SMED30007732

Overview
NameSMED30007732
Smed IDSMED30007732
Length (bp)311
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




SMED30007732

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30007732SMESG000032777.1 Contig922newmark_estsPMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30007732SMESG000032777.1 Contig922uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012
FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30007732 vs. Planmine SMEST
Match: SMESG000008880.1 (SMESG000008880.1)

HSP 1 Score: 143.665 bits (361), Expect = 2.936e-44
Identity = 72/99 (72.73%), Postives = 86/99 (86.87%), Query Frame = -3
Query:   13 EQVEMVDPPPAYEEVEFPALDPDVIYAPVSPFFHRASASQINLNMAENEQPSQIRISTMLNLTAIEKGILDKQTSPDIQPRIELANSSRTEPNQVAITP 309
            EQ+E++D PPAYEEVE P LDPDVIYA VSPFFHR S++QINLNM E++QPSQIRISTMLNLT IE GIL ++ SP+IQPRI+ ANS++ EP+QVA TP
Sbjct:  127 EQMEIIDLPPAYEEVELPLLDPDVIYALVSPFFHRPSSAQINLNMVESKQPSQIRISTMLNLTLIEIGILSERASPNIQPRIKPANSTQAEPSQVAPTP 225          
BLAST of SMED30007732 vs. Planmine SMEST
Match: SMESG000076770.1 (SMESG000076770.1)

HSP 1 Score: 131.724 bits (330), Expect = 2.854e-39
Identity = 66/100 (66.00%), Postives = 81/100 (81.00%), Query Frame = -3
Query:   13 EQVEMVDPPPAYEEVEFPALDPDVIYAPVSPFFHRASASQINLNMAENEQPSQIRISTMLNLTAIEKGIL-DKQTSPDIQPRIELANSSRTEPNQVAITP 309
            EQ E+VDPPPAYEEVE  ALDPDV+Y P SPFFHR+SA QI+LN  +N+  ++IRISTML+LT+IE GIL ++ T+PD QPR+E ANSSR EP+Q   TP
Sbjct:  144 EQPEIVDPPPAYEEVELSALDPDVVYPPSSPFFHRSSAVQIDLNAVKNDPSNRIRISTMLDLTSIEIGILGERTTTPDSQPRVETANSSRVEPSQATTTP 243          
BLAST of SMED30007732 vs. Planmine SMEST
Match: SMESG000035723.1 (SMESG000035723.1)

HSP 1 Score: 129.413 bits (324), Expect = 9.245e-39
Identity = 67/96 (69.79%), Postives = 78/96 (81.25%), Query Frame = -3
Query:   22 EQVEMVDPPPAYEEVEFPALDPDVIYAPVSPFFHRASASQINLNMAENEQPSQIRISTMLNLTAIEKGILDKQTSPDIQPRIELANSSRTEPNQVA 309
            EQ+EMVD PPAYEEV+  + DPDVIYAPVSPFFHR S+SQINLNM ++EQPSQIRISTMLNLT IE GIL ++T+P IQ  IE A SS+   +Q A
Sbjct:  108 EQMEMVDLPPAYEEVKLHSRDPDVIYAPVSPFFHRPSSSQINLNMVDSEQPSQIRISTMLNLTPIEIGILSERTAPIIQSTIEPATSSQEGSSQSA 203          
BLAST of SMED30007732 vs. Planmine SMEST
Match: SMESG000052982.1 (SMESG000052982.1)

HSP 1 Score: 108.227 bits (269), Expect = 2.926e-31
Identity = 54/77 (70.13%), Postives = 61/77 (79.22%), Query Frame = -3
Query:   79 EQVEMVDPPPAYEEVEFPALDPDVIYAPVSPFFHRASASQINLNMAENEQPSQIRISTMLNLTAIEKGILDKQTSPD 309
            +Q E+VDPPPAYEEVE  ALDPDVIYAP SPFFHR SA  I+LN AE++   +IRISTMLNLT IE GIL + TS D
Sbjct:   67 DQAEIVDPPPAYEEVELSALDPDVIYAPSSPFFHRPSAVHIDLNTAEHDPSKRIRISTMLNLTPIEIGILSELTSTD 143          
BLAST of SMED30007732 vs. Planmine SMEST
Match: SMESG000053105.1 (SMESG000053105.1)

HSP 1 Score: 97.8265 bits (242), Expect = 2.417e-27
Identity = 55/99 (55.56%), Postives = 66/99 (66.67%), Query Frame = -3
Query:   13 EQVEMVDPPPAYEEVEFPALDPDVIYAPVSPFFHRASASQINLNMAENEQPSQIRISTMLNLTAIEKGILDKQTSPDIQPRIELANSSRTEPNQVAITP 309
            E +E+VD PPAYEEVE  + +PDVIYAP  PFF   +++ INLN+ ENEQ  QIRISTMLNLT IE GI  ++ SP   P I    SS+  P QV   P
Sbjct:   48 EPMEIVDLPPAYEEVEQYSFEPDVIYAPALPFFQPPTSTHINLNVEENEQVDQIRISTMLNLTPIEIGIFRERASPSTHPTIGPETSSQEGPIQVTPAP 146          
The following BLAST results are available for this feature:
BLAST of SMED30007732 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 SMED30007732 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 SMED30007732 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 SMED30007732 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 SMED30007732 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 SMED30007732 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 SMED30007732 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 SMED30007732 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 SMED30007732 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 SMED30007732 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 SMED30007732 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 SMED30007732 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 SMED30007732 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 SMED30007732 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000008880.12.936e-4472.73SMESG000008880.1[more]
SMESG000076770.12.854e-3966.00SMESG000076770.1[more]
SMESG000035723.19.245e-3969.79SMESG000035723.1[more]
SMESG000052982.12.926e-3170.13SMESG000052982.1[more]
SMESG000053105.12.417e-2755.56SMESG000053105.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007732 ID=SMED30007732|Name=SMED30007732|organism=Schmidtea mediterranea sexual|type=transcript|length=311bp
AACGGGGGGGGGCGGAGTTATCGCCACTTGGTTCGGTTCCGTTCGAGACG
AATTGGCCAATTCGATCCTAGGTTGGATATCCGGGGAGGTCTGTTTGTCT
AGGATACCTTTTTCGATAGCGGTGAGGTTGAGCATCGTGGAGATGCGGAT
TTGGCTGGGTTGTTCATTTTCTGCCATGTTTAGGTTTATTTGGGAAGCGG
ACGCGCGGTGAAAGAACGGCGATACCGGAGCATAAATCACATCTGGGTCC
AATGCAGGGAACTCCACTTCCTCGTAAGCTGGAGGTGGGTCGACCATTTC
CACTTGTTCTA
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protein sequence of SMED30007732-orf-1

>SMED30007732-orf-1 ID=SMED30007732-orf-1|Name=SMED30007732-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=103bp
EQVEMVDPPPAYEEVEFPALDPDVIYAPVSPFFHRASASQINLNMAENEQ
PSQIRISTMLNLTAIEKGILDKQTSPDIQPRIELANSSRTEPNQVAITPP
PPV
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte