SMED30002272
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., 2020SMED30002272 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 11
Alignments
SMED30002272 aligns in the following genomic locations:
Homology
BLAST of SMED30002272 vs. Ensembl Sea Lamprey
Match: rbpms2a (RNA binding protein, mRNA processing factor 2a [Source:ZFIN;Acc:ZDB-GENE-040718-106]) HSP 1 Score: 46.595 bits (109), Expect = 1.768e-6 Identity = 19/31 (61.29%), Postives = 24/31 (77.42%), Query Frame = 3 Query: 645 GIKFDPDSDQLMRLEFARTNTKMLKNKMCNS 737 GI+FDPD Q +RLEFA+ NTKM KNK+ + Sbjct: 23 GIRFDPDIPQTLRLEFAKANTKMAKNKLLGT 53
BLAST of SMED30002272 vs. Planmine SMEST
Match: SMESG000071928.1 (SMESG000071928.1) HSP 1 Score: 359.377 bits (921), Expect = 3.629e-121 Identity = 175/175 (100.00%), Postives = 175/175 (100.00%), Query Frame = 3 Query: 645 GIKFDPDSDQLMRLEFARTNTKMLKNKMCNSHIYNSGLNQQLSAGSIDANLLNSDMNLFLGYDGRLAFFAQSAFSPFGPALLPFNGTTFRPPNCSFAPIAVAAPNGLLNVTGTHSLSPFIGPQSGLLGETISQVLMHPSQNGLLYVQPFSIDLNEISAQPLETQFRMNSWNSNGE 1169 GIKFDPDSDQLMRLEFARTNTKMLKNKMCNSHIYNSGLNQQLSAGSIDANLLNSDMNLFLGYDGRLAFFAQSAFSPFGPALLPFNGTTFRPPNCSFAPIAVAAPNGLLNVTGTHSLSPFIGPQSGLLGETISQVLMHPSQNGLLYVQPFSIDLNEISAQPLETQFRMNSWNSNGE Sbjct: 110 GIKFDPDSDQLMRLEFARTNTKMLKNKMCNSHIYNSGLNQQLSAGSIDANLLNSDMNLFLGYDGRLAFFAQSAFSPFGPALLPFNGTTFRPPNCSFAPIAVAAPNGLLNVTGTHSLSPFIGPQSGLLGETISQVLMHPSQNGLLYVQPFSIDLNEISAQPLETQFRMNSWNSNGE 284
BLAST of SMED30002272 vs. Planmine SMEST
Match: SMESG000055387.1 (SMESG000055387.1) HSP 1 Score: 239.965 bits (611), Expect = 2.292e-92 Identity = 116/116 (100.00%), Postives = 116/116 (100.00%), Query Frame = 3 Query: 138 MGNCNHICCMLCGLESLRLQMKCPLDKTNVKKIKIFSNKFCCEKNENIQENILTIESGNEEETLKFQTVLDAVLSMEELDDREEIGNMFEMDRYLLWMGPFVENKSKITREMVHNH 485 MGNCNHICCMLCGLESLRLQMKCPLDKTNVKKIKIFSNKFCCEKNENIQENILTIESGNEEETLKFQTVLDAVLSMEELDDREEIGNMFEMDRYLLWMGPFVENKSKITREMVHNH Sbjct: 1 MGNCNHICCMLCGLESLRLQMKCPLDKTNVKKIKIFSNKFCCEKNENIQENILTIESGNEEETLKFQTVLDAVLSMEELDDREEIGNMFEMDRYLLWMGPFVENKSKITREMVHNH 116 HSP 2 Score: 119.398 bits (298), Expect = 2.292e-92 Identity = 54/54 (100.00%), Postives = 54/54 (100.00%), Query Frame = 1 Query: 484 MSKYGPIEDIIVFPQCSYVLFGSSKHGFAAEHSCKREEFYGEAITTDSFHPDFW 645 MSKYGPIEDIIVFPQCSYVLFGSSKHGFAAEHSCKREEFYGEAITTDSFHPDFW Sbjct: 117 MSKYGPIEDIIVFPQCSYVLFGSSKHGFAAEHSCKREEFYGEAITTDSFHPDFW 170
BLAST of SMED30002272 vs. Planmine SMEST
Match: SMESG000071605.1 (SMESG000071605.1) HSP 1 Score: 239.965 bits (611), Expect = 5.437e-92 Identity = 116/116 (100.00%), Postives = 116/116 (100.00%), Query Frame = 3 Query: 138 MGNCNHICCMLCGLESLRLQMKCPLDKTNVKKIKIFSNKFCCEKNENIQENILTIESGNEEETLKFQTVLDAVLSMEELDDREEIGNMFEMDRYLLWMGPFVENKSKITREMVHNH 485 MGNCNHICCMLCGLESLRLQMKCPLDKTNVKKIKIFSNKFCCEKNENIQENILTIESGNEEETLKFQTVLDAVLSMEELDDREEIGNMFEMDRYLLWMGPFVENKSKITREMVHNH Sbjct: 1 MGNCNHICCMLCGLESLRLQMKCPLDKTNVKKIKIFSNKFCCEKNENIQENILTIESGNEEETLKFQTVLDAVLSMEELDDREEIGNMFEMDRYLLWMGPFVENKSKITREMVHNH 116 HSP 2 Score: 118.627 bits (296), Expect = 5.437e-92 Identity = 53/54 (98.15%), Postives = 54/54 (100.00%), Query Frame = 1 Query: 484 MSKYGPIEDIIVFPQCSYVLFGSSKHGFAAEHSCKREEFYGEAITTDSFHPDFW 645 MSKYGPIEDII+FPQCSYVLFGSSKHGFAAEHSCKREEFYGEAITTDSFHPDFW Sbjct: 117 MSKYGPIEDIILFPQCSYVLFGSSKHGFAAEHSCKREEFYGEAITTDSFHPDFW 170
BLAST of SMED30002272 vs. Planmine SMEST
