SMED30017255

Overview
NameSMED30017255
Smed IDSMED30017255
Length (bp)360
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30017255 (SMED30017255) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30017255 (SMED30017255) in cells (dots) of each of the 12 neoblast clusters.

 

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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



SMED30017255

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30017255 SmedASXL_001220SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30017255 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000076:91938..92296 +1702
Homology
[Close]
BLAST of SMED30017255 vs. TrEMBL
Match: A0A183N6V9 (Uncharacterized protein OS=Schistosoma margrebowiei OX=48269 GN=SMRZ_LOCUS24034 PE=4 SV=1)

HSP 1 Score: 65.0846 bits (157), Expect = 2.257e-11
Identity = 34/82 (41.46%), Postives = 49/82 (59.76%), Query Frame = 3 
Query:   36 IYDIVLPPPKEVSALVRISRWSALIAGIVYGFMHRRELAEKEVEIQNCFHRIMDKRIKDFNEATEKRVFLETKELEEMMKAS 281
            +Y   LP P+EVS L+R +RW  L AGIVYG +  + L  +E +I      I++KR+K++NE    R     K LEE+ KA+
Sbjct:    5 VYVTKLPAPREVSPLIRTARWGLLAAGIVYGALRLKYLTRREKKISERDRAIIEKRLKEYNEL---RALQAQKSLEELSKAT 83
[Close]
BLAST of SMED30017255 vs. TrEMBL
Match: A0A183Q1D4 (Uncharacterized protein OS=Schistosoma mattheei OX=31246 GN=SMTD_LOCUS20420 PE=4 SV=1)

HSP 1 Score: 63.1586 bits (152), Expect = 1.183e-10
Identity = 33/82 (40.24%), Postives = 49/82 (59.76%), Query Frame = 3 
Query:   36 IYDIVLPPPKEVSALVRISRWSALIAGIVYGFMHRRELAEKEVEIQNCFHRIMDKRIKDFNEATEKRVFLETKELEEMMKAS 281
            +Y   LP P+EVS L+R +RW  L AGIVYG +  + L  +E +I      I++KR+K++NE    R     K LEE+ +A+
Sbjct:    5 VYVTKLPAPREVSPLIRTARWGLLAAGIVYGALRLKYLTRREKKISERDRAIIEKRLKEYNEL---RALQAQKSLEELSEAT 83
[Close]
BLAST of SMED30017255 vs. TrEMBL
Match: A0A183R021 (Uncharacterized protein OS=Schistosoma rodhaini OX=6188 PE=4 SV=1)

HSP 1 Score: 61.6178 bits (148), Expect = 4.626e-10
Identity = 33/82 (40.24%), Postives = 49/82 (59.76%), Query Frame = 3 
Query:   36 IYDIVLPPPKEVSALVRISRWSALIAGIVYGFMHRRELAEKEVEIQNCFHRIMDKRIKDFNEATEKRVFLETKELEEMMKAS 281
            +Y   LP P+EVS L+R +RW  L AGIVYG +  + L ++E +I      I++KR+K++NE          K LEE+ KA+
Sbjct:    5 VYVNKLPAPREVSPLIRTARWGLLAAGIVYGALRLKYLTKREKKITERDRAIIEKRLKEYNEL---HALQAQKSLEELSKAT 83
[Close]
BLAST of SMED30017255 vs. TrEMBL
Match: A0A430QDY6 (Uncharacterized protein OS=Schistosoma bovis OX=6184 GN=DC041_0005297 PE=4 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 9.997e-10
Identity = 32/82 (39.02%), Postives = 48/82 (58.54%), Query Frame = 3 
Query:   36 IYDIVLPPPKEVSALVRISRWSALIAGIVYGFMHRRELAEKEVEIQNCFHRIMDKRIKDFNEATEKRVFLETKELEEMMKAS 281
            +Y   LP P+EVS L+R +RW  L AGIVYG +  + L  +E +I      I++KR++++NE          K LEE+ KA+
Sbjct:    5 VYVTKLPAPREVSPLIRTARWGLLAAGIVYGALRLKYLTRREKKISERDRAIIEKRLEEYNELC---ALQAQKSLEELSKAT 83
[Close]
BLAST of SMED30017255 vs. TrEMBL
Match: A0A095BVB5 (Uncharacterized protein (Fragment) OS=Schistosoma haematobium OX=6185 GN=MS3_01026 PE=4 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 1.019e-9
Identity = 32/82 (39.02%), Postives = 48/82 (58.54%), Query Frame = 3 
Query:   36 IYDIVLPPPKEVSALVRISRWSALIAGIVYGFMHRRELAEKEVEIQNCFHRIMDKRIKDFNEATEKRVFLETKELEEMMKAS 281
            +Y   LP P+EVS L+R +RW  L AGIVYG +  + L  +E +I      I++KR++++NE          K LEE+ KA+
Sbjct:    5 VYVTKLPAPREVSPLIRTARWGLLAAGIVYGALRLKYLTRREKKISERDRAIIEKRLEEYNELC---ALQAQKSLEELSKAT 83
[Close]
BLAST of SMED30017255 vs. Planmine SMEST
Match: SMESG000061177.1 (SMESG000061177.1)

