SMED30027489
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., 2020SMED30027489 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 3
Alignments
SMED30027489 aligns in the following genomic locations:
Homology
BLAST of SMED30027489 vs. Planmine SMEST
Match: SMESG000004279.1 (SMESG000004279.1) HSP 1 Score: 163.31 bits (412), Expect = 4.488e-52 Identity = 81/115 (70.43%), Postives = 90/115 (78.26%), Query Frame = 3 Query: 132 NQKHYYMIETI**RWKSSFQI*KTSFHIVLLNFLATRIYQMTGINIEEIIRIHYESVQ*SGLKCLDDCIVCADPSMFTCTFRCRC*RDYKKKEVVHILLAELRRAYYKMICDDVN 476 +++ Y+ ETI + + F K +LATRIYQMTGINIEEI+R+HYESVQ SGLKCLDDCIVCADPSM TC FRCRC RDYKKKEVVHILLAELRRAYYK ICDDVN Sbjct: 3 DEQEAYVFETILMKMEELFPNMKNKLSYCAPEYLATRIYQMTGINIEEIVRMHYESVQGSGLKCLDDCIVCADPSMLTCPFRCRCCRDYKKKEVVHILLAELRRAYYKQICDDVN 117
BLAST of SMED30027489 vs. Planmine SMEST
Match: SMESG000030237.1 (SMESG000030237.1) HSP 1 Score: 163.31 bits (412), Expect = 6.802e-50 Identity = 80/114 (70.18%), Postives = 89/114 (78.07%), Query Frame = 3 Query: 132 NQKHYYMIETI**RWKSSFQI*KTSFHIVLLNFLATRIYQMTGINIEEIIRIHYESVQ*SGLKCLDDCIVCADPSMFTCTFRCRC*RDYKKKEVVHILLAELRRAYYKMICDDV 473 +++ Y+ ETI + + F K +LATRIYQMTGINIEEI+R+HYESVQ SGLKCLDDCIVCADPSM TC FRCRC RDYKKKEVVHILLAELRRAYYK ICDDV Sbjct: 3 DEQEAYVFETILMKMEELFPNMKNKLFYCAPEYLATRIYQMTGINIEEIVRMHYESVQGSGLKCLDDCIVCADPSMLTCPFRCRCCRDYKKKEVVHILLAELRRAYYKQICDDV 116
BLAST of SMED30027489 vs. Planmine SMEST
Match: SMESG000047442.1 (SMESG000047442.1) HSP 1 Score: 169.474 bits (428), Expect = 4.283e-49 Identity = 79/113 (69.91%), Postives = 88/113 (77.88%), Query Frame = 3 Query: 132 NQKHYYMIETI**RWKSSFQI*KTSFHIVLLNFLATRIYQMTGINIEEIIRIHYESVQ*SGLKCLDDCIVCADPSMFTCTFRCRC*RDYKKKEVVHILLAELRRAYYKMICDD 470 +++ Y+ ETI + + F K +LATRIYQMTGINIEEI+R+HYESVQ SGLKCLDDCIVCADPSM TC FRCRC RDYKKKEVVHILLAELRRAYYK ICDD Sbjct: 3 DEQEAYVFETILMKMEELFPNMKNKLSYCAPEYLATRIYQMTGINIEEIVRMHYESVQGSGLKCLDDCIVCADPSMLTCPFRCRCCRDYKKKEVVHILLAELRRAYYKQICDD 115
BLAST of SMED30027489 vs. Planmine SMEST
Match: SMESG000058567.1 (SMESG000058567.1) HSP 1 Score: 160.999 bits (406), Expect = 5.095e-49 Identity = 79/113 (69.91%), Postives = 88/113 (77.88%), Query Frame = 3 Query: 132 NQKHYYMIETI**RWKSSFQI*KTSFHIVLLNFLATRIYQMTGINIEEIIRIHYESVQ*SGLKCLDDCIVCADPSMFTCTFRCRC*RDYKKKEVVHILLAELRRAYYKMICDD 470 +++ Y+ ETI + + F K +LATRIYQMTGINIEEI+R+HYESVQ SGLKCLDDCIVCADPSM TC FRCRC RDYKKKEVVHILLAELRRAYYK ICDD Sbjct: 3 DEQEAYVFETILMKMEELFPNMKNKLSYCAPKYLATRIYQMTGINIEEIVRMHYESVQGSGLKCLDDCIVCADPSMLTCPFRCRCCRDYKKKEVVHILLAELRRAYYKQICDD 115
BLAST of SMED30027489 vs. Planmine SMEST
Match: SMESG000000439.1 (SMESG000000439.1) HSP 1 Score: 152.91 bits (385), Expect = 4.429e-48 Identity = 78/109 (71.56%), Postives = 86/109 (78.90%), Query Frame = 3 Query: 150 MIETI**RWKSSFQI*KTSFHIVLLNFLATRIYQMTGINIEEIIRIHYESVQ*SGLKCLDDCIVCADPSMFTCTFRCRC*RDYKKKEVVHILLAELRRAYYKMICDDVN 476 MIETI + + F K L +LAT IYQMTGINIEEI+R+HYESVQ +GLKCLDD IVCADPSM TC F CRC RDYKKKEVVHILLA+LRRAYYK+ICDDVN Sbjct: 1 MIETILTKIEELFPNIKNKLSYCALEYLATWIYQMTGINIEEIVRMHYESVQGTGLKCLDDSIVCADPSMLTCPFICRCCRDYKKKEVVHILLADLRRAYYKLICDDVN 109 The following BLAST results are available for this feature:
BLAST of SMED30027489 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30027489 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30027489 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30027489 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30027489 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30027489 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30027489 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30027489 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30027489 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30027489 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30027489 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30027489 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30027489 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30027489 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 >SMED30027489 ID=SMED30027489|Name=SMED30027489|organism=Schmidtea mediterranea sexual|type=transcript|length=589bpback to top Annotated Terms
The following terms have been associated with this transcript:
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