SMED30004601
|
Overview
Neoblast Clusters
Zeng et. al., 2018
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 AppEmbryonic 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., 2020SMED30004601 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 1
Alignments
SMED30004601 aligns in the following genomic locations:
Homology
BLAST of SMED30004601 vs. Planmine SMEST
Match: SMESG000003962.1 (SMESG000003962.1) HSP 1 Score: 86.6557 bits (213), Expect = 2.339e-27 Identity = 39/69 (56.52%), Postives = 49/69 (71.01%), Query Frame = 1
Query: 427 RECRGSCSNNYDDVDLPHVAIKREPGRNPARESRSRAEYILVRLEERQKQTDREVVMARYHFARVNSDI 633
RE R + ++DLP VAIKREPGRNPARE R +AE++L RLEE Q+QT+R+V AR H A +N I
Sbjct: 43 REFRAGIQRDDGEIDLPFVAIKREPGRNPAREIRGQAEFLLARLEEHQRQTNRQVDRARRHLAEINKAI 111 HSP 2 Score: 53.5286 bits (127), Expect = 2.339e-27 Identity = 20/28 (71.43%), Postives = 25/28 (89.29%), Query Frame = 3
Query: 348 SWIDAS*ITVRFPARTAARCRKEMWDAG 431
SWIDAS +TVRFPAR+A RC++ +WDAG
Sbjct: 9 SWIDASRVTVRFPARSATRCQQSLWDAG 36
BLAST of SMED30004601 vs. Planmine SMEST
Match: SMESG000003962.1 (SMESG000003962.1) HSP 1 Score: 86.6557 bits (213), Expect = 2.339e-27 Identity = 39/69 (56.52%), Postives = 49/69 (71.01%), Query Frame = 1
Query: 427 RECRGSCSNNYDDVDLPHVAIKREPGRNPARESRSRAEYILVRLEERQKQTDREVVMARYHFARVNSDI 633
RE R + ++DLP VAIKREPGRNPARE R +AE++L RLEE Q+QT+R+V AR H A +N I
Sbjct: 43 REFRAGIQRDDGEIDLPFVAIKREPGRNPAREIRGQAEFLLARLEEHQRQTNRQVDRARRHLAEINKAI 111 HSP 2 Score: 53.5286 bits (127), Expect = 2.339e-27 Identity = 20/28 (71.43%), Postives = 25/28 (89.29%), Query Frame = 3
Query: 348 SWIDAS*ITVRFPARTAARCRKEMWDAG 431
SWIDAS +TVRFPAR+A RC++ +WDAG
Sbjct: 9 SWIDASRVTVRFPARSATRCQQSLWDAG 36
BLAST of SMED30004601 vs. Planmine SMEST
Match: SMESG000023390.1 (SMESG000023390.1) HSP 1 Score: 80.8777 bits (198), Expect = 4.329e-26 Identity = 43/78 (55.13%), Postives = 52/78 (66.67%), Query Frame = 1
Query: 403 DAGKKCG-TRECRGSCSNNYDDVDLPHVAIKREPGRNPARESRSRAEYILVRLEERQKQTDREVVMARYHFARVNSDI 633
DAG RE R + + + VDLP VAIKREPGRNPARE R +AE++L RLEE Q+QT R+V AR H A +N I
Sbjct: 386 DAGFSVSPVRESRTATRRDDEKVDLPFVAIKREPGRNPAREIRGQAEFLLARLEEHQRQTKRQVNRARRHLAEINKAI 463 HSP 2 Score: 55.0694 bits (131), Expect = 4.329e-26 Identity = 24/36 (66.67%), Postives = 28/36 (77.78%), Query Frame = 3
Query: 324 EFRFVSGESWIDAS*ITVRFPARTAARCRKEMWDAG 431
EFR SWIDAS +TVRFPAR+ ARCR+ +WDAG
Sbjct: 353 EFRAKDDHSWIDASRVTVRFPARSVARCRQVLWDAG 388
BLAST of SMED30004601 vs. Planmine SMEST
Match: SMESG000068014.1 (SMESG000068014.1) HSP 1 Score: 97.4413 bits (241), Expect = 6.824e-26 Identity = 50/89 (56.18%), Postives = 60/89 (67.42%), Query Frame = 1
Query: 388 HGLPQDAGKKCGTR-------ECRGSCSNNYDDVDLPHVAIKREPGRNPARESRSRAEYILVRLEERQKQTDREVVMARYHFARVNSDI 633
H P DAGK+CGTR E R ++Y+D DLP+VAIK EPGRNPARE R R E+ L LE RQ+QT+ +V MAR H RVN+DI
Sbjct: 11 HDQPPDAGKQCGTRDFHFPVRESREGRLDDYEDADLPYVAIKMEPGRNPAREIRQRKEFTLAHLETRQRQTNWQVAMARRHLVRVNADI 99
BLAST of SMED30004601 vs. Planmine SMEST
Match: SMESG000019398.1 (SMESG000019398.1) HSP 1 Score: 84.3445 bits (207), Expect = 1.352e-25 Identity = 39/68 (57.35%), Postives = 48/68 (70.59%), Query Frame = 1
Query: 427 RECRGSCSNNYDDVDLPHVAIKREPGRNPARESRSRAEYILVRLEERQKQTDREVVMARYHFARVNSD 630
RE R ++V+LP VAIKREPGRNPARE R +AE++L RLEE Q+QTD +V AR + A VN D
Sbjct: 1145 RESRSGTLQQMEEVELPFVAIKREPGRNPAREIRGQAEFLLARLEEHQRQTDLQVARARLYLANVNED 1212 HSP 2 Score: 50.0618 bits (118), Expect = 1.352e-25 Identity = 18/29 (62.07%), Postives = 23/29 (79.31%), Query Frame = 3
Query: 345 ESWIDAS*ITVRFPARTAARCRKEMWDAG 431
ESW++ S +T+RFPA A RCR+ MWDAG
Sbjct: 1110 ESWVNESRVTIRFPAHAANRCRQAMWDAG 1138 The following BLAST results are available for this feature:
BLAST of SMED30004601 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30004601 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30004601 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30004601 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30004601 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30004601 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30004601 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30004601 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30004601 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30004601 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30004601 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30004601 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30004601 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30004601 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 >SMED30004601 ID=SMED30004601|Name=SMED30004601|organism=Schmidtea mediterranea sexual|type=transcript|length=635bpback to top protein sequence of SMED30004601-orf-1 >SMED30004601-orf-1 ID=SMED30004601-orf-1|Name=SMED30004601-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=104bp MSFVLSQVNHGSMPRESPYASLHGLPQDAGKKCGTRECRGSCSNNYDDVDback to top Annotated Terms
The following terms have been associated with this transcript:
|
