SMED30015759

Overview
NameSMED30015759
Smed IDSMED30015759
Length (bp)329
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



SMED30015759

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
oocyteSMED30015759SMESG000037481.1 Contig43493newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30015759SMESG000037481.1 Contig43493uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30015759SMESG000037481.1 Contig43493newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30015759SMESG000037481.1 Contig43493uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30015759 vs. Planmine SMEST
Match: SMESG000005270.1 (SMESG000005270.1)

HSP 1 Score: 72.4034 bits (176), Expect = 5.928e-16
Identity = 49/97 (50.52%), Postives = 64/97 (65.98%), Query Frame = -3 
Query:   31 YEGVNVLVQKARIIETVQRDRFNSAIDAVEIQE--IEKEKITSNDKDDNILWDEMKQLYLYYVKNXXXXXXXXSHNQP-SDRFNSPRGRSN-NLINL 309
            Y  +N LVQKA+ +E +QRDRFN++IDAVEIQ+  I K K+   +KD ++ W+EMKQLYL +VKNRR+       N P S R  SP  R   N +NL
Sbjct:  127 YRDLNELVQKAKRVEAIQRDRFNASIDAVEIQKPTIAKPKL---EKDYDVPWEEMKQLYLNFVKNRRK-------NSPNSSRSQSPENRKRFNALNL 213
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BLAST of SMED30015759 vs. Planmine SMEST
Match: SMESG000026061.1 (SMESG000026061.1)

HSP 1 Score: 68.5514 bits (166), Expect = 1.309e-14
Identity = 35/65 (53.85%), Postives = 48/65 (73.85%), Query Frame = -3 
Query:  121 YEGVNVLVQKARIIETVQRDRFNSAIDAVEIQE--IEKEKITSNDKDDNILWDEMKQLYLYYVKN 309
            Y  +N LV KA+ +E +QRDRFN++IDAVEIQ   + K K+   + DD++ W+EMKQLYL +VKN
Sbjct: 1565 YRDLNELVHKAKRVEAIQRDRFNASIDAVEIQRPTMAKPKL---ENDDDVPWEEMKQLYLNFVKN 1626
The following BLAST results are available for this feature:
BLAST of SMED30015759 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 SMED30015759 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 SMED30015759 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 SMED30015759 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 SMED30015759 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 SMED30015759 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 SMED30015759 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 SMED30015759 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 SMED30015759 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 SMED30015759 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 SMED30015759 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 SMED30015759 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 SMED30015759 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 SMED30015759 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000005270.15.928e-1650.52SMESG000005270.1[more]
SMESG000026061.11.309e-1453.85SMESG000026061.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015759 ID=SMED30015759|Name=SMED30015759|organism=Schmidtea mediterranea sexual|type=transcript|length=329bp
TTTCAAAATAAGTCTTTCTATCATTTTGATTAAATTGATTAGATTATTCG
ATCTACCTCTTGGGCTATTAAATCTATCAGATGGCTGATTATGACTCGGA
CTTGGACTAGATCTTCTTCTATTCTTAACATAATATAAATACAATTGTTT
CATTTCATCCCAAAGAATATTATCATCTTTATCGTTTGATGTAATTTTTT
CCTTTTCAATTTCCTGAATCTCTACTGCATCAATTGCGGAATTAAATCTA
TCTCTTTGTACTGTTTCAATTATTCGAGCTTTTTGTACTAATACGTTTAC
ACCTTCGTATACACTAGAGCCTCGAGTTG
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protein sequence of SMED30015759-orf-1

>SMED30015759-orf-1 ID=SMED30015759-orf-1|Name=SMED30015759-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=109bp
TRGSSVYEGVNVLVQKARIIETVQRDRFNSAIDAVEIQEIEKEKITSNDK
DDNILWDEMKQLYLYYVKNRRRSSPSPSHNQPSDRFNSPRGRSNNLINLI
KMIERLILK
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland