SMED30000746
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., 2020SMED30000746 has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGEPAGE Curations: 13Note: Hover over icons to view figure legend
Alignments
SMED30000746 aligns in the following genomic locations:
Homology
BLAST of SMED30000746 vs. TrEMBL
Match: I1ZI82 (Uncharacterized protein (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1) HSP 1 Score: 98.2117 bits (243), Expect = 3.024e-23 Identity = 51/118 (43.22%), Postives = 72/118 (61.02%), Query Frame = 2 Query: 44 IQIGLLVVLALINVECVSK---SKKAFDCLTMLDKIDNECDKRYLVLDGHCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCLGAYDKVDSYCDKRYNVLDTHCDGLY 388 I +++ +++ V C S KK F C +L +ID ECD +Y LD CD SY +H+ CDIKY +LSGRC+ KL+ CI++YG LD CL + + C ++YN +D HCD LY Sbjct: 1 ILFAAVLIQSMLVVHCASVKAVEKKGF-CSGILHRIDTECDDKYRRLDRECDHSYESIHEVCDIKYTMLSGRCRVKLTEDCIKRYGNLDHSCLESLRNIQEKCQEKYNRVDDHCDALY 117
BLAST of SMED30000746 vs. Planmine SMEST
Match: SMESG000024754.1 (SMESG000024754.1) HSP 1 Score: 249.98 bits (637), Expect = 1.682e-86 Identity = 128/129 (99.22%), Postives = 128/129 (99.22%), Query Frame = 2 Query: 32 MKLMIQIGLLVVLALINVECVSKSKKAFDCLTMLDKIDNECDKRYLVLDGHCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCLGAYDKVDSYCDKRYNVLDTHCDGLYKLQEKCENNS 418 MKLMIQIGLLVVLALINVECVSKSKKAFDCLTMLDKIDNECDKRYLVLDGHCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCL AYDKVDSYCDKRYNVLDTHCDGLYKLQEKCENNS Sbjct: 1 MKLMIQIGLLVVLALINVECVSKSKKAFDCLTMLDKIDNECDKRYLVLDGHCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCLRAYDKVDSYCDKRYNVLDTHCDGLYKLQEKCENNS 129
BLAST of SMED30000746 vs. Planmine SMEST
Match: SMESG000024821.1 (SMESG000024821.1) HSP 1 Score: 203.756 bits (517), Expect = 1.594e-68 Identity = 103/103 (100.00%), Postives = 103/103 (100.00%), Query Frame = 2 Query: 110 AFDCLTMLDKIDNECDKRYLVLDGHCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCLGAYDKVDSYCDKRYNVLDTHCDGLYKLQEKCENNS 418 AFDCLTMLDKIDNECDKRYLVLDGHCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCLGAYDKVDSYCDKRYNVLDTHCDGLYKLQEKCENNS Sbjct: 6 AFDCLTMLDKIDNECDKRYLVLDGHCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCLGAYDKVDSYCDKRYNVLDTHCDGLYKLQEKCENNS 108
BLAST of SMED30000746 vs. Planmine SMEST
Match: SMESG000072142.1 (SMESG000072142.1) HSP 1 Score: 204.142 bits (518), Expect = 2.212e-68 Identity = 99/129 (76.74%), Postives = 111/129 (86.05%), Query Frame = 2 Query: 32 MKLMIQIGLLVVLALINVECVSKSKKAFDCLTMLDKIDNECDKRYLVLDGHCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCLGAYDKVDSYCDKRYNVLDTHCDGLYKLQEKCENNS 418 MKLMIQIG + LAL+NVECVSKSK + DCLTMLDKID ECD++YLVLD HCD YA LHK CDI YD LSGRCK +SMRCI KYG+LD KCLGAYD+VD++CDKRYNVLDTHCD LYK+QEKCE+NS Sbjct: 1 MKLMIQIGFFMTLALLNVECVSKSKNSADCLTMLDKIDRECDRKYLVLDNHCDSRYAHLHKTCDINYDKLSGRCKNNMSMRCILKYGRLDRKCLGAYDRVDTFCDKRYNVLDTHCDELYKIQEKCEDNS 129
BLAST of SMED30000746 vs. Planmine SMEST
Match: SMESG000072142.1 (SMESG000072142.1) HSP 1 Score: 198.749 bits (504), Expect = 2.868e-66 Identity = 96/126 (76.19%), Postives = 108/126 (85.71%), Query Frame = 2 Query: 41 MIQIGLLVVLALINVECVSKSKKAFDCLTMLDKIDNECDKRYLVLDGHCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCLGAYDKVDSYCDKRYNVLDTHCDGLYKLQEKCENNS 418 MIQIG + LAL+NVECVSKSK + DCLTMLDKID ECD++YLVLD HCD YA LHK CDI YD LSGRCK +SMRCI KYG+LD KCLGAYD+VD++CDKRYNVLDTHCD LYK+QEKCE+NS Sbjct: 1 MIQIGFFMTLALLNVECVSKSKNSADCLTMLDKIDRECDRKYLVLDNHCDSRYAHLHKTCDINYDKLSGRCKNNMSMRCILKYGRLDRKCLGAYDRVDTFCDKRYNVLDTHCDELYKIQEKCEDNS 126
BLAST of SMED30000746 vs. Planmine SMEST
Match: SMESG000021388.1 (SMESG000021388.1) HSP 1 Score: 114.39 bits (285), Expect = 6.853e-33 Identity = 62/136 (45.59%), Postives = 79/136 (58.09%), Query Frame = 2 Query: 38 LMIQIGLLVVLALINVECVSKSK------------KAFDCLTMLDKIDNECDKRYLVLDGHCDRSYADLHKNCDIKYDLLSGRCKGKLSMRCIRKYGKLDGKCLGAYDKVDSYCDKRYNVLDTHCDGLYKLQEKCE 409 L I V LA++ V C+ K K C LDK+D ECDK+Y +LD C+ SY L+K CD+ Y LSGRC+ +LS CI+KYGKLD C+ AY ++D CDKRY LD +CD LY +E CE Sbjct: 2 LRIIYAFSVTLAVLRVNCLESPKVFKDEIVNNYEKKWMKCTKFLDKVDAECDKKYDLLDNDCNGSYKQLYKTCDVNYLKLSGRCQMRLSKNCIKKYGKLDRHCIKAYGEIDESCDKRYAKLDPYCDALYTKEENCE 137 The following BLAST results are available for this feature:
BLAST of SMED30000746 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99) Total hits: 0
BLAST of SMED30000746 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99) Total hits: 0
BLAST of SMED30000746 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99) Total hits: 0
BLAST of SMED30000746 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99) Total hits: 0
BLAST of SMED30000746 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99) Total hits: 0
BLAST of SMED30000746 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99) Total hits: 0
BLAST of SMED30000746 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt) Total hits: 0
BLAST of SMED30000746 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL) Total hits: 1
BLAST of SMED30000746 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99) Total hits: 0
BLAST of SMED30000746 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99) Total hits: 0
BLAST of SMED30000746 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46) Total hits: 0
BLAST of SMED30000746 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46) Total hits: 0
BLAST of SMED30000746 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99) Total hits: 0
BLAST of SMED30000746 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 >SMED30000746 ID=SMED30000746|Name=SMED30000746|organism=Schmidtea mediterranea sexual|type=transcript|length=506bpback to top protein sequence of SMED30000746-orf-1 >SMED30000746-orf-1 ID=SMED30000746-orf-1|Name=SMED30000746-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=130bp MKLMIQIGLLVVLALINVECVSKSKKAFDCLTMLDKIDNECDKRYLVLDGback 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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