X1.A.G7.1

Overview
NameX1.A.G7.1
Smed IDSMED30025608
Length (bp)902
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 X1.A.G7.1 (SMED30025608) t-SNE clustered cells

Violin plots show distribution of expression levels for X1.A.G7.1 (SMED30025608) 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 X1.A.G7.1 (SMED30025608) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for X1.A.G7.1 (SMED30025608) 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




SMED30025608

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30025608SMESG000046817.1 SMESG000046814.1 dd_Smed_v4_1507_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
epidermal cellSMED30025608SMESG000046817.1 SMESG000046814.1 dd_Smed_v4_1507_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30025608SMESG000046817.1 SMESG000046814.1 dd_Smed_v4_1507_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30025608SMESG000046817.1 SMESG000046814.1 dd_Smed_v4_1507_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult colorimetric in situ hybridization evidence
dorsal region of the epidermisSMED30025608SMESG000046817.1 SMESG000046814.1 dd_Smed_v4_1507_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
whole organismSMED30025608SMESG000046817.1 SMESG000046814.1 dd_Smed_v4_1507_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
BLAST of X1.A.G7.1 vs. Planmine SMEST
Match: SMESG000046817.1 (SMESG000046817.1)

HSP 1 Score: 384.415 bits (986), Expect = 9.332e-136
Identity = 235/235 (100.00%), Postives = 235/235 (100.00%), Query Frame = 3
Query:   66 MARPNEGFTTDEYATVSEXXXXXXXXXXXXXXXXXXDIIKIPTDVNVMYLPPPRYDGLVMNNQVIVVSQPAPEPPQNVILRFKKAHLKLGILLTIVGGIQMILDPLLPALFMYPYSLFPGGLFMLISGICSIHGSRREDRCSLRASLTFDXXXXXXXXXXXXXXXXXXXXGDSILFCKSSIYLCYPSVDFYSSGLKGFSIFNLIYGIILFVLLCWDSGIKCGDVCCCKRRQPRVT 770
            MARPNEGFTTDEYATVSEPVPPYPQTFQPPNPPNYNDIIKIPTDVNVMYLPPPRYDGLVMNNQVIVVSQPAPEPPQNVILRFKKAHLKLGILLTIVGGIQMILDPLLPALFMYPYSLFPGGLFMLISGICSIHGSRREDRCSLRASLTFDILALVLVFIAIIIAIVVIIAGDSILFCKSSIYLCYPSVDFYSSGLKGFSIFNLIYGIILFVLLCWDSGIKCGDVCCCKRRQPRVT
Sbjct:    1 MARPNEGFTTDEYATVSEPVPPYPQTFQPPNPPNYNDIIKIPTDVNVMYLPPPRYDGLVMNNQVIVVSQPAPEPPQNVILRFKKAHLKLGILLTIVGGIQMILDPLLPALFMYPYSLFPGGLFMLISGICSIHGSRREDRCSLRASLTFDILALVLVFIAIIIAIVVIIAGDSILFCKSSIYLCYPSVDFYSSGLKGFSIFNLIYGIILFVLLCWDSGIKCGDVCCCKRRQPRVT 235          
BLAST of X1.A.G7.1 vs. Planmine SMEST
Match: SMESG000046814.1 (SMESG000046814.1)

HSP 1 Score: 384.415 bits (986), Expect = 9.332e-136
Identity = 235/235 (100.00%), Postives = 235/235 (100.00%), Query Frame = 3
Query:   66 MARPNEGFTTDEYATVSEXXXXXXXXXXXXXXXXXXDIIKIPTDVNVMYLPPPRYDGLVMNNQVIVVSQPAPEPPQNVILRFKKAHLKLGILLTIVGGIQMILDPLLPALFMYPYSLFPGGLFMLISGICSIHGSRREDRCSLRASLTFDXXXXXXXXXXXXXXXXXXXXGDSILFCKSSIYLCYPSVDFYSSGLKGFSIFNLIYGIILFVLLCWDSGIKCGDVCCCKRRQPRVT 770
            MARPNEGFTTDEYATVSEPVPPYPQTFQPPNPPNYNDIIKIPTDVNVMYLPPPRYDGLVMNNQVIVVSQPAPEPPQNVILRFKKAHLKLGILLTIVGGIQMILDPLLPALFMYPYSLFPGGLFMLISGICSIHGSRREDRCSLRASLTFDILALVLVFIAIIIAIVVIIAGDSILFCKSSIYLCYPSVDFYSSGLKGFSIFNLIYGIILFVLLCWDSGIKCGDVCCCKRRQPRVT
Sbjct:    1 MARPNEGFTTDEYATVSEPVPPYPQTFQPPNPPNYNDIIKIPTDVNVMYLPPPRYDGLVMNNQVIVVSQPAPEPPQNVILRFKKAHLKLGILLTIVGGIQMILDPLLPALFMYPYSLFPGGLFMLISGICSIHGSRREDRCSLRASLTFDILALVLVFIAIIIAIVVIIAGDSILFCKSSIYLCYPSVDFYSSGLKGFSIFNLIYGIILFVLLCWDSGIKCGDVCCCKRRQPRVT 235          
BLAST of X1.A.G7.1 vs. Planmine SMEST
Match: SMESG000046812.1 (SMESG000046812.1)

