SMED30008108

Overview
NameSMED30008108
Smed IDSMED30008108
Length (bp)922
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 SMED30008108 (SMED30008108) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30008108 (SMED30008108) 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




SMED30008108

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
gutSMED30008108SMESG000025456.1 dd_Smed_v4_72642_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
SMED30008108 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000021:15231..16152 +4610
Homology
BLAST of SMED30008108 vs. TrEMBL
Match: A0A448WWI4 (Uncharacterized protein (Fragment) OS=Protopolystoma xenopodis OX=117903 GN=PXEA_LOCUS15414 PE=4 SV=1)

HSP 1 Score: 63.1586 bits (152), Expect = 2.537e-7
Identity = 26/55 (47.27%), Postives = 39/55 (70.91%), Query Frame = 3
Query:  624 LLAIERRTRCQIKTSNETFLYRGKVVKPLIIDGPNKNSVLRCRNCLPDSLRECII 788
             ++IE RT C+I+     FL+RG+ V+ L+IDGP KN++LRC++ LPD L   +I
Sbjct:  492 FVSIEARTGCEIRLGARRFLHRGRTVRHLVIDGPTKNNILRCKSSLPDRLTRLLI 546          
BLAST of SMED30008108 vs. TrEMBL
Match: A0A2H1CXR6 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_000443 PE=4 SV=1)

HSP 1 Score: 62.003 bits (149), Expect = 4.203e-7
Identity = 33/99 (33.33%), Postives = 51/99 (51.52%), Query Frame = 3
Query:  540 GQTRLIMLMPHDSKEGWTKIMKFARY----------------RTLLAIERRTRCQIKTSNETFLYRGKVVKPLIIDGPNKNSVLRCRNCLPDSLRECII 788
            G + +I     D +EGW +   F                    TLL++E RT C+I+ S   F++RGK V+ ++IDGP++  +LRC + LP  L + II
Sbjct:  268 GSSGVIRSEKTDYREGWLRYTMFLHQEKTDALNFYATIRKAKHTLLSLEARTGCEIRLSKRLFVHRGKHVRTVVIDGPSRKHILRCYSSLPTLLTKMII 366          
BLAST of SMED30008108 vs. TrEMBL
Match: A0A504Z8W8 (Uncharacterized protein OS=Fasciola gigantica OX=46835 GN=FGIG_05293 PE=4 SV=1)

HSP 1 Score: 61.2326 bits (147), Expect = 9.393e-7
Identity = 32/99 (32.32%), Postives = 51/99 (51.52%), Query Frame = 3
Query:  540 GQTRLIMLMPHDSKEGWTKIMKFARY----------------RTLLAIERRTRCQIKTSNETFLYRGKVVKPLIIDGPNKNSVLRCRNCLPDSLRECII 788
            G + +I     D +EGW +   F                    TLL++E RT C+I+ S   F++RGK V+ ++IDGP++  ++RC + LP  L + II
Sbjct:  268 GSSGVIRSEKTDYREGWLRYTMFLHQEKTDALNFYATIRKAKHTLLSLEARTGCEIRLSKRLFVHRGKHVRTVVIDGPSRKHIIRCYSSLPTLLTKMII 366          
BLAST of SMED30008108 vs. TrEMBL
Match: A0A074YWV0 (Uncharacterized protein (Fragment) OS=Opisthorchis viverrini OX=6198 GN=T265_15597 PE=4 SV=1)

HSP 1 Score: 59.6918 bits (143), Expect = 2.431e-6
Identity = 32/103 (31.07%), Postives = 54/103 (52.43%), Query Frame = 3
Query:  528 PEFSGQTRLIMLMPHDSKEGWTKIMKF------------ARYR----TLLAIERRTRCQIKTSNETFLYRGKVVKPLIIDGPNKNSVLRCRNCLPDSLRECII 788
            PEF G       + +  +EGW +   F            A+ R      L++E +T C+++ S   FL+RGK+V+ ++IDGP++  +LRC + LP  L + +I
Sbjct:  262 PEFVGSESATKEV-YGHREGWIRYTMFLHQERADICGFYAKLRNAKHVFLSLEAKTGCELRLSKRLFLHRGKLVRTVVIDGPSRKHILRCHSSLPSILTKLMI 363          
BLAST of SMED30008108 vs. TrEMBL
Match: A0A3R7CFB0 (Uncharacterized protein OS=Clonorchis sinensis OX=79923 GN=CSKR_4442s PE=4 SV=1)

