SMED30000857

Overview
NameSMED30000857
Smed IDSMED30000857
Length (bp)314
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



SMED30000857

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
epidermisSMED30000857 dd_Smed_v4_21753_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30000857 dd_Smed_v4_21753_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
Homology
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BLAST of SMED30000857 vs. Planmine SMEST
Match: SMESG000002835.1 (SMESG000002835.1)

HSP 1 Score: 113.235 bits (282), Expect = 2.187e-30
Identity = 54/68 (79.41%), Postives = 58/68 (85.29%), Query Frame = -1 
Query:    9 AYSDSELRIRVPGNIRVEQLDIVPAHHLPNAEDQSNPTTNAPTLSVNLTQLPPPGTVENQANVSAPTA 212
            A+SD+ELRI VPGNIR EQLDIVPAHHLPN EDQSNPTT+A   S NLTQLPPPGTVE +AN S PTA
Sbjct: 1329 AFSDTELRIWVPGNIRAEQLDIVPAHHLPNIEDQSNPTTSAFPSSANLTQLPPPGTVETRANSSTPTA 1396
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BLAST of SMED30000857 vs. Planmine SMEST
Match: SMESG000054981.1 (SMESG000054981.1)

HSP 1 Score: 97.0561 bits (240), Expect = 4.364e-27
Identity = 51/70 (72.86%), Postives = 56/70 (80.00%), Query Frame = -1 
Query:  105 RQNISRLTQVRDELITESRAQRLLIREQSVALHQAYSDSELRIRVPGNIRVEQLDIVPAHHLPNAEDQSN 314
            RQ ISRL++  DELI ESRAQRLLIREQSVALHQAYSDSELRIRVPGN+R EQLD++    L  A   SN
Sbjct:   58 RQKISRLSRALDELIAESRAQRLLIREQSVALHQAYSDSELRIRVPGNLRAEQLDVLRGVVLVMALTCSN 127
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BLAST of SMED30000857 vs. Planmine SMEST
Match: SMESG000011446.1 (SMESG000011446.1)

HSP 1 Score: 91.6633 bits (226), Expect = 7.212e-25
Identity = 44/75 (58.67%), Postives = 58/75 (77.33%), Query Frame = -1 
Query:   90 RQNISRLTQVRDELITESRAQRLLIREQSVALHQAYSDSELRIRVPGNIRVEQLDIVPAHHLPNAEDQSNPTTNA 314
            RQ I+R+TQ RDELI ESR+QRLLIREQ+ AL +A++D E R  VPG++R  QL+++PAHHLP   D+  PT +A
Sbjct:   60 RQKIARITQARDELIAESRSQRLLIREQATALRRAFTDVEFRTHVPGSVRASQLNLIPAHHLPV--DEVPPTPSA 132
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BLAST of SMED30000857 vs. Planmine SMEST
Match: SMESG000020958.1 (SMESG000020958.1)

HSP 1 Score: 97.4413 bits (241), Expect = 7.878e-25
Identity = 46/72 (63.89%), Postives = 59/72 (81.94%), Query Frame = -1 
Query:   99 RQNISRLTQVRDELITESRAQRLLIREQSVALHQAYSDSELRIRVPGNIRVEQLDIVPAHHLPNAEDQSNPT 314
            R+ I RLT+ RDELITESRAQRLLI+EQS AL +A++D+EL+  VPG+IR  QLDI+PA+HLP A   S+P+
Sbjct:  956 RRKIERLTRARDELITESRAQRLLIKEQSTALRRAFTDTELQACVPGSIRASQLDIIPAYHLPTANVSSSPS 1027
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BLAST of SMED30000857 vs. Planmine SMEST
Match: SMESG000009535.1 (SMESG000009535.1)

HSP 1 Score: 95.9005 bits (237), Expect = 1.824e-24
Identity = 55/101 (54.46%), Postives = 70/101 (69.31%), Query Frame = -1 
Query:   36 RQNISRLTQVRDELITESRAQRLLIREQSVALHQAYSDSELRIRVPGNIRVEQLDIVPAHHLP-----NAEDQSNPTTN---APTLSVNLTQLPPPGTVEN 314
            RQ I RLT+ RDEL+TESR QRLLIREQS AL +A++D ELR  VPGN+R  QL+I+PAHH+P      +   SNP+T+   AP  +  ++Q PP G VE 
Sbjct:   92 RQKIERLTRARDELVTESRIQRLLIREQSTALRRAFTDIELRTLVPGNVRASQLEIIPAHHIPVMGILPSLPVSNPSTSEARAPAATPVVSQ-PPTGAVET 191
The following BLAST results are available for this feature:
BLAST of SMED30000857 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 SMED30000857 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 SMED30000857 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 SMED30000857 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 SMED30000857 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 SMED30000857 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 SMED30000857 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 SMED30000857 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 SMED30000857 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 SMED30000857 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 SMED30000857 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 SMED30000857 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 SMED30000857 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 SMED30000857 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000002835.12.187e-3079.41SMESG000002835.1[more]
SMESG000054981.14.364e-2772.86SMESG000054981.1[more]
SMESG000011446.17.212e-2558.67SMESG000011446.1[more]
SMESG000020958.17.878e-2563.89SMESG000020958.1[more]
SMESG000009535.11.824e-2454.46SMESG000009535.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000857 ID=SMED30000857|Name=SMED30000857|organism=Schmidtea mediterranea sexual|type=transcript|length=314bp
CGATGACGGGCCGTAGGGGCAGAAACATTAGCCTGGTTTTCCACAGTTCC
GGGAGGTGGTAACTGTGTGAGATTTACGCTCAATGTAGGAGCGTTTGTTG
TGGGGTTGGATTGGTCTTCAGCGTTGGGGAGATGGTGAGCCGGGACGATA
TCGAGCTGTTCTACGCGAATATTTCCCGGAACTCGGATTCGAAGTTCGGA
ATCCGAGTACGCCTGATGCAGTGCCACGGACTGTTCCCGAATTAGCAGAC
GTTGAGCGCGCGACTCGGTAATTAATTCGTCGCGCACTTGAGTAAGACGA
GAGATGTTCTGGCG
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protein sequence of SMED30000857-orf-1

>SMED30000857-orf-1 ID=SMED30000857-orf-1|Name=SMED30000857-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=104bp
RQNISRLTQVRDELITESRAQRLLIREQSVALHQAYSDSELRIRVPGNIR
VEQLDIVPAHHLPNAEDQSNPTTNAPTLSVNLTQLPPPGTVENQANVSAP
TARH
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002032epidermal cell