HSP 1 Score: 195.282 bits (495), Expect = 2.689e-61
Identity = 113/232 (48.71%), Postives = 164/232 (70.69%), Query Frame = 3
Query:   66 MARPNEGFTTDEYATVSEXXXXXXXXXXXXXXXXXXDIIKIPTDVNVMYLPPPRYDGLVMNNQVIVVSQPAPEPPQNVILRFKKAHLKLGILLTIVGGIQMILDPLLPALFMYPYSLFPGGLFMLISGICSIHGSRREDRCSLRASLTFDXXXXXXXXXXXXX-XXXXXXXGDSILFCKSSIYLCYPSVDFYSSGLKGFSIFNLIYGIILFVLLCWDSGIKCGDVCCCKRRQ 758
            M + + GFTT+E+A +        QTF+P +PPNYNDI+K P +   + +PPP+Y+G       IVV     E  QN +LR+K+ HL  G +  ++GGIQ+ +DP+LP++F YPYS++PGGLFM+ISG+CSI+GSR+ ++CSL ASL F+ILA++++F   II  + +  +G S   C     +CYPSV FY+ G+KGF+IFN+++GIILFVL+ WDS +KCGDVC  K++Q
Sbjct:    1 MEQSDAGFTTEEHAIILNSDRHNLQTFEPLSPPNYNDIVKSPLNGPTLSIPPPQYEG-------IVVPPQTTEESQNSMLRYKRMHLIYGTIYVVLGGIQVAIDPILPSIFQYPYSMYPGGLFMIISGLCSIYGSRKNNKCSLIASLIFNILAMIVIFTNYIIGILALNQSGFSFTPCNQYNSICYPSVSFYTEGVKGFAIFNVVFGIILFVLMIWDSSLKCGDVCFKKQKQ 225          
BLAST of X1.A.G7.1 vs. Planmine SMEST
Match: SMESG000046815.1 (SMESG000046815.1)

HSP 1 Score: 193.741 bits (491), Expect = 1.028e-60
Identity = 113/232 (48.71%), Postives = 161/232 (69.40%), Query Frame = 3
Query:   66 MARPNEGFTTDEYATVSEXXXXXXXXXXXXXXXXXXDIIKIPTDVNVMYLPPPRYDGLVMNNQVIVVSQPAPEPPQNVILRFKKAHLKLGILLTIVGGIQMILDPLLPALFMYPYSLFPGGLFMLISGICSIHGSRREDRCSLRASLTFDXXXXXXXXXXXXX-XXXXXXXGDSILFCKSSIYLCYPSVDFYSSGLKGFSIFNLIYGIILFVLLCWDSGIKCGDVCCCKRRQ 758
            M + N GFTT+EYA +        QTF+P +PPNYNDI+K P     + +PPP+Y+G+ +  Q         E  QN +LR+K+ HL  G +  ++GGIQ+ +DP+LP++F YPYS++PGGLFM+ISG+CSI+GSR+ ++CSL ASL F+ILAL+++F   II  +    +G     C     +CYPSV FY+ G+KGF+IFN+++GIILFVL+ WDS +KCGDVC  K++Q
Sbjct:    1 MEQSNAGFTTEEYAIILNSDRHNLQTFEPLSPPNYNDIVKSPLTGPTLSIPPPQYEGIAVPPQTT-------EESQNSMLRYKRMHLIYGTISVVLGGIQVAIDPILPSIFQYPYSMYPGGLFMIISGLCSIYGSRKNNKCSLIASLIFNILALIVIFTNYIIGILASNQSGFFFTPCNQYNAICYPSVSFYTEGVKGFAIFNVVFGIILFVLMIWDSSLKCGDVCFKKQKQ 225          
BLAST of X1.A.G7.1 vs. Planmine SMEST
Match: SMESG000046819.1 (SMESG000046819.1)

