SMED30024409
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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., 2020SMED30024409 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 3
Homology
BLAST of SMED30024409 vs. Planmine SMEST
Match: SMESG000074943.1 (SMESG000074943.1) HSP 1 Score: 235.728 bits (600), Expect = 2.271e-75 Identity = 144/147 (97.96%), Postives = 146/147 (99.32%), Query Frame = 1
Query: 82 MNKXXXXXXXXXXXDKCRNEDPKFSCVKNLFKTQNASCAGFHNFCMKNEDVDCINFQNVCNQCPPSNYSILMLIDLINVKTELNQTKHQLEAIKVQSQIYENQISESLKKQNLQINNLYTXXXXXXXXXXXXXXXSVDVRFRFLSKY 522
MNKFVFIILIIIFIDKCRNEDPKFSCVKNLFKTQNASCAGFHNFCMKNEDVDCINFQNVCNQCPPSNYSILMLIDLINVKTELNQTKHQLEAIKVQSQIYENQISESLKKQNLQINNLYTFFWIIIILLIFLALISVDVRFRFL+ +
Sbjct: 1 MNKFVFIILIIIFIDKCRNEDPKFSCVKNLFKTQNASCAGFHNFCMKNEDVDCINFQNVCNQCPPSNYSILMLIDLINVKTELNQTKHQLEAIKVQSQIYENQISESLKKQNLQINNLYTFFWIIIILLIFLALISVDVRFRFLTNF 147
BLAST of SMED30024409 vs. Planmine SMEST
Match: SMESG000074943.1 (SMESG000074943.1) HSP 1 Score: 213.386 bits (542), Expect = 9.450e-67 Identity = 134/147 (91.16%), Postives = 136/147 (92.52%), Query Frame = 1
Query: 82 MNKXXXXXXXXXXXDKCRNEDPKFSCVKNLFKTQNASCAGFHNFCMKNEDVDCINFQNVCNQCPPSNYSILMLIDLINVKTELNQTKHQLEAIKVQSQIYENQISESLKKQNLQINNLYTXXXXXXXXXXXXXXXSVDVRFRFLSKY 522
MNKFVFIILIIIFIDKCRNEDPKFSCVKNLFKTQNASCAGFHNFCMKNEDVDCINFQNVCNQCPPSNYSILMLIDLINVKTELNQTKHQLEAIKVQSQIYENQISESLKKQNLQ IIILLIFLALISVDVRFRFL+ +
Sbjct: 1 MNKFVFIILIIIFIDKCRNEDPKFSCVKNLFKTQNASCAGFHNFCMKNEDVDCINFQNVCNQCPPSNYSILMLIDLINVKTELNQTKHQLEAIKVQSQIYENQISESLKKQNLQ----------IIILLIFLALISVDVRFRFLTNF 137
BLAST of SMED30024409 vs. Planmine SMEST
Match: SMESG000074941.1 (SMESG000074941.1) HSP 1 Score: 105.531 bits (262), Expect = 2.158e-26 Identity = 50/103 (48.54%), Postives = 74/103 (71.84%), Query Frame = 1
Query: 136 NEDPKFSC-VKNLFKTQNASCAGFHNFCMKNEDVDCINFQNVCNQCPPSNYSILMLIDLINVKTELNQTKHQLEAIKVQSQIYENQISESLKKQNLQINNLYT 441
+E P+ C + + FKT++ C F+ C+K D++C+NFQ +C QCPPSNYS+LM +DL+ VK EL +TK QLEA+K QS++ +N+ S +L KQN QI ++T
Sbjct: 18 HEIPRSHCPIGSPFKTKDNLCKDFYEVCVKQNDLECLNFQTICKQCPPSNYSVLMFMDLLTVKNELIKTKDQLEALKTQSELCQNKTSGTLMKQNQQIKKIFT 120
BLAST of SMED30024409 vs. Planmine SMEST
Match: SMESG000074941.1 (SMESG000074941.1) HSP 1 Score: 105.531 bits (262), Expect = 2.325e-26 Identity = 50/103 (48.54%), Postives = 74/103 (71.84%), Query Frame = 1
Query: 136 NEDPKFSC-VKNLFKTQNASCAGFHNFCMKNEDVDCINFQNVCNQCPPSNYSILMLIDLINVKTELNQTKHQLEAIKVQSQIYENQISESLKKQNLQINNLYT 441
+E P+ C + + FKT++ C F+ C+K D++C+NFQ +C QCPPSNYS+LM +DL+ VK EL +TK QLEA+K QS++ +N+ S +L KQN QI ++T
Sbjct: 18 HEIPRSHCPIGSPFKTKDNLCKDFYEVCVKQNDLECLNFQTICKQCPPSNYSVLMFMDLLTVKNELIKTKDQLEALKTQSELCQNKTSGTLMKQNQQIKKIFT 120
BLAST of SMED30024409 vs. Planmine SMEST
Match: SMESG000074945.1 (SMESG000074945.1) HSP 1 Score: 77.411 bits (189), Expect = 7.426e-17 Identity = 38/82 (46.34%), Postives = 56/82 (68.29%), Query Frame = 1
Query: 136 NEDPKFSCV-KNLFKTQNASCAGFHNFCMKNEDVDCINFQNVCNQCPPSNYSILMLIDLINVKTELNQTKHQLEAI--KVQS 372
E P+F C F+T + SCA +++ C+K D DC NFQ CNQCPPSNYSI+M ID++N+K ++ +K Q++ + KV+S
Sbjct: 18 GEKPRFICQNPKSFRTNDNSCADYNDVCIKTGDPDCANFQTACNQCPPSNYSIMMYIDMMNMKNQIIISKSQMKNLTDKVES 99 The following BLAST results are available for this feature:
BLAST of SMED30024409 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30024409 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30024409 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30024409 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30024409 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30024409 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30024409 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30024409 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30024409 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30024409 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30024409 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30024409 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30024409 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30024409 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 >SMED30024409 ID=SMED30024409|Name=SMED30024409|organism=Schmidtea mediterranea sexual|type=transcript|length=588bpback to top protein sequence of SMED30024409-orf-1 >SMED30024409-orf-1 ID=SMED30024409-orf-1|Name=SMED30024409-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=153bp MNKFVFIILIIIFIDKCRNEDPKFSCVKNLFKTQNASCAGFHNFCMKNEDback 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
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