SMED30013611
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Overview
Neoblast Clusters
Zeng et. al., 2018▻ Overview▻ Neoblast 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
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., 2020SMED30013611 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 4
Alignments
SMED30013611 aligns in the following genomic locations: Homology
BLAST of SMED30013611 vs. Planmine SMEST
Match: SMESG000008330.1 (SMESG000008330.1) HSP 1 Score: 140.969 bits (354), Expect = 2.161e-69 Identity = 65/73 (89.04%), Postives = 66/73 (90.41%), Query Frame = 1
Query: 238 QFSKRFDKFVFTGFWMDESRITMRFPSHSAAKCRQAMWDEGYSISPVRKARFERQDDMEDAERPYIAIKREPG 456
F +FDKFVFTGFWMDESRITMRFPSHSAAKCRQAMWDEGYSISPVR RFERQDD E AERPYIAIKREPG
Sbjct: 49 HFELQFDKFVFTGFWMDESRITMRFPSHSAAKCRQAMWDEGYSISPVRTVRFERQDDTEVAERPYIAIKREPG 121 HSP 2 Score: 140.198 bits (352), Expect = 2.161e-69 Identity = 68/80 (85.00%), Postives = 71/80 (88.75%), Query Frame = 3
Query: 456 RNPARELRGRAEDILARLEAHQRKTNREVNRAHQHLKQINKDIATGLIPSTGGYAPSYGISFELDDPRVNQPIPPMTVSV 695
RNP RELR RAEDILARLEAHQ+KTNREVNRA QHLKQINKDIA GLIPST GYAP+YGI FELDDP +NQ I PMTVSV
Sbjct: 122 RNPTRELRERAEDILARLEAHQQKTNREVNRARQHLKQINKDIAAGLIPSTDGYAPAYGILFELDDPHMNQSILPMTVSV 201
BLAST of SMED30013611 vs. Planmine SMEST
Match: SMESG000075969.1 (SMESG000075969.1) HSP 1 Score: 122.865 bits (307), Expect = 7.990e-53 Identity = 57/80 (71.25%), Postives = 68/80 (85.00%), Query Frame = 3
Query: 456 RNPARELRGRAEDILARLEAHQRKTNREVNRAHQHLKQINKDIATGLIPSTGGYAPSYGISFELDDPRVNQPIPPMTVSV 695
RNPARELR R E+ILAR EAHQR+TN++V +A + L+Q N+DIA GLIPST GY PSYGISF+LDDPRVNQP+ MTVS+
Sbjct: 70 RNPARELRSRVEEILARPEAHQRRTNKQVEKARRQLEQTNEDIAAGLIPSTDGYTPSYGISFQLDDPRVNQPVQAMTVSM 149 HSP 2 Score: 102.834 bits (255), Expect = 7.990e-53 Identity = 44/64 (68.75%), Postives = 52/64 (81.25%), Query Frame = 1
Query: 265 VFTGFWMDESRITMRFPSHSAAKCRQAMWDEGYSISPVRKARFERQDDMEDAERPYIAIKREPG 456
+ W+DESRITMRFPSHSA +CRQAMWD G+SISPVR++RF RQ ED E P++AIKREPG
Sbjct: 6 ILIDSWVDESRITMRFPSHSAVRCRQAMWDAGFSISPVRESRFGRQGGTEDVELPFVAIKREPG 69
BLAST of SMED30013611 vs. Planmine SMEST
Match: SMESG000004613.1 (SMESG000004613.1) HSP 1 Score: 108.227 bits (269), Expect = 6.354e-42 Identity = 46/65 (70.77%), Postives = 52/65 (80.00%), Query Frame = 1
Query: 262 FVFTGFWMDESRITMRFPSHSAAKCRQAMWDEGYSISPVRKARFERQDDMEDAERPYIAIKREPG 456
F+ W+DESRITMRFPSH AA+CRQAMWD YSISPVR++ FERQ ED E PY+AIKREPG
Sbjct: 3 FISIDSWVDESRITMRFPSHPAARCRQAMWDARYSISPVRESLFERQGGAEDVELPYVAIKREPG 67 HSP 2 Score: 80.8777 bits (198), Expect = 6.354e-42 Identity = 34/49 (69.39%), Postives = 45/49 (91.84%), Query Frame = 3
Query: 456 RNPARELRGRAEDILARLEAHQRKTNREVNRAHQHLKQINKDIATGLIP 602
RNPAR+LRG+AE+I ARLEAHQR+T+++V +A + L+QIN+DIATGLIP
Sbjct: 68 RNPARKLRGQAEEIFARLEAHQRRTDKQVEKARRQLEQINEDIATGLIP 116
BLAST of SMED30013611 vs. Planmine SMEST
