SMED30002879

Overview
NameSMED30002879
Smed IDSMED30002879
Length (bp)836
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



SMED30002879

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
X1 cellSMED30002879SMESG000008184.1 SmedASXL_009826SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
reproductive organSMED30002879 Contig22799newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30002879 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000256:56813..57749 -4102
Homology
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BLAST of SMED30002879 vs. Planmine SMEST
Match: SMESG000008184.1 (SMESG000008184.1)

HSP 1 Score: 179.489 bits (454), Expect = 1.627e-53
Identity = 109/129 (84.50%), Postives = 110/129 (85.27%), Query Frame = 2 
Query:  161 LVMELSKPQLIQLMGTIACQLAGSTNNHVENTETFAXXXXXXXXXXXXXXIPNSSQSFSNLYRKTDDSNSKSCRSNVNSMRQLNSTTKEIINRQCGKHHSLINENEMLQMHSDFFMPRIFNEINENVAS 547
            LVMELSKPQLIQLMGTIACQLAGSTNNHVENTETFAESLELDTSLSELQEIPNSS SFSNLYRKTDDS SKSCRSNVNSMRQLNSTTKEIINRQC                 DFFMPRIFNEINENVA+
Sbjct:   25 LVMELSKPQLIQLMGTIACQLAGSTNNHVENTETFAESLELDTSLSELQEIPNSSPSFSNLYRKTDDSKSKSCRSNVNSMRQLNSTTKEIINRQC-----------------DFFMPRIFNEINENVAT 136
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BLAST of SMED30002879 vs. Planmine SMEST
Match: SMESG000008184.1 (SMESG000008184.1)

HSP 1 Score: 175.252 bits (443), Expect = 3.519e-52
Identity = 107/127 (84.25%), Postives = 108/127 (85.04%), Query Frame = 2 
Query:  167 MELSKPQLIQLMGTIACQLAGSTNNHVENTETFAXXXXXXXXXXXXXXIPNSSQSFSNLYRKTDDSNSKSCRSNVNSMRQLNSTTKEIINRQCGKHHSLINENEMLQMHSDFFMPRIFNEINENVAS 547
            MELSKPQLIQLMGTIACQLAGSTNNHVENTETFAESLELDTSLSELQEIPNSS SFSNLYRKTDDS SKSCRSNVNSMRQLNSTTKEIINRQC                 DFFMPRIFNEINENVA+
Sbjct:    1 MELSKPQLIQLMGTIACQLAGSTNNHVENTETFAESLELDTSLSELQEIPNSSPSFSNLYRKTDDSKSKSCRSNVNSMRQLNSTTKEIINRQC-----------------DFFMPRIFNEINENVAT 110
[Close]
BLAST of SMED30002879 vs. Planmine SMEST
Match: SMESG000008184.1 (SMESG000008184.1)

HSP 1 Score: 155.606 bits (392), Expect = 1.026e-45
Identity = 93/96 (96.88%), Postives = 93/96 (96.88%), Query Frame = 2 
Query:  161 LVMELSKPQLIQLMGTIACQLAGSTNNHVENTETFAXXXXXXXXXXXXXXIPNSSQSFSNLYRKTDDSNSKSCRSNVNSMRQLNSTTKEIINRQCG 448
            LVMELSKPQLIQLMGTIACQLAGSTNNHVENTETFAESLELDTSLSELQEIPNSS SFSNLYRKTDDS SKSCRSNVNSMRQLNSTTKEIINRQC 
Sbjct:   25 LVMELSKPQLIQLMGTIACQLAGSTNNHVENTETFAESLELDTSLSELQEIPNSSPSFSNLYRKTDDSKSKSCRSNVNSMRQLNSTTKEIINRQCA 120

HSP 2 Score: 46.595 bits (109), Expect = 1.026e-45
Identity = 23/23 (100.00%), Postives = 23/23 (100.00%), Query Frame = 3 
Query:   90 MENNTKKAKKIQLSRKNIFDLSK 158
            MENNTKKAKKIQLSRKNIFDLSK
Sbjct:    1 MENNTKKAKKIQLSRKNIFDLSK 23
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BLAST of SMED30002879 vs. Planmine SMEST
Match: SMESG000008184.1 (SMESG000008184.1)

