SMED30022646

Overview
NameSMED30022646
Smed IDSMED30022646
Length (bp)799
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




SMED30022646

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
nervous systemSMED30022646 dd_Smed_v4_12065_0_2dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30022646 dd_Smed_v4_12065_0_2dd_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
Homology
BLAST of SMED30022646 vs. Planmine SMEST
Match: SMESG000031752.1 (SMESG000031752.1)

HSP 1 Score: 123.635 bits (309), Expect = 1.372e-34
Identity = 62/111 (55.86%), Postives = 80/111 (72.07%), Query Frame = 1
Query:  331 ESGYSIFPVNGSSWNKFSIRHDEVELPYVAIKREPGRNSAREARQKAELKLAQLMEHQQQTQVQIVTAHHHLNQVNTDIAAGRIPSTDSYAPSYGISYKLDDQTLEEMEAP 663
            ++GYSI  V  S  +  S RHDEVEL YVA+KREP RN AREARQ+AE  L +L  H++QT  Q++ A   +++V  DIAAGRIPSTD +   YG+SY+LDD  L+EM+AP
Sbjct:   23 DAGYSISTVKESREHHLS-RHDEVELAYVAMKREPVRNLAREARQRAEFTLIRLEIHKRQTNWQVLVARRRMDRVKADIAAGRIPSTDGHTSEYGVSYELDDLALKEMDAP 132          
BLAST of SMED30022646 vs. Planmine SMEST
Match: SMESG000036641.1 (SMESG000036641.1)

HSP 1 Score: 126.331 bits (316), Expect = 1.616e-34
Identity = 64/111 (57.66%), Postives = 80/111 (72.07%), Query Frame = 1
Query:  331 ESGYSIFPVNGSSWNKFSIRHDEVELPYVAIKREPGRNSAREARQKAELKLAQLMEHQQQTQVQIVTAHHHLNQVNTDIAAGRIPSTDSYAPSYGISYKLDDQTLEEMEAP 663
            ++GYSI PV  S  ++    +DEVELPYVAIK+EPGRN AREARQ+AE  L  L  HQ+QT  Q+  A   L++VN DIAAG+IPSTD YAP  G+S++LDD  L EM+ P
Sbjct:    3 DAGYSISPVRESRESRH-FNNDEVELPYVAIKQEPGRNPAREARQRAESTLDCLEIHQKQTNWQVAMARQWLDKVNADIAAGKIPSTDGYAPECGVSFELDDPALMEMDTP 112          
BLAST of SMED30022646 vs. Planmine SMEST
Match: SMESG000008360.1 (SMESG000008360.1)

HSP 1 Score: 123.635 bits (309), Expect = 5.621e-34
Identity = 61/111 (54.95%), Postives = 79/111 (71.17%), Query Frame = 1
Query:  331 ESGYSIFPVNGSSWNKFSIRHDEVELPYVAIKREPGRNSAREARQKAELKLAQLMEHQQQTQVQIVTAHHHLNQVNTDIAAGRIPSTDSYAPSYGISYKLDDQTLEEMEAP 663
            ++G+SI PV  S   + +  + E +LPYVAIK+EPGRN ARE RQ+AE  LA+L  HQ+QT  Q+V A   L+++N +IAAGRIP TD YAPSYG+SY+LDD  L E   P
Sbjct:    3 DAGFSISPVRESREGRLN-DYKEADLPYVAIKKEPGRNPARETRQRAEFTLARLELHQRQTNSQVVMARRRLSRINAEIAAGRIPITDGYAPSYGVSYELDDPALVESTIP 112          
BLAST of SMED30022646 vs. Planmine SMEST
Match: SMESG000038777.1 (SMESG000038777.1)

HSP 1 Score: 118.627 bits (296), Expect = 3.408e-31
Identity = 56/90 (62.22%), Postives = 68/90 (75.56%), Query Frame = 1
Query:  391 HDEVELPYVAIKREPGRNSAREARQKAELKLAQLMEHQQQTQVQIVTAHHHLNQVNTDIAAGRIPSTDSYAPSYGISYKLDDQTLEEMEA 660
            HDE ELPY+AIKREPGRN A EARQ+ E  +A+L  HQ+QT  Q+  A   L++VN DIA GRIPSTD YAP+YG+SY+LDD  L EM+ 
Sbjct:   54 HDEGELPYMAIKREPGRNLALEARQRTEFTIARLEMHQKQTNWQVAMARRRLDRVNADIATGRIPSTDVYAPNYGVSYELDDPALVEMDT 143          
BLAST of SMED30022646 vs. Planmine SMEST
Match: SMESG000038895.1 (SMESG000038895.1)

