SMED30001731

Overview
NameSMED30001731
Smed IDSMED30001731
Length (bp)627
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 SMED30001731 (SMED30001731) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30001731 (SMED30001731) 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 SMED30001731 (SMED30001731) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30001731 (SMED30001731) 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



SMED30001731

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30001731 SmedASXL_006297SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
epidermisSMED30001731 dd_Smed_v4_4859_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30001731 dd_Smed_v4_4859_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30001731 dd_Smed_v4_4859_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
SMED30001731 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001430:82134..83408 +2975
Homology
[Close]
BLAST of SMED30001731 vs. Ensembl Xenopus
Match: c6orf203 (chromosome 6 open reading frame 203 [Source:NCBI gene;Acc:779478])

HSP 1 Score: 46.9802 bits (110), Expect = 4.932e-6
Identity = 25/74 (33.78%), Postives = 42/74 (56.76%), Query Frame = -2 
Query:   96 EDEAFSKDYHHMHISVTVLRSDKIISSCLKVTRNLIDKIFYQGSIMVNGAPLQKKSAPLSEGDIIELSIDGRKR 317
            ED    KDY  +  +V   R D I+++ L ++RN I++ FY   + +NG  L KKS  +  GD ++L ++  K+
Sbjct:  116 EDLNVQKDYKDLEKAVQSFRFDVILTAGLDISRNKIEEAFYNSLLRLNGEKLWKKSRAVKVGDTLDLIVEEDKQ 189
[Close]
BLAST of SMED30001731 vs. Ensembl Mouse
Match: 1700021F05Rik (RIKEN cDNA 1700021F05 gene [Source:MGI Symbol;Acc:MGI:1915101])

HSP 1 Score: 46.2098 bits (108), Expect = 7.217e-6
Identity = 23/64 (35.94%), Postives = 35/64 (54.69%), Query Frame = -2 
Query:  117 AFSKDYHHMHISVTVLRSDKIISSCLKVTRNLIDKIFYQGSIMVNGAPLQKKSAPLSEGDIIEL 308
              +KDY  +   V   R D I+ + L V RN ++  FY+G + +NG  L KKS  +  GD ++L
Sbjct:  127 GVAKDYKDLEKVVQSFRYDVILKTGLDVGRNKVEDAFYKGELRLNGEKLWKKSRTVKVGDTLDL 190
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BLAST of SMED30001731 vs. TrEMBL
Match: R7U0X3 (S4 RNA-binding domain-containing protein OS=Capitella teleta OX=283909 GN=CAPTEDRAFT_205157 PE=4 SV=1)

HSP 1 Score: 65.4698 bits (158), Expect = 4.525e-10
Identity = 39/107 (36.45%), Postives = 59/107 (55.14%), Query Frame = -2 
Query:   30 YFAEDEAFSKDYHHMHISVTVLRSDKIISSCLKVTRNLIDKIFYQGSIMVNGAPLQKKSAPLSEGDIIEL--SIDGRKR---RIRICSIKEKNY---RQVVKARVWK 326
            +F ED     +Y  + + V  LR D I++  L V RN +D+ F   ++ +NG  + KK   LSEGD I++  S DG  R   R+RI ++  K     R+VV+ RVW+
Sbjct:   18 FFDEDADLPNNYRDLTVHVKSLRLDAILAQGLNVARNKVDEHFLGSNLELNGNRVLKKGKQLSEGDYIDVITSNDGEARRFKRVRITNVSSKTTKSDRKVVQLRVWR 124
[Close]
BLAST of SMED30001731 vs. TrEMBL
Match: A0A2A4JKS7 (S4 RNA-binding domain-containing protein OS=Heliothis virescens OX=7102 GN=B5V51_837 PE=4 SV=1)

HSP 1 Score: 59.3066 bits (142), Expect = 1.326e-7
Identity = 32/80 (40.00%), Postives = 48/80 (60.00%), Query Frame = -2 
Query:  117 DEDDIEIKDEYFAEDEAFSKDYHHMHISVTVLRSDKIISSCLKVTRNLIDKIFYQGSIMVNGAPLQKKSAPLSEGDIIEL 356
            D DD E+    F  D + SKD   +  + T +R+D I+ S L V+RN ++++FY+  I VNG  + KKSA L  GD I++
Sbjct:   18 DSDDEEVD---FEGDSSLSKDSKVVKFNTTSMRTDVILKSALGVSRNKVEQMFYESKIRVNGKKIMKKSASLKLGDEIDV 94
[Close]
BLAST of SMED30001731 vs. TrEMBL
Match: C1LF40 (Asparaginyl-tRNA synthetase OS=Schistosoma japonicum OX=6182 PE=2 SV=1)

