ATP-dependent DNA helicase

Overview
NameATP-dependent DNA helicase
Smed IDSMED30007244
Length (bp)507
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-dependent DNA helicase (SMED30007244) t-SNE clustered cells

Violin plots show distribution of expression levels for ATP-dependent DNA helicase (SMED30007244) 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-dependent DNA helicase (SMED30007244) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for ATP-dependent DNA helicase (SMED30007244) 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



SMED30007244

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
X1 cellSMED30007244 SmedASXL_072639SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30007244 dd_Smed_v6_54952_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of ATP-dependent DNA helicase vs. TrEMBL
Match: A0A0C2N3H9 (ATP-dependent DNA helicase OS=Thelohanellus kitauei OX=669202 GN=RF11_10810 PE=3 SV=1)

HSP 1 Score: 80.4925 bits (197), Expect = 5.613e-15
Identity = 50/92 (54.35%), Postives = 56/92 (60.87%), Query Frame = 3 
Query:    9 KAKIISTWNHNDIVLILRIDLAPTDTALPFILKCRQFPNFPAYAITINKTRCRS-----------IFTWP-----LSRSTVARQVKAYIESN 236
            KAKIIS  N  D VLI RIDLAPT+T L F LK RQFP  PAYAITINK + +S           +F+       LSRS  +RQVK YIE N
Sbjct:  164 KAKIISECNRGDSVLIPRIDLAPTETTLNFTLKRRQFPVVPAYAITINKAQGQSFDHVGIQLKTTVFSHGQLYVALSRSRNSRQVKLYIEPN 255
[Close]
BLAST of ATP-dependent DNA helicase vs. TrEMBL
Match: A0A4Y2PVR7 (ATP-dependent DNA helicase OS=Araneus ventricosus OX=182803 GN=AVEN_105794_1 PE=3 SV=1)

HSP 1 Score: 67.781 bits (164), Expect = 1.285e-11
Identity = 30/54 (55.56%), Postives = 42/54 (77.78%), Query Frame = 3 
Query:    9 KAKIISTWNHNDIVLILRIDLAPTDTALPFILKCRQFPNFPAYAITINKTRCRS 170
            +AKI+   N  D+V I RI+LAP+D  LPF+LK RQFP+ PAYA+TINK++ ++
Sbjct:   37 RAKIVFECNRGDVVFIPRIELAPSDANLPFVLKRRQFPSIPAYAMTINKSQGQT 90
[Close]
BLAST of ATP-dependent DNA helicase vs. TrEMBL
Match: A0A226E9L3 (ATP-dependent DNA helicase OS=Folsomia candida OX=158441 GN=Fcan01_11178 PE=3 SV=1)

HSP 1 Score: 71.2478 bits (173), Expect = 3.177e-11
Identity = 36/53 (67.92%), Postives = 42/53 (79.25%), Query Frame = 3 
Query:   12 AKIISTWNHNDIVLILRIDLAPTDTALPFILKCRQFPNFPAYAITINKTRCRS 170
            A+IIS  N  DIV I RIDLAP+DT LPFIL+ RQFP  PAYAITINK++ +S
Sbjct: 1449 AEIISECNRGDIVFIPRIDLAPSDTTLPFILRRRQFPITPAYAITINKSQGQS 1501
[Close]
BLAST of ATP-dependent DNA helicase vs. TrEMBL
Match: A0A4Y2AVB9 (ATP-dependent DNA helicase OS=Araneus ventricosus OX=182803 GN=AVEN_6544_1 PE=3 SV=1)

HSP 1 Score: 65.0846 bits (157), Expect = 1.117e-10
Identity = 29/53 (54.72%), Postives = 41/53 (77.36%), Query Frame = 3 
Query:   12 AKIISTWNHNDIVLILRIDLAPTDTALPFILKCRQFPNFPAYAITINKTRCRS 170
            AKI+S  N + +V + RI+LAP+D  LPF+LK RQFP  PAYA+TINK++ ++
Sbjct:   38 AKIVSECNPSGVVFLTRIELAPSDVTLPFVLKRRQFPLIPAYAMTINKSQGQT 90
[Close]
BLAST of ATP-dependent DNA helicase vs. TrEMBL
Match: A0A4Y2HS16 (Uncharacterized protein OS=Araneus ventricosus OX=182803 GN=AVEN_150011_1 PE=4 SV=1)

