SMED30003421
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., 2020SMED30003421 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 4
Alignments
SMED30003421 aligns in the following genomic locations:
Homology
BLAST of SMED30003421 vs. Planmine SMEST
Match: SMESG000072456.1 (SMESG000072456.1) HSP 1 Score: 491.886 bits (1265), Expect = 4.610e-178 Identity = 242/242 (100.00%), Postives = 242/242 (100.00%), Query Frame = 3 Query: 150 MRLLLLVFIATFVKVYSDEASEKETYENLISEIEFNKVFVDQFNRFSGAPAQINNLAKSILHHLKDVGTLVTEIIFLTVGHVVSNTTYNLTLAGHSSVLFAQLVGVLDAENRLPEIIYTTEDGTRFESIINFTNSNYESLLETLHHSSKQSWLDFRKTINEKTLQKNIHELVSINKIVLDKSLFQCNQANIAKFCVASTNNLIKLLIIQSALKATKGDKLDERVTSKLSITKSCEKYIMRCY 875 MRLLLLVFIATFVKVYSDEASEKETYENLISEIEFNKVFVDQFNRFSGAPAQINNLAKSILHHLKDVGTLVTEIIFLTVGHVVSNTTYNLTLAGHSSVLFAQLVGVLDAENRLPEIIYTTEDGTRFESIINFTNSNYESLLETLHHSSKQSWLDFRKTINEKTLQKNIHELVSINKIVLDKSLFQCNQANIAKFCVASTNNLIKLLIIQSALKATKGDKLDERVTSKLSITKSCEKYIMRCY Sbjct: 1 MRLLLLVFIATFVKVYSDEASEKETYENLISEIEFNKVFVDQFNRFSGAPAQINNLAKSILHHLKDVGTLVTEIIFLTVGHVVSNTTYNLTLAGHSSVLFAQLVGVLDAENRLPEIIYTTEDGTRFESIINFTNSNYESLLETLHHSSKQSWLDFRKTINEKTLQKNIHELVSINKIVLDKSLFQCNQANIAKFCVASTNNLIKLLIIQSALKATKGDKLDERVTSKLSITKSCEKYIMRCY 242
BLAST of SMED30003421 vs. Planmine SMEST
Match: SMESG000072423.1 (SMESG000072423.1) HSP 1 Score: 66.6254 bits (161), Expect = 1.002e-12 Identity = 50/216 (23.15%), Postives = 93/216 (43.06%), Query Frame = 3 Query: 246 IEFNKVFVDQFNRFSGAPAQINNLAKSILHHLKDVGTLVTEIIFLTVGHVVSNTTYNLTLAGHSSVLFAQLVGVLDAENRLPEIIYTTEDGTRFESIINFTNSNYESLLETLHHSSKQSWLDFRKTINEKTLQKNIHELVSINKIVLDKSL------FQCNQANIAKFCVASTNNLIKLLIIQSALKATKGDKLDE-RVTSKLSITKSCEKYIMRC 872 +E N+ D F F G +QI A+ + HL + + + + +YN T GH+ LF Q V + L + T+ G ++ + + L+ + S +SW F +T + + N+ +L+ + L F+C+ IA FC ++ + KLL+ +SA++A + KL+ R+ + + C Y+ C Sbjct: 1 MENNRRIADDFLNFKGESSQIYPFARRMFFHLIKTTKYSCSELNYVIECIFTGKSYNATKVGHADSLFIQFVNAMQEIEPLTTEMVETKVGKHYKDTLRKISYMMLDLVFASYEHSVKSWTKFSQTYD----KGNVTKLIPVFYKAFHDELYEVGREFKCDNVQIANFCASAITGMTKLLLSRSAIRAAQRVKLNRLRLRIVWKMRQKCLNYMNFC 212
BLAST of SMED30003421 vs. Planmine SMEST
Match: SMESG000068770.1 (SMESG000068770.1) HSP 1 Score: 65.0846 bits (157), Expect = 4.123e-12 Identity = 55/246 (22.36%), Postives = 103/246 (41.87%), Query Frame = 3 Query: 165 LVFIATFVKVYSDEASEKETYENLISEIEFNKVFVDQFNRFSGAPAQINNLAKSILHHLKDVGTLVTEIIFLTVGHVVSNTTYNLTLAGHSSVLFAQLVGVLDAENRLPEIIYTTEDGTRFESIINFTNSN--------YESLLETLHHSSKQSWLDFRKTINEKTLQKNIHELVSINKIVLD-KSLFQCNQANIAKFCVASTNNLIKLLIIQSALKATKGD-KLDERVTSKLSITKSCEKYIMRC 872 ++F F+ ++ S Y ++ ++ K D F R S P + + + L L + + + V V++N + A +SV FAQL+G LD+ E ++ D + +IN N Y + H + ++W FR+ + L + + + ++L S CN+ ++ K+C + K+L ++ A +A KGD K+D S+ SC + C Sbjct: 1 MIFFIAFLAIFIPALSCDNLYVDITEDMRVAKENFDAFIRLSDKPKESESQIITFLESLVKITANLESAGYRNVADVLNNKLDDAKTAAIASVKFAQLIGDLDS----VEPLFKNFDA--YTEVINLFTKNEHAVNQMYYNPFMAAFHVNDLEAWTKFRENYLQSKLDETVASITKSQTVILKLLSEKDCNKVDVGKYCAFTFGEFFKVLAMRGAARAVKGDSKIDNVNIDYNSVLSSCLSTLKSC 240 The following BLAST results are available for this feature:
BLAST of SMED30003421 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30003421 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30003421 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30003421 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30003421 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30003421 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30003421 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30003421 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30003421 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30003421 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30003421 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30003421 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30003421 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30003421 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST) Total hits: 3
Analyses
This transcript is derived from or has results from the following analyses Sequences
The following sequences are available for this feature:
transcript sequence >SMED30003421 ID=SMED30003421|Name=SMED30003421|organism=Schmidtea mediterranea sexual|type=transcript|length=929bpback to top protein sequence of SMED30003421-orf-1 >SMED30003421-orf-1 ID=SMED30003421-orf-1|Name=SMED30003421-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=243bp MRLLLLVFIATFVKVYSDEASEKETYENLISEIEFNKVFVDQFNRFSGAPback to top Annotated Terms
The following terms have been associated with this transcript:
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