SMED30003051

Overview
NameSMED30003051
Smed IDSMED30003051
Length (bp)545
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 SMED30003051 (SMED30003051) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30003051 (SMED30003051) 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 SMED30003051 (SMED30003051) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30003051 (SMED30003051) 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



SMED30003051

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30003051SMESG000072417.1 SmedASXL_019765SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30003051SMESG000072417.1 SmedASXL_019765SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
neoblastSMED30003051SMESG000072417.1 dd_Smed_v4_6349_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30003051 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000935:75568..76154 +2664
Homology
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BLAST of SMED30003051 vs. Ensembl Fly
Match: Surf6 (gene:FBgn0038746 transcript:FBtr0083854)

HSP 1 Score: 49.6766 bits (117), Expect = 3.090e-7
Identity = 36/94 (38.30%), Postives = 60/94 (63.83%), Query Frame = 3 
Query:  231 KAADLKINRIWESTMSRIKGEKVKDNNKLIEKTFKNKRKLKERQAKKWSERKFAQNLTQKKAADKRKANIEXXXXXXXXXXXXXXXXXGRLITG 512
            KAA+++ +  W +   +++G+KVKD+ KL++K  K +R  K++   KW+ERK      ++K   KR+ N+EKR  DK + K+K   K+GR+I G
Sbjct:  230 KAAEIQTDIAWRNAFDKVEGKKVKDDTKLLQKAIKKRRVEKKKSKTKWTERKQKVEHDKEKRQKKRQENLEKRSKDKKNRKLKTASKRGRIIPG 323
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BLAST of SMED30003051 vs. UniProt/SwissProt
Match: sp|Q9VDS6|SURF6_DROME (Surfeit locus protein 6 homolog OS=Drosophila melanogaster OX=7227 GN=Surf6 PE=1 SV=1)

HSP 1 Score: 49.6766 bits (117), Expect = 3.098e-6
Identity = 36/94 (38.30%), Postives = 60/94 (63.83%), Query Frame = 3 
Query:  231 KAADLKINRIWESTMSRIKGEKVKDNNKLIEKTFKNKRKLKERQAKKWSERKFAQNLTQKKAADKRKANIEXXXXXXXXXXXXXXXXXGRLITG 512
            KAA+++ +  W +   +++G+KVKD+ KL++K  K +R  K++   KW+ERK      ++K   KR+ N+EKR  DK + K+K   K+GR+I G
Sbjct:  230 KAAEIQTDIAWRNAFDKVEGKKVKDDTKLLQKAIKKRRVEKKKSKTKWTERKQKVEHDKEKRQKKRQENLEKRSKDKKNRKLKTASKRGRIIPG 323
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BLAST of SMED30003051 vs. TrEMBL
Match: A0A2T7NM66 (SURF6 domain-containing protein OS=Pomacea canaliculata OX=400727 GN=C0Q70_18067 PE=4 SV=1)

HSP 1 Score: 63.1586 bits (152), Expect = 1.917e-8
Identity = 56/153 (36.60%), Postives = 84/153 (54.90%), Query Frame = 3 
Query:   69 EGQFLYNKFE----TIDKRDEPILFIKKNRYKVNLKTQYRKNKEFEEKIQATAENDKAKAADLKINRIWESTMSRIKGEKVKDNNKLIEKTFKNKRKLKERQAKKWSERKFAQNLTQKKAADKRKANIEXXXXXXXXXXXXXXXXXGRLITGL 515
            EG+ L++KFE    + +K       + K+  ++ +K + R     + KI    E D A A  L+   +W+  +S+ +GEKVKD+  L++K  K K K+K    KKW +R+   N  +K   +KR  NIE RK+ K   K KKL KKGRL+ GL
Sbjct:  182 EGKMLFSKFEIPKSSHEKDTHKSKLVGKDYKRLLMKLEQR-----DAKIAKVKEKDPAAATKLEEKYVWQDVLSKARGEKVKDDPGLLKKALKRKEKIKSIHKKKWGDRQKTVNKQKKTQQEKRTRNIEARKDAKKEKKRKKLIKKGRLLPGL 329
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BLAST of SMED30003051 vs. TrEMBL
Match: A0A3S1AZD4 (SURF6 domain-containing protein OS=Elysia chlorotica OX=188477 GN=EGW08_021133 PE=4 SV=1)

HSP 1 Score: 61.2326 bits (147), Expect = 1.175e-7
Identity = 41/85 (48.24%), Postives = 58/85 (68.24%), Query Frame = 3 
Query:  261 WESTMSRIKGEKVKDNNKLIEKTFKNKRKLKERQAKKWSERKFAQNLTQKKAADKRKANIEXXXXXXXXXXXXXXXXXGRLITGL 515
            W++ MS+ +GEKVKD+  L++K  K K K+KE++ +KW +RK A    QKK  D+R+ANI +RK+     K KKL KKGRL+ G 
Sbjct:  292 WQAMMSKARGEKVKDDPTLLKKAAKRKEKVKEQKGRKWDDRKKATEEAQKKRQDRREANIGRRKDATKEKKRKKLIKKGRLVPGF 376
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BLAST of SMED30003051 vs. TrEMBL
Match: F1L5H5 (SURF6 domain-containing protein OS=Ascaris suum OX=6253 PE=2 SV=1)

HSP 1 Score: 61.2326 bits (147), Expect = 1.201e-7
Identity = 46/132 (34.85%), Postives = 71/132 (53.79%), Query Frame = 3 
Query:   72 GQFLYNKFETIDKRDE--------PILFIKKNRYKVNLKTQYRKNKEFEEKIQATAENDKAKAADLKINRIWESTMSRIKGEKVKDNNKLIEKTFKNKRKLKERQAKKWSERKFAQNLTQKKAADKRKANIE 443
            GQ +Y+KF+ I K D+           F+ K+  ++  K + R     +E+I+   E +  KA  ++ N  W   MSR++G KVKDN +L+ K  K K K+KER  +KW++R       Q K  +KR ANI+
Sbjct:  336 GQLVYSKFDFIVKDDQQEEKKKDKRDKFVGKDYGRLLKKAEMR-----QERIEKIREKNPEKAVRIEENIRWNKAMSRVEGHKVKDNPELLRKGMKRKEKMKERSKEKWAKRMDYVKEKQAKQQEKRIANIQ 462
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BLAST of SMED30003051 vs. TrEMBL
Match: A0A1I8CQ59 (SURF6 domain-containing protein OS=Rhabditophanes sp. KR3021 OX=114890 PE=4 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 8.640e-7
Identity = 37/95 (38.95%), Postives = 58/95 (61.05%), Query Frame = 3 
Query:  156 NLKTQYRKNKEFEEKIQATAENDKAKAADLKINRIWESTMSRIKGEKVKDNNKLIEKTFKNKRKLKERQAKKWSERKFAQNLTQKKAADKRKANI 440
            + K   +K ++ EEKI +  E D  KA  ++ +  W+S M R +GEK+KDN ++++   K K  +KE + KKW ERK A   T++K  DKR+ N+
Sbjct:  198 DFKALLKKVEKREEKIASIREKDPEKADTIEKDIKWKSAMKRAEGEKIKDNPQMLKAAAKRKEIIKESRGKKWDERKNAITETKEKKQDKREGNL 292
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BLAST of SMED30003051 vs. TrEMBL
Match: A0A0M3IC87 (SURF6 domain-containing protein OS=Ascaris lumbricoides OX=6252 PE=4 SV=1)

HSP 1 Score: 54.299 bits (129), Expect = 2.480e-6
Identity = 34/84 (40.48%), Postives = 50/84 (59.52%), Query Frame = 3 
Query:  192 EEKIQATAENDKAKAADLKINRIWESTMSRIKGEKVKDNNKLIEKTFKNKRKLKERQAKKWSERKFAQNLTQKKAADKRKANIE 443
            +E+I+   E +  KA  ++ N  W   MSR++G KVKDN +L+ K  K K K+KER  +KW++R       Q K  +KR ANI+
Sbjct:    3 QERIEKIREKNPEKAVRIEENIRWNKAMSRVEGHKVKDNPELLRKGMKRKEKMKERSKEKWAKRMDYVKEKQAKQQEKRIANIQ 86
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BLAST of SMED30003051 vs. Planmine SMEST
Match: SMESG000072417.1 (SMESG000072417.1)