HSP 1 Score: 66.2402 bits (160), Expect = 1.719e-10
Identity = 29/48 (60.42%), Postives = 37/48 (77.08%), Query Frame = 3 
Query:   12 AKIISTWNHNDIVLILRIDLAPTDTALPFILKCRQFPNFPAYAITINK 155
            AKI+S +N   +V + RI+LAP+D  LPF+LK RQFP  PAYA+TINK
Sbjct:   30 AKIVSEYNRGGVVFLSRIELAPSDVNLPFVLKRRQFPLIPAYAMTINK 77
The following BLAST results are available for this feature:
BLAST of ATP-dependent DNA helicase 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-dependent DNA helicase 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-dependent DNA helicase 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-dependent DNA helicase 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-dependent DNA helicase 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-dependent DNA helicase 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-dependent DNA helicase 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-dependent DNA helicase vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A0C2N3H95.613e-1554.35ATP-dependent DNA helicase OS=Thelohanellus kitaue... [more]
A0A4Y2PVR71.285e-1155.56ATP-dependent DNA helicase OS=Araneus ventricosus ... [more]
A0A226E9L33.177e-1167.92ATP-dependent DNA helicase OS=Folsomia candida OX=... [more]
A0A4Y2AVB91.117e-1054.72ATP-dependent DNA helicase OS=Araneus ventricosus ... [more]
A0A4Y2HS161.719e-1060.42Uncharacterized protein OS=Araneus ventricosus OX=... [more]
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BLAST of ATP-dependent DNA helicase 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-dependent DNA helicase 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-dependent DNA helicase 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-dependent DNA helicase 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-dependent DNA helicase 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-dependent DNA helicase 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

>SMED30007244 ID=SMED30007244|Name=ATP-dependent DNA helicase|organism=Schmidtea mediterranea sexual|type=transcript|length=507bp
ATTTAAGAAAAGCAAAAATTATTTCAACATGGAATCATAACGATATAGTT
TTAATTCTCAGGATTGATCTCGCTCCAACTGACACAGCGTTACCTTTCAT
ATTAAAATGCCGCCAATTTCCGAATTTTCCTGCGTATGCTATTACAATAA
ACAAGACTCGGTGCCGCAGTATTTTCACATGGCCTTTGTCACGATCAACA
GTTGCAAGGCAAGTTAAGGCGTATATTGAATCGAATCCACAGCAAGGAAG
ATTATTGAATAACCAGAGACAACTCACACGAAATGCAGTTTTTCAAAAGG
TTCTTTGTTAAAAACGATTCATTTTTTCTTACATTTATTTGTAACACATT
TTTAATTTTAATATTTTGCTTTGTATAAATTTTAACGATCTCTTAACAGT
TTTAATTTATATGTTAGTGCAGTCATTCTCAAAGTGGGCGATAACGCCCC
CTTGTTGGCGTTTGAGACAGGGGGGGTTAAAGGGCCCAGAAAAATGGGGG
GAGGAGA
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protein sequence of SMED30007244-orf-1

>SMED30007244-orf-1 ID=SMED30007244-orf-1|Name=SMED30007244-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=103bp
LRKAKIISTWNHNDIVLILRIDLAPTDTALPFILKCRQFPNFPAYAITIN
KTRCRSIFTWPLSRSTVARQVKAYIESNPQQGRLLNNQRQLTRNAVFQKV
LC*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0000166nucleotide binding
GO:0005524ATP binding
GO:0016787hydrolase activity
GO:0003678DNA helicase activity
GO:0004386helicase activity
Vocabulary: biological process
TermDefinition
GO:0006310DNA recombination
GO:0006974cellular response to DNA damage stimulus
GO:0000723telomere maintenance
GO:0006281DNA repair
GO:0032508DNA duplex unwinding
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000420parapharyngeal region
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR015086Phage_T4_Gp59_C