ATP synthase subunit f

Overview
NameATP synthase subunit f
Smed IDSMED30014130
Length (bp)624
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 subunit f (SMED30014130) t-SNE clustered cells

Violin plots show distribution of expression levels for ATP synthase subunit f (SMED30014130) 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 subunit f (SMED30014130) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for ATP synthase subunit f (SMED30014130) 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.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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



SMED30014130

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30014130SMESG000067649.1 SMESG000060121.1 dd_Smed_v4_776_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30014130SMESG000067649.1 SMESG000060121.1 dd_Smed_v4_776_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30014130SMESG000067649.1 SMESG000060121.1 dd_Smed_v4_776_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30014130SMESG000067649.1 SMESG000060121.1 dd_Smed_v4_776_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 ATP synthase subunit f vs. Ensembl Fly
Match: ATPsynF (gene:FBgn0035032 transcript:FBtr0072340)

HSP 1 Score: 53.9138 bits (128), Expect = 2.027e-9
Identity = 31/113 (27.43%), Postives = 58/113 (51.33%), Query Frame = 3 
Query:   84 LGIGKLPNDYNVRIHGQYNPSIYYGPMKNRYDAMKWYNVTIGELPMYLLSRRFYNPLAILRGIGRWYWKFNLKWVSVKYRTLVPLYQMHIFAALWYYKEFYYEHRTDRRSKYH 422
            +  G  P +YN ++HG Y+P+ +YG     +  +K     +GE+  + L RR   P A+   + R +W++  K+V  K   + P +Q+ + +  ++Y   Y + +  R  KYH
Sbjct:    1 MAFGDYPAEYNPKVHGPYDPARFYGKADVPFGQVK-----LGEIGAW-LGRRNKTPNAVAGAVSRAWWRWQHKYVFPKRAGIAPFFQLTVASMTFFYLINYTKLKHHRNYKYH 107
[Close]
BLAST of ATP synthase subunit f vs. Ensembl Fly
Match: ATPsynF (gene:FBgn0035032 transcript:FBtr0072339)

HSP 1 Score: 53.9138 bits (128), Expect = 2.027e-9
Identity = 31/113 (27.43%), Postives = 58/113 (51.33%), Query Frame = 3 
Query:   84 LGIGKLPNDYNVRIHGQYNPSIYYGPMKNRYDAMKWYNVTIGELPMYLLSRRFYNPLAILRGIGRWYWKFNLKWVSVKYRTLVPLYQMHIFAALWYYKEFYYEHRTDRRSKYH 422
            +  G  P +YN ++HG Y+P+ +YG     +  +K     +GE+  + L RR   P A+   + R +W++  K+V  K   + P +Q+ + +  ++Y   Y + +  R  KYH
Sbjct:    1 MAFGDYPAEYNPKVHGPYDPARFYGKADVPFGQVK-----LGEIGAW-LGRRNKTPNAVAGAVSRAWWRWQHKYVFPKRAGIAPFFQLTVASMTFFYLINYTKLKHHRNYKYH 107
[Close]
BLAST of ATP synthase subunit f vs. UniProt/SwissProt
Match: sp|Q9W141|ATPK_DROME (Putative ATP synthase subunit f, mitochondrial OS=Drosophila melanogaster OX=7227 GN=ATPsynF PE=3 SV=1)

HSP 1 Score: 53.9138 bits (128), Expect = 2.032e-8
Identity = 31/113 (27.43%), Postives = 58/113 (51.33%), Query Frame = 3 
Query:   84 LGIGKLPNDYNVRIHGQYNPSIYYGPMKNRYDAMKWYNVTIGELPMYLLSRRFYNPLAILRGIGRWYWKFNLKWVSVKYRTLVPLYQMHIFAALWYYKEFYYEHRTDRRSKYH 422
            +  G  P +YN ++HG Y+P+ +YG     +  +K     +GE+  + L RR   P A+   + R +W++  K+V  K   + P +Q+ + +  ++Y   Y + +  R  KYH
Sbjct:    1 MAFGDYPAEYNPKVHGPYDPARFYGKADVPFGQVK-----LGEIGAW-LGRRNKTPNAVAGAVSRAWWRWQHKYVFPKRAGIAPFFQLTVASMTFFYLINYTKLKHHRNYKYH 107
[Close]
BLAST of ATP synthase subunit f vs. TrEMBL
Match: A0A1S8X4M2 (Uncharacterized protein OS=Opisthorchis viverrini OX=6198 GN=X801_02425 PE=4 SV=1)

