SMED30028142
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., 2020SMED30028142 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 9Note: Hover over icons to view figure legend
Alignments
SMED30028142 aligns in the following genomic locations:
Homology
BLAST of SMED30028142 vs. Planmine SMEST
Match: SMESG000061765.1 (SMESG000061765.1) HSP 1 Score: 267.7 bits (683), Expect = 1.445e-92 Identity = 129/129 (100.00%), Postives = 129/129 (100.00%), Query Frame = 3 Query: 207 MKTSILIFCVLISAVFTDEEFQLSKHCIEVLTPLSKDCDRRYHVADTFCSQGYAKINKICTGKESVYCGLQYENHDKACKQVQNNFWNHCDDIYRNYRQQCASVKEIKEETLEIAADANANKKKYEVDI 593 MKTSILIFCVLISAVFTDEEFQLSKHCIEVLTPLSKDCDRRYHVADTFCSQGYAKINKICTGKESVYCGLQYENHDKACKQVQNNFWNHCDDIYRNYRQQCASVKEIKEETLEIAADANANKKKYEVDI Sbjct: 1 MKTSILIFCVLISAVFTDEEFQLSKHCIEVLTPLSKDCDRRYHVADTFCSQGYAKINKICTGKESVYCGLQYENHDKACKQVQNNFWNHCDDIYRNYRQQCASVKEIKEETLEIAADANANKKKYEVDI 129
BLAST of SMED30028142 vs. Planmine SMEST
Match: SMESG000061762.1 (SMESG000061762.1) HSP 1 Score: 267.7 bits (683), Expect = 1.445e-92 Identity = 129/129 (100.00%), Postives = 129/129 (100.00%), Query Frame = 3 Query: 207 MKTSILIFCVLISAVFTDEEFQLSKHCIEVLTPLSKDCDRRYHVADTFCSQGYAKINKICTGKESVYCGLQYENHDKACKQVQNNFWNHCDDIYRNYRQQCASVKEIKEETLEIAADANANKKKYEVDI 593 MKTSILIFCVLISAVFTDEEFQLSKHCIEVLTPLSKDCDRRYHVADTFCSQGYAKINKICTGKESVYCGLQYENHDKACKQVQNNFWNHCDDIYRNYRQQCASVKEIKEETLEIAADANANKKKYEVDI Sbjct: 1 MKTSILIFCVLISAVFTDEEFQLSKHCIEVLTPLSKDCDRRYHVADTFCSQGYAKINKICTGKESVYCGLQYENHDKACKQVQNNFWNHCDDIYRNYRQQCASVKEIKEETLEIAADANANKKKYEVDI 129
BLAST of SMED30028142 vs. Planmine SMEST
Match: SMESG000061767.1 (SMESG000061767.1) HSP 1 Score: 123.635 bits (309), Expect = 1.018e-35 Identity = 59/127 (46.46%), Postives = 82/127 (64.57%), Query Frame = 3 Query: 207 MKTSILIFCVL-ISAVFTDEEFQLSKHCIEVLTPLSKDCDRRYHVADTFCSQGYAKINKICTGKESVYCGLQYENHDKACKQVQNNFWNHCDDIYRNYRQQCASVKEIKEETLEIAADANANKKKYE 584 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 MKNLSIFLCFLSVAVVFSTKWVPPSNRCSKILTPAARRCDRKYKEADNFCSAGYVAINKDCKGKETIDCGKRFDQHDADCKEKQDIFWDLCDSVYTAYRNECASPKEIKEELQEIADDSKESKKHYK 127
BLAST of SMED30028142 vs. Planmine SMEST
Match: SMESG000022139.1 (SMESG000022139.1) HSP 1 Score: 116.701 bits (291), Expect = 3.458e-33 Identity = 54/123 (43.90%), Postives = 76/123 (61.79%), Query Frame = 3 Query: 204 IMKTSILIFCVLISAVFTDEEFQLSKHCIEVLTPLSKDCDRRYHVADTFCSQGYAKINKICTGKESVYCGLQYENHDKACKQVQNNFWNHCDDIYRNYRQQCASVKEIKEETLEIAADANANK 572 + K SI+ F + ++ D S C VL P SK CD+ Y D FC+ G+AK+NK+C GK++V CG Y+ CK+ Q+NFW+ CD +Y YR++CA+ +EIKEE EIA +A NK Sbjct: 1 MKKFSIIAFSIFVTLAVADVWIPPSARCKNVLVPASKQCDKNYKETDEFCNGGFAKLNKVCYGKDTVECGDAYKAFTTLCKEKQDNFWDECDPVYTAYRKECATPEEIKEENQEIAEEAKDNK 123
BLAST of SMED30028142 vs. Planmine SMEST
Match: SMESG000028420.1 (SMESG000028420.1) HSP 1 Score: 94.7449 bits (234), Expect = 1.004e-24 Identity = 45/115 (39.13%), Postives = 66/115 (57.39%), Query Frame = 3 Query: 204 IMKTSILIFCVLISAVFTDEEFQLSKHCIEVLTPLSKDCDRRYHVADTFCSQGYAKINKICTGKESVYCGLQYENHDKACKQVQNNFWNHCDDIYRNYRQQCASVKEIKEETLEI 548 + K S+ ++ V + + + C+++LTP +K CD RY D FCS GY I+K C G +SV CG+QY H C + Q+ FW C +Y+ Y +CAS +E KEE+ EI Sbjct: 1 MNKISVYALFAVVVIVNSTKWVPSPEKCLKILTPAAKGCDSRYTETDLFCSVGYKHIDKSCKGHDSVECGVQYAKHKDDCTEKQDYFWKVCGPVYKTYSDECASNEERKEESAEI 115 The following BLAST results are available for this feature:
BLAST of SMED30028142 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30028142 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30028142 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30028142 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30028142 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30028142 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30028142 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30028142 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30028142 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30028142 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30028142 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30028142 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30028142 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30028142 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 >SMED30028142 ID=SMED30028142|Name=SMED30028142|organism=Schmidtea mediterranea sexual|type=transcript|length=685bpback to top protein sequence of SMED30028142-orf-1 >SMED30028142-orf-1 ID=SMED30028142-orf-1|Name=SMED30028142-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=130bp MKTSILIFCVLISAVFTDEEFQLSKHCIEVLTPLSKDCDRRYHVADTFCSback 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
|