SMED30007738
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., 2020SMED30007738 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 3
Alignments
SMED30007738 aligns in the following genomic locations:
Homology
BLAST of SMED30007738 vs. Planmine SMEST
Match: SMESG000035479.1 (SMESG000035479.1) HSP 1 Score: 360.918 bits (925), Expect = 1.314e-127 Identity = 201/202 (99.50%), Postives = 201/202 (99.50%), Query Frame = 2 Query: 32 MFYISTIVDCLCSAFDCCINLCYTDYETEKGKVFRENSRSPFVINKQSSVTPQSEDKFSFKEQTDEKMFLLNPFNVFKKVSISNIPLDFVDSPESNIGVSIDVTHEKIEHILIIRVYSSEGLSGKFDISILGLEDXXXXXXXXXXXXXXXXXXESDLKISTLKVRFYDENIPKNAPIVGEIDYDLSQLLLVEMVENKRRLQT 637 MFYISTIVDCLCSAFDCCINLCYTDYETEKGKVFRENSRSPFVINKQSSVTPQSEDKFSFKEQTDEKMFLLNPFNVFKKVSISNIPLDFVDSPESNIGV IDVTHEKIEHILIIRVYSSEGLSGKFDISILGLEDFKPKKSKFKKAVKFKGIFESDLKISTLKVRFYDENIPKNAPIVGEIDYDLSQLLLVEMVENKRRLQT Sbjct: 1 MFYISTIVDCLCSAFDCCINLCYTDYETEKGKVFRENSRSPFVINKQSSVTPQSEDKFSFKEQTDEKMFLLNPFNVFKKVSISNIPLDFVDSPESNIGVLIDVTHEKIEHILIIRVYSSEGLSGKFDISILGLEDFKPKKSKFKKAVKFKGIFESDLKISTLKVRFYDENIPKNAPIVGEIDYDLSQLLLVEMVENKRRLQT 202
BLAST of SMED30007738 vs. Planmine SMEST
Match: SMESG000035479.1 (SMESG000035479.1) HSP 1 Score: 351.673 bits (901), Expect = 7.947e-122 Identity = 196/199 (98.49%), Postives = 198/199 (99.50%), Query Frame = 2 Query: 41 ISTIVDCLCSAFDCCINLCYTDYETEKGKVFRENSRSPFVINKQSSVTPQSEDKFSFKEQTDEKMFLLNPFNVFKKVSISNIPLDFVDSPESNIGVSIDVTHEKIEHILIIRVYSSEGLSGKFDISILGLEDXXXXXXXXXXXXXXXXXXESDLKISTLKVRFYDENIPKNAPIVGEIDYDLSQLLLVEMVENKRRLQT 637 ++TIVDCLCSAFDCCINLCYTDYETEKGKVFRENSRSPFVINKQSSVTPQSEDKFSFKEQTDEKMFLLNPFNVFKKVSISNIPLDFVDSPESNIGV IDVTHEKIEHILIIRVYSSEGLSGKFDISILGLEDFKPKKSKFKKAVKFKGIFESDLKISTLKVRFYDENIPKNAPIVGEIDYDLSQLLLVEMVENKRRLQT Sbjct: 143 LTTIVDCLCSAFDCCINLCYTDYETEKGKVFRENSRSPFVINKQSSVTPQSEDKFSFKEQTDEKMFLLNPFNVFKKVSISNIPLDFVDSPESNIGVLIDVTHEKIEHILIIRVYSSEGLSGKFDISILGLEDFKPKKSKFKKAVKFKGIFESDLKISTLKVRFYDENIPKNAPIVGEIDYDLSQLLLVEMVENKRRLQT 341 HSP 2 Score: 63.929 bits (154), Expect = 1.440e-11 Identity = 48/137 (35.04%), Postives = 80/137 (58.39%), Query Frame = 2 Query: 32 MFYISTIVDCLCSAFDCCINLCYTDYETEKGKVFRENSRSPFVINKQSS-----VTPQSEDKFSFKEQTDEKMFLLNPFNVFKKVSISNIPLDFVDSPESNIGVSIDVTHEKIEHILIIRVYSSEGLSGKFDISILG 427 MF ST+ +C C+ FDCCINLCY + E +K K+ +E ++SPFV+ KQ S V ++ + ++T EK LL+ F+ S LD V E++ V I+++ +K HIL I+++ ++ ++ FD+ + G Sbjct: 1 MFLCSTVSNCFCNVFDCCINLCYKENEKKKSKISKEYNKSPFVVYKQYSLDSENVRNDADSTENILDKTTEKTSLLSA-KTFRGSSKCG-SLDCVIKNENDCRVFIEISFDKAAHILSIKLFPTK-ITNIFDVCLKG 134
BLAST of SMED30007738 vs. Planmine SMEST