HSP 1 Score: 58.9214 bits (141), Expect = 4.405e-6
Identity = 31/103 (30.10%), Postives = 54/103 (52.43%), Query Frame = 3
Query:  528 PEFSGQTRLIMLMPHDSKEGWTKIMKF------------ARYR----TLLAIERRTRCQIKTSNETFLYRGKVVKPLIIDGPNKNSVLRCRNCLPDSLRECII 788
            PE +G       + +  +EGW +   F            A+ R      L++E +T C+++ S   FL+RGK+V+ ++IDGP++  +LRC + LP  L + +I
Sbjct:  263 PELAGSESATREV-YGHREGWVRYTMFLHQERADICEFYAKLRNAKHVFLSLEAKTGCELRLSKRLFLHRGKLVRTVVIDGPSRKHILRCHSSLPSILTKLMI 364          
BLAST of SMED30008108 vs. Planmine SMEST
Match: SMESG000025456.1 (SMESG000025456.1)

HSP 1 Score: 536.184 bits (1380), Expect = 0.000e+0
Identity = 278/278 (100.00%), Postives = 278/278 (100.00%), Query Frame = 3
Query:   24 MGNCLLNDLNEKSLSEILTRKHLCXXXXXXXXXXXXXXXCIKIDRTFTFDSKSIEQINFTETISENNSTYDLSNKQKVFSSSTLSYNESTYNIQQNPDQCSIFSGDLCDNQTNVVRLDNRMLSQDPADLLVPPKLCRPEKIIDDFQNNRAMNFTKSKIITNQELGFCIPEFSGQTRLIMLMPHDSKEGWTKIMKFARYRTLLAIERRTRCQIKTSNETFLYRGKVVKPLIIDGPNKNSVLRCRNCLPDSLRECIIYHEFDAKFGNFMQIDQKEFISFN 857
            MGNCLLNDLNEKSLSEILTRKHLCSINNIINSDNNEQSNCIKIDRTFTFDSKSIEQINFTETISENNSTYDLSNKQKVFSSSTLSYNESTYNIQQNPDQCSIFSGDLCDNQTNVVRLDNRMLSQDPADLLVPPKLCRPEKIIDDFQNNRAMNFTKSKIITNQELGFCIPEFSGQTRLIMLMPHDSKEGWTKIMKFARYRTLLAIERRTRCQIKTSNETFLYRGKVVKPLIIDGPNKNSVLRCRNCLPDSLRECIIYHEFDAKFGNFMQIDQKEFISFN
Sbjct:    1 MGNCLLNDLNEKSLSEILTRKHLCSINNIINSDNNEQSNCIKIDRTFTFDSKSIEQINFTETISENNSTYDLSNKQKVFSSSTLSYNESTYNIQQNPDQCSIFSGDLCDNQTNVVRLDNRMLSQDPADLLVPPKLCRPEKIIDDFQNNRAMNFTKSKIITNQELGFCIPEFSGQTRLIMLMPHDSKEGWTKIMKFARYRTLLAIERRTRCQIKTSNETFLYRGKVVKPLIIDGPNKNSVLRCRNCLPDSLRECIIYHEFDAKFGNFMQIDQKEFISFN 278          
BLAST of SMED30008108 vs. Planmine SMEST
Match: SMESG000023299.1 (SMESG000023299.1)

