SMED30013083
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., 2020SMED30013083 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 2
Alignments
SMED30013083 aligns in the following genomic locations:
Homology
BLAST of SMED30013083 vs. TrEMBL
Match: G4VFR1 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 GN=Smp_144350 PE=4 SV=1) HSP 1 Score: 183.341 bits (464), Expect = 7.337e-52 Identity = 82/153 (53.59%), Postives = 110/153 (71.90%), Query Frame = 1 Query: 703 PVVIVNPQEKKEIFVGGNENVRLPFWAYRKCLTCIRGKPNELSSRLCLRLLQAKFGRKYMLSHNYNGSGDKVPIDRQIMSSILVQAKMQFPDQEDFQNNPAKFAMFRDYINNAFRVVAYRHRKGIQSNTPFWDQNGEPIADLDPP-SWIADNI 1158 PVV++NP E +EIF+GG ++V LP WAY KCLT +RG+P+EL RLCLRLLQ+ F Y+++HNYNGSG K PID +MS++L QA++QF F P RDY+NNAFRV+A+R RKG + +PFW++ GEPI DL+ P W+ + I Sbjct: 97 PVVVLNPDEPREIFIGGVQSVALPLWAYCKCLTMVRGEPHELGPRLCLRLLQSLFSLHYLVTHNYNGSGGKAPIDPIVMSAVLRQAQLQF-GSGYFFTEPMALGKLRDYLNNAFRVMAFRQRKGERVRSPFWNEKGEPIHDLEAPKEWLLNVI 248
BLAST of SMED30013083 vs. TrEMBL
Match: A0A183PXD5 (Uncharacterized protein OS=Schistosoma mattheei OX=31246 GN=SMTD_LOCUS19021 PE=4 SV=1) HSP 1 Score: 183.341 bits (464), Expect = 2.995e-51 Identity = 80/145 (55.17%), Postives = 106/145 (73.10%), Query Frame = 1 Query: 703 PVVIVNPQEKKEIFVGGNENVRLPFWAYRKCLTCIRGKPNELSSRLCLRLLQAKFGRKYMLSHNYNGSGDKVPIDRQIMSSILVQAKMQFPDQEDFQNNPAKFAMFRDYINNAFRVVAYRHRKGIQSNTPFWDQNGEPIADLDPP 1137 PVV++NP E +EIF+GG ++V LP WAY KCLT +RG+P+EL RLCLRLLQ+ F Y+++HNYNGSG K PID +MS++L QA++QF F P RDY+NNAFRV+A+R RKG + +PFW++ GEPI DL+ P Sbjct: 105 PVVVLNPDEPREIFIGGVQSVALPLWAYCKCLTMVRGEPHELGPRLCLRLLQSLFSLHYLVTHNYNGSGGKAPIDPIVMSAVLRQAQLQF-GSGYFFTEPMALGKLRDYLNNAFRVMAFRQRKGERVRSPFWNEKGEPIHDLEAP 248
BLAST of SMED30013083 vs. TrEMBL
Match: A0A095CBW8 (Uncharacterized protein OS=Schistosoma haematobium OX=6185 GN=MS3_08494 PE=4 SV=1) HSP 1 Score: 183.341 bits (464), Expect = 3.620e-51 Identity = 80/145 (55.17%), Postives = 106/145 (73.10%), Query Frame = 1 Query: 703 PVVIVNPQEKKEIFVGGNENVRLPFWAYRKCLTCIRGKPNELSSRLCLRLLQAKFGRKYMLSHNYNGSGDKVPIDRQIMSSILVQAKMQFPDQEDFQNNPAKFAMFRDYINNAFRVVAYRHRKGIQSNTPFWDQNGEPIADLDPP 1137 PVV++NP E +EIF+GG ++V LP WAY KCLT +RG+P+EL RLCLRLLQ+ F Y+++HNYNGSG K PID +MS++L QA++QF F P RDY+NNAFRV+A+R RKG + +PFW++ GEPI DL+ P Sbjct: 103 PVVVLNPDEPREIFIGGVQSVALPLWAYCKCLTMVRGEPHELGPRLCLRLLQSLFSLHYLVTHNYNGSGGKAPIDPIVMSAVLRQAQLQF-GSGYFFTEPMALGKLRDYLNNAFRVMAFRQRKGERVRSPFWNEKGEPIHDLEAP 246
BLAST of SMED30013083 vs. TrEMBL
Match: A0A183M5B3 (Uncharacterized protein OS=Schistosoma margrebowiei OX=48269 GN=SMRZ_LOCUS11238 PE=4 SV=1) HSP 1 Score: 182.956 bits (463), Expect = 3.810e-51 Identity = 80/145 (55.17%), Postives = 106/145 (73.10%), Query Frame = 1 Query: 703 PVVIVNPQEKKEIFVGGNENVRLPFWAYRKCLTCIRGKPNELSSRLCLRLLQAKFGRKYMLSHNYNGSGDKVPIDRQIMSSILVQAKMQFPDQEDFQNNPAKFAMFRDYINNAFRVVAYRHRKGIQSNTPFWDQNGEPIADLDPP 1137 PVV++NP E +EIF+GG ++V LP WAY KCLT +RG+P+EL RLCLRLLQ+ F Y+++HNYNGSG K PID +MS++L QA++QF F P RDY+NNAFRV+A+R RKG + +PFW++ GEPI DL+ P Sbjct: 103 PVVVLNPDEPREIFIGGVQSVALPLWAYCKCLTMVRGEPHELGPRLCLRLLQSLFSLHYLVTHNYNGSGGKAPIDPIVMSAVLRQAQLQF-GSGYFFTEPMALGKLRDYLNNAFRVMAFRQRKGERVRSPFWNEKGEPIHDLEAP 246
BLAST of SMED30013083 vs. TrEMBL
