SMED30003773
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., 2020SMED30003773 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 3
Alignments
SMED30003773 aligns in the following genomic locations:
Homology
BLAST of SMED30003773 vs. Planmine SMEST
Match: SMESG000021279.1 (SMESG000021279.1) HSP 1 Score: 70.0922 bits (170), Expect = 2.208e-14 Identity = 54/140 (38.57%), Postives = 79/140 (56.43%), Query Frame = -1 Query: 402 ERILKLMVILKEYS*KFV*AYLSAKATKKYXSNSRTLQLFIVSKFL-ILRKSFKKQMNFVYNLQEVFKYHQDNDSVN------RKVHQQILRQSQ*KG-IA*IFNFLARKVLK*RKFSKITKFKTMEKM*ERIKKHEKVN 797 ER+ M IL+EY KF A+LSA A KY + S S +L L+++FKK +NF+ + QE KY+Q NDS N K+ + IL+ K + F A + + K ++ +FKT+E++ ER+KKHEKVN Sbjct: 7 ERVFDFMGILEEYRGKFDKAFLSANAINKYEATSEN------SNYLDCLKEAFKKPLNFMDDFQEALKYYQRNDSANEFCTKIEKLAKVILQHKLNKEKLQKFLIFHAVEDNEMNKDLRMNEFKTVEELKERLKKHEKVN 140
BLAST of SMED30003773 vs. Planmine SMEST
Match: SMESG000066474.1 (SMESG000066474.1) HSP 1 Score: 65.4698 bits (158), Expect = 6.693e-13 Identity = 37/78 (47.44%), Postives = 46/78 (58.97%), Query Frame = -1 Query: 567 FERILKLMVILKEYS*KFV*AYLSAKATKKYXSNSRTLQLFIVSKFLILRKSFKKQMNFVYNLQEVFKYHQDNDSVNR 800 FER LM I KEY KFV A+LS ATKKY ++ + L+++FKK MNF+ +LQE KY Q NDS N Sbjct: 40 FERFFDLMWISKEYRGKFVKAFLSVNATKKYEASREDINYLDR-----LKETFKKPMNFMGDLQEAVKYRQGNDSANE 112
BLAST of SMED30003773 vs. Planmine SMEST
Match: SMESG000023258.1 (SMESG000023258.1) HSP 1 Score: 47.3654 bits (111), Expect = 4.595e-8 Identity = 44/141 (31.21%), Postives = 71/141 (50.35%), Query Frame = -1 Query: 405 ERILKLMVILKEYS*KFV*AYLSAKATKKYXSNSRTLQLFIVSKFLILRKSFKKQMNFVYNLQEVFKYHQDNDSVN------RKVHQQILR----QSQ*KGIA*IFNFLARKVLK*RKFSKITKFKTMEKM*ERIKKHEKV 797 ER ++ I+ EY KFV A+LS +TKKY + TL LR +F K + + +L E Y Q N++ K+ + IL+ + + K +FN L K +K K K+ K+ ++M ER+K+H++V Sbjct: 1077 ERFFEMTNIVDEYRSKFVKAFLSINSTKKYELTNETLHYTER-----LRNAFSKNRSLIDDLNEALNYRQGNEAAEEFCSKIEKLAKNILKHKLDEEELKKFL-LFNSLEDKEVK--KDLKMQDLKSFDEMKERLKRHDQV 1209 HSP 2 Score: 28.4906 bits (62), Expect = 4.595e-8 Identity = 11/19 (57.89%), Postives = 16/19 (84.21%), Query Frame = -3 Query: 799 NFIKPPENYEIRANVKDCI 855 NFIKPPE Y++ ++V+D I Sbjct: 1055 NFIKPPETYDMDSDVEDFI 1073
BLAST of SMED30003773 vs. Planmine SMEST
Match: SMESG000023258.1 (SMESG000023258.1) HSP 1 Score: 47.3654 bits (111), Expect = 4.861e-8 Identity = 44/141 (31.21%), Postives = 71/141 (50.35%), Query Frame = -1 Query: 405 ERILKLMVILKEYS*KFV*AYLSAKATKKYXSNSRTLQLFIVSKFLILRKSFKKQMNFVYNLQEVFKYHQDNDSVN------RKVHQQILR----QSQ*KGIA*IFNFLARKVLK*RKFSKITKFKTMEKM*ERIKKHEKV 797 ER ++ I+ EY KFV A+LS +TKKY + TL LR +F K + + +L E Y Q N++ K+ + IL+ + + K +FN L K +K K K+ K+ ++M ER+K+H++V Sbjct: 1085 ERFFEMTNIVDEYRSKFVKAFLSINSTKKYELTNETLHYTER-----LRNAFSKNRSLIDDLNEALNYRQGNEAAEEFCSKIEKLAKNILKHKLDEEELKKFL-LFNSLEDKEVK--KDLKMQDLKSFDEMKERLKRHDQV 1217 HSP 2 Score: 28.4906 bits (62), Expect = 4.861e-8 Identity = 11/19 (57.89%), Postives = 16/19 (84.21%), Query Frame = -3 Query: 799 NFIKPPENYEIRANVKDCI 855 NFIKPPE Y++ ++V+D I Sbjct: 1063 NFIKPPETYDMDSDVEDFI 1081
BLAST of SMED30003773 vs. Planmine SMEST
Match: SMESG000063281.1 (SMESG000063281.1) HSP 1 Score: 44.669 bits (104), Expect = 4.669e-6 Identity = 33/84 (39.29%), Postives = 42/84 (50.00%), Query Frame = -1 Query: 546 MVILKEYS*KFV*AYLSAKATKKYXSNSRTLQLFIVSKFLILRKSFKKQMNFVYNLQEVFKYHQDNDSVN------RKVHQQIL 779 M I +EY FV A+LSA KKY S + + L+ FKK M F+ +LQE KY + ND VN K +QIL Sbjct: 1 MGISEEYREIFVKAFLSANVAKKYESTRKDINYLNR-----LKDVFKKPMKFMDDLQEALKYRKGNDLVNEFCTKIEKFEKQIL 79 The following BLAST results are available for this feature:
BLAST of SMED30003773 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30003773 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30003773 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30003773 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30003773 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30003773 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30003773 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30003773 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30003773 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30003773 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30003773 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30003773 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30003773 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30003773 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 >SMED30003773 ID=SMED30003773|Name=SMED30003773|organism=Schmidtea mediterranea sexual|type=transcript|length=1076bpback to top Annotated Terms
The following terms have been associated with this transcript:
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