HSP 1 Score: 87.4261 bits (215), Expect = 1.981e-19
Identity = 41/94 (43.62%), Postives = 62/94 (65.96%), Query Frame = 3
Query:  510 ELGFCIPEFSGQTRLIMLMPHDSKEGWTKIMKFARY-RTLLAIERRTRCQIKTSNETFLYRGKVVKPLIIDGPNKNSVLRCRNCLPDSLRECII 788
            +LGFC P  +G+ R +M +   S  GW  +  F +Y RTL+A ER+T C I+ S   FLYRG  VKPLII+G +KN +++C++ LP  +++ +I
Sbjct:  226 KLGFC-PTDTGRLRYLMFIKASSSNGWKNVNIFQQYARTLIANERKTGCDIQISESLFLYRGTEVKPLIIEGNSKNQIIKCKSLLPKFIKQHLI 318          
BLAST of SMED30008108 vs. Planmine SMEST
Match: SMESG000062441.1 (SMESG000062441.1)

HSP 1 Score: 60.8474 bits (146), Expect = 1.133e-10
Identity = 29/99 (29.29%), Postives = 53/99 (53.54%), Query Frame = 3
Query:  549 RLIMLMPHDSKEGWTKIMKFARYRTLLAIERRTRCQIKTSNETFLYRGKVVKPLIIDGPNKNSVLRCRNCLPDSLRECIIYHE--------FDAKFGNF 821
            + +  +  D ++GW++I      RT +  E+R  C++    E  +YRG +   +  +  NKN++++CRN  PD L+E +I +E        F ++FGN 
Sbjct:  137 KYVAYVNADDEQGWSRIKNLMN-RTSIGFEKRFECKVIFEEEPIIYRGNMCYAIRFEAHNKNNIIKCRNSFPDYLKEKLILNEDSIMEINHFISEFGNL 234          
BLAST of SMED30008108 vs. Planmine SMEST
Match: SMESG000062451.1 (SMESG000062451.1)

HSP 1 Score: 60.8474 bits (146), Expect = 1.144e-10
Identity = 29/99 (29.29%), Postives = 53/99 (53.54%), Query Frame = 3
Query:  549 RLIMLMPHDSKEGWTKIMKFARYRTLLAIERRTRCQIKTSNETFLYRGKVVKPLIIDGPNKNSVLRCRNCLPDSLRECIIYHE--------FDAKFGNF 821
            + +  +  D ++GW++I      RT +  E+R  C++    E  +YRG +   +  +  NKN++++CRN  PD L+E +I +E        F ++FGN 
Sbjct:  137 KYVAYVNADDEQGWSRIKNLMN-RTSIGFEKRFECKVIFEEEPIIYRGNMCYAIRFEAHNKNNIIKCRNSFPDYLKEKLILNEDSIMEINHFISEFGNL 234          
BLAST of SMED30008108 vs. Planmine SMEST
Match: SMESG000043405.1 (SMESG000043405.1)