Match: G7YEM1 (Uncharacterized protein OS=Clonorchis sinensis OX=79923 GN=CLF_106053 PE=4 SV=1) HSP 1 Score: 179.874 bits (455), Expect = 1.737e-50 Identity = 79/154 (51.30%), Postives = 108/154 (70.13%), Query Frame = 1 Query: 694 ILEPVVIVNPQEKKEIFVGGNENVRLPFWAYRKCLTCIRGKPNELSSRLCLRLLQAKFGRKYMLSHNYNGSGDKVPIDRQIMSSILVQAKMQFPDQEDFQNNPAKFAMFRDYINNAFRVVAYRHRKGIQSNTPFWDQNGEPIADLDPPSWIADN 1155 I P+VI+NP+E +EIF+GG +V LP WAY+KCLT +RG+P+EL RLCLRLLQ+ F Y+++HNYNGSG K PID +M ++L QA++QF F P RDY+NNAFRV+A+R RKG + +PFW++ GEP+ L+ P A+ Sbjct: 67 IGNPIVILNPKEPREIFIGGIPSVPLPLWAYKKCLTMVRGEPHELGPRLCLRLLQSLFSLHYLVTHNYNGSGGKAPIDPIVMGAVLRQAQIQF-GSGYFFTEPMALGKLRDYLNNAFRVMAFRQRKGERVRSPFWNEQGEPVHGLEAPVEFAET 219
BLAST of SMED30013083 vs. Planmine SMEST
Match: SMESG000062614.1 (SMESG000062614.1) HSP 1 Score: 671.389 bits (1731), Expect = 0.000e+0 Identity = 330/330 (100.00%), Postives = 330/330 (100.00%), Query Frame = 1 Query: 172 MNSNFGFNNGMTIQIPAFNIANDQLFLAIQTYFDNRFNELKDQIQQIQIKSEKLIVNTKKIELEIRNLKMNKYKDVNRGKNKLKYRKSLSKITKKGKVLESDVNELNPKKDCIDQNMESNEILETNSFLLGINKIEDLENKYPAELSPKNFELPLDNIIKKYLKANESKIVYKDILEPVVIVNPQEKKEIFVGGNENVRLPFWAYRKCLTCIRGKPNELSSRLCLRLLQAKFGRKYMLSHNYNGSGDKVPIDRQIMSSILVQAKMQFPDQEDFQNNPAKFAMFRDYINNAFRVVAYRHRKGIQSNTPFWDQNGEPIADLDPPSWIADNIN 1161 MNSNFGFNNGMTIQIPAFNIANDQLFLAIQTYFDNRFNELKDQIQQIQIKSEKLIVNTKKIELEIRNLKMNKYKDVNRGKNKLKYRKSLSKITKKGKVLESDVNELNPKKDCIDQNMESNEILETNSFLLGINKIEDLENKYPAELSPKNFELPLDNIIKKYLKANESKIVYKDILEPVVIVNPQEKKEIFVGGNENVRLPFWAYRKCLTCIRGKPNELSSRLCLRLLQAKFGRKYMLSHNYNGSGDKVPIDRQIMSSILVQAKMQFPDQEDFQNNPAKFAMFRDYINNAFRVVAYRHRKGIQSNTPFWDQNGEPIADLDPPSWIADNIN Sbjct: 1 MNSNFGFNNGMTIQIPAFNIANDQLFLAIQTYFDNRFNELKDQIQQIQIKSEKLIVNTKKIELEIRNLKMNKYKDVNRGKNKLKYRKSLSKITKKGKVLESDVNELNPKKDCIDQNMESNEILETNSFLLGINKIEDLENKYPAELSPKNFELPLDNIIKKYLKANESKIVYKDILEPVVIVNPQEKKEIFVGGNENVRLPFWAYRKCLTCIRGKPNELSSRLCLRLLQAKFGRKYMLSHNYNGSGDKVPIDRQIMSSILVQAKMQFPDQEDFQNNPAKFAMFRDYINNAFRVVAYRHRKGIQSNTPFWDQNGEPIADLDPPSWIADNIN 330 The following BLAST results are available for this feature:
BLAST of SMED30013083 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30013083 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30013083 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30013083 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30013083 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30013083 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30013083 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30013083 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 5
BLAST of SMED30013083 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30013083 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30013083 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30013083 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30013083 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30013083 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 1
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30013083 ID=SMED30013083|Name=SMED30013083|organism=Schmidtea mediterranea sexual|type=transcript|length=1170bpback to top protein sequence of SMED30013083-orf-1 >SMED30013083-orf-1 ID=SMED30013083-orf-1|Name=SMED30013083-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=331bp MNSNFGFNNGMTIQIPAFNIANDQLFLAIQTYFDNRFNELKDQIQQIQIKback 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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