDEFCNGGFAKLNKVCYGKDTVECGDAYKAFTTLCKEKQDNFWDECDPVYTAYRKECATPEEIKEENQEIAEEAKDNK 123
BLAST of SMED30014713 vs. Planmine SMEST
Match: SMESG000028420.1 (SMESG000028420.1) HSP 1 Score: 132.109 bits (331), Expect = 1.326e-39 Identity = 61/120 (50.83%), Postives = 80/120 (66.67%), Query Frame = 1 Query: 124 MKNLSIFLCFLSVAVVFSTKWVPPSNRCSKILTPAARRCDRKYKEADNFCSAGYVAINKDCKGKETIDCGKRFDQHDADCKEKQDIFWDLCDSVYTAYRNECASPKEIKEELQEIAEDSK 483 M +S++ F V +V STKWVP +C KILTPAA+ CD +Y E D FCS GY I+K CKG ++++CG ++ +H DC EKQD FW +C VY Y +ECAS +E KEE EI E +K Sbjct: 1 MNKISVYALFAVVVIVNSTKWVPSPEKCLKILTPAAKGCDSRYTETDLFCSVGYKHIDKSCKGHDSVECGVQYAKHKDDCTEKQDYFWKVCGPVYKTYSDECASNEERKEESAEIKEGNK 120
BLAST of SMED30014713 vs. Planmine SMEST
Match: SMESG000061765.1 (SMESG000061765.1) HSP 1 Score: 123.635 bits (309), Expect = 3.055e-36 Identity = 59/127 (46.46%), Postives = 82/127 (64.57%), Query Frame = 1 Query: 124 MKNLSIFLCFLSVAVVFSTKWVPPSNRCSKILTPAARRCDRKYKEADNFCSAGYVAINKDCKGKETIDCGKRFDQHDADCKEKQDIFWDLCDSVYTAYRNECASPKEIKEELQEIAEDSKESKKHYK 504 MK + C L ++ VF+ + S C ++LTP ++ CDR+Y AD FCS GY INK C GKE++ CG +++ HD CK+ Q+ FW+ CD +Y YR +CAS KEIKEE EIA D+ +KK Y+ Sbjct: 1 MKTSILIFCVL-ISAVFTDEEFQLSKHCIEVLTPLSKDCDRRYHVADTFCSQGYAKINKICTGKESVYCGLQYENHDKACKQVQNNFWNHCDDIYRNYRQQCASVKEIKEETLEIAADANANKKKYE 126
BLAST of SMED30014713 vs. Planmine SMEST
Match: SMESG000061762.1 (SMESG000061762.1) HSP 1 Score: 123.635 bits (309), Expect = 3.055e-36 Identity = 59/127 (46.46%), Postives = 82/127 (64.57%), Query Frame = 1 Query: 124 MKNLSIFLCFLSVAVVFSTKWVPPSNRCSKILTPAARRCDRKYKEADNFCSAGYVAINKDCKGKETIDCGKRFDQHDADCKEKQDIFWDLCDSVYTAYRNECASPKEIKEELQEIAEDSKESKKHYK 504 MK + C L ++ VF+ + S C ++LTP ++ CDR+Y AD FCS GY INK C GKE++ CG +++ HD CK+ Q+ FW+ CD +Y YR +CAS KEIKEE EIA D+ +KK Y+ Sbjct: 1 MKTSILIFCVL-ISAVFTDEEFQLSKHCIEVLTPLSKDCDRRYHVADTFCSQGYAKINKICTGKESVYCGLQYENHDKACKQVQNNFWNHCDDIYRNYRQQCASVKEIKEETLEIAADANANKKKYE 126 The following BLAST results are available for this feature:
BLAST of SMED30014713 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30014713 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30014713 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30014713 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30014713 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30014713 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30014713 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30014713 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30014713 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30014713 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30014713 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30014713 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30014713 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30014713 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 >SMED30014713 ID=SMED30014713|Name=SMED30014713|organism=Schmidtea mediterranea sexual|type=transcript|length=602bpback to top protein sequence of SMED30014713-orf-1 >SMED30014713-orf-1 ID=SMED30014713-orf-1|Name=SMED30014713-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=137bp MKNLSIFLCFLSVAVVFSTKWVPPSNRCSKILTPAARRCDRKYKEADNFCback 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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