Match: SMESG000035479.1 (SMESG000035479.1) HSP 1 Score: 150.984 bits (380), Expect = 5.829e-45 Identity = 111/207 (53.62%), Postives = 145/207 (70.05%), Query Frame = 2 Query: 32 MFYISTIVDCLCSAFDCCINLCYTDYETEKGKVFRENSRSPFVINKQSS-----VTPQSEDKFSFKEQTDEKMFLLNPFNVFKKVSISNIPLDFVDSPESNIGVSIDVTHEKIEHILIIRVYSSEGLSGKFDISILGLEDXXXXXXXXXXXXXXXXXXESDLKISTLKVRFYDENIPKNAPIVGEIDYDLSQLLLVEMVENKRRLQT 637 MF ST+ +C C+ FDCCINLCY + E +K K+ +E ++SPFV+ KQ S V ++ + ++T EK LL+ F+ S LD V E++ V I+++ +K HIL I+++ ++ ++ FD+ + G + +K KK FKKAVKFKGIFESDLKISTLKVRFYDENIPKNAPIVGEIDYDLSQLLLVEMVENKRRLQT Sbjct: 1 MFLCSTVSNCFCNVFDCCINLCYKENEKKKSKISKEYNKSPFVVYKQYSLDSENVRNDADSTENILDKTTEKTSLLSA-KTFRGSSKCG-SLDCVIKNENDCRVFIEISFDKAAHILSIKLFPTK-ITNIFDVCLKGPDIYKSKKLTFKKAVKFKGIFESDLKISTLKVRFYDENIPKNAPIVGEIDYDLSQLLLVEMVENKRRLQT 204
BLAST of SMED30007738 vs. Planmine SMEST
Match: SMESG000035473.1 (SMESG000035473.1) HSP 1 Score: 51.9878 bits (123), Expect = 1.381e-7 Identity = 53/198 (26.77%), Postives = 95/198 (47.98%), Query Frame = 2 Query: 80 CCINLCYTDYETEKGKVFRENSRSPFVINKQSSVTP------------QSEDKFSFKEQTDEKMFLLNPFNVFKKV-SISNIPLDF-VDSPESNIGVSIDVTHEKIEHILIIRVYSSEGLSGKFDISILGLEDXXXXXXXXXXXXXXXXXXESDLKISTLKVRFYDENIPKNAPIVGEIDYDLSQLLLVEMVENKRRL 631 CC C+ EKGK++ + SP ++N++ S+ Q+E+ + ++Q+ FL+ + +K+ S+ + D + N +++ H I ++L I+V+ +E + KFDIS+ + K S F K + F I E DL S L + FY P + GEI + L +L+L + ++N R Sbjct: 18 CC--FCFHSETEEKGKLYIHDRTSPMILNQKPSIMNQEIEIKNISLNLQTENTLNPRKQSLGGNFLVPNAGLNEKLPSVIKVKRHSESDLGDMNYNFPVEINHNHILNVLSIKVFPNEKIPDKFDISVKTNDKITKKISYFYKVITFDNISEDDLNTSFLSLTFYKRKTPDDKKSFGEIKFPL-KLILKKKIQNSIRF 212 The following BLAST results are available for this feature:
BLAST of SMED30007738 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30007738 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30007738 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30007738 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30007738 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30007738 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30007738 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30007738 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30007738 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30007738 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30007738 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30007738 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30007738 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30007738 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 4
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30007738 ID=SMED30007738|Name=SMED30007738|organism=Schmidtea mediterranea sexual|type=transcript|length=775bpback to top protein sequence of SMED30007738-orf-1 >SMED30007738-orf-1 ID=SMED30007738-orf-1|Name=SMED30007738-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=218bp MFYISTIVDCLCSAFDCCINLCYTDYETEKGKVFRENSRSPFVINKQSSVback to top Annotated Terms
The following terms have been associated with this transcript:
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