HSP 1 Score: 82.8037 bits (203), Expect = 6.472e-17
Identity = 47/112 (41.96%), Postives = 63/112 (56.25%), Query Frame = 3 
Query:   87 GIGKLPNDYNVRIHGQYNPSIYYGPMKNRYDAMKWYNVTIGELPMYLLSRRFYNPLAILRGIGRWYWKFNLKWVSVKYRTLVPLYQMHIFAALWYYKEFYYEHRTDRRSKYH 422
            G G LP +YNVRIHG Y P  +YG  K     M   +V IGELP +L SRR  NP    R I R+ W++  KW++ K  T  P++Q  +      Y + Y EH+ ++ SKYH
Sbjct:    3 GFGLLPKEYNVRIHGAYFPGYFYG--KPDTPIM---DVKIGELPAWL-SRRSRNPADWARAIARFGWRYTFKWIACKQLTFAPVFQFAVVLGAVRYFQDYGEHQNEKHSKYH 108
[Close]
BLAST of ATP synthase subunit f vs. TrEMBL
Match: G4LVE7 (ATP synthase f chain, mitochondrial-related OS=Schistosoma mansoni OX=6183 GN=Smp_140480 PE=4 SV=1)

HSP 1 Score: 82.0333 bits (201), Expect = 1.069e-16
Identity = 44/114 (38.60%), Postives = 68/114 (59.65%), Query Frame = 3 
Query:   84 LGIGKLPNDYNVRIHGQYNPSIYYGPMKNRYDAMKWYNVTIGELPMYLLSRRFYNPLAILRGIGRWYWKFNLKWVSVKYRTLVPLYQMHI-FAALWYYKEFYYEHRTDRRSKYH 422
            +  G LP +YN R+HG Y P  YYG        + + +V +G+L  +  SRR  NP+ +LR + R+YW++  +WV  K  ++VP +Q+   FAA  Y+ + Y EHR+ + SKYH
Sbjct:    2 MNFGLLPKEYNARVHGVYFPGTYYGKKD-----IPFGDVQLGQLSEWF-SRRSKNPVDMLRAVSRFYWRYAFRWVMTKRPSVVPFFQLTFSFAAFRYFSD-YAEHRSHKHSKYH 108
[Close]
BLAST of ATP synthase subunit f vs. TrEMBL
Match: A0A4S2LVD0 (Uncharacterized protein OS=Opisthorchis felineus OX=147828 GN=CRM22_004817 PE=4 SV=1)

HSP 1 Score: 81.6481 bits (200), Expect = 1.783e-16
Identity = 44/112 (39.29%), Postives = 61/112 (54.46%), Query Frame = 3 
Query:   87 GIGKLPNDYNVRIHGQYNPSIYYGPMKNRYDAMKWYNVTIGELPMYLLSRRFYNPLAILRGIGRWYWKFNLKWVSVKYRTLVPLYQMHIFAALWYYKEFYYEHRTDRRSKYH 422
            G G LP +YNVRIHG Y P  +YG   +        +V IGELP +  SRR  NP    R I R+ W++  KW++ K  T  P++Q  +      Y + Y EH+ ++ SKYH
Sbjct:    3 GFGLLPKEYNVRIHGAYFPGYFYGKPDSPI-----MDVKIGELPAWF-SRRSRNPADWARAIARFGWRYTFKWIACKRLTFAPVFQAAVVVGAIRYFQDYGEHQNEKHSKYH 108
[Close]
BLAST of ATP synthase subunit f vs. TrEMBL
Match: A0A183S3H9 (Uncharacterized protein OS=Schistosoma rodhaini OX=6188 PE=4 SV=1)

