NADH dehydrogenase subunit 2

Overview
NameNADH dehydrogenase subunit 2 (YP_008592436.1)
Smed IDSMED30003686
Length (bp)870
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 dehydrogenase subunit 2 (SMED30003686) t-SNE clustered cells

Violin plots show distribution of expression levels for NADH dehydrogenase subunit 2 (SMED30003686) 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 dehydrogenase subunit 2 (SMED30003686) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for NADH dehydrogenase subunit 2 (SMED30003686) 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




SMED30003686

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



PAGE Curations: 17

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30003686 dd_Smed_v4_505_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30003686 dd_Smed_v4_505_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30003686 dd_Smed_v4_505_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30003686 dd_Smed_v4_505_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30003686 dd_Smed_v4_505_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30003686 dd_Smed_v4_505_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30003686 dd_Smed_v4_505_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30003686 dd_Smed_v4_505_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30003686 dd_Smed_v4_505_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30003686 dd_Smed_v4_505_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30003686 dd_Smed_v4_505_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30003686 Contig50888newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30003686 Contig50888uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30003686 dd_Smed_v6_505_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
progenitor cellSMED30003686 dd_Smed_v6_505_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30003686 dd_Smed_v6_505_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gamma neoblastSMED30003686 dd_Smed_v6_505_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 dehydrogenase subunit 2 vs. TrEMBL
Match: T1PUK7 (NADH dehydrogenase subunit 2 OS=Schmidtea mediterranea OX=79327 GN=ND2 PE=4 SV=2)

HSP 1 Score: 325.479 bits (833), Expect = 4.841e-108
Identity = 257/263 (97.72%), Postives = 257/263 (97.72%), Query Frame = 1
Query:    1 MSFYFYVLLNSLSSIMIFN*LNSFSLDLGVFTYYLFTLVSDILII*SSVYGESFIFALAIXXXXXXXXXXXXXXXXIPYLNYSLLFFILVIHKSIYCLVYLNLAKLSFXXXXXXXXXXXXXXXXYMLFTYRDLMYYLF*SSTFHTGWYVLACSIFPNVALKYWVMYXXXXXXXXXXXXYKSNLSSLYDVSQIGSVSVYFMLVLYVTLTGFPPFVLFACKFILFLIVNPXXXXXXXXXXXXXXXXXXXXXXXXXXXXELFIYSN 789
            MSFYFYVLLNSLSSIMIFN LNSFSLDLGVFTYYLFTLVSDILII SSVYGESFIFALAILFKLSFFPLFWWFFPLIPYLNYSLLFFILVIHKSIYCLVYLNLAKLSFI INLCCLIIILISLIYMLFTYRDLMYYLF SSTFHTGWYVLACSIFPNVALKYWVMYLVLTLVLFSFLVY SNLSSLYDVSQIGSVSVYFMLVLYVTLTGFPPFVLFACKFILFLIVNPLIV SVYILLLLLCVMVLSMVILVLFLSELFIYSN
Sbjct:   27 MSFYFYVLLNSLSSIMIFNWLNSFSLDLGVFTYYLFTLVSDILIIWSSVYGESFIFALAILFKLSFFPLFWWFFPLIPYLNYSLLFFILVIHKSIYCLVYLNLAKLSFISINLCCLIIILISLIYMLFTYRDLMYYLFWSSTFHTGWYVLACSIFPNVALKYWVMYLVLTLVLFSFLVYNSNLSSLYDVSQIGSVSVYFMLVLYVTLTGFPPFVLFACKFILFLIVNPLIVSSVYILLLLLCVMVLSMVILVLFLSELFIYSN 289          
BLAST of NADH dehydrogenase subunit 2 vs. TrEMBL
Match: A0A0B4VJT2 (NADH dehydrogenase subunit 2 (Fragment) OS=Schmidtea mediterranea OX=79327 GN=ND2 PE=4 SV=1)