HSP 1 Score: 59.6918 bits (143), Expect = 1.637e-7
Identity = 36/110 (32.73%), Postives = 58/110 (52.73%), Query Frame = -2 
Query:   18 YFAEDEAFSKDYHHMHISVTVLRSDKIISSCLKVTRNLIDKIFYQGSIMVNGAPLQKKSAPLSEGDIIELSIDGRK----RRIRICSIK---EKNYRQVVKARVWKNVVE 326
            Y+ ED  FS ++  +  +V  LR DKII   L +TR++ D  F+     +NGA L K    +  GD +++ ID  +    +R+R+  IK   + NY+  +  R W+N V 
Sbjct:   84 YYMEDMTFSPNFRQISSNVKSLRFDKIIRVGLDITRSVADNTFFSSRFRLNGAKLLKMGTTVYVGDKLDMIIDDTEEPVGKRVRVLDIKQLRQNNYK--ISLRCWRNQVR 191
[Close]
BLAST of SMED30001731 vs. TrEMBL
Match: A0A1S3K4U3 (uncharacterized protein C6orf203 homolog OS=Lingula unguis OX=7574 GN=LOC106178693 PE=4 SV=1)

HSP 1 Score: 60.077 bits (144), Expect = 2.532e-7
Identity = 35/117 (29.91%), Postives = 67/117 (57.26%), Query Frame = -2 
Query:   18 IEIKDEYFAEDEAFSKDYHHMHISVTVLRSDKIISSCLKVTRNLIDKIFYQGSIMVNGAPLQKKSAPLSEGDIIELSIDG----RKRRIRICSIKEKNYRQVVKARV----WKNVVE 344
            +E+ D+   E +   +DY  M+I+V  +R D +++S L ++    + +F    I+VNG  ++KK+  +  GDI+++  +G    +KRR+++ SI  +N  +  +ARV    W+N  E
Sbjct:  134 VELGDDVEEETDG-PEDYRTMNITVKTVRVDSVVASGLAISNKQTEALFLGTKILVNGEKIRKKARRVKVGDILDVIGEGHESNKKRRVKVLSIDTENVTKKGRARVTIRAWRNPFE 249
[Close]
BLAST of SMED30001731 vs. TrEMBL
Match: A0A2T7P783 (S4 RNA-binding domain-containing protein OS=Pomacea canaliculata OX=400727 GN=C0Q70_11850 PE=4 SV=1)

HSP 1 Score: 57.7658 bits (138), Expect = 4.647e-7
Identity = 30/100 (30.00%), Postives = 54/100 (54.00%), Query Frame = -2 
Query:   27 YHHMHISVTVLRSDKIISSCLKVTRNLIDKIFYQGSIMVNGAPLQKKSAPLSEGDIIELSIDGRK--------RRIRICSIKEKNYRQ---VVKARVWKN 293
            +  + I V  LR+D ++SS L V+RN +D++FY   + +NG  L KKS  + EGD ++L ++           +R+++  + E+   +    V  +VWK 
Sbjct:   35 FRKITIHVKSLRADSVVSSALDVSRNKVDELFYSSRLRLNGQTLLKKSKQIDEGDFVDLVLERSTQNEGEIMVKRVKVIGVSEERTNKDKVAVTVKVWKG 134
[Close]
BLAST of SMED30001731 vs. Planmine SMEST
Match: SMESG000042728.1 (SMESG000042728.1)

HSP 1 Score: 325.479 bits (833), Expect = 1.861e-112
Identity = 193/196 (98.47%), Postives = 194/196 (98.98%), Query Frame = -2 
Query:   24 MSFIARLNIKLFSKAKYLFVNKLSKKTNFSTVFRNYKPYYLSNANHFNIIINYYXXXXXXXXXXXXXXXXXXXXXXXXXXXVFVPDEDDIEIKDEYFAEDEAFSKDYHHMHISVTVLRSDKIISSCLKVTRNLIDKIFYQGSIMVNGAPLQKKSAPLSEGDIIELSIDGRKRRIRICSIKEKNYRQVVKARVWKNV 611
            MSFIARLNI LFSKA YLFVNKLSKKTNFSTVFRNYKPYYLSNANHFNIIINYYSKKSKSTVKKSSVSEEHEESDDEFDSEVFVPDEDDIEIKDEYFAEDEAF+KDYHHMHISVTVLRSDKIISSCLKVTRNLIDKIFYQGSIMVNGAPLQKKSAPLSEGDIIELSIDGRKRRIRICSIKEKNYRQVVKARVWKNV
Sbjct:    1 MSFIARLNINLFSKANYLFVNKLSKKTNFSTVFRNYKPYYLSNANHFNIIINYYSKKSKSTVKKSSVSEEHEESDDEFDSEVFVPDEDDIEIKDEYFAEDEAFNKDYHHMHISVTVLRSDKIISSCLKVTRNLIDKIFYQGSIMVNGAPLQKKSAPLSEGDIIELSIDGRKRRIRICSIKEKNYRQVVKARVWKNV 196
The following BLAST results are available for this feature:
BLAST of SMED30001731 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 SMED30001731 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 SMED30001731 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 SMED30001731 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 SMED30001731 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 1
Match NameE-valueIdentityDescription
c6orf2034.932e-633.78chromosome 6 open reading frame 203 [Source:NCBI g... [more]
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BLAST of SMED30001731 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 1
Match NameE-valueIdentityDescription
1700021F05Rik7.217e-635.94RIKEN cDNA 1700021F05 gene [Source:MGI Symbol;Acc:... [more]
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BLAST of SMED30001731 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 SMED30001731 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
R7U0X34.525e-1036.45S4 RNA-binding domain-containing protein OS=Capite... [more]
A0A2A4JKS71.326e-740.00S4 RNA-binding domain-containing protein OS=Heliot... [more]
C1LF401.637e-732.73Asparaginyl-tRNA synthetase OS=Schistosoma japonic... [more]
A0A1S3K4U32.532e-729.91uncharacterized protein C6orf203 homolog OS=Lingul... [more]
A0A2T7P7834.647e-730.00S4 RNA-binding domain-containing protein OS=Pomace... [more]
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BLAST of SMED30001731 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 SMED30001731 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 SMED30001731 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 SMED30001731 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 SMED30001731 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 SMED30001731 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000042728.11.861e-11298.47SMESG000042728.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30001731 ID=SMED30001731|Name=SMED30001731|organism=Schmidtea mediterranea sexual|type=transcript|length=627bp
ACAAATTAATACATTTATTCAACTACATTTTTCCACACTCTTGCTTTAAC
CACTTGTCTGTAATTTTTTTCTTTGATTGAACAAATTCTTATCCTTCGTT
TTCGACCATCAATACTGAGTTCAATAATATCTCCTTCACTTAGTGGAGCA
CTTTTCTTTTGTAAAGGAGCACCATTTACCATAATGCTTCCTTGATAAAA
AATTTTGTCTATTAAATTTCTTGTAACTTTTAAGCAGCTTGATATTATTT
TGTCTGATCTTAAAACAGTTACACTAATGTGCATATGATGATAATCTTTA
CTGAAAGCCTCATCTTCAGCAAAATATTCATCTTTAATTTCAATATCATC
TTCATCTGGTACAAATACCTCTGAATCAAATTCATCGTCAGATTCTTCAT
GCTCTTCGGACACTGAAGATTTTTTAACAGTAGATTTCGATTTTTTCGAA
TAATAATTAATTATAATGTTAAAATGATTGGCATTTGATAAATAATAAGG
TTTATAATTACGAAAAACTGTTGAAAAATTTGTTTTTTTACTTAATTTAT
TAACAAATAGATATTTAGCTTTCGAAAATAACTTGATATTTAAACGTGCT
ATAAAACTCATTATTTATCAAATGCCA
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protein sequence of SMED30001731-orf-1

>SMED30001731-orf-1 ID=SMED30001731-orf-1|Name=SMED30001731-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=199bp
MSFIARLNIKLFSKAKYLFVNKLSKKTNFSTVFRNYKPYYLSNANHFNII
INYYSKKSKSTVKKSSVSEEHEESDDEFDSEVFVPDEDDIEIKDEYFAED
EAFSKDYHHMHISVTVLRSDKIISSCLKVTRNLIDKIFYQGSIMVNGAPL
QKKSAPLSEGDIIELSIDGRKRRIRICSIKEKNYRQVVKARVWKNVVE*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000429neoblast
PLANA:0002032epidermal cell
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR036986S4_RNA-bd_sf
IPR039167MTRES1
IPR002942S4_RNA-bd
Vocabulary: biological process
TermDefinition
GO:1903108regulation of transcription from mitochondrial promoter
Vocabulary: cellular component
TermDefinition
GO:0005739mitochondrion
Vocabulary: molecular function
TermDefinition
GO:0003723RNA binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR036986RNA-binding S4 domain superfamilyGENE3DG3DSA:3.10.290.10coord: 117..196
e-value: 5.0E-8
score: 35.2
IPR039167Mitochondrial transcription rescue factor 1PANTHERPTHR13633UNCHARACTERIZEDcoord: 24..195
IPR002942RNA-binding S4 domainPROSITEPS50889S4coord: 117..179
score: 10.146
IPR002942RNA-binding S4 domainCDDcd00165S4coord: 118..185
e-value: 0.00319675
score: 32.9918
NoneNo IPR availableSUPERFAMILYSSF55174Alpha-L RNA-binding motifcoord: 110..180