HSP 1 Score: 113.62 bits (283), Expect = 4.111e-31
Identity = 60/111 (54.05%), Postives = 77/111 (69.37%), Query Frame = 1
Query:  331 ESGYSIFPVNGSSWNKFSIRHDEVELPYVAIKREPGRNSAREARQKAELKLAQLMEHQQQTQVQIVTAHHHLNQVNTDIAAGRIPSTDSYAPSYGISYKLDDQTLEEMEAP 663
            ++GYSI  V  S  ++ S R+DEVEL YVAIKREP RN   EA Q+AE  LA+L  HQ+QT  Q+    +  ++VN +IA GRIPSTD Y P Y +SY+L+D  LEEM+AP
Sbjct:    7 DAGYSISSVRESMDHRLS-RNDEVELSYVAIKREPWRNPVIEAGQRAEFTLARLDIHQRQTNWQVAMVRNRSDRVNAEIATGRIPSTDGYIPGYRVSYELNDPALEEMDAP 116          
The following BLAST results are available for this feature:
BLAST of SMED30022646 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 SMED30022646 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 SMED30022646 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 SMED30022646 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 SMED30022646 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 SMED30022646 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 SMED30022646 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 SMED30022646 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 SMED30022646 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 SMED30022646 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 SMED30022646 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 SMED30022646 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 SMED30022646 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 SMED30022646 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000031752.11.372e-3455.86SMESG000031752.1[more]
SMESG000036641.11.616e-3457.66SMESG000036641.1[more]
SMESG000008360.15.621e-3454.95SMESG000008360.1[more]
SMESG000038777.13.408e-3162.22SMESG000038777.1[more]
SMESG000038895.14.111e-3154.05SMESG000038895.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022646 ID=SMED30022646|Name=SMED30022646|organism=Schmidtea mediterranea sexual|type=transcript|length=799bp
GTCTATAAACGATGTGACGAATCAAAACAAAGAGATCCTACAAGGAGATA
TGCTATTGAGATAGGCTTACTCAGAGATAATAAATGTCAAACAGGAGTTG
AATGATTACATGAAATAAAGTTATGAGTTTCAATTCATAATAATCGTAGA
AATAAACAGGATTAGTAAAACAAAAATTAATGAATTAATAATGCTCTATA
ATATTTTAATTTACCTACCCCAATGTTTAGCAGGCAGTACGTCACCCATG
GACGGATTTTGGGACTATGACACCCGAATTACGATTCGATTTACAGACTG
GTCAGCCACCCGATGTCGACAAGCGATGTGGAATCCGGATACTCGATATT
CCCAGTAAACGGATCGAGCTGGAACAAATTCTCTATCCGCCACGATGAGG
TCGAGCTACCTTATGTCGCGATTAAACGCGAACCAGGTCGAAACTCTGCG
CGAGAAGCTCGGCAGAAGGCTGAGTTAAAATTGGCCCAACTGATGGAACA
TCAACAACAAACGCAAGTGCAGATAGTTACGGCTCACCATCACTTAAACC
AAGTCAATACGGACATAGCCGCAGGCCGGATCCCAAGTACCGATAGCTAC
GCACCAAGCTACGGGATATCCTACAAGTTGGATGACCAAACCCTAGAAGA
AATGGAAGCGCCTGATTCGAACAACCGCGCTAGACCGTATCGGAGTGCCG
CACCACAACGAGGGGCACGCGTACGTCAGTTACAAGCCGAAGAAAAACTC
GATATTACGATTTTATGATGGTCAGCGAAGATATGGCCCCCCATGAGAA
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protein sequence of SMED30022646-orf-1

>SMED30022646-orf-1 ID=SMED30022646-orf-1|Name=SMED30022646-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=152bp
MSTSDVESGYSIFPVNGSSWNKFSIRHDEVELPYVAIKREPGRNSAREAR
QKAELKLAQLMEHQQQTQVQIVTAHHHLNQVNTDIAAGRIPSTDSYAPSY
GISYKLDDQTLEEMEAPDSNNRARPYRSAAPQRGARVRQLQAEEKLDITI
L*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron