SMED30016976

Overview
NameSMED30016976
Smed IDSMED30016976
Length (bp)367
Neoblast Clusters

Zeng et. al., 2018



 

 

Overview

 

Single cell RNA-seq of pluripotent neoblasts and its early progenies


We 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



Embryonic Expression

Davies et. al., 2017

Hover the mouse over a column in the graph to view average RPKM values per sample.
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Embryonic Stages: Y: yolk. S2-S8: Stages 2-8. C4: asexual adult. SX: virgin, sexually mature adult.
For further information about sample preparation and analysis for the single animal RNA-Seq experiment, please refer to the Materials and Methods

 

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Anatomical Expression

PAGE et. al., 2020



SMED30016976

has been reported as being expressed in these anatomical structures and/or regions. Read more about PAGE



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymaSMED30016976 dd_Smed_v4_1041_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30016976 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000401:85681..86149 -1763
Homology
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BLAST of SMED30016976 vs. Planmine SMEST
Match: SMESG000054106.1 (SMESG000054106.1)

HSP 1 Score: 71.2478 bits (173), Expect = 3.448e-17
Identity = 36/75 (48.00%), Postives = 45/75 (60.00%), Query Frame = 3 
Query:   78 FMGTGYYTNGIPYVNIRGQEYSATTQKRIQIGTGDQCIVCYIYPAANSKSKPYYNCNEPMPFSGDDGQISYISSC 302
            F+G G   NG  YV I G EYSA +Q+ I IGTGD+C +C I P  N K+ P YNC EP+      G++ Y S C
Sbjct:   21 FIGVGVVRNGKQYVTITGVEYSADSQRNILIGTGDKCNLCKIVPGKN-KTNPTYNCLEPIKVISASGKVMYKSQC 94
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BLAST of SMED30016976 vs. Planmine SMEST
Match: SMESG000062897.1 (SMESG000062897.1)

HSP 1 Score: 64.6994 bits (156), Expect = 1.479e-14
Identity = 32/73 (43.84%), Postives = 43/73 (58.90%), Query Frame = 3 
Query:   84 GTGYYTNGIPYVNIRGQEYSATTQKRIQIGTGDQCIVCYIYPAANSKSKPYYNCNEPMPFSGDDGQISYISSC 302
            G GYY NG P V I  Q + A      QIG+GD+C+ C+I   AN+  KP + C+ P P    DG+++YIS C
Sbjct:   34 GIGYYENGKPVVKINNQVFPADKNSVQQIGSGDRCLKCFINAPANNDEKPKFQCHGPSPVYM-DGKMAYISEC 105
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BLAST of SMED30016976 vs. Planmine SMEST
Match: SMESG000020860.1 (SMESG000020860.1)

HSP 1 Score: 62.003 bits (149), Expect = 1.227e-13
Identity = 32/92 (34.78%), Postives = 48/92 (52.17%), Query Frame = 3 
Query:   27 NVFVLLIFVMNPLLCNAFMGTGYYTNGIPYVNIRGQEYSATTQKRIQIGTGDQCIVCYIYPAANSKSKPYYNCNEPMPFSGDDGQISYISSC 302
             V +L++ V+     +   G GY+ +G  YV I G EY A     IQ G GD+C+VC  + + +    P Y+C  P P    DG+++Y S C
Sbjct:    2 KVILLVLSVLTVAYASVSFGRGYFRDGKGYVKINGVEYLAEEDGEIQYGEGDRCVVCNYFASKDKVKPPTYSCYGPSPMM-IDGKLTYRSQC 92
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BLAST of SMED30016976 vs. Planmine SMEST
Match: SMESG000054105.1 (SMESG000054105.1)

HSP 1 Score: 61.2326 bits (147), Expect = 2.664e-13
Identity = 30/93 (32.26%), Postives = 51/93 (54.84%), Query Frame = 3 
Query:   27 NVFVLLIFVMNPLLCNAFM-GTGYYTNGIPYVNIRGQEYSATTQKRIQIGTGDQCIVCYIYPAANSKSKPYYNCNEPMPFSGDDGQISYISSC 302
            ++ +L + + + L C++   G G++  G  YV + G EYSA  +  + IGTGD+CI C I P+ ++     + C +PM      G ++Y S C
Sbjct:    3 SILLLTVILFSILSCSSDTNGRGFWRKGKQYVVLNGTEYSADLKASVNIGTGDKCIYCSITPSKSANQNSTFYCQDPMTTKTITGYVTYYSFC 95
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BLAST of SMED30016976 vs. Planmine SMEST
Match: SMESG000055805.1 (SMESG000055805.1)

HSP 1 Score: 58.5362 bits (140), Expect = 3.526e-12
Identity = 28/93 (30.11%), Postives = 46/93 (49.46%), Query Frame = 3 
Query:   42 LIFVMNPLLCNAFM------GTGYYTNGIPYVNIRGQEYSATTQKRIQIGTGDQCIVCYIYPAANSKSKPYYNCNEPMPFSGDDGQISYISSC 302
            +I  +  + C  F+      G GY+ +G P+V I   EY A     +++G GD C +C I P  ++ + P + C  P P +  DG+  Y+  C
Sbjct:    3 VIIALCAIFCTKFVHSSVSFGNGYFKDGKPFVKISETEYPADESLEVEVGEGDNCNLCSISPPTSTDTNPTFECQGPSP-AEIDGETIYLPVC 94
The following BLAST results are available for this feature:
BLAST of SMED30016976 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30016976 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30016976 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30016976 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30016976 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30016976 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30016976 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30016976 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30016976 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30016976 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30016976 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30016976 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30016976 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30016976 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000054106.13.448e-1748.00SMESG000054106.1[more]
SMESG000062897.11.479e-1443.84SMESG000062897.1[more]
SMESG000020860.11.227e-1334.78SMESG000020860.1[more]
SMESG000054105.12.664e-1332.26SMESG000054105.1[more]
SMESG000055805.13.526e-1230.11SMESG000055805.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016976 ID=SMED30016976|Name=SMED30016976|organism=Schmidtea mediterranea sexual|type=transcript|length=367bp
TGCATTCAGCTAAAAAAATGAAACCAAATGTATTTGTTTTGCTAATATTT
GTAATGAATCCCTTACTTTGCAACGCCTTTATGGGAACCGGCTATTATAC
GAATGGTATCCCGTATGTGAATATCCGGGGGCAGGAATATTCAGCAACCA
CTCAGAAAAGAATTCAAATTGGAACAGGAGACCAATGCATTGTTTGCTAT
ATTTATCCCGCGGCAAATTCAAAATCAAAACCCTATTACAATTGTAACGA
ACCGATGCCATTTTCTGGGGACGACGGTCAAATATCATACATTTCTTCCT
GTACATAATTCAGATTTGCAACTGTGATAACTTTGGTTCTTTCTCTAAAT
ATATTTTGGATTGTGTC
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protein sequence of SMED30016976-orf-1

>SMED30016976-orf-1 ID=SMED30016976-orf-1|Name=SMED30016976-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=102bp
HSAKKMKPNVFVLLIFVMNPLLCNAFMGTGYYTNGIPYVNIRGQEYSATT
QKRIQIGTGDQCIVCYIYPAANSKSKPYYNCNEPMPFSGDDGQISYISSC
T*
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InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..20
score: 0.904
NoneNo IPR availableTMHMMTMhelixcoord: 5..27