HSP 1 Score: 188.348 bits (477), Expect = 1.086e-58
Identity = 111/232 (47.84%), Postives = 158/232 (68.10%), Query Frame = 3
Query:   66 MARPNEGFTTDEYATVSEXXXXXXXXXXXXXXXXXXDIIKIPTDVNVMYLPPPRYDGLVMNNQVIVVSQPAPEPPQNVILRFKKAHLKLGILLTIVGGIQMILDPLLPALFMYPYSLFPGGLFMLISGICSIHGSRREDRCSLRASLTFDXXXXXXXXXXXXX-XXXXXXXGDSILFCKSSIYLCYPSVDFYSSGLKGFSIFNLIYGIILFVLLCWDSGIKCGDVCCCKRRQ 758
            M + N GFTT+EYA +        QTF+P +PPNYNDI+K P     + +PPP+Y+G       I V     E  QN +LR+K+ HL  G +  ++GGIQ+ +DP+LP++F YPYS++PGGLFM+ISG+CSI+GSR+ ++CSL ASL F+ILAL+++F   II  +    +G     C     +CYPSV FY+ G+KG +IFN+++G+ILFVL+ WDS +KCGDVC   ++Q
Sbjct:    1 MEQSNAGFTTEEYAIILNSDRHNLQTFEPLSPPNYNDIVKSPLTGPTLSIPPPQYEG-------IAVPPQTTEESQNSMLRYKRMHLIYGTISVVLGGIQVAIDPILPSIFQYPYSMYPGGLFMIISGLCSIYGSRKNNKCSLIASLIFNILALIVIFTNYIIGILASNQSGFFFTPCNQYNAICYPSVSFYTEGVKGLAIFNVVFGMILFVLMIWDSSLKCGDVCFKNQKQ 225          
The following BLAST results are available for this feature:
BLAST of X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 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 X1.A.G7.1 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000046817.19.332e-136100.00SMESG000046817.1[more]
SMESG000046814.19.332e-136100.00SMESG000046814.1[more]
SMESG000046812.12.689e-6148.71SMESG000046812.1[more]
SMESG000046815.11.028e-6048.71SMESG000046815.1[more]
SMESG000046819.11.086e-5847.84SMESG000046819.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30025608 ID=SMED30025608|Name=X1.A.G7.1|organism=Schmidtea mediterranea sexual|type=transcript|length=902bp
GTCATACGAAAGATTGTATTGCGTTTTCATAATCACTGACCAGTTTTTTA
AAACTAGAAAAAGCAATGGCACGGCCAAATGAAGGATTTACGACGGATGA
ATATGCAACAGTTAGTGAACCCGTTCCACCTTATCCGCAAACATTTCAGC
CTCCTAATCCTCCAAATTATAACGATATTATAAAGATTCCAACGGACGTC
AATGTAATGTATCTTCCACCTCCGCGATATGATGGGCTAGTAATGAATAA
TCAAGTGATTGTAGTTTCACAACCTGCTCCTGAACCACCTCAAAATGTAA
TATTAAGATTCAAAAAGGCTCATCTTAAATTGGGAATTCTGTTGACAATA
GTAGGAGGCATTCAGATGATACTTGATCCGTTATTACCAGCATTATTTAT
GTACCCTTATTCTTTATTTCCCGGAGGATTGTTTATGTTAATCAGTGGGA
TTTGCTCCATTCATGGAAGTCGAAGAGAAGATAGGTGTAGCTTGAGAGCG
TCATTAACATTCGACATTCTAGCGTTGGTACTTGTATTTATAGCCATTAT
AATAGCTATTGTTGTCATAATTGCGGGTGACTCCATATTATTCTGCAAAA
GCTCAATTTATTTGTGTTACCCTAGCGTGGATTTCTACTCCTCTGGACTT
AAAGGCTTTAGTATTTTCAATCTGATTTATGGGATTATTTTGTTTGTTCT
TCTTTGCTGGGATTCCGGCATAAAGTGCGGAGATGTTTGCTGTTGTAAAC
GACGACAACCAAGAGTGACTTACAATCCGAATGGGCCTAATTAGATTTAT
TAAAACATATTTATGTACCAGAAAGAAAATAACTAATTATTCCACAAAAT
GCTTTCGCTGTGAATAAATTTTAATTAACAAATTTTATTAACACAATTAA
TT
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protein sequence of SMED30025608-orf-1

>SMED30025608-orf-1 ID=SMED30025608-orf-1|Name=SMED30025608-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=243bp
MARPNEGFTTDEYATVSEPVPPYPQTFQPPNPPNYNDIIKIPTDVNVMYL
PPPRYDGLVMNNQVIVVSQPAPEPPQNVILRFKKAHLKLGILLTIVGGIQ
MILDPLLPALFMYPYSLFPGGLFMLISGICSIHGSRREDRCSLRASLTFD
ILALVLVFIAIIIAIVVIIAGDSILFCKSSIYLCYPSVDFYSSGLKGFSI
FNLIYGIILFVLLCWDSGIKCGDVCCCKRRQPRVTYNPNGPN*
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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:0000016pharynx
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0000136whole organism
PLANA:0002032epidermal cell
Vocabulary: INTERPRO
TermDefinition
IPR007237CD20-like
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR007237CD20-like familyPFAMPF04103CD20coord: 86..182
e-value: 2.8E-8
score: 34.0
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..22
NoneNo IPR availableTMHMMTMhelixcoord: 89..111
NoneNo IPR availableTMHMMTMhelixcoord: 197..219
NoneNo IPR availableTMHMMTMhelixcoord: 147..169
NoneNo IPR availableTMHMMTMhelixcoord: 115..134