ATP synthase F0 subunit 6

Overview
NameATP synthase F0 subunit 6 (YP_008592432.1)
Smed IDSMED30031308
Length (bp)636
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 ATP synthase F0 subunit 6 (SMED30031308) t-SNE clustered cells

Violin plots show distribution of expression levels for ATP synthase F0 subunit 6 (SMED30031308) 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 ATP synthase F0 subunit 6 (SMED30031308) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for ATP synthase F0 subunit 6 (SMED30031308) 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



SMED30031308

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



PAGE Curations: 15

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30031308 dd_Smed_v4_258_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30031308 dd_Smed_v4_258_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30031308 dd_Smed_v4_258_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30031308 dd_Smed_v4_258_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30031308 dd_Smed_v4_258_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30031308 dd_Smed_v4_258_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30031308 dd_Smed_v4_258_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30031308 dd_Smed_v4_258_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30031308 dd_Smed_v4_258_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30031308 dd_Smed_v4_258_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30031308 dd_Smed_v4_258_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30031308 dd_Smed_v4_258_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30031308 dd_Smed_v4_258_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30031308 Contig51827newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30031308 Contig51827uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of ATP synthase F0 subunit 6 vs. TrEMBL
Match: T1PTK3 (ATP synthase subunit a OS=Schmidtea mediterranea OX=79327 GN=ATP6 PE=4 SV=1)

HSP 1 Score: 181.8 bits (460), Expect = 3.043e-54
Identity = 205/211 (97.16%), Postives = 205/211 (97.16%), Query Frame = 1 
Query:    1 MTNIFSALDLKFFNSLFFDPWXXXXXXXXXXXXDFYSCNIYSLFGLFINFFKGLSLLVYGXXXXXXXXXXXXXXXXXXXXXXXXXXGVSSHLFANLLVSVFVYFNIVFFGLYKDVVRYFSHXXXXXXXXXXXXXXXXXXXXX*IRIITLTLRLSVNMTAGHXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXIQASVYCLLIKRYVCD 633
            MTNIFSALDLKFFNSLFFDPWFILLVLLFVFILDFYSCNIYSLFGLFINFF GLSLLVYGPFLFFSYIVFVFFFFF LSGLFPYFFGVSSHLFANLLVSVFVYFNIVFFGLYKDVV YFSHFVPLGSGSLSFFLFFVEFLSF IRIITLTLRLSVNMTAGHVFLHLFGSSFSSSFNIFLLLLVVFYMFFEVFVCVIQASVYCLLI  YVCD
Sbjct:    1 MTNIFSALDLKFFNSLFFDPWFILLVLLFVFILDFYSCNIYSLFGLFINFFNGLSLLVYGPFLFFSYIVFVFFFFFNLSGLFPYFFGVSSHLFANLLVSVFVYFNIVFFGLYKDVVSYFSHFVPLGSGSLSFFLFFVEFLSFWIRIITLTLRLSVNMTAGHVFLHLFGSSFSSSFNIFLLLLVVFYMFFEVFVCVIQASVYCLLINSYVCD 211
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BLAST of ATP synthase F0 subunit 6 vs. TrEMBL
Match: A0A0B4VJ65 (ATP synthase subunit a OS=Schmidtea mediterranea OX=79327 GN=ATP6 PE=4 SV=1)

HSP 1 Score: 174.096 bits (440), Expect = 3.345e-51
Identity = 198/211 (93.84%), Postives = 202/211 (95.73%), Query Frame = 1 
Query:    1 MTNIFSALDLKFFNSLFFDPWXXXXXXXXXXXXDFYSCNIYSLFGLFINFFKGLSLLVYGXXXXXXXXXXXXXXXXXXXXXXXXXXGVSSHLFANLLVSVFVYFNIVFFGLYKDVVRYFSHXXXXXXXXXXXXXXXXXXXXX*IRIITLTLRLSVNMTAGHXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXIQASVYCLLIKRYVCD 633
            MTNIFSALDLKFFNSLFFDPWFILLVLLFVFI+DFY+CNIYSLFGLFINFF GLSLLVYGPFLFFSYIVFVFFFFF LSGLFPYFFG+SSHLFANLLVSVFVYFNIV FG YKD+V YFSHFVPLGSGSLSFFLFFVEFLSF IRIITLTLRLSVNMTAGHVFLHLFGSSFSSSFNIFLLLLVVFYMFFEVFVCVIQASVYCLLI  YV D
Sbjct:    2 MTNIFSALDLKFFNSLFFDPWFILLVLLFVFIVDFYACNIYSLFGLFINFFNGLSLLVYGPFLFFSYIVFVFFFFFNLSGLFPYFFGISSHLFANLLVSVFVYFNIVLFGFYKDMVSYFSHFVPLGSGSLSFFLFFVEFLSFWIRIITLTLRLSVNMTAGHVFLHLFGSSFSSSFNIFLLLLVVFYMFFEVFVCVIQASVYCLLINSYVSD 212
The following BLAST results are available for this feature:
BLAST of ATP synthase F0 subunit 6 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 ATP synthase F0 subunit 6 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 ATP synthase F0 subunit 6 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 ATP synthase F0 subunit 6 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 ATP synthase F0 subunit 6 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 ATP synthase F0 subunit 6 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 ATP synthase F0 subunit 6 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 ATP synthase F0 subunit 6 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
T1PTK33.043e-5497.16ATP synthase subunit a OS=Schmidtea mediterranea O... [more]
A0A0B4VJ653.345e-5193.84ATP synthase subunit a OS=Schmidtea mediterranea O... [more]
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BLAST of ATP synthase F0 subunit 6 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 ATP synthase F0 subunit 6 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 ATP synthase F0 subunit 6 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 ATP synthase F0 subunit 6 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 ATP synthase F0 subunit 6 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 ATP synthase F0 subunit 6 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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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30031308
GenBankYP_008592432.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031308 ID=SMED30031308|Name=ATP synthase F0 subunit 6|organism=Schmidtea mediterranea sexual|type=transcript|length=636bp
atgactaatattttttcagcattggatttgaagttctttaattctttgtt
ctttgatccttggtttattttgttagttttgctttttgtttttattttag
acttttattcttgtaatatttattctttgtttggactatttattaacttt
tttaaaggtttaagtcttttggtttatggtccatttttgttttttagtta
tattgtatttgttttcttttttttttttaaattatctggattatttcctt
atttttttggtgtttcttcgcatttgtttgccaatctcttagtcagtgtg
tttgtttattttaatattgttttttttggcttgtataaggatgtggttag
atatttttcacattttgttcctttaggttctggttctctttctttctttt
tattttttgttgagtttcttagtttttgaattcgtattattactttaact
cttcgtttatctgttaatatgactgctggtcatgtttttttacacttgtt
tgggtcttctttttcttcttcgtttaatatttttttattgttacttgtgg
ttttttatatgttttttgaagtttttgtctgtgtaattcaagctagtgtt
tattgtttgttaattaaaagatatgtttgtgattag
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000101muscle cell
PLANA:0000429neoblast
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR000568ATPase_F0-cplx_asu
IPR023011ATPase_F0-cplx_asu_AS
Vocabulary: molecular function
TermDefinition
GO:0015078hydrogen ion transmembrane transporter activity
Vocabulary: biological process
TermDefinition
GO:0015986ATP synthesis coupled proton transport
Vocabulary: cellular component
TermDefinition
GO:0005739mitochondrion
GO:0005743mitochondrial inner membrane
GO:0016020membrane
GO:0016021integral component of membrane
GO:0045263proton-transporting ATP synthase complex, coupling factor F(o)