SMED30004959
Overview
Neoblast Clusters
Zeng et. al., 2018
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 AppEmbryonic 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., 2020SMED30004959 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 2
Alignments
SMED30004959 aligns in the following genomic locations:
Homology
BLAST of SMED30004959 vs. TrEMBL
Match: V9XRT9 (X1.A.G7.1 (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1) HSP 1 Score: 62.003 bits (149), Expect = 7.909e-8 Identity = 38/96 (39.58%), Postives = 55/96 (57.29%), Query Frame = -2 Query: 386 ETSEI-----LIYQKLHFIFGIVTTICGCVLLVFDPLLPAIFRYNYSLVFAGIFMFISGICSIKATRTVSKHFLIISLSFNIMAGVLLFTGYIVSL 658 E+ EI I K H IFG + CG +L DPLLP + Y +S+ AG+FM ISGI SI+A + K +LI + NI+A + + G +V++ Sbjct: 50 ESKEIRSGSKFINSKSHRIFGYILIACGIFVLCIDPLLPILLEYPFSISIAGVFMIISGIFSIQAVKRNLKLYLIFAKILNILALINIGIGILVAI 145
BLAST of SMED30004959 vs. Planmine SMEST
Match: SMESG000046821.1 (SMESG000046821.1) HSP 1 Score: 206.068 bits (523), Expect = 6.282e-99 Identity = 104/107 (97.20%), Postives = 106/107 (99.07%), Query Frame = -2 Query: 356 KILNKSETSEILIYQKLHFIFGIVTTICGCVLLVFDPLLPAIFRYNYSLVFAGIFMFISGICSIKATRTVSKHFLIISLSFNIMAGVLLFTGYIVSLRNLLNSCMNF 676 +ILNKSETSEILIYQKLHFIFGIVTTICGCVLLVFDPLLPAIFRYNYSLVFAGIFMFISGICSIKATRTVSKHFLIISLSFNIMAGVLLFTGY+VSLRN LNSCMNF Sbjct: 32 QILNKSETSEILIYQKLHFIFGIVTTICGCVLLVFDPLLPAIFRYNYSLVFAGIFMFISGICSIKATRTVSKHFLIISLSFNIMAGVLLFTGYVVSLRN-LNSCMNF 137 HSP 2 Score: 125.561 bits (314), Expect = 6.282e-99 Identity = 59/60 (98.33%), Postives = 60/60 (100.00%), Query Frame = -3 Query: 175 CTKFQQGQRNLAFYHAIVAVGLIVLIYWDLSLKFGEIISKKSRITENFQTENVEFGIRRE 354 CTKFQQGQRNLAFYHAIVAVGLIVLIYWDLSLKFGEIISK+SRITENFQTENVEFGIRRE Sbjct: 138 CTKFQQGQRNLAFYHAIVAVGLIVLIYWDLSLKFGEIISKRSRITENFQTENVEFGIRRE 197 HSP 3 Score: 69.707 bits (169), Expect = 6.282e-99 Identity = 31/32 (96.88%), Postives = 31/32 (96.88%), Query Frame = -1 Query: 675 MDLVPCTNSMESSEPRLSLDHPELTQVQMRYQ 770 MDLVPCTNSME SEPRLSLDHPELTQVQMRYQ Sbjct: 1 MDLVPCTNSMEISEPRLSLDHPELTQVQMRYQ 32
BLAST of SMED30004959 vs. Planmine SMEST
Match: SMESG000046821.1 (SMESG000046821.1) HSP 1 Score: 124.405 bits (311), Expect = 4.691e-36 Identity = 59/60 (98.33%), Postives = 60/60 (100.00%), Query Frame = -3 Query: 175 CTKFQQGQRNLAFYHAIVAVGLIVLIYWDLSLKFGEIISKKSRITENFQTENVEFGIRRE 354 CTKFQQGQRNLAFYHAIVAVGLIVLIYWDLSLKFGEIISK+SRITENFQTENVEFGIRRE Sbjct: 37 CTKFQQGQRNLAFYHAIVAVGLIVLIYWDLSLKFGEIISKRSRITENFQTENVEFGIRRE 96
BLAST of SMED30004959 vs. Planmine SMEST
Match: SMESG000046812.1 (SMESG000046812.1) HSP 1 Score: 84.7297 bits (208), Expect = 1.186e-20 Identity = 41/103 (39.81%), Postives = 67/103 (65.05%), Query Frame = -2 Query: 356 KSETSEILIYQKLHFIFGIVTTICGCVLLVFDPLLPAIFRYNYSLVFAGIFMFISGICSIKATRTVSKHFLIISLSFNIMAGVLLFTGYIVSLRNLLNSCMNF 664 + + +L Y+++H I+G + + G + + DP+LP+IF+Y YS+ G+FM ISG+CSI +R +K LI SL FNI+A +++FT YI+ + L S +F Sbjct: 66 EESQNSMLRYKRMHLIYGTIYVVLGGIQVAIDPILPSIFQYPYSMYPGGLFMIISGLCSIYGSRKNNKCSLIASLIFNILAMIVIFTNYIIGILALNQSGFSF 168 HSP 2 Score: 33.113 bits (74), Expect = 1.186e-20 Identity = 14/42 (33.33%), Postives = 25/42 (59.52%), Query Frame = -3 Query: 220 FQQGQRNLAFYHAIVAVGLIVLIYWDLSLKFGEIISKKSRIT 345 + +G + A ++ + + L VL+ WD SLK G++ KK + T Sbjct: 185 YTEGVKGFAIFNVVFGIILFVLMIWDSSLKCGDVCFKKQKQT 226