Match: SMESG000004613.1 (SMESG000004613.1) HSP 1 Score: 108.227 bits (269), Expect = 6.354e-42 Identity = 46/65 (70.77%), Postives = 52/65 (80.00%), Query Frame = 1
Query: 262 FVFTGFWMDESRITMRFPSHSAAKCRQAMWDEGYSISPVRKARFERQDDMEDAERPYIAIKREPG 456
F+ W+DESRITMRFPSH AA+CRQAMWD YSISPVR++ FERQ ED E PY+AIKREPG
Sbjct: 2 FISIDSWVDESRITMRFPSHPAARCRQAMWDARYSISPVRESLFERQGGAEDVELPYVAIKREPG 66 HSP 2 Score: 80.8777 bits (198), Expect = 6.354e-42 Identity = 34/49 (69.39%), Postives = 45/49 (91.84%), Query Frame = 3
Query: 456 RNPARELRGRAEDILARLEAHQRKTNREVNRAHQHLKQINKDIATGLIP 602
RNPAR+LRG+AE+I ARLEAHQR+T+++V +A + L+QIN+DIATGLIP
Sbjct: 67 RNPARKLRGQAEEIFARLEAHQRRTDKQVEKARRQLEQINEDIATGLIP 115
BLAST of SMED30013611 vs. Planmine SMEST
Match: SMESG000027872.1 (SMESG000027872.1) HSP 1 Score: 105.916 bits (263), Expect = 9.483e-42 Identity = 49/80 (61.25%), Postives = 62/80 (77.50%), Query Frame = 3
Query: 456 RNPARELRGRAEDILARLEAHQRKTNREVNRAHQHLKQINKDIATGLIPSTGGYAPSYGISFELDDPRVNQPIPPMTVSV 695
RNPARE+RG+A+ +LARLE HQR+T +++ RA +HL +IN+DIA GLIPST GYAP Y SF LDDPR N+P + V V
Sbjct: 70 RNPAREIRGQAKHLLARLEEHQRQTAQQIRRAQRHLDEINRDIAVGLIPSTNGYAPPYNTSFNLDDPRFNRPTEAINVVV 149 HSP 2 Score: 82.8037 bits (203), Expect = 9.483e-42 Identity = 35/59 (59.32%), Postives = 49/59 (83.05%), Query Frame = 1
Query: 280 WMDESRITMRFPSHSAAKCRQAMWDEGYSISPVRKARFERQDDMEDAERPYIAIKREPG 456
W+D SR+T+RFP+HSAA+CRQAMWD +SISPVR+++ + Q +D + P++AIKREPG
Sbjct: 11 WIDASRVTLRFPAHSAARCRQAMWDAEFSISPVRESQGKDQKISDDVDLPFVAIKREPG 69 The following BLAST results are available for this feature:
BLAST of SMED30013611 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30013611 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30013611 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30013611 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30013611 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30013611 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30013611 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30013611 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30013611 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30013611 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30013611 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30013611 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30013611 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30013611 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 >SMED30013611 ID=SMED30013611|Name=SMED30013611|organism=Schmidtea mediterranea sexual|type=transcript|length=695bpback to top protein sequence of SMED30013611-orf-1 >SMED30013611-orf-1 ID=SMED30013611-orf-1|Name=SMED30013611-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=100bp MRGILSPRYERPDSKGRMTWRTPNGHILPSNGSPAKPGSRTSRKGRRYPSback to top Annotated Terms
The following terms have been associated with this transcript:
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