NADH-ubiquinone oxidoreductase chain 3

Overview
NameNADH-ubiquinone oxidoreductase chain 3
Smed IDSMED30008414
Length (bp)270
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 NADH-ubiquinone oxidoreductase chain 3 (SMED30008414) t-SNE clustered cells

Violin plots show distribution of expression levels for NADH-ubiquinone oxidoreductase chain 3 (SMED30008414) 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 NADH-ubiquinone oxidoreductase chain 3 (SMED30008414) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for NADH-ubiquinone oxidoreductase chain 3 (SMED30008414) 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




SMED30008414

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30008414 dd_Smed_v4_289_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30008414 dd_Smed_v4_289_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
neoblastSMED30008414 dd_Smed_v4_289_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30008414 dd_Smed_v4_289_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
progenitor cellSMED30008414 dd_Smed_v6_289_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30008414 dd_Smed_v6_289_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gamma neoblastSMED30008414 dd_Smed_v6_289_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of NADH-ubiquinone oxidoreductase chain 3 vs. TrEMBL
Match: T1PTG8 (NADH-ubiquinone oxidoreductase chain 3 OS=Schmidtea mediterranea OX=79327 GN=ND3 PE=3 SV=2)

HSP 1 Score: 87.4261 bits (215), Expect = 3.284e-20
Identity = 85/89 (95.51%), Postives = 85/89 (95.51%), Query Frame = 1
Query:    1 LGYNSFRESQSVYECGFDSKDVSRFPFSFRXXXXXXXXXXXXXELCFVLQMPFELFYVMYGKRXXXXXXXXXXXXXXXXEYFKGLLV*K 267
            LGYNSFRESQSVYECGFDSKDVSRFPFSFRFFLIVILFVILDVELCFVLQMPFELFYVMYG RLYYLYFILLLVFGV LEYF GLLV K
Sbjct:   29 LGYNSFRESQSVYECGFDSKDVSRFPFSFRFFLIVILFVILDVELCFVLQMPFELFYVMYGNRLYYLYFILLLVFGVWLEYFNGLLVWK 117          
BLAST of NADH-ubiquinone oxidoreductase chain 3 vs. TrEMBL
Match: A0A0B4VIX4 (NADH-ubiquinone oxidoreductase chain 3 (Fragment) OS=Schmidtea mediterranea OX=79327 GN=ND3 PE=3 SV=1)

HSP 1 Score: 86.6557 bits (213), Expect = 5.424e-20
Identity = 83/89 (93.26%), Postives = 84/89 (94.38%), Query Frame = 1
Query:    1 LGYNSFRESQSVYECGFDSKDVSRFPFSFRXXXXXXXXXXXXXELCFVLQMPFELFYVMYGKRXXXXXXXXXXXXXXXXEYFKGLLV*K 267
            LGYNSFRESQSVYECGFDSKDVSRFPFSFRFFLIVILFVILDVELCFVLQMPFELFY MYG RLYYLYFI+LLVFGV LEYF GLLV K
Sbjct:   29 LGYNSFRESQSVYECGFDSKDVSRFPFSFRFFLIVILFVILDVELCFVLQMPFELFYFMYGNRLYYLYFIVLLVFGVWLEYFNGLLVWK 117          
BLAST of NADH-ubiquinone oxidoreductase chain 3 vs. TrEMBL
Match: G9M8V8 (NADH-ubiquinone oxidoreductase chain 3 (Fragment) OS=Dugesia japonica OX=6161 GN=nd3 PE=3 SV=1)