HSP 1 Score: 117.472 bits (293), Expect = 1.106e-34
Identity = 81/82 (98.78%), Postives = 82/82 (100.00%), Query Frame = 3 
Query:  273 MSRIKGEKVKDNNKLIEKTFKNKRKLKERQAKKWSERKFAQNLTQKKAADKRKANIEXXXXXXXXXXXXXXXXXGRLITGLN 518
            MSRIKGEKVKDNNKLIEKTFKNKRKLKERQ+KKWSERKFAQNLTQKKAADKRKANIEKRKNDKLSNKVKKLKKKGRLITGLN
Sbjct:    1 MSRIKGEKVKDNNKLIEKTFKNKRKLKERQSKKWSERKFAQNLTQKKAADKRKANIEKRKNDKLSNKVKKLKKKGRLITGLN 82
The following BLAST results are available for this feature:
BLAST of SMED30003051 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 SMED30003051 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 SMED30003051 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 1
Match NameE-valueIdentityDescription
Surf63.090e-738.30gene:FBgn0038746 transcript:FBtr0083854[more]
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BLAST of SMED30003051 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 SMED30003051 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 SMED30003051 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 SMED30003051 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|Q9VDS6|SURF6_DROME3.098e-638.30Surfeit locus protein 6 homolog OS=Drosophila mela... [more]
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BLAST of SMED30003051 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A2T7NM661.917e-836.60SURF6 domain-containing protein OS=Pomacea canalic... [more]
A0A3S1AZD41.175e-748.24SURF6 domain-containing protein OS=Elysia chloroti... [more]
F1L5H51.201e-734.85SURF6 domain-containing protein OS=Ascaris suum OX... [more]
A0A1I8CQ598.640e-738.95SURF6 domain-containing protein OS=Rhabditophanes ... [more]
A0A0M3IC872.480e-640.48SURF6 domain-containing protein OS=Ascaris lumbric... [more]
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BLAST of SMED30003051 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 SMED30003051 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 SMED30003051 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 SMED30003051 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 SMED30003051 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 SMED30003051 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000072417.11.106e-3498.78SMESG000072417.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003051 ID=SMED30003051|Name=SMED30003051|organism=Schmidtea mediterranea sexual|type=transcript|length=545bp
AAACATGTTAAAATTTTAAATTGAATGTGACTAATAAGAAAAACGTTGTT
TAAATATTCAACATTATGGAGGGCCAATTTTTATATAATAAATTTGAAAC
CATTGATAAACGTGATGAACCAATATTGTTTATTAAGAAAAATCGTTACA
AAGTAAATTTAAAGACTCAATATCGTAAAAATAAAGAATTTGAAGAAAAA
ATACAAGCAACCGCTGAAAATGATAAAGCTAAAGCAGCTGATTTAAAAAT
AAATCGTATTTGGGAGTCAACAATGTCGCGTATAAAAGGTGAAAAGGTGA
AAGATAACAATAAATTAATTGAGAAAACGTTTAAGAATAAACGCAAATTG
AAGGAAAGACAAGCCAAAAAGTGGAGTGAAAGGAAATTTGCTCAAAATCT
TACTCAAAAGAAGGCAGCTGATAAAAGAAAAGCCAATATTGAGAAACGTA
AAAATGACAAACTTTCCAATAAGGTTAAAAAGTTAAAGAAGAAGGGTCGC
TTAATTACTGGTTTAAATTAATAAATTTATTTAGTTTTAAAAAAA
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protein sequence of SMED30003051-orf-1

>SMED30003051-orf-1 ID=SMED30003051-orf-1|Name=SMED30003051-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=152bp
MEGQFLYNKFETIDKRDEPILFIKKNRYKVNLKTQYRKNKEFEEKIQATA
ENDKAKAADLKINRIWESTMSRIKGEKVKDNNKLIEKTFKNKRKLKERQA
KKWSERKFAQNLTQKKAADKRKANIEKRKNDKLSNKVKKLKKKGRLITGL
N*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000429neoblast
PLANA:0002109X1 cell
PLANA:0002111X2 cell
Vocabulary: INTERPRO
TermDefinition
IPR007019SURF6
IPR029190Rrp14/SURF6_C
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
GO:0003677DNA binding
GO:0003723RNA binding
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
GO:0005730nucleolus
GO:0022625cytosolic large ribosomal subunit
Vocabulary: biological process
TermDefinition
GO:0007419ventral cord development
GO:0022008neurogenesis
GO:0042254ribosome biogenesis
GO:0042273ribosomal large subunit biogenesis
GO:0042274ribosomal small subunit biogenesis
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 123..143
NoneNo IPR availableCOILSCoilCoilcoord: 25..52
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 101..133
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 95..151
IPR029190Ribosomal RNA-processing protein 14/surfeit locus protein 6, C-terminal domainPFAMPF04935SURF6coord: 26..137
e-value: 6.5E-16
score: 58.7
IPR007019Surfeit locus 6PANTHERPTHR14369SURFEIT LOCUS PROTEIN 6coord: 2..146