HSP 1 Score: 316.235 bits (809), Expect = 2.434e-104
Identity = 248/263 (94.30%), Postives = 252/263 (95.82%), Query Frame = 1
Query:    1 MSFYFYVLLNSLSSIMIFN*LNSFSLDLGVFTYYLFTLVSDILII*SSVYGESFIFALAIXXXXXXXXXXXXXXXXIPYLNYSLLFFILVIHKSIYCLVYLNLAKLSFXXXXXXXXXXXXXXXXYMLFTYRDLMYYLF*SSTFHTGWYVLACSIFPNVALKYWVMYXXXXXXXXXXXXYKSNLSSLYDVSQIGSVSVYFMLVLYVTLTGFPPFVLFACKFILFLIVNPXXXXXXXXXXXXXXXXXXXXXXXXXXXXELFIYSN 789
            MSFYFYVLLNSLSSIM+FN LNSFSLDLGVFTYYLFTLVSDI II SSVYGESFIFALAILFKLSFFPLFWWFFPLIPY NYSLLFFILVIHKS+YCLVYLNLAKLSFI INLCCLIIILISLIYMLFTYRDLMYYLF SSTFHTGWYVLACSI PNVALKYWVMYLVLTLVLFSFLVY SNLSSLYDVSQIGSVS YFMLVLYVTLTGFPPFVLFACKFILFLIVNPL V SV+ILLLLLCVMVLSM+ILVLFLSELFIYSN
Sbjct:   27 MSFYFYVLLNSLSSIMVFNWLNSFSLDLGVFTYYLFTLVSDIFIIWSSVYGESFIFALAILFKLSFFPLFWWFFPLIPYFNYSLLFFILVIHKSLYCLVYLNLAKLSFISINLCCLIIILISLIYMLFTYRDLMYYLFWSSTFHTGWYVLACSISPNVALKYWVMYLVLTLVLFSFLVYNSNLSSLYDVSQIGSVSTYFMLVLYVTLTGFPPFVLFACKFILFLIVNPLTVSSVFILLLLLCVMVLSMIILVLFLSELFIYSN 289          
The following BLAST results are available for this feature:
BLAST of NADH dehydrogenase subunit 2 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 dehydrogenase subunit 2 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 dehydrogenase subunit 2 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 dehydrogenase subunit 2 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 dehydrogenase subunit 2 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 dehydrogenase subunit 2 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 dehydrogenase subunit 2 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 dehydrogenase subunit 2 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
T1PUK74.841e-10897.72NADH dehydrogenase subunit 2 OS=Schmidtea mediterr... [more]
A0A0B4VJT22.434e-10494.30NADH dehydrogenase subunit 2 (Fragment) OS=Schmidt... [more]
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BLAST of NADH dehydrogenase subunit 2 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 dehydrogenase subunit 2 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 dehydrogenase subunit 2 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 dehydrogenase subunit 2 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 dehydrogenase subunit 2 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 dehydrogenase subunit 2 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 GBrowseSMED30003686
GenBankYP_008592436.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003686 ID=SMED30003686|Name=NADH dehydrogenase subunit 2|organism=Schmidtea mediterranea sexual|type=transcript|length=870bp
atgtctttttatttctatgttcttttgaattctttgagttctattatgat
ttttaattgattgaattcttttagcttagatttaggtgtgtttacttatt
atttgtttactttggttagtgatatattaattatttgatcttctgtttat
ggagaatcttttatttttgctttggctattttatttaagttgtctttttt
ccctttattttggtggttttttcctttgattccttatttaaattattctt
tattgttttttattttagtgattcataagagcatttattgtttagtttat
ttgaatttagcaaagctttcttttattaggattaacttgtgttgtttaat
tataatattgatttctttgatttacatgctttttacttatcgggatttaa
tgtattatttgttttgatcttctacttttcatactggttggtatgtgtta
gcttgttctatttttccaaatgttgctttgaagtattgggttatgtactt
ggttttgacgttagtcttgttttcttttcttgtttataaatctaatttaa
gttctttgtatgatgttagtcaaattggtagtgtttctgtttattttatg
ttggtattatatgtaactctcacaggttttcctccgtttgttttgtttgc
ttgtaagtttattttgtttttaatagtcaatcctttgatagttagatctg
tttatattttattgttgttgctttgtgttatggttttatctatggttatt
ttggttttgtttttatcggagttgtttatttattctaattttagttattt
agttagttcttgtttatttttagtttctgttagttttgttctattattaa
tgttctttttattagcttaa
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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:0000418head
PLANA:0000429neoblast
Vocabulary: cellular component
TermDefinition
GO:0005739mitochondrion
GO:0016020membrane
GO:0016021integral component of membrane