HSP 1 Score: 58.5362 bits (140), Expect = 6.958e-10
Identity = 33/99 (33.33%), Postives = 53/99 (53.54%), Query Frame = 3
Query:  507 QELGFCIPEFSGQTRLIMLMPHDSKEGWTKIMKFARYRTLLAIERRTRCQIKTSNETFLYRGKVVKPLIIDGPNKNSVLRCRNCLPDSLRE-CIIYHEF 800
            Q LGF   E   +     L+  D       +  F   R  L++ER+ +C+I  S     Y+G +V+P+ I G NK+SVL CR+ LP++++  CII  ++
Sbjct:  120 QRLGFVNDEARQKVIYTFLVCQDKTYCENILKVFILSRRFLSLERQNKCEILLSTTNVQYKGIIVRPISIVGKNKSSVLSCRSSLPETIKSICIISEDY 218          
The following BLAST results are available for this feature:
BLAST of SMED30008108 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 SMED30008108 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 SMED30008108 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 SMED30008108 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 SMED30008108 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 SMED30008108 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 SMED30008108 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 SMED30008108 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A448WWI42.537e-747.27Uncharacterized protein (Fragment) OS=Protopolysto... [more]
A0A2H1CXR64.203e-733.33Uncharacterized protein OS=Fasciola hepatica OX=61... [more]
A0A504Z8W89.393e-732.32Uncharacterized protein OS=Fasciola gigantica OX=4... [more]
A0A074YWV02.431e-631.07Uncharacterized protein (Fragment) OS=Opisthorchis... [more]
A0A3R7CFB04.405e-630.10Uncharacterized protein OS=Clonorchis sinensis OX=... [more]
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BLAST of SMED30008108 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 SMED30008108 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 SMED30008108 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 SMED30008108 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 SMED30008108 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 SMED30008108 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000025456.10.000e+0100.00SMESG000025456.1[more]
SMESG000023299.11.981e-1943.62SMESG000023299.1[more]
SMESG000062441.11.133e-1029.29SMESG000062441.1[more]
SMESG000062451.11.144e-1029.29SMESG000062451.1[more]
SMESG000043405.16.958e-1033.33SMESG000043405.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30008108 ID=SMED30008108|Name=SMED30008108|organism=Schmidtea mediterranea sexual|type=transcript|length=922bp
TTCCAAATCAATAAATATTTAATATGGGAAATTGTTTATTAAATGATTTA
AATGAGAAATCACTGTCAGAAATTTTAACTAGAAAACATTTATGTAGCAT
AAATAATATTATTAATTCAGATAACAATGAGCAATCTAACTGCATAAAAA
TCGACAGAACATTTACATTTGATAGTAAATCCATTGAGCAAATTAACTTT
ACAGAAACGATATCGGAAAATAATTCCACGTACGATTTATCGAATAAACA
GAAAGTTTTCTCCTCTTCAACTTTGTCATATAATGAGTCGACATATAATA
TTCAGCAAAATCCTGACCAATGCTCCATATTTAGCGGTGATCTTTGTGAC
AATCAAACAAATGTTGTCCGACTGGATAACAGGATGCTTTCCCAAGATCC
AGCAGATCTGTTGGTACCACCAAAATTATGTCGCCCTGAAAAAATAATTG
ACGACTTTCAAAATAATCGAGCTATGAATTTTACGAAATCAAAAATAATC
ACCAATCAGGAATTAGGATTTTGTATTCCAGAATTCAGTGGACAAACGCG
ATTGATAATGTTAATGCCACACGATTCGAAAGAAGGATGGACAAAAATTA
TGAAATTCGCAAGATATAGAACGCTGTTAGCTATTGAGAGAAGAACACGT
TGTCAAATTAAAACGAGCAACGAAACATTTCTATATCGTGGTAAAGTTGT
CAAACCATTGATAATAGATGGCCCAAATAAAAATTCCGTTCTCCGATGTA
GAAATTGTCTTCCTGACTCGTTAAGAGAATGTATCATTTATCATGAATTC
GACGCAAAATTTGGGAATTTCATGCAAATCGACCAAAAAGAATTCATTAG
CTTTAATTAATGTGAACTTATTCCATAATGTTGAGTTAAATTATAGATTT
ACTAACCATATTGATATCGTAC
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protein sequence of SMED30008108-orf-1

>SMED30008108-orf-1 ID=SMED30008108-orf-1|Name=SMED30008108-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=279bp
MGNCLLNDLNEKSLSEILTRKHLCSINNIINSDNNEQSNCIKIDRTFTFD
SKSIEQINFTETISENNSTYDLSNKQKVFSSSTLSYNESTYNIQQNPDQC
SIFSGDLCDNQTNVVRLDNRMLSQDPADLLVPPKLCRPEKIIDDFQNNRA
MNFTKSKIITNQELGFCIPEFSGQTRLIMLMPHDSKEGWTKIMKFARYRT
LLAIERRTRCQIKTSNETFLYRGKVVKPLIIDGPNKNSVLRCRNCLPDSL
RECIIYHEFDAKFGNFMQIDQKEFISFN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut