SMED30017298
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., 2020SMED30017298 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 3
Homology
BLAST of SMED30017298 vs. Planmine SMEST
Match: SMESG000013157.1 (SMESG000013157.1) HSP 1 Score: 117.472 bits (293), Expect = 9.734e-45 Identity = 54/84 (64.29%), Postives = 67/84 (79.76%), Query Frame = 2 Query: 470 NNSWIDASRITLRFPVQTAARCRQAMWDTSFSISPVRESRESRQFDNDEMELPHVAIKSEPGRNPVREAR*RAEFTLARLERHQ 721 ++SWIDASR+ RFP +AARCRQAMWD FSI PVRE+R Q D++E++L +VAIK EPGR+P RE R +AE+ LARLERHQ Sbjct: 89 HDSWIDASRVIARFPAHSAARCRQAMWDAGFSIFPVRETRGGTQGDSNEVDLSYVAIKREPGRSPAREMRGQAEYLLARLERHQ 172 HSP 2 Score: 82.0333 bits (201), Expect = 9.734e-45 Identity = 46/84 (54.76%), Postives = 59/84 (70.24%), Query Frame = 1 Query: 721 AKTNWQVAMARRRLNRVNQDIATGKIPSTVGYAIKYGVSYELDDPVLVEMDTPMDVVILR*LLPRELQ-DYDGQPPQRQEHSYA 969 A+TN QV AR+ L RVN+DIA G+IPST GYA +Y VS+ELDDP L + M V + R +LP+E++ + D PQR EHSYA Sbjct: 173 AETNRQVEQARQYLRRVNEDIAAGRIPSTDGYAPQYNVSFELDDPRLQRQMSEMRVAVPRHILPKEMRNENDIAEPQR-EHSYA 255
BLAST of SMED30017298 vs. Planmine SMEST
Match: SMESG000023390.1 (SMESG000023390.1) HSP 1 Score: 119.783 bits (299), Expect = 1.385e-43 Identity = 53/87 (60.92%), Postives = 72/87 (82.76%), Query Frame = 2 Query: 467 ENNSWIDASRITLRFPVQTAARCRQAMWDTSFSISPVRESRESRQFDNDEMELPHVAIKSEPGRNPVREAR*RAEFTLARLERHQQK 727 +++SWIDASR+T+RFP ++ ARCRQ +WD FS+SPVRESR + + D+++++LP VAIK EPGRNP RE R +AEF LARLE HQ++ Sbjct: 358 DDHSWIDASRVTVRFPARSVARCRQVLWDAGFSVSPVRESRTATRRDDEKVDLPFVAIKREPGRNPAREIRGQAEFLLARLEEHQRQ 444 HSP 2 Score: 75.8702 bits (185), Expect = 1.385e-43 Identity = 42/82 (51.22%), Postives = 52/82 (63.41%), Query Frame = 1 Query: 724 KTNWQVAMARRRLNRVNQDIATGKIPSTVGYAIKYGVSYELDDPVLVEMDTPMDVVILR*LLPRELQDYDGQPPQRQEHSYA 969 +T QV ARR L +N+ IATG IPST YA Y VS+ LDDP L M+VV+ R +L RE++D D + Q QEHSYA Sbjct: 444 QTKRQVNRARRHLAEINKAIATGDIPSTDRYAPPYNVSFNLDDPNLAGEAEAMNVVVPRRILTREMKDKDRRSNQDQEHSYA 525
BLAST of SMED30017298 vs. Planmine SMEST
Match: SMESG000030287.1 (SMESG000030287.1) HSP 1 Score: 118.627 bits (296), Expect = 9.034e-42 Identity = 55/86 (63.95%), Postives = 70/86 (81.40%), Query Frame = 2 Query: 470 NNSWIDASRITLRFPVQTAARCRQAMWDTSFSISPVRESRESRQFDNDEMELPHVAIKSEPGRNPVREAR*RAEFTLARLERHQQK 727 ++SWIDASR+T+RFP ++AARCRQA+WD FS+SPVRESR +++E+EL VAIK EPGRNP RE R +AEF LARLE HQ++ Sbjct: 306 DHSWIDASRVTVRFPARSAARCRQALWDLGFSVSPVRESRVGTYREDEEVELLFVAIKREPGRNPAREIRGQAEFLLARLEEHQRQ 391 HSP 2 Score: 70.8626 bits (172), Expect = 9.034e-42 Identity = 40/82 (48.78%), Postives = 49/82 (59.76%), Query Frame = 1 Query: 724 KTNWQVAMARRRLNRVNQDIATGKIPSTVGYAIKYGVSYELDDPVLVEMDTPMDVVILR*LLPRELQDYDGQPPQRQEHSYA 969 + N QV +RR L +N+ IATG IPST YA+ Y VSY LDDP L M+VV+ PR + D +P Q QEHSYA Sbjct: 391 QNNRQVDRSRRHLAEINKAIATGDIPSTDWYALPYNVSYNLDDPNLAGETEAMNVVV-----PRRMLAADRRPYQDQEHSYA 467
BLAST of SMED30017298 vs. Planmine SMEST
Match: SMESG000031752.1 (SMESG000031752.1) HSP 1 Score: 107.071 bits (266), Expect = 5.483e-41 Identity = 54/93 (58.06%), Postives = 68/93 (73.12%), Query Frame = 1 Query: 724 KTNWQVAMARRRLNRVNQDIATGKIPSTVGYAIKYGVSYELDDPVLVEMDTPMDVVILR*LLPRELQDYDGQPPQRQEHSYA*NQSGWSSNPR 1002 +TNWQV +ARRR++RV DIA G+IPST G+ +YGVSYELDD L EMD P+DVV+ R L+P + D + + PQRQEHSYA N+ SN R Sbjct: 81 QTNWQVLVARRRMDRVKADIAAGRIPSTDGHTSEYGVSYELDDLALKEMDAPIDVVVPRRLIPSNILDRNRRSPQRQEHSYARNRPVNPSNFR 173 HSP 2 Score: 80.1073 bits (196), Expect = 5.483e-41 Identity = 41/67 (61.19%), Postives = 50/67 (74.63%), Query Frame = 2 Query: 527 ARCRQAMWDTSFSISPVRESRESRQFDNDEMELPHVAIKSEPGRNPVREAR*RAEFTLARLERHQQK 727 ARC QAMWD +SIS V+ESRE +DE+EL +VA+K EP RN REAR RAEFTL RLE H+++ Sbjct: 15 ARCWQAMWDAGYSISTVKESREHHLSRHDEVELAYVAMKREPVRNLAREARQRAEFTLIRLEIHKRQ 81
BLAST of SMED30017298 vs. Planmine SMEST
Match: SMESG000038895.1 (SMESG000038895.1) HSP 1 Score: 107.457 bits (267), Expect = 2.376e-40 Identity = 57/100 (57.00%), Postives = 71/100 (71.00%), Query Frame = 1 Query: 724 KTNWQVAMARRRLNRVNQDIATGKIPSTVGYAIKYGVSYELDDPVLVEMDTPMDVVILR*LLPRELQDYDGQPPQRQEHSYA*NQSGWSSNPRVESHPRR 1023 +TNWQVAM R R +RVN +IATG+IPST GY Y VSYEL+DP L EMD PMDVV+ R LLP + + + + PQRQEHSYA ++ + SN R + RR Sbjct: 65 QTNWQVAMVRNRSDRVNAEIATGRIPSTDGYIPGYRVSYELNDPALEEMDAPMDVVVPRRLLPSNILERNRRSPQRQEHSYACSRPVYPSNSRNINRQRR 164 HSP 2 Score: 77.411 bits (189), Expect = 2.376e-40 Identity = 40/63 (63.49%), Postives = 48/63 (76.19%), Query Frame = 2 Query: 539 QAMWDTSFSISPVRESRESRQFDNDEMELPHVAIKSEPGRNPVREAR*RAEFTLARLERHQQK 727 +AMWD +SIS VRES + R NDE+EL +VAIK EP RNPV EA RAEFTLARL+ HQ++ Sbjct: 3 EAMWDAGYSISSVRESMDHRLSRNDEVELSYVAIKREPWRNPVIEAGQRAEFTLARLDIHQRQ 65 The following BLAST results are available for this feature:
BLAST of SMED30017298 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30017298 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30017298 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30017298 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30017298 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30017298 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30017298 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30017298 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30017298 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30017298 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30017298 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30017298 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30017298 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30017298 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 >SMED30017298 ID=SMED30017298|Name=SMED30017298|organism=Schmidtea mediterranea sexual|type=transcript|length=1071bpback to top protein sequence of SMED30017298-orf-1 >SMED30017298-orf-1 ID=SMED30017298-orf-1|Name=SMED30017298-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=113bp MITPRDFIIMTKKTSDENQNGPNVKQRGETRKRELLRRKEDENNSWIDASback to top Annotated Terms
The following terms have been associated with this transcript:
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