SMED30027751
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., 2020SMED30027751 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 4
Alignments
SMED30027751 aligns in the following genomic locations:
Homology
BLAST of SMED30027751 vs. UniProt/SwissProt
Match: sp|P29129|ICP0_SUHVF (E3 ubiquitin-protein ligase ICP0 OS=Suid herpesvirus 1 (strain Indiana-Funkhauser / Becker) OX=31523 GN=EP0 PE=2 SV=1) HSP 1 Score: 56.225 bits (134), Expect = 8.478e-8 Identity = 25/61 (40.98%), Postives = 37/61 (60.66%), Query Frame = 3 Query: 180 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVE 362 M+C ICL ++ A+ + C H+FC DCI +W L + CP C +R+ + H SD +FVE Sbjct: 44 MDCPICLDVAATE-AQTLPCMHKFCLDCIQRWTLTSTACPLCNARVTSILHHVDSDASFVE 103
BLAST of SMED30027751 vs. Planmine SMEST
Match: SMESG000037691.1 (SMESG000037691.1) HSP 1 Score: 258.07 bits (658), Expect = 7.712e-88 Identity = 127/128 (99.22%), Postives = 127/128 (99.22%), Query Frame = 3 Query: 180 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLVRAIDSDEGDSEEYYSDMDCVEDLFFNHSLSDSNNYVITNYIDESGYLS 563 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLVRAIDSDEGDSEEYYSDMDCVEDLF NHSLSDSNNYVITNYIDESGYLS Sbjct: 1 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLVRAIDSDEGDSEEYYSDMDCVEDLFCNHSLSDSNNYVITNYIDESGYLS 128
BLAST of SMED30027751 vs. Planmine SMEST
Match: SMESG000037688.1 (SMESG000037688.1) HSP 1 Score: 256.914 bits (655), Expect = 2.539e-87 Identity = 126/128 (98.44%), Postives = 127/128 (99.22%), Query Frame = 3 Query: 180 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLVRAIDSDEGDSEEYYSDMDCVEDLFFNHSLSDSNNYVITNYIDESGYLS 563 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLVRAIDSDEGDSEEYYSDMDCV+DLF NHSLSDSNNYVITNYIDESGYLS Sbjct: 1 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLVRAIDSDEGDSEEYYSDMDCVDDLFCNHSLSDSNNYVITNYIDESGYLS 128
BLAST of SMED30027751 vs. Planmine SMEST
Match: SMESG000054762.1 (SMESG000054762.1) HSP 1 Score: 254.603 bits (649), Expect = 2.335e-86 Identity = 125/128 (97.66%), Postives = 126/128 (98.44%), Query Frame = 3 Query: 180 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLVRAIDSDEGDSEEYYSDMDCVEDLFFNHSLSDSNNYVITNYIDESGYLS 563 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNL+RAIDSDEGDSEEYYSDMDCVEDLF NHSLSDSNNYVITNYIDESG LS Sbjct: 1 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLIRAIDSDEGDSEEYYSDMDCVEDLFCNHSLSDSNNYVITNYIDESGNLS 128
BLAST of SMED30027751 vs. Planmine SMEST
Match: SMESG000054763.1 (SMESG000054763.1) HSP 1 Score: 252.677 bits (644), Expect = 1.067e-85 Identity = 124/128 (96.88%), Postives = 126/128 (98.44%), Query Frame = 3 Query: 180 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLVRAIDSDEGDSEEYYSDMDCVEDLFFNHSLSDSNNYVITNYIDESGYLS 563 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNL++AIDSDEGDSEEYYSDMDCVEDLF NHSLSDSNNYVITNYIDESG LS Sbjct: 1 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLIQAIDSDEGDSEEYYSDMDCVEDLFCNHSLSDSNNYVITNYIDESGNLS 128
BLAST of SMED30027751 vs. Planmine SMEST
Match: SMESG000054764.1 (SMESG000054764.1) HSP 1 Score: 216.853 bits (551), Expect = 1.574e-71 Identity = 109/128 (85.16%), Postives = 115/128 (89.84%), Query Frame = 3 Query: 180 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLVRAIDSDEGDSEEYYSDMDCVEDLFFNHSLSDSNNYVITNYIDESGYLS 563 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILT PPL+NKSLEENWNL+RAIDSDE DSE+ + C+EDLF +H LSDS YVITNYIDES LS Sbjct: 1 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTNPPLMNKSLEENWNLIRAIDSDEEDSEK---GIGCIEDLFRDHFLSDSKKYVITNYIDESECLS 125 The following BLAST results are available for this feature:
BLAST of SMED30027751 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30027751 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30027751 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30027751 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30027751 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30027751 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30027751 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 1
BLAST of SMED30027751 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30027751 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30027751 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30027751 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30027751 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30027751 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30027751 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 >SMED30027751 ID=SMED30027751|Name=SMED30027751|organism=Schmidtea mediterranea sexual|type=transcript|length=830bpback to top protein sequence of SMED30027751-orf-1 >SMED30027751-orf-1 ID=SMED30027751-orf-1|Name=SMED30027751-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=143bp MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYback 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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