Vacuolar ATPase assembly integral membrane protein VMA21 homolog

Overview
NameVacuolar ATPase assembly integral membrane protein VMA21 homolog
Smed IDSMED30007091
Length (bp)614
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 Vacuolar ATPase assembly integral membrane protein VMA21 homolog (SMED30007091) t-SNE clustered cells

Violin plots show distribution of expression levels for Vacuolar ATPase assembly integral membrane protein VMA21 homolog (SMED30007091) 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 Vacuolar ATPase assembly integral membrane protein VMA21 homolog (SMED30007091) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Vacuolar ATPase assembly integral membrane protein VMA21 homolog (SMED30007091) 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



SMED30007091

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
posterior sideSMED30007091SMESG000059638.1 dd_Smed_v4_2976_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30007091SMESG000059638.1 dd_Smed_v4_2976_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
[Close]
BLAST of Vacuolar ATPase assembly integral membrane protein VMA21 homolog vs. Planmine SMEST
Match: SMESG000059638.1 (SMESG000059638.1)

HSP 1 Score: 92.4337 bits (228), Expect = 2.201e-24
Identity = 64/64 (100.00%), Postives = 64/64 (100.00%), Query Frame = 3 
Query:  147 AMLFFTVLIIFLPLFSYFVSRSVLFEGYFGYDASQSSLYGXXXXXXXXXXXXXXXXCLAFSDNE 338
            AMLFFTVLIIFLPLFSYFVSRSVLFEGYFGYDASQSSLYGAIVAVVVVHVVLIAFICLAFSDNE
Sbjct:   22 AMLFFTVLIIFLPLFSYFVSRSVLFEGYFGYDASQSSLYGAIVAVVVVHVVLIAFICLAFSDNE 85
The following BLAST results are available for this feature:
BLAST of Vacuolar ATPase assembly integral membrane protein VMA21 homolog 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 Vacuolar ATPase assembly integral membrane protein VMA21 homolog 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 Vacuolar ATPase assembly integral membrane protein VMA21 homolog 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 Vacuolar ATPase assembly integral membrane protein VMA21 homolog 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 Vacuolar ATPase assembly integral membrane protein VMA21 homolog 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 Vacuolar ATPase assembly integral membrane protein VMA21 homolog 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 Vacuolar ATPase assembly integral membrane protein VMA21 homolog 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 Vacuolar ATPase assembly integral membrane protein VMA21 homolog 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 Vacuolar ATPase assembly integral membrane protein VMA21 homolog 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 Vacuolar ATPase assembly integral membrane protein VMA21 homolog 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 Vacuolar ATPase assembly integral membrane protein VMA21 homolog 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 Vacuolar ATPase assembly integral membrane protein VMA21 homolog 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 Vacuolar ATPase assembly integral membrane protein VMA21 homolog 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 Vacuolar ATPase assembly integral membrane protein VMA21 homolog vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000059638.12.201e-24100.00SMESG000059638.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007091 ID=SMED30007091|Name=Vacuolar ATPase assembly integral membrane protein VMA21 homolog|organism=Schmidtea mediterranea sexual|type=transcript|length=614bp
TTTTGTTTAAATATATGTACTAAAAAACAAATATTACATTTTTTGAAATA
GGAAAATCTAATCCGTTTTAAGGTTTTTTAAAAATGAAGACAACTAAAAT
CAATTCATCTAAAAACAAAGTAACAAAAACAAGTAAAGTTATGAAAGCTA
TGCTATTTTTTACTGTTCTCATTATTTTTCTTCCATTATTTTCTTACTTT
GTTTCAAGATCAGTTTTATTTGAAGGATATTTTGGATATGATGCTAGTCA
AAGTTCTCTCTATGGAGCTATAGTTGCTGTTGTAGTTGTACATGTAGTTT
TAATTGCTTTCATATGTTTAGCATTTTCTGATAACGAACAAGTTCATATA
TTGTGGAAAAGACAGATTAAAATTGTTTAATATTTCTTTTGAATTTTGAT
CAATGTAAATAAGTTTTTGGTATTTTTTGTAGTAATGGAAATAAATCTGG
GTTTTTTTTAAATTAAACATTAATATTTAAACTAAACTGTTAAATAAGTA
CATAAGTATTGAAAATTGTAATAATAATTTTAGTTCTTATCAATTAGCCA
AAAAATCATTTGTAAAATGCATTCTGTTATGTGAATGTATTTGTGTTTTG
AAATACAAATTTTT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0005783endoplasmic reticulum
GO:0005789endoplasmic reticulum membrane
GO:0012507ER to Golgi transport vesicle membrane
GO:0016020membrane
GO:0016021integral component of membrane
GO:0031410cytoplasmic vesicle
GO:0033116endoplasmic reticulum-Golgi intermediate compartment membrane
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell
PLANA:0000142posterior region of the whole animal
Vocabulary: INTERPRO
TermDefinition
IPR019013Vma21
Vocabulary: biological process
TermDefinition
GO:0070072vacuolar proton-transporting V-type ATPase complex assembly