SMED30022827

Overview
NameSMED30022827
Smed IDSMED30022827
Length (bp)308
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



SMED30022827

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
epidermisSMED30022827 dd_Smed_v4_2335_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30022827 dd_Smed_v4_2335_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30022827 dd_Smed_v4_2335_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30022827 dd_Smed_v4_2335_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30022827 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000082:128854..129161 +1513
Homology
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BLAST of SMED30022827 vs. Planmine SMEST
Match: SMESG000020775.1 (SMESG000020775.1)

HSP 1 Score: 149.443 bits (376), Expect = 1.830e-45
Identity = 76/102 (74.51%), Postives = 84/102 (82.35%), Query Frame = -3 
Query:    1 EVNDPPQAYEEFEFPEIDPSVVYAPTVTFYPPSPPIYINLEQDENEAQILNRYLEQMNLAPDEIAVLSERVPTSTIPTFKPETSAQEGQNLTVPSPLHRQPK 306
            EVND P AYEEFEFP++DP VVYAP VTFYPP P IYI+LE+DENEA ILN  LEQ++LAPDEIAVLS RVPTS   T +PETS QEGQN T+ SPLH QPK
Sbjct:  153 EVNDLPPAYEEFEFPDLDPDVVYAPAVTFYPPPPSIYIDLEEDENEAPILNHSLEQLDLAPDEIAVLSGRVPTSLTQTNEPETSTQEGQNPTISSPLHLQPK 254
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BLAST of SMED30022827 vs. Planmine SMEST
Match: SMESG000055981.1 (SMESG000055981.1)

HSP 1 Score: 141.739 bits (356), Expect = 5.326e-43
Identity = 73/102 (71.57%), Postives = 82/102 (80.39%), Query Frame = -3 
Query:    1 EVNDPPQAYEEFEFPEIDPSVVYAPTVTFYPPSPPIYINLEQDENEAQILNRYLEQMNLAPDEIAVLSERVPTSTIPTFKPETSAQEGQNLTVPSPLHRQPK 306
            E  DPP AYEEFEFP+IDP VVYAPTVTFYP  P IYI+L +DE EA IL+  LEQ++L PDEI VLSERVP STIPT +P T  Q GQNLT+PSPLHRQP+
Sbjct:  164 ESTDPPPAYEEFEFPDIDPDVVYAPTVTFYPQPPSIYIDLGEDEYEAPILDHALEQLDLTPDEIDVLSERVPISTIPTTEPGTLFQGGQNLTIPSPLHRQPE 265
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BLAST of SMED30022827 vs. Planmine SMEST
Match: SMESG000056201.1 (SMESG000056201.1)

HSP 1 Score: 110.923 bits (276), Expect = 2.461e-32
Identity = 59/100 (59.00%), Postives = 69/100 (69.00%), Query Frame = -3 
Query:    1 NDPPQAYEEFEFPEIDPSVVYAPTVTFYPPSPPIYINLEQDENEAQILNRYLEQMNLAPDEIAVLSERVPTSTIPTFKPETSAQEGQNLTVPSPLHRQPK 300
            NDPP  YEEFEFPE+DP VVYAP +T Y P P IYI+  ++   A +LN  LEQ+ L  DEIAVLS+RVPT+  P   PETS Q  Q  T  SPL+RQPK
Sbjct:   27 NDPPLVYEEFEFPELDPDVVYAPAITVYQPPPSIYIDFVEELKNAPVLNHSLEQLKLKLDEIAVLSDRVPTNPAPINVPETSTQVRQTSTTTSPLYRQPK 126
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BLAST of SMED30022827 vs. Planmine SMEST
Match: SMESG000074438.1 (SMESG000074438.1)

HSP 1 Score: 104.375 bits (259), Expect = 5.342e-29
Identity = 64/102 (62.75%), Postives = 75/102 (73.53%), Query Frame = -3 
Query:    1 EVNDPPQAYEEFEFPEIDPSVVYAPTVTFYPPSPPIYINLEQDENEAQILNRYLEQMNLAPDEIAVLSERVPTSTIPTFKPETSAQEGQNLTVPSPLHRQPK 306
            EV DPP  Y EFEFP++DP +      TFYPP P IYI+LE++ENE   LNR LEQ++L PDEIAVLS RVP S IPT +P TS+QE QNLT P P+HR PK
Sbjct:  127 EVADPPPDYAEFEFPDLDPDL------TFYPPPPSIYIDLEEEENEPPNLNRNLEQIDLTPDEIAVLSGRVPFSNIPTIEPTTSSQERQNLTTPFPIHRHPK 222
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BLAST of SMED30022827 vs. Planmine SMEST
Match: SMESG000038618.1 (SMESG000038618.1)

HSP 1 Score: 103.605 bits (257), Expect = 3.135e-28
Identity = 56/102 (54.90%), Postives = 70/102 (68.63%), Query Frame = -3 
Query:    1 EVNDPPQAYEEFEFPEIDPSVVYAPTVTFYPPSPPIYINLEQDENEAQILNRYLEQMNLAPDEIAVLSERVPTSTIPTFKPETSAQEGQNLTVPSPLHRQPK 306
            EVNDPP AY EFEFPE+DP +VYAP+   YP  PPIYI+LE DE E   +N  LE++ L PD+IA+LS +VP++     +P TS QE  + TV    HRQPK
Sbjct:  173 EVNDPPFAYTEFEFPEMDPEIVYAPSSIIYPLPPPIYIDLEADEPETPNVNLILERLRLTPDKIALLSGQVPSNAYSAIEPSTSMQEDPSPTVSISNHRQPK 274
The following BLAST results are available for this feature:
BLAST of SMED30022827 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 SMED30022827 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 SMED30022827 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 SMED30022827 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 SMED30022827 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 SMED30022827 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 SMED30022827 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 SMED30022827 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 SMED30022827 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 SMED30022827 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 SMED30022827 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 SMED30022827 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 SMED30022827 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 SMED30022827 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000020775.11.830e-4574.51SMESG000020775.1[more]
SMESG000055981.15.326e-4371.57SMESG000055981.1[more]
SMESG000056201.12.461e-3259.00SMESG000056201.1[more]
SMESG000074438.15.342e-2962.75SMESG000074438.1[more]
SMESG000038618.13.135e-2854.90SMESG000038618.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30022827 ID=SMED30022827|Name=SMED30022827|organism=Schmidtea mediterranea sexual|type=transcript|length=308bp
CTTCGGTTGGCGGTGAAGAGGAGATGGGACTGTTAGATTTTGTCCCTCCT
GAGCTGAGGTTTCCGGTTTGAATGTTGGGATAGTGCTGGTTGGTACGCGT
TCACTTAGGACGGCTATCTCGTCTGGGGCGAGGTTCATTTGTTCCAAATA
GCGATTCAGGATTTGGGCTTCGTTTTCATCCTGCTCCAAATTGATGTATA
TAGGCGGGGACGGGGGATAAAACGTTACTGTCGGCGCATAGACTACGCTT
GGGTCTATTTCCGGGAACTCAAATTCCTCGTAGGCCTGGGGCGGGTCATT
CACTTCGA
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protein sequence of SMED30022827-orf-1

>SMED30022827-orf-1 ID=SMED30022827-orf-1|Name=SMED30022827-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=102bp
EVNDPPQAYEEFEFPEIDPSVVYAPTVTFYPPSPPIYINLEQDENEAQIL
NRYLEQMNLAPDEIAVLSERVPTSTIPTFKPETSAQEGQNLTVPSPLHRQ
PK
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0002032epidermal cell