Zinc finger MYM-type protein 5

Overview
NameZinc finger MYM-type protein 5
Smed IDSMED30023872
Length (bp)1211
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

 

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



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of Zinc finger MYM-type protein 5 (SMED30023872) t-SNE clustered cells

Violin plots show distribution of expression levels for Zinc finger MYM-type protein 5 (SMED30023872) in cells (dots) of each of the 12 neoblast clusters.

 

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Sub-lethal Irradiated Surviving X1 and X2 Cell Population

 

t-SNE plot of surviving X1 and X2 cells (n = 1,039 after QC filter) after sub-lethal irradiation. Colors indicate unbiased cell classification via graph-based clustering. SL, sub-lethal irradiated cell groups.

Expression of Zinc finger MYM-type protein 5 (SMED30023872) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Zinc finger MYM-type protein 5 (SMED30023872) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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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



SMED30023872

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30023872h1SMcG0004194 dd_Smed_v4_11239_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30023872h1SMcG0004194 dd_Smed_v4_11239_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30023872h1SMcG0004194 dd_Smed_v4_11239_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
parenchymal cellSMED30023872h1SMcG0004194 dd_Smed_v4_11239_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30023872h1SMcG0004194 dd_Smed_v4_11239_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30023872h1SMcG0004194 dd_Smed_v4_11239_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior sideSMED30023872h1SMcG0004194 dd_Smed_v4_11239_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30023872h1SMcG0004194 dd_Smed_v4_11239_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 Zinc finger MYM-type protein 5 vs. TrEMBL
Match: A0A3B3C8M6 (Uncharacterized protein OS=Oryzias melastigma OX=30732 PE=4 SV=1)

HSP 1 Score: 61.6178 bits (148), Expect = 2.259e-6
Identity = 28/56 (50.00%), Postives = 41/56 (73.21%), Query Frame = 3 
Query:  675 YHFPRMKKVENISCFH--FYRRMSNGDKIKRTCLVYFSTKDTVFCFCCQIFSQNKF 836
            ++FP  K  +  SC H  F+R++SNG++IKRT L+Y   KD++FCFCC++FSQ  F
Sbjct:  177 FNFP--KNQDGRSCHHHYFFRKLSNGERIKRTWLMYSPKKDSLFCFCCKLFSQKSF 230
[Close]
BLAST of Zinc finger MYM-type protein 5 vs. TrEMBL
Match: A0A3S2PND3 (Uncharacterized protein OS=Oryzias javanicus OX=123683 GN=OJAV_G00051350 PE=4 SV=1)

HSP 1 Score: 59.6918 bits (143), Expect = 8.731e-6
Identity = 26/56 (46.43%), Postives = 41/56 (73.21%), Query Frame = 3 
Query:  675 YHFPRMKKVENISCFH--FYRRMSNGDKIKRTCLVYFSTKDTVFCFCCQIFSQNKF 836
            ++FP  K  +  SC H  F+R+++NG++IKRT L+Y   +D++FCFCC++FSQ  F
Sbjct:  176 FNFP--KNQDGRSCHHHYFFRKLANGERIKRTWLMYSPKRDSLFCFCCKLFSQKSF 229
The following BLAST results are available for this feature:
BLAST of Zinc finger MYM-type protein 5 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 Zinc finger MYM-type protein 5 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 Zinc finger MYM-type protein 5 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 Zinc finger MYM-type protein 5 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 Zinc finger MYM-type protein 5 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 Zinc finger MYM-type protein 5 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 Zinc finger MYM-type protein 5 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 Zinc finger MYM-type protein 5 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
A0A3B3C8M62.259e-650.00Uncharacterized protein OS=Oryzias melastigma OX=3... [more]
A0A3S2PND38.731e-646.43Uncharacterized protein OS=Oryzias javanicus OX=12... [more]
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BLAST of Zinc finger MYM-type protein 5 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 Zinc finger MYM-type protein 5 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 Zinc finger MYM-type protein 5 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 Zinc finger MYM-type protein 5 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 Zinc finger MYM-type protein 5 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 Zinc finger MYM-type protein 5 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023872 ID=SMED30023872|Name=Zinc finger MYM-type protein 5|organism=Schmidtea mediterranea sexual|type=transcript|length=1211bp
TCCATATTGAATTTTTAAATAAAGTGTAGTTCGCTGGTGGCTTATATTGG
GTTGAATGTGTTAATATATGATTTTTAGTATATTACATTTAAAAATAGGT
CTCGAATGTAAAAGATTGGAATTTCTAATTACACCAGCTTACTTTTTTCT
AAAACATCTTTGCGGGACCTCAAGGAAGAAAATTTAATGAATTTGTTTAA
GTTAAACCGATACAATATGATGGATACGAATAAGGGACAACGCTGTCCGG
ATCACAAAAGAGAATCAGAAGAATTCTTTGTTACAGTTTTTGAGAAGTTC
GTCAAGCGGTACAGCACGAGTATCTATAGTAGCTTCAAATCAAAGTGAAA
AAGAAATTGAAATCGATCTGCGGCGGAGAAATAAAGTGTGCCGACAATGT
TATTGAATATAACGATTCAGATTCTGACTACGAAAGTATTGCTAAAGAAC
CACGAAATTTAAATGAAGTAGAATATATTTCTAATTTAAGTGAAGTTGTT
TCACAGAACATCAATGATATAGGATAAAAGGAAAAAATGAAGGTCAAAGT
GATCAAGACCCCAAAAACAATAAAAATCTGCCTCTTAATCTTAATAATCC
GGCAAACTGGCCTATAATAGATGGTAAATTTAAAGCATTGTTGGTAAAGT
ATGGCCCGATTCAGAAAATTCCGTTATCATTTCCCGAGGATGAAGAAGGT
AGAGAATATTTCCTGCTTTCATTTTTATCGCCGAATGTCTAACGGTGATA
AAATTAAACGCACTTGCCTTGTATACTTCAGTACAAAAGACACTGTATTT
TGCTTTTGCTGTCAAATATTCAGTCAAAATAAATTCTCCTTGTCATCTTC
AAGTGGCCACAGCCTCTATACAGTAAGCTATGTTGATAAGCTATTGAGCA
TGTTTTGTAAACATTACGACCACAATAAATTTGATCATTTCAAAATGAAC
AGACCCGTCTATTTCCGATAGGATAACGGTGGGTAATATTATGCATACCT
TTCCGTTACTTCCATCGAAAGTGATTCGCTCAACTTATCACTGTAAGGAT
ACCATTTCTGGACTGCTTAACATGCATAGGACAAGACAAAGCGCTCAAGC
GACCTTTAAGTTGTGTTGAAAATATAGAATATTTACCTTTGGCCAAGTGT
TATGAACCCATTTTACACTTTAGTTCTTCATTTATTTCAAAACGATATAG
TACAATAGCAG
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protein sequence of SMED30023872-orf-1

>SMED30023872-orf-1 ID=SMED30023872-orf-1|Name=SMED30023872-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=107bp
MARFRKFRYHFPRMKKVENISCFHFYRRMSNGDKIKRTCLVYFSTKDTVF
CFCCQIFSQNKFSLSSSSGHSLYTVSYVDKLLSMFCKHYDHNKFDHFKMN
RPVYFR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000142posterior region of the whole animal