SMED30026973

Overview
NameSMED30026973
Smed IDSMED30026973
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



SMED30026973

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Category 3 cellSMED30026973SMESG000033974.1 dd_Smed_v4_34155_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
SMED30026973 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002443:44685..44995 +1555
Homology
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BLAST of SMED30026973 vs. Planmine SMEST
Match: SMESG000033974.1 (SMESG000033974.1)

HSP 1 Score: 208.379 bits (529), Expect = 1.626e-69
Identity = 103/103 (100.00%), Postives = 103/103 (100.00%), Query Frame = 3 
Query:    3 NSDLEIISPPRLMDFPQSAPIPFQFNISMENLSTDNATNAQIIISARSSPIREERHETSSGRSTPQIISVTEPPQVRNSINSTAGDTSRQNQTQFHRDLGKDT 311
            NSDLEIISPPRLMDFPQSAPIPFQFNISMENLSTDNATNAQIIISARSSPIREERHETSSGRSTPQIISVTEPPQVRNSINSTAGDTSRQNQTQFHRDLGKDT
Sbjct:  153 NSDLEIISPPRLMDFPQSAPIPFQFNISMENLSTDNATNAQIIISARSSPIREERHETSSGRSTPQIISVTEPPQVRNSINSTAGDTSRQNQTQFHRDLGKDT 255
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BLAST of SMED30026973 vs. Planmine SMEST
Match: SMESG000068983.1 (SMESG000068983.1)

HSP 1 Score: 114.775 bits (286), Expect = 2.840e-33
Identity = 60/90 (66.67%), Postives = 68/90 (75.56%), Query Frame = 3 
Query:    3 NSDLEIISPPRLMDFPQSAPIPFQFNISMENLSTDNATNAQIIISARSSPIREERHETSSGRSTPQIISVTEPPQVRNSINSTAGDTSRQ 272
            +SDLEII  PRL+ F Q  P+  QFNISMENL+T N  N  I IS RSSP+REE HE +SGRSTPQIISV EPPQVR S+NST  + SRQ
Sbjct:   96 DSDLEIIYAPRLVAFSQLDPVRSQFNISMENLTTGNPANVPITISTRSSPVREEGHEITSGRSTPQIISVIEPPQVRTSVNSTVENISRQ 185
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BLAST of SMED30026973 vs. Planmine SMEST
Match: SMESG000046397.1 (SMESG000046397.1)

HSP 1 Score: 103.99 bits (258), Expect = 3.176e-30
Identity = 57/88 (64.77%), Postives = 65/88 (73.86%), Query Frame = 3 
Query:    9 DLEIISPPRLMDFPQSAPIPFQFNISMENLSTDNATNAQIIISARSSPIREERHETSSGRSTPQIISVTEPPQVRNSINSTAGDTSRQ 272
            DLEII  PRLMDF Q AP P QFNISM+NLS D  TN QI+I    SP+REE HE SSGRSTPQIISVTEPP +RN  + T  + ++Q
Sbjct:    6 DLEIIYSPRLMDFSQPAPTPSQFNISMDNLSADTPTNVQIMI----SPVREEVHENSSGRSTPQIISVTEPP-IRNDFDLTVRNVAQQ 88
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BLAST of SMED30026973 vs. Planmine SMEST
Match: SMESG000056168.1 (SMESG000056168.1)

HSP 1 Score: 100.138 bits (248), Expect = 6.902e-26
Identity = 56/93 (60.22%), Postives = 61/93 (65.59%), Query Frame = 3 
Query:    3 NSDLEIISPPRLMDFPQSAPIPFQFNISMENLSTDNATNAQIIISARSSPIREERHETSSGRSTPQIISVTEPPQVRNSINSTAGDTSRQNQT 281
            NSDLEII  P L+DF Q AP   QFNI++ENL TDN  + QI I  RSSPIREERHE SS RST QIISV E PQ R  I+   G    Q  T
Sbjct:   71 NSDLEIIYGPLLVDFSQLAPTSSQFNIAIENLITDNPASVQITIFTRSSPIREERHEISSRRSTLQIISVIESPQKREVISFYIGQGGVQTGT 163
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BLAST of SMED30026973 vs. Planmine SMEST
Match: SMESG000056168.1 (SMESG000056168.1)

HSP 1 Score: 99.7525 bits (247), Expect = 9.897e-26
Identity = 56/93 (60.22%), Postives = 61/93 (65.59%), Query Frame = 3 
Query:    3 NSDLEIISPPRLMDFPQSAPIPFQFNISMENLSTDNATNAQIIISARSSPIREERHETSSGRSTPQIISVTEPPQVRNSINSTAGDTSRQNQT 281
            NSDLEII  P L+DF Q AP   QFNI++ENL TDN  + QI I  RSSPIREERHE SS RST QIISV E PQ R  I+   G    Q  T
Sbjct:   71 NSDLEIIYGPLLVDFSQLAPTSSQFNIAIENLITDNPASVQITIFTRSSPIREERHEISSRRSTLQIISVIESPQKREVISFYIGQGGVQTGT 163
The following BLAST results are available for this feature:
BLAST of SMED30026973 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 SMED30026973 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 SMED30026973 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 SMED30026973 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 SMED30026973 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 SMED30026973 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 SMED30026973 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 SMED30026973 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 SMED30026973 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 SMED30026973 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 SMED30026973 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 SMED30026973 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 SMED30026973 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 SMED30026973 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000033974.11.626e-69100.00SMESG000033974.1[more]
SMESG000068983.12.840e-3366.67SMESG000068983.1[more]
SMESG000046397.13.176e-3064.77SMESG000046397.1[more]
SMESG000056168.16.902e-2660.22SMESG000056168.1[more]
SMESG000056168.19.897e-2660.22SMESG000056168.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026973 ID=SMED30026973|Name=SMED30026973|organism=Schmidtea mediterranea sexual|type=transcript|length=311bp
CCAACTCCGATCTGGAGATAATCTCTCCTCCCAGATTGATGGATTTCCCC
CAGTCAGCTCCAATACCGTTTCAATTCAACATTTCTATGGAAAACCTATC
CACGGATAATGCAACTAATGCTCAAATAATTATATCTGCCAGATCATCTC
CCATCAGAGAGGAAAGACACGAAACATCCAGCGGAAGATCCACCCCGCAA
ATTATTTCAGTTACCGAGCCACCACAAGTCCGTAATAGCATCAACTCGAC
AGCTGGAGATACTTCTCGACAAAATCAAACCCAATTTCACAGAGACTTAG
GAAAAGATACG
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protein sequence of SMED30026973-orf-1

>SMED30026973-orf-1 ID=SMED30026973-orf-1|Name=SMED30026973-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=103bp
NSDLEIISPPRLMDFPQSAPIPFQFNISMENLSTDNATNAQIIISARSSP
IREERHETSSGRSTPQIISVTEPPQVRNSINSTAGDTSRQNQTQFHRDLG
KDT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000035Category 3 cell