HSP 1 Score: 151.369 bits (381), Expect = 3.132e-43
Identity = 91/94 (96.81%), Postives = 91/94 (96.81%), Query Frame = 2 
Query:  167 MELSKPQLIQLMGTIACQLAGSTNNHVENTETFAXXXXXXXXXXXXXXIPNSSQSFSNLYRKTDDSNSKSCRSNVNSMRQLNSTTKEIINRQCG 448
            MELSKPQLIQLMGTIACQLAGSTNNHVENTETFAESLELDTSLSELQEIPNSS SFSNLYRKTDDS SKSCRSNVNSMRQLNSTTKEIINRQC 
Sbjct:    1 MELSKPQLIQLMGTIACQLAGSTNNHVENTETFAESLELDTSLSELQEIPNSSPSFSNLYRKTDDSKSKSCRSNVNSMRQLNSTTKEIINRQCA 94
The following BLAST results are available for this feature:
BLAST of SMED30002879 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 SMED30002879 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 SMED30002879 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 SMED30002879 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 SMED30002879 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 SMED30002879 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 SMED30002879 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 SMED30002879 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 SMED30002879 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 SMED30002879 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 SMED30002879 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 SMED30002879 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 SMED30002879 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 SMED30002879 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000008184.11.627e-5384.50SMESG000008184.1[more]
SMESG000008184.13.519e-5284.25SMESG000008184.1[more]
SMESG000008184.11.026e-4596.88SMESG000008184.1[more]
SMESG000008184.13.132e-4396.81SMESG000008184.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002879 ID=SMED30002879|Name=SMED30002879|organism=Schmidtea mediterranea sexual|type=transcript|length=836bp
TTTAAACGTTGTCATGATTATCAATATTATTTTAAATTGAATATTTGTGT
AATAATTTCTGCTTTTGTTAAACTTATTAGATTTTCTAAATGGAAAACAA
TACGAAAAAAGCAAAAAAAATACAATTATCAAGAAAAAACATTTTCGATT
TAAGTAAAAGTTAGTAATGGAATTATCTAAGCCTCAATTAATTCAATTAA
TGGGGACTATCGCTTGCCAACTGGCGGGAAGCACTAATAATCACGTGGAA
AACACTGAAACCTTTGCAGAATCGTTAGAATTAGACACTAGTTTATCGGA
ATTGCAAGAGATTCCCAACAGTAGCCAGAGTTTTTCGAATTTGTACAGGA
AAACTGATGATTCTAACTCGAAATCCTGCCGATCGAATGTCAATTCAATG
AGACAGTTGAACAGTACAACGAAGGAAATAATAAATCGCCAATGCGGTAA
ACATCACAGTTTGATAAATGAAAATGAAATGTTACAAATGCATTCAGATT
TTTTTATGCCTCGAATTTTTAATGAAATTAATGAAAACGTTGCAAGTGAA
AATTTTATAATTCAGTTAATTTTTACATTTGATAATTATTAATACTTTCG
AATGAAACTCTCGGACAAATTCACAAAATGAATGAATATTTGAGTAGAGT
TGGATCACTGTTACGCAAGGTCACCTGAAATCAGCTTCAAGGTTTAGATA
GATAGGGTCAGTTGAAACCTTGTAGGGTTCTGGGGAAATTAAAAGCGTAT
TAGTAGCTGTGCGCATAACTAATGCTATATCCATGTGGCACACACACACT
GATGAGCAGTGTGTAATCAATCACATTAAATTGCAC
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protein sequence of SMED30002879-orf-1

>SMED30002879-orf-1 ID=SMED30002879-orf-1|Name=SMED30002879-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=142bp
MELSKPQLIQLMGTIACQLAGSTNNHVENTETFAESLELDTSLSELQEIP
NSSQSFSNLYRKTDDSNSKSCRSNVNSMRQLNSTTKEIINRQCGKHHSLI
NENEMLQMHSDFFMPRIFNEINENVASENFIIQLIFTFDNY*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ
PLANA:0002109X1 cell