HSP 1 Score: 81.2629 bits (199), Expect = 2.379e-16
Identity = 42/113 (37.17%), Postives = 65/113 (57.52%), Query Frame = 3 
Query:   84 LGIGKLPNDYNVRIHGQYNPSIYYGPMKNRYDAMKWYNVTIGELPMYLLSRRFYNPLAILRGIGRWYWKFNLKWVSVKYRTLVPLYQMHIFAALWYYKEFYYEHRTDRRSKYH 422
            +  G LP +YN R+HG Y P  YYG        + + +V +G+L  +  SRR  NP+ +LR + R+YW++  +WV  K  ++VP +Q+    A + Y   Y EHR+ + SKYH
Sbjct:    2 MNFGLLPKEYNARVHGVYFPGTYYGK-----KDIPFGDVQLGQLSEWF-SRRSKNPVDMLRAVSRFYWRYAFRWVMTKRPSVVPFFQLTFSFATFRYFSDYAEHRSHKHSKYH 108
[Close]
BLAST of ATP synthase subunit f vs. TrEMBL
Match: A0A5K3FU46 (Uncharacterized protein OS=Mesocestoides corti OX=53468 PE=4 SV=1)

HSP 1 Score: 81.2629 bits (199), Expect = 2.563e-16
Identity = 41/112 (36.61%), Postives = 66/112 (58.93%), Query Frame = 3 
Query:   87 GIGKLPNDYNVRIHGQYNPSIYYGPMKNRYDAMKWYNVTIGELPMYLLSRRFYNPLAILRGIGRWYWKFNLKWVSVKYRTLVPLYQMHIFAALWYYKEFYYEHRTDRRSKYH 422
            G+G LP +YNVR+HG Y P  YYGP + +       +V +G+L  +L +R   +P+  +R + R+ W++ L+W+  +  TLVP + +    AL  Y   Y  H+T+R +KYH
Sbjct:    3 GLGLLPKEYNVRVHGAYFPGYYYGPKETKLG-----DVKLGDLKAWLKTRSL-DPMYYMRALARFTWRYRLRWIYPRNTTLVPFFHLGCVFALCQYVINYKSHQTERHAKYH 108
[Close]
BLAST of ATP synthase subunit f vs. Planmine SMEST
Match: SMESG000060121.1 (SMESG000060121.1)

HSP 1 Score: 236.498 bits (602), Expect = 9.977e-81
Identity = 115/115 (100.00%), Postives = 115/115 (100.00%), Query Frame = 3 
Query:   78 MGLGIGKLPNDYNVRIHGQYNPSIYYGPMKNRYDAMKWYNVTIGELPMYLLSRRFYNPLAILRGIGRWYWKFNLKWVSVKYRTLVPLYQMHIFAALWYYKEFYYEHRTDRRSKYH 422
            MGLGIGKLPNDYNVRIHGQYNPSIYYGPMKNRYDAMKWYNVTIGELPMYLLSRRFYNPLAILRGIGRWYWKFNLKWVSVKYRTLVPLYQMHIFAALWYYKEFYYEHRTDRRSKYH
Sbjct:    1 MGLGIGKLPNDYNVRIHGQYNPSIYYGPMKNRYDAMKWYNVTIGELPMYLLSRRFYNPLAILRGIGRWYWKFNLKWVSVKYRTLVPLYQMHIFAALWYYKEFYYEHRTDRRSKYH 115
[Close]
BLAST of ATP synthase subunit f vs. Planmine SMEST
Match: SMESG000067649.1 (SMESG000067649.1)