HSP 1 Score: 63.929 bits (154), Expect = 4.821e-11
Identity = 40/61 (65.57%), Postives = 48/61 (78.69%), Query Frame = 1
Query:    7 YNSFRESQSVYECGFDSKDVSRFPFSFRXXXXXXXXXXXXXELCFVLQMPFELFYVMYGKR 189
            Y S RE  SVYECGFDSKDVSR PFS  FFL++++F+I DVE+CFVLQ+P+E F   YG R
Sbjct:   27 YYSSREVISVYECGFDSKDVSRLPFSLYFFLVLLVFIIFDVEICFVLQIPYECFNFFYGNR 87          
BLAST of NADH-ubiquinone oxidoreductase chain 3 vs. TrEMBL
Match: A0A0C4ZKM3 (NADH-ubiquinone oxidoreductase chain 3 (Fragment) OS=Girardia sp. ER-2015 OX=1608986 GN=ND3 PE=3 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 3.062e-9
Identity = 49/83 (59.04%), Postives = 63/83 (75.90%), Query Frame = 1
Query:   19 RESQSVYECGFDSKDVSRFPFSFRXXXXXXXXXXXXXELCFVLQMPFELFYVMYGKRXXXXXXXXXXXXXXXXEYFKGLLV*K 267
            RE  S YECGFDSKD SR PFS  FFLI+++F++ DVELCF+LQ+P+E F   YG RL++L+ + LLV GV LE F G+L+ K
Sbjct:   18 REIISSYECGFDSKDTSRLPFSLYFFLILLVFIVFDVELCFLLQVPYESFGFYYGNRLFFLFVVYLLVSGVLLELFSGILLWK 100          
BLAST of NADH-ubiquinone oxidoreductase chain 3 vs. TrEMBL
Match: A0A0C5D534 (NADH-ubiquinone oxidoreductase chain 3 OS=Crenobia alpina OX=27898 GN=nad3 PE=3 SV=1)

HSP 1 Score: 53.9138 bits (128), Expect = 3.984e-7
Identity = 36/57 (63.16%), Postives = 45/57 (78.95%), Query Frame = 1
Query:   19 RESQSVYECGFDSKDVSRFPFSFRXXXXXXXXXXXXXELCFVLQMPFELFYVMYGKR 189
            RE+ S +ECGFD KD SR PFS RFFLIVILFVI DVE+C +LQ+PFE+ + ++  R
Sbjct:   36 RETVSSFECGFDGKDTSRLPFSLRFFLIVILFVIFDVEICVLLQIPFEITFELFENR 92          
The following BLAST results are available for this feature:
BLAST of NADH-ubiquinone oxidoreductase chain 3 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 NADH-ubiquinone oxidoreductase chain 3 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 NADH-ubiquinone oxidoreductase chain 3 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 NADH-ubiquinone oxidoreductase chain 3 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 NADH-ubiquinone oxidoreductase chain 3 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 NADH-ubiquinone oxidoreductase chain 3 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 NADH-ubiquinone oxidoreductase chain 3 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 NADH-ubiquinone oxidoreductase chain 3 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
T1PTG83.284e-2095.51NADH-ubiquinone oxidoreductase chain 3 OS=Schmidte... [more]
A0A0B4VIX45.424e-2093.26NADH-ubiquinone oxidoreductase chain 3 (Fragment) ... [more]
G9M8V84.821e-1165.57NADH-ubiquinone oxidoreductase chain 3 (Fragment) ... [more]
A0A0C4ZKM33.062e-959.04NADH-ubiquinone oxidoreductase chain 3 (Fragment) ... [more]
A0A0C5D5343.984e-763.16NADH-ubiquinone oxidoreductase chain 3 OS=Crenobia... [more]
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BLAST of NADH-ubiquinone oxidoreductase chain 3 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 NADH-ubiquinone oxidoreductase chain 3 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 NADH-ubiquinone oxidoreductase chain 3 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 NADH-ubiquinone oxidoreductase chain 3 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 NADH-ubiquinone oxidoreductase chain 3 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 NADH-ubiquinone oxidoreductase chain 3 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

>SMED30008414 ID=SMED30008414|Name=NADH-ubiquinone oxidoreductase chain 3|organism=Schmidtea mediterranea sexual|type=transcript|length=270bp
ttgggttataatagctttcgtgagtctcagtctgtgtatgagtgtgggtt
tgattctaaggatgtttctcgttttcctttttcttttcgtttttttttga
ttgtcatattgtttgttattttggatgttgagttgtgttttgtattacag
atgccttttgaattgttttatgttatgtatggtaaacgtttgtattactt
gtatttcattctcttattagtgtttggtgtttgattagagtattttaaag
gtttattggtttgaaagtag
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000039gamma neoblast
PLANA:0000101muscle cell
PLANA:0000120progenitor cell
PLANA:0000429neoblast
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR000440NADH_UbQ/plastoQ_OxRdtase_su3
Vocabulary: molecular function
TermDefinition
GO:0008137NADH dehydrogenase (ubiquinone) activity
GO:0016491oxidoreductase activity
Vocabulary: biological process
TermDefinition
GO:0055114oxidation-reduction process
Vocabulary: cellular component
TermDefinition
GO:0005739mitochondrion
GO:0016020membrane
GO:0016021integral component of membrane
GO:0031966mitochondrial membrane
GO:0070469respiratory chain
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 10..30