SMED30005839
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., 2020SMED30005839 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 2
Alignments
SMED30005839 aligns in the following genomic locations:
Homology
BLAST of SMED30005839 vs. Planmine SMEST
Match: SMESG000005595.1 (SMESG000005595.1) HSP 1 Score: 83.5741 bits (205), Expect = 9.964e-18 Identity = 38/39 (97.44%), Postives = 39/39 (100.00%), Query Frame = 2 Query: 245 VPSVYKQTHHNANRRPEKRIREQNSRYSRKDNCAPDLRS 361 +PSVYKQTHHNANRRPEKRIREQNSRYSRKDNCAPDLRS Sbjct: 360 LPSVYKQTHHNANRRPEKRIREQNSRYSRKDNCAPDLRS 398
BLAST of SMED30005839 vs. Planmine SMEST
Match: SMESG000005595.1 (SMESG000005595.1) HSP 1 Score: 72.4034 bits (176), Expect = 4.851e-14 Identity = 33/33 (100.00%), Postives = 33/33 (100.00%), Query Frame = 2 Query: 392 MTEARKRIHKQIYSSYKRKCHPECRIASHSSIY 490 MTEARKRIHKQIYSSYKRKCHPECRIASHSSIY Sbjct: 1 MTEARKRIHKQIYSSYKRKCHPECRIASHSSIY 33
BLAST of SMED30005839 vs. Planmine SMEST
Match: SMESG000051975.1 (SMESG000051975.1) HSP 1 Score: 50.0618 bits (118), Expect = 5.693e-11 Identity = 25/46 (54.35%), Postives = 31/46 (67.39%), Query Frame = 3 Query: 525 YENERVKNIYQQLDTTRVTLLEFNQLIKAQKAQIRAIETSLSASQE 662 +E +R+K IY D R L E NQL +AQK QIRA+E +LSAS E Sbjct: 49 FEQKRLKRIYPVFDANRAALKEANQLKQAQKTQIRALEVALSASHE 94 HSP 2 Score: 35.4242 bits (80), Expect = 5.693e-11 Identity = 22/45 (48.89%), Postives = 28/45 (62.22%), Query Frame = 1 Query: 685 GIHPAQLAYKEQGTRNVTGE*TNPIRHKQGKAERARFWLLRVEPK 819 G PAQL +E+ T + G +N R K GKAERAR L+RV+ K Sbjct: 103 GFVPAQLPDRERATTSDGGP-SNQRRCKPGKAERARLQLMRVKSK 146
BLAST of SMED30005839 vs. Planmine SMEST
Match: SMESG000062790.1 (SMESG000062790.1) HSP 1 Score: 43.1282 bits (100), Expect = 4.461e-7 Identity = 21/47 (44.68%), Postives = 30/47 (63.83%), Query Frame = 3 Query: 522 AYENERVKNIYQQLDTTRVTLLEFNQLIKAQKAQIRAIETSLSASQE 662 +E +R + IY++LD R L E NQ AQ+ IRA E +L+ASQ+ Sbjct: 23 CFEPKRPQKIYRELDACRTALKEANQTNHAQRTLIRAFELALTASQD 69 HSP 2 Score: 29.261 bits (64), Expect = 4.461e-7 Identity = 23/45 (51.11%), Postives = 26/45 (57.78%), Query Frame = 1 Query: 688 IHPAQLAYKEQGTRNVTGE*TNPIR-HKQGKAERARFWLLRVEPK 819 PAQL Y+E+ T E T P R HK GKAE AR L R +PK Sbjct: 79 FDPAQLIYRER-----TAE-TFPQRKHKPGKAEPARRRLQRADPK 117
BLAST of SMED30005839 vs. Planmine SMEST
Match: SMESG000068632.1 (SMESG000068632.1) HSP 1 Score: 36.1946 bits (82), Expect = 8.880e-7 Identity = 18/39 (46.15%), Postives = 25/39 (64.10%), Query Frame = 1 Query: 694 PAQLAYKEQGTRNVTGE*TNPIRHKQGKAERARFWLLRV 810 PAQLAY++Q + + P RH+ GKAERA+ L+V Sbjct: 1156 PAQLAYRDQMSPATPKD--KPNRHRPGKAERAKLRRLKV 1192 HSP 2 Score: 34.6538 bits (78), Expect = 8.880e-7 Identity = 17/45 (37.78%), Postives = 28/45 (62.22%), Query Frame = 3 Query: 528 ENERVKNIYQQLDTTRVTLLEFNQLIKAQKAQIRAIETSLSASQE 662 E ++ K +YQ+++ + QL + K QI+ +ET+LSASQE Sbjct: 1100 EPKKAKAVYQRMEAAQKGWASERQLTQNLKTQIKGLETALSASQE 1144 The following BLAST results are available for this feature:
BLAST of SMED30005839 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30005839 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30005839 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30005839 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30005839 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30005839 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30005839 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30005839 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30005839 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30005839 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30005839 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30005839 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30005839 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30005839 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 >SMED30005839 ID=SMED30005839|Name=SMED30005839|organism=Schmidtea mediterranea sexual|type=transcript|length=881bpback 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
|