BLAST of SMED30004959 vs. Planmine SMEST
Match: SMESG000046815.1 (SMESG000046815.1) HSP 1 Score: 84.3445 bits (207), Expect = 1.621e-20 Identity = 38/93 (40.86%), Postives = 64/93 (68.82%), Query Frame = -2 Query: 386 KSETSEILIYQKLHFIFGIVTTICGCVLLVFDPLLPAIFRYNYSLVFAGIFMFISGICSIKATRTVSKHFLIISLSFNIMAGVLLFTGYIVSL 664 + + +L Y+++H I+G ++ + G + + DP+LP+IF+Y YS+ G+FM ISG+CSI +R +K LI SL FNI+A +++FT YI+ + Sbjct: 66 EESQNSMLRYKRMHLIYGTISVVLGGIQVAIDPILPSIFQYPYSMYPGGLFMIISGLCSIYGSRKNNKCSLIASLIFNILALIVIFTNYIIGI 158 HSP 2 Score: 33.113 bits (74), Expect = 1.621e-20 Identity = 14/42 (33.33%), Postives = 25/42 (59.52%), Query Frame = -3 Query: 220 FQQGQRNLAFYHAIVAVGLIVLIYWDLSLKFGEIISKKSRIT 345 + +G + A ++ + + L VL+ WD SLK G++ KK + T Sbjct: 185 YTEGVKGFAIFNVVFGIILFVLMIWDSSLKCGDVCFKKQKQT 226
BLAST of SMED30004959 vs. Planmine SMEST
Match: SMESG000046819.1 (SMESG000046819.1) HSP 1 Score: 84.3445 bits (207), Expect = 2.653e-20 Identity = 38/93 (40.86%), Postives = 64/93 (68.82%), Query Frame = -2 Query: 386 KSETSEILIYQKLHFIFGIVTTICGCVLLVFDPLLPAIFRYNYSLVFAGIFMFISGICSIKATRTVSKHFLIISLSFNIMAGVLLFTGYIVSL 664 + + +L Y+++H I+G ++ + G + + DP+LP+IF+Y YS+ G+FM ISG+CSI +R +K LI SL FNI+A +++FT YI+ + Sbjct: 66 EESQNSMLRYKRMHLIYGTISVVLGGIQVAIDPILPSIFQYPYSMYPGGLFMIISGLCSIYGSRKNNKCSLIASLIFNILALIVIFTNYIIGI 158 HSP 2 Score: 32.3426 bits (72), Expect = 2.653e-20 Identity = 14/42 (33.33%), Postives = 25/42 (59.52%), Query Frame = -3 Query: 220 FQQGQRNLAFYHAIVAVGLIVLIYWDLSLKFGEIISKKSRIT 345 + +G + LA ++ + + L VL+ WD SLK G++ K + T Sbjct: 185 YTEGVKGLAIFNVVFGMILFVLMIWDSSLKCGDVCFKNQKQT 226 The following BLAST results are available for this feature:
BLAST of SMED30004959 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30004959 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30004959 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30004959 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30004959 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30004959 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30004959 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30004959 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 1
BLAST of SMED30004959 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30004959 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30004959 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30004959 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30004959 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30004959 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 >SMED30004959 ID=SMED30004959|Name=SMED30004959|organism=Schmidtea mediterranea sexual|type=transcript|length=815bpback to top Annotated Terms
The following terms have been associated with this transcript:
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