SMED30026763
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., 2020SMED30026763 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 4
Alignments
SMED30026763 aligns in the following genomic locations:
Homology
BLAST of SMED30026763 vs. Planmine SMEST
Match: SMESG000025004.1 (SMESG000025004.1) HSP 1 Score: 221.09 bits (562), Expect = 6.929e-73 Identity = 108/108 (100.00%), Postives = 108/108 (100.00%), Query Frame = 1 Query: 265 GKKELSRSCQNELNLIYSEFETAIEKVDEDCEDKYFKIKKEYKPDSGPVQSICTNIIDKMSKKCSDEMILEQDLFSEAIGNLDTSCDQEYERMIRYFNRKIAILLGKC 588 GKKELSRSCQNELNLIYSEFETAIEKVDEDCEDKYFKIKKEYKPDSGPVQSICTNIIDKMSKKCSDEMILEQDLFSEAIGNLDTSCDQEYERMIRYFNRKIAILLGKC Sbjct: 136 GKKELSRSCQNELNLIYSEFETAIEKVDEDCEDKYFKIKKEYKPDSGPVQSICTNIIDKMSKKCSDEMILEQDLFSEAIGNLDTSCDQEYERMIRYFNRKIAILLGKC 243 HSP 2 Score: 62.7734 bits (151), Expect = 6.986e-12 Identity = 41/133 (30.83%), Postives = 65/133 (48.87%), Query Frame = 1 Query: 193 MKKLAILLFVLIFDNLESESRIIK---GKKELSRSCQNELNLIYSEFETAIEKVDEDCEDKYFKIKKEYKPDSGPVQSICTNIIDKMSKKCSDEMILEQDLFSEAIGNLDTSCDQEYERMIRYFNRKIAILLG 582 MK I+ ++F ++E R + K+ELS C E+ + TA +K+D C+ Y + + + ++ C N IDKMSK+C E D FS+ I LD SCD+EY +++ + LL Sbjct: 1 MKTFLIICLAILFVSIECRYRARRVELNKRELSAECSKEVEKLDEALNTATDKIDASCQKAYDDLVMKNSVEYLKIEKDCGNYIDKMSKECYAEAKKLDDSFSKEIDKLDQSCDEEYANLVKNMKAEKVKLLA 133
BLAST of SMED30026763 vs. Planmine SMEST
Match: SMESG000025001.1 (SMESG000025001.1) HSP 1 Score: 84.3445 bits (207), Expect = 6.907e-21 Identity = 48/134 (35.82%), Postives = 80/134 (59.70%), Query Frame = 1 Query: 193 MKKLAILLFVLIFDNLESESRIIK--GKKELSRSCQNELNLIYSEFETAIEKVDEDCEDKYFKIKKEYKPDSGPVQSICTNIIDKMSKKCSDEMILEQDLFSEAIGNLDTSCDQEYERMIRYFNRKIAILLGKC 588 M KL I F L+F ++E ++++ K+ELS SCQ EL+ + +++ A+ K+D DC+ + KI+K + P V+S C DKMS++C DE D F++ I LD+SCD E+ + + +++ A L +C Sbjct: 1 MNKLLIFAFALLFVSIECRYKLVQELSKRELSESCQKELDKMNEDYDKAVAKIDSDCDAAFLKIEKPFSPLYLDVESRCGLDYDKMSEECIDETKKLDDDFTKEIEKLDSSCDAEFAKTVENLSKEKAKLKKEC 134
BLAST of SMED30026763 vs. Planmine SMEST
Match: SMESG000025000.1 (SMESG000025000.1) HSP 1 Score: 68.9366 bits (167), Expect = 5.905e-15 Identity = 42/135 (31.11%), Postives = 71/135 (52.59%), Query Frame = 1 Query: 193 MKKLAILLFVLIFDNLESESRIIK---GKKELSRSCQNELNLIYSEFETAIEKVDEDCEDKYFKIKKEYKPDSGPVQSICTNIIDKMSKKCSDEMILEQDLFSEAIGNLDTSCDQEYERMIRYFNRKIAILLGKC 588 M K+ +L FV+ F ++E R+ K+E+S C+ EL + +F A K+D+DC+ Y K K+Y P+ ++ C KM+K C E+ +LF+E +D CD EY ++R +++ L +C Sbjct: 1 MNKILLLTFVIFFVSVECRFRLRLDKIAKREMSSECKAELKKLDDQFTAAANKIDDDCDAVYVKWSKKYLPEYVALKEKCGLDTSKMTKDCKTELKRLFNLFAEGNYKVDLECDNEYAALVRQTSKEKEKLKQQC 135
BLAST of SMED30026763 vs. Planmine SMEST
Match: SMESG000054780.1 (SMESG000054780.1) HSP 1 Score: 65.4698 bits (158), Expect = 1.117e-13 Identity = 42/135 (31.11%), Postives = 67/135 (49.63%), Query Frame = 1 Query: 193 MKKLAILLFVLIFDNLESESRIIK---GKKELSRSCQNELNLIYSEFETAIEKVDEDCEDKYFKIKKEYKPDSGPVQSICTNIIDKMSKKCSDEMILEQDLFSEAIGNLDTSCDQEYERMIRYFNRKIAILLGKC 588 MK I+ ++F ++E R + K+ELS C E+ + TA +K+D C+ Y + + + ++ C N IDKMSK+C E D FS+ I LD SCD+EY +++ + LL +C Sbjct: 1 MKTFLIICLAILFVSIECRYRARRVELNKRELSAECSKEVEKLDEALNTATDKIDATCQKAYDDLVMKNSVEYLKIEKDCGNYIDKMSKECYAEAKKLDDSFSKEIDKLDQSCDEEYANLVKNMKAEKVKLLAEC 135
BLAST of SMED30026763 vs. Planmine SMEST
Match: SMESG000025014.1 (SMESG000025014.1) HSP 1 Score: 65.4698 bits (158), Expect = 1.117e-13 Identity = 42/135 (31.11%), Postives = 67/135 (49.63%), Query Frame = 1 Query: 193 MKKLAILLFVLIFDNLESESRIIK---GKKELSRSCQNELNLIYSEFETAIEKVDEDCEDKYFKIKKEYKPDSGPVQSICTNIIDKMSKKCSDEMILEQDLFSEAIGNLDTSCDQEYERMIRYFNRKIAILLGKC 588 MK I+ ++F ++E R + K+ELS C E+ + TA +K+D C+ Y + + + ++ C N IDKMSK+C E D FS+ I LD SCD+EY +++ + LL +C Sbjct: 1 MKTFLIICLAILFVSIECRYRARRVELNKRELSAECSKEVEKLDEALNTATDKIDATCQKAYDDLVMKNSVEYLKIEKDCGNYIDKMSKECYAEAKKLDDSFSKEIDKLDQSCDEEYANLVKNMKAEKVKLLAEC 135 The following BLAST results are available for this feature:
BLAST of SMED30026763 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30026763 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30026763 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30026763 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30026763 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30026763 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30026763 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30026763 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 0
BLAST of SMED30026763 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30026763 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30026763 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30026763 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30026763 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30026763 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 >SMED30026763 ID=SMED30026763|Name=SMED30026763|organism=Schmidtea mediterranea sexual|type=transcript|length=603bpback to top protein sequence of SMED30026763-orf-1 >SMED30026763-orf-1 ID=SMED30026763-orf-1|Name=SMED30026763-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=133bp MKKLAILLFVLIFDNLESESRIIKGKKELSRSCQNELNLIYSEFETAIEKback 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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