Match: SMESG000055916.1 (SMESG000055916.1) HSP 1 Score: 240.736 bits (613), Expect = 1.005e-91 Identity = 116/116 (100.00%), Postives = 116/116 (100.00%), Query Frame = 3 Query: 138 MGNCNHICCMLCGLESLRLQMKCPLDKTNVKKIKIFSNKFCCEKNENIQENILTIESGNEEETLKFQTVLDAVLSMEELDDREEIGNMFEMDRYLLWMGPFVENKSKITREMVHNH 485 MGNCNHICCMLCGLESLRLQMKCPLDKTNVKKIKIFSNKFCCEKNENIQENILTIESGNEEETLKFQTVLDAVLSMEELDDREEIGNMFEMDRYLLWMGPFVENKSKITREMVHNH Sbjct: 1 MGNCNHICCMLCGLESLRLQMKCPLDKTNVKKIKIFSNKFCCEKNENIQENILTIESGNEEETLKFQTVLDAVLSMEELDDREEIGNMFEMDRYLLWMGPFVENKSKITREMVHNH 116 HSP 2 Score: 116.701 bits (291), Expect = 1.005e-91 Identity = 53/54 (98.15%), Postives = 53/54 (98.15%), Query Frame = 1 Query: 484 MSKYGPIEDIIVFPQCSYVLFGSSKHGFAAEHSCKREEFYGEAITTDSFHPDFW 645 MSKYGPIEDIIVFPQCSYVLFGSSKHGFAAEHSCKREEFYGEAITTDSFH DFW Sbjct: 117 MSKYGPIEDIIVFPQCSYVLFGSSKHGFAAEHSCKREEFYGEAITTDSFHTDFW 170
BLAST of SMED30002272 vs. Planmine SMEST
Match: SMESG000028861.1 (SMESG000028861.1) HSP 1 Score: 132.494 bits (332), Expect = 1.245e-35 Identity = 62/131 (47.33%), Postives = 94/131 (71.76%), Query Frame = 3 Query: 93 ECLLCLQTDNKLLLSMGNCNHICCMLCGLESLRLQMKCPLDKTNVKKIKIFSNKFCCEKNENIQENILTIESGNEEETLKFQTVLDAVLSMEELDDREEIGNMFEMDRYLLWMGPFVENKSKITREMVHNH 485 ECL+CL+TDNKLL+S+G CNH CC++CGLES+R M CPLD+ + +I I+ N EK + L I+S N +E L F+ V A+LS+E +++R EI ++ +D YL+++GPFV N++K++REM+ N+ Sbjct: 5 ECLICLETDNKLLMSIGGCNHKCCIICGLESMRNTMTCPLDREQITEITIYENTNGIEKEK------LKIKSLNSDENLTFEMVQRAILSIENIENRSEIEQIYTLDPYLIYIGPFVLNRNKVSREMIENY 129 HSP 2 Score: 72.0182 bits (175), Expect = 2.100e-14 Identity = 34/77 (44.16%), Postives = 50/77 (64.94%), Query Frame = 1 Query: 418 IYYGWARL*KTKARSQEKWFTIMSKYGPIEDIIVFPQCSYVLFGSSKHGFAAEHSCKREEFYGEAITTDSFHPDFWE 648 IY G L + K S+E ++++GPI D+IV P +Y +F SS+HG A++ +E FYGE++T +SFHPD WE Sbjct: 109 IYIGPFVLNRNKV-SREMIENYLNEFGPINDVIVKPNSAYAMFSSSQHGMRAKYERNKELFYGESVTIESFHPDTWE 184 The following BLAST results are available for this feature:
BLAST of SMED30002272 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30002272 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30002272 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30002272 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30002272 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30002272 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30002272 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30002272 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30002272 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30002272 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 1
BLAST of SMED30002272 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30002272 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30002272 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30002272 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 >SMED30002272 ID=SMED30002272|Name=SMED30002272|organism=Schmidtea mediterranea sexual|type=transcript|length=1726bpback to top protein sequence of SMED30002272-orf-1 >SMED30002272-orf-1 ID=SMED30002272-orf-1|Name=SMED30002272-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=141bp MTSNNYYDECLLCLQTDNKLLLSMGNCNHICCMLCGLESLRLQMKCPLDKback to top protein sequence of SMED30002272-orf-2 >SMED30002272-orf-2 ID=SMED30002272-orf-2|Name=SMED30002272-orf-2|organism=Schmidtea mediterranea sexual|type=polypeptide|length=165bp MRLEFARTNTKMLKNKMCNSHIYNSGLNQQLSAGSIDANLLNSDMNLFLGback to top Annotated Terms
The following terms have been associated with this transcript:
|