HSP 1 Score: 234.958 bits (598), Expect = 3.152e-80
Identity = 114/115 (99.13%), Postives = 114/115 (99.13%), Query Frame = 3 
Query:   78 MGLGIGKLPNDYNVRIHGQYNPSIYYGPMKNRYDAMKWYNVTIGELPMYLLSRRFYNPLAILRGIGRWYWKFNLKWVSVKYRTLVPLYQMHIFAALWYYKEFYYEHRTDRRSKYH 422
            MGLGIGKLPNDYNVRIHGQYNPSIYYGPMKNRYDAMKWYNVTIGELPMYLLSRRFYNPLAI RGIGRWYWKFNLKWVSVKYRTLVPLYQMHIFAALWYYKEFYYEHRTDRRSKYH
Sbjct:    1 MGLGIGKLPNDYNVRIHGQYNPSIYYGPMKNRYDAMKWYNVTIGELPMYLLSRRFYNPLAIFRGIGRWYWKFNLKWVSVKYRTLVPLYQMHIFAALWYYKEFYYEHRTDRRSKYH 115
The following BLAST results are available for this feature:
BLAST of ATP synthase subunit f 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 subunit f 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 subunit f vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 2
Match NameE-valueIdentityDescription
ATPsynF2.027e-927.43gene:FBgn0035032 transcript:FBtr0072340[more]
ATPsynF2.027e-927.43gene:FBgn0035032 transcript:FBtr0072339[more]
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BLAST of ATP synthase subunit f 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 subunit f 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 subunit f 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 subunit f vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|Q9W141|ATPK_DROME2.032e-827.43Putative ATP synthase subunit f, mitochondrial OS=... [more]
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BLAST of ATP synthase subunit f vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1S8X4M26.472e-1741.96Uncharacterized protein OS=Opisthorchis viverrini ... [more]
G4LVE71.069e-1638.60ATP synthase f chain, mitochondrial-related OS=Sch... [more]
A0A4S2LVD01.783e-1639.29Uncharacterized protein OS=Opisthorchis felineus O... [more]
A0A183S3H92.379e-1637.17Uncharacterized protein OS=Schistosoma rodhaini OX... [more]
A0A5K3FU462.563e-1636.61Uncharacterized protein OS=Mesocestoides corti OX=... [more]
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BLAST of ATP synthase subunit f 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 subunit f 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 subunit f 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 subunit f 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 subunit f 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 subunit f vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000060121.19.977e-81100.00SMESG000060121.1[more]
SMESG000067649.13.152e-8099.13SMESG000067649.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014130 ID=SMED30014130|Name=ATP synthase subunit f|organism=Schmidtea mediterranea sexual|type=transcript|length=624bp
TTTTNTTTTTTTTGTTTAGCTTATTTGTTATTTACTGTTAAATTTGAAAT
TTTCAAGTTTTACTTTTCAGCTTTCTTATGGGTTTGGGAATCGGTAAGCT
CCCAAATGATTATAATGTTAGAATACATGGGCAATATAACCCTAGTATAT
ACTACGGTCCTATGAAGAATAGATATGATGCAATGAAATGGTATAACGTA
ACTATTGGTGAATTGCCTATGTATCTTTTGTCAAGACGATTTTATAATCC
TTTGGCGATTCTTAGAGGTATTGGCAGATGGTATTGGAAATTTAATTTAA
AATGGGTGTCTGTGAAATATCGAACCTTAGTGCCACTATACCAGATGCAC
ATTTTCGCAGCTCTCTGGTATTACAAAGAATTCTATTATGAACATCGTAC
CGATAGACGTAGTAAATATCATTAAATTAACAGCTCGTTTTAGTTGAATT
AGGAATAATGTTCTATTTGAAATATAAGTTATTATAAATTCTTAATTTAA
CCTTAAATTAGTTTAGTTTAATTGTTTTAATTCAAAATTAATCAGATAAG
TATATTATTTCACATTTATATTAATATTTATTTTGAGAACATGCTTGTTT
AATAAATAAATTCTAATTCATTCA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000429neoblast
Vocabulary: INTERPRO
TermDefinition
IPR019344F1F0-ATPsyn_F_prd
Vocabulary: molecular function
TermDefinition
GO:0016787hydrolase activity
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR019344Mitochondrial F1-F0 ATP synthase subunit F, predictedPFAMPF10206WRWcoord: 5..110
e-value: 8.7E-18
score: 64.6