SMED30004721

Overview
NameSMED30004721
Smed IDSMED30004721
Length (bp)460
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 SMED30004721 (SMED30004721) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30004721 (SMED30004721) in cells (dots) of each of the 12 neoblast clusters.

 

back to top

 

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 SMED30004721 (SMED30004721) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30004721 (SMED30004721) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top

 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020



SMED30004721

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



PAGE Curations: 13

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30004721SMESG000046687.1 Contig3931newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004721SMESG000046687.1 Contig3931uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004721SMESG000069155.1 Contig3931newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004721SMESG000069155.1 Contig3931uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
X1 cellSMED30004721SMESG000046687.1 SmedASXL_017470SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
nervous systemSMED30004721SMESG000046687.1 dd_Smed_v4_1325_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30004721SMESG000046687.1 dd_Smed_v4_1325_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30004721SMESG000046687.1 dd_Smed_v4_1325_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30004721SMESG000046687.1 dd_Smed_v4_1325_1_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
whole organismSMED30004721SMESG000046687.1 Contig41039newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
whole organismSMED30004721SMESG000046687.1 Contig41039uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
reproductive organSMED30004721SMESG000046687.1 Contig12572newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30004721SMESG000046687.1 Contig12572uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30004721 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.014586:8849..9472 -2067
v31.002989:67826..68448 -2067
Homology
[Close]
BLAST of SMED30004721 vs. Ensembl Mouse
Match: Atpif1 (ATPase inhibitory factor 1 [Source:MGI Symbol;Acc:MGI:1196457])

HSP 1 Score: 45.0542 bits (105), Expect = 1.704e-6
Identity = 25/58 (43.10%), Postives = 42/58 (72.41%), Query Frame = 2 
Query:  212 FGKREAYLEEEYFRXXXXXXXXXXXXXXXDEVDTHVHEIEKHEEAIKRHKRKVEEIKN 385
            FGKRE   E+ YFR+  + ++  L++  EDE+D H  EIE+ ++ I+RHK+K++++KN
Sbjct:   47 FGKREKAEEDRYFREKTKEQLAALRKHHEDEIDHHSKEIERLQKQIERHKKKIQQLKN 104
[Close]
BLAST of SMED30004721 vs. Ensembl Mouse
Match: Atpif1 (ATPase inhibitory factor 1 [Source:MGI Symbol;Acc:MGI:1196457])

HSP 1 Score: 44.2838 bits (103), Expect = 1.885e-6
Identity = 25/58 (43.10%), Postives = 42/58 (72.41%), Query Frame = 2 
Query:  212 FGKREAYLEEEYFRXXXXXXXXXXXXXXXDEVDTHVHEIEKHEEAIKRHKRKVEEIKN 385
            FGKRE   E+ YFR+  + ++  L++  EDE+D H  EIE+ ++ I+RHK+K++++KN
Sbjct:   15 FGKREKAEEDRYFREKTKEQLAALRKHHEDEIDHHSKEIERLQKQIERHKKKIQQLKN 72
[Close]
BLAST of SMED30004721 vs. Planmine SMEST
Match: SMESG000046687.1 (SMESG000046687.1)

HSP 1 Score: 143.665 bits (361), Expect = 7.405e-45
Identity = 120/120 (100.00%), Postives = 120/120 (100.00%), Query Frame = 2 
Query:   47 MNRLLGFSRVVKLKGSLPLRNISCSPLIFXXXXXXXXXXXXXXXXXXXXXXXXXXFGKREAYLEEEYFRXXXXXXXXXXXXXXXDEVDTHVHEIEKHEEAIKRHKRKVEEIKNLVKEQNK 406
            MNRLLGFSRVVKLKGSLPLRNISCSPLIFSGDGSLGSGDGKGGGKGGSIRDSGGSFGKREAYLEEEYFRKLNENKVKELKEQLEDEVDTHVHEIEKHEEAIKRHKRKVEEIKNLVKEQNK
Sbjct:    1 MNRLLGFSRVVKLKGSLPLRNISCSPLIFSGDGSLGSGDGKGGGKGGSIRDSGGSFGKREAYLEEEYFRKLNENKVKELKEQLEDEVDTHVHEIEKHEEAIKRHKRKVEEIKNLVKEQNK 120
[Close]
BLAST of SMED30004721 vs. Planmine SMEST
Match: SMESG000074861.1 (SMESG000074861.1)

HSP 1 Score: 50.0618 bits (118), Expect = 1.326e-8
Identity = 30/60 (50.00%), Postives = 46/60 (76.67%), Query Frame = 2 
Query:  212 FGKREAYLEEEYFRXXXXXXXXXXXXXXXDEVDTHVHEIEKHEEAIKRHKRKVEEIKNLV 391
            FGKREA  EEEYF+++   K+  +K+ L+DE+ +H  EIE H +AI+RHK++++EIK +V
Sbjct:   31 FGKREAAHEEEYFKRMEREKINGMKKYLQDELKSHEEEIENHTDAIERHKQRIKEIKEVV 90
[Close]
BLAST of SMED30004721 vs. Planmine SMEST
Match: SMESG000074861.1 (SMESG000074861.1)