HSP 1 Score: 200.29 bits (508), Expect = 3.392e-68
Identity = 96/97 (98.97%), Postives = 97/97 (100.00%), Query Frame = 3 
Query:   21 DSKSFIYDIVLPPPKEVSALVRISRWSALIAGIVYGFMHRRELAEKEVEIQNCFHRIMDKRIKDFNEATEKRVFLETKELEEMMKASLGSVKPPGKH 311
            DS+SFIYDIVLPPPKEVSALVRISRWSALIAGIVYGFMHRRELAEKEVEIQNCFHRIMDKRIKDFNEATEKRVFLETKELEEMMKASLGSVKPPGKH
Sbjct:    4 DSRSFIYDIVLPPPKEVSALVRISRWSALIAGIVYGFMHRRELAEKEVEIQNCFHRIMDKRIKDFNEATEKRVFLETKELEEMMKASLGSVKPPGKH 100
[Close]
BLAST of SMED30017255 vs. Planmine SMEST
Match: SMESG000045448.1 (SMESG000045448.1)

HSP 1 Score: 56.6102 bits (135), Expect = 1.033e-11
Identity = 32/83 (38.55%), Postives = 49/83 (59.04%), Query Frame = 3 
Query:   18 MDSKSFIYDIVLPPPKEVSALVRISRWSALIAGIVYGFMHRRELAEKEVEIQNCFHRIMDKRIKDFN-----EATEKRVFLET 251
            M  K F YDI L  PK+V+ L+R +R+  L  GI+YGF   R L ++EVEI+     I+ KR+ + +     +A + + F+ET
Sbjct:    1 MSGKVFPYDIQLRVPKQVTPLIRTARYFFLGTGILYGFFRHRYLEKREVEIKKRNDVILQKRLDELHHHNKLQAEKDKEFIET 83
The following BLAST results are available for this feature:
BLAST of SMED30017255 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 SMED30017255 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 SMED30017255 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 SMED30017255 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 SMED30017255 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 SMED30017255 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 SMED30017255 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 SMED30017255 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A183N6V92.257e-1141.46Uncharacterized protein OS=Schistosoma margrebowie... [more]
A0A183Q1D41.183e-1040.24Uncharacterized protein OS=Schistosoma mattheei OX... [more]
A0A183R0214.626e-1040.24Uncharacterized protein OS=Schistosoma rodhaini OX... [more]
A0A430QDY69.997e-1039.02Uncharacterized protein OS=Schistosoma bovis OX=61... [more]
A0A095BVB51.019e-939.02Uncharacterized protein (Fragment) OS=Schistosoma ... [more]
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BLAST of SMED30017255 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 SMED30017255 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 SMED30017255 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 SMED30017255 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 SMED30017255 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 SMED30017255 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000061177.13.392e-6898.97SMESG000061177.1[more]
SMESG000045448.11.033e-1138.55SMESG000045448.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017255 ID=SMED30017255|Name=SMED30017255|organism=Schmidtea mediterranea sexual|type=transcript|length=360bp
ATCTATATAAATCTTATATGGACTCTAAATCCTTTATTTATGATATTGTC
CTTCCGCCACCGAAAGAAGTAAGTGCTCTCGTTCGAATATCGAGGTGGAG
TGCCCTTATTGCGGGAATTGTGTACGGATTTATGCATCGCCGGGAATTAG
CTGAAAAAGAAGTAGAAATCCAAAATTGTTTTCATCGGATAATGGACAAA
AGGATTAAAGATTTTAATGAGGCAACTGAAAAGCGAGTGTTTTTAGAAAC
AAAGGAGTTGGAAGAAATGATGAAAGCAAGTCTAGGATCAGTTAAGCCGC
CCGGAAAACACTGAATAAATTTTAGTGAAAGTATTTTTGTATATAACAAT
AATATTTGTG
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protein sequence of SMED30017255-orf-1

>SMED30017255-orf-1 ID=SMED30017255-orf-1|Name=SMED30017255-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=104bp
LYKSYMDSKSFIYDIVLPPPKEVSALVRISRWSALIAGIVYGFMHRRELA
EKEVEIQNCFHRIMDKRIKDFNEATEKRVFLETKELEEMMKASLGSVKPP
GKH*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000419prepharyngeal region
Vocabulary: INTERPRO
TermDefinition
IPR008386ATP_synth_F0_esu_mt
Vocabulary: molecular function
TermDefinition
GO:0015078hydrogen ion transmembrane transporter activity
Vocabulary: biological process
TermDefinition
GO:0015986ATP synthesis coupled proton transport
Vocabulary: cellular component
TermDefinition
GO:0000276mitochondrial proton-transporting ATP synthase complex, coupling factor F(o)
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR008386ATP synthase, F0 complex, subunit E, mitochondrialPFAMPF05680ATP-synt_Ecoord: 17..90
e-value: 8.9E-14
score: 51.6