HSP 1 Score: 50.447 bits (119), Expect = 1.516e-8
Identity = 30/60 (50.00%), Postives = 46/60 (76.67%), Query Frame = 2 
Query:  212 FGKREAYLEEEYFRXXXXXXXXXXXXXXXDEVDTHVHEIEKHEEAIKRHKRKVEEIKNLV 391
            FGKREA  EEEYF+++   K+  +K+ L+DE+ +H  EIE H +AI+RHK++++EIK +V
Sbjct:   63 FGKREAAHEEEYFKRMEREKINGMKKYLQDELKSHEEEIENHTDAIERHKQRIKEIKEVV 122
The following BLAST results are available for this feature:
BLAST of SMED30004721 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30004721 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30004721 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30004721 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30004721 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30004721 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 2
Match NameE-valueIdentityDescription
Atpif11.704e-643.10ATPase inhibitory factor 1 [Source:MGI Symbol;Acc:... [more]
Atpif11.885e-643.10ATPase inhibitory factor 1 [Source:MGI Symbol;Acc:... [more]
back to top
BLAST of SMED30004721 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30004721 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30004721 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30004721 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30004721 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30004721 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30004721 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30004721 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000046687.17.405e-45100.00SMESG000046687.1[more]
SMESG000074861.11.326e-850.00SMESG000074861.1[more]
SMESG000074861.11.516e-850.00SMESG000074861.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004721 ID=SMED30004721|Name=SMED30004721|organism=Schmidtea mediterranea sexual|type=transcript|length=460bp
GGAAGTCTAGGTAGTGGAGTAAAGTAATTGTTATTTTTTGAATTTAATGA
ATCGCTTATTAGGATTTTCAAGAGTTGTAAAATTGAAAGGATCTTTGCCA
TTAAGGAATATATCATGTTCGCCTTTAATATTTAGTGGAGATGGAAGTCT
AGGTAGTGGAGATGGAAAAGGTGGCGGAAAAGGTGGTTCTATTAGAGATT
CTGGTGGATCTTTTGGTAAAAGAGAAGCTTATCTTGAAGAAGAATATTTT
CGAAAATTGAATGAAAACAAAGTTAAAGAACTAAAAGAGCAGCTTGAAGA
TGAAGTTGATACTCATGTTCATGAAATTGAAAAACATGAAGAAGCAATTA
AACGTCATAAAAGAAAAGTTGAAGAAATTAAAAATTTAGTGAAAGAACAA
AATAAATAATTCCTACTCCGATATCATTTGTTCATTTCGATGATTAATTA
TACATAGGGG
back to top

protein sequence of SMED30004721-orf-1

>SMED30004721-orf-1 ID=SMED30004721-orf-1|Name=SMED30004721-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=121bp
MNRLLGFSRVVKLKGSLPLRNISCSPLIFSGDGSLGSGDGKGGGKGGSIR
DSGGSFGKREAYLEEEYFRKLNENKVKELKEQLEDEVDTHVHEIEKHEEA
IKRHKRKVEEIKNLVKEQNK*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
PLANA:0000136whole organism
PLANA:0000429neoblast
PLANA:0002089reproductive organ
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR007648ATPase_inhibitor_mt
Vocabulary: cellular component
TermDefinition
GO:0005739mitochondrion
GO:0005753mitochondrial proton-transporting ATP synthase complex
GO:0009986cell surface
Vocabulary: molecular function
TermDefinition
GO:0042030ATPase inhibitor activity
GO:0005515protein binding
GO:0005516calmodulin binding
GO:0042803protein homodimerization activity
GO:0043532angiostatin binding
GO:0051117ATPase binding
Vocabulary: biological process
TermDefinition
GO:0032780negative regulation of ATPase activity
GO:0001937negative regulation of endothelial cell proliferation
GO:0006783heme biosynthetic process
GO:0030218erythrocyte differentiation
GO:0051260protein homooligomerization
GO:0051289protein homotetramerization
GO:0051346negative regulation of hydrolase activity
GO:0051882mitochondrial depolarization
GO:0072593reactive oxygen species metabolic process
GO:1901030positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway
GO:1903052positive regulation of proteolysis involved in cellular protein catabolic process
GO:1903214regulation of protein targeting to mitochondrion
GO:1903578regulation of ATP metabolic process
GO:1904925positive regulation of mitophagy in response to mitochondrial depolarization
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 69..120
NoneNo IPR availableGENE3DG3DSA:1.20.5.500coord: 36..119
e-value: 2.0E-19
score: 71.3
NoneNo IPR availablePANTHERPTHR23407ATPASE INHIBITOR/5-FORMYLTETRAHYDROFOLATE CYCLO-LIGASEcoord: 28..113
NoneNo IPR availablePANTHERPTHR23407:SF7ATPASE INHIBITOR MAI-1, MITOCHONDRIALcoord: 28..113
NoneNo IPR availableSUPERFAMILYSSF64602F1 ATPase inhibitor, IF1, C-terminal domaincoord: 53..113
IPR007648Mitochondrial ATPase inhibitorPFAMPF04568IATPcoord: 33..103
e-value: 1.3E-21
score: 76.9