SMED30009524

Overview
NameSMED30009524
Smed IDSMED30009524
Length (bp)2177
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 SMED30009524 (SMED30009524) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30009524 (SMED30009524) 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 SMED30009524 (SMED30009524) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30009524 (SMED30009524) 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




SMED30009524

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
zeta neoblastSMED30009524 dd_Smed_v4_14230_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30009524 vs. Planmine SMEST
Match: SMESG000005270.1 (SMESG000005270.1)

HSP 1 Score: 215.698 bits (548), Expect = 2.834e-58
Identity = 150/420 (35.71%), Postives = 226/420 (53.81%), Query Frame = 3
Query:  945 IMFIDVNLVSNSNDSMRPVDVNIRNFKGVTVYDKKSHPEQRSHILKKQWSTEKISSEIKTNIKR**TSRNCCE---------------KIIIGFDIS-KLKALTLNLYNVIGVREISEDTFMCSFAMNVAPHKIKFCLSSHLAP*MV*RQNHQ*N-------ITETRTFLYNNKHYDSKSYLWNNRKAV*KSCQMELGNLK*Q*GIFIITSSR*HQRKHVHQTIQRELKFNKNGTRKTFEDELRDSDDEVIFIKQESGPKLVKTVKIEPQ---------------EATTFQEELMKCNLRTRQK*KSDINKEKE---------------KVTEKDLCRHFVRRINEGEILNLALEKGFSRTKIMIQDVEVELVRTEKDNSDIILTALGKMLDDEGKLITTFILNKYFKTWSRKYRVNVYA 2045
            I F+DV LV + N++ RPV+V IR+F    +++KK  P  R+ IL       +++ E   NI        C E               +I++G+DI+ KLKALTL++YNV+GVR+++ED+FMCSF  NVAPHKIK    S+LA  ++   +   N       +     F     +   KSYLW +R  V     +E    K +     +  +   +  ++  + + ELKF +NGTRKTFE EL DSDD++IF+ +E       ++K EPQ               E  +F+E+  + +  +  +   +   E +               +V+ K+LCRHF R I +G+ILNLAL+KGF RT + I D E++LV ++K   DI LT  G MLDDEGKL+ TF+L KY++T   +YR+N++A
Sbjct: 1964 IKFVDVKLVCDINNNQRPVEVCIRDFNETVLFNKKITP--RTKILHYYPEKTRVNKE---NII-------CNEGEYQALVDIRKLLYGQIVVGYDITNKLKALTLDIYNVMGVRKMAEDSFMCSFVKNVAPHKIKL---SNLAYQLIRYHDKWFNDKIINRILQTAEPFSAKRNNNTCKSYLWYHRAKV----GIEGDQEKKETTTNALEDNDMVEDMYIEPS-EWELKFKRNGTRKTFESELMDSDDDIIFVSEERPQNNKISIKSEPQLRENNEMQCDMDSDEEYFSFEEDNQESSQSSTTEDSDEYGPEPDIILEDPDFVIGENQTEVSHKELCRHFGRPIKDGDILNLALKKGFRRTTMKINDCEIKLVLSDKGTEDITLTTQGGMLDDEGKLLDTFVLTKYYRTGPNRYRINIHA 2363          

HSP 2 Score: 53.1434 bits (126), Expect = 7.438e-14
Identity = 25/47 (53.19%), Postives = 37/47 (78.72%), Query Frame = 2
Query:  683 IITTNMCTAVTKTINNDRSVPNNFNDMIIQMNNFPSVIAIKILYVPT 823
            +ITT+ C+ + KTI N R + N FN+++IQMNN P ++AI+ILY+PT
Sbjct: 1877 LITTSNCSIMIKTIKN-RKMSNEFNNLMIQMNNLPCLMAIEILYIPT 1922          

HSP 3 Score: 43.5134 bits (101), Expect = 7.438e-14
Identity = 16/28 (57.14%), Postives = 25/28 (89.29%), Query Frame = 1
Query:  595 EAVKKKRKMPHRILFHITKTELSICQQK 678
            ++  + +K+PHRI+FH+TKTE+SICQQ+
Sbjct: 1847 QSAAEGKKVPHRIIFHMTKTEVSICQQR 1874          
BLAST of SMED30009524 vs. Planmine SMEST
Match: SMESG000044899.1 (SMESG000044899.1)

HSP 1 Score: 104.76 bits (260), Expect = 4.088e-26
Identity = 45/88 (51.14%), Postives = 63/88 (71.59%), Query Frame = 1
Query:  367 CMLHKHYSSFYKNLKYNKCKDGNSIIVRSFPNQVCIPNEMKVEIEERELHLIKFNEAQRVKLHELIGAYDRYPNADEAVKKKRKMPHR 630
            C L+KH+ SFYKN++     DG  I +RSFP+QVCIPN+MK++IE  E+H++KFNEA  +KL ELI  +  + N D+A  + RK+ HR
Sbjct:   55 CFLNKHFHSFYKNIQNRIAADGTPITIRSFPSQVCIPNDMKIDIEVSEMHIVKFNEAMSIKLKELIRTFKEFSNVDKAAAEGRKVSHR 142          
BLAST of SMED30009524 vs. Planmine SMEST
Match: SMESG000027806.1 (SMESG000027806.1)

HSP 1 Score: 109.768 bits (273), Expect = 1.724e-25
Identity = 91/261 (34.87%), Postives = 131/261 (50.19%), Query Frame = 3
Query:  951 FIDVNLVSNSNDSMRPVDVNIRNFKGVTVYDKKSHPEQRSHILKKQWSTEKISSEIKTNIKR**TSRNCCE-------KIIIGFDIS-KLKALTLNLYNVIGVREISEDTFMCSFAMNVAPHKIKFCLSSHLAP*MV*RQNHQ*NITETRTFLYNNKHYDSKSYLWNNRKAV*KSCQMELGNLK*Q*GIFIITSSR*HQRKHVHQTIQRELKFNKNGTRKTFEDELRDSDDEVIFIKQE----------SGPKLVKTVKIE 1679
            F++V LV + N++ RPV+V IR+F G+ +++KK  P  R+  L   +  EK  +  +  I      +   +       +II+G+ I+ K +ALTL++YNV+GVREI+ED+FMCSF  NVAPHKIK    S+LA                         Y    Y   N K   +S  M    L+ +     I  S            Q ELKF +NGTR+TFE EL DSDD++IF+ +E          S P+L +  K+E
Sbjct:  139 FVNVKLVCDINNNQRPVEVCIRDFNGIVLFNKKITP--RTKFL--HYYPEKTRANKENIIGNEDEYQALIDIQKLRYGQIIVGYGITEKFEALTLDIYNVMGVREIAEDSFMCSFVKNVAPHKIKL---SNLA-------------------------YQVIRYHDKNEKEDQESEGMTTNTLEDKDIDMYIEPS------------QWELKFKRNGTRRTFESELMDSDDDIIFVSEEKPQSNKIFIKSKPQLRENNKME 355          
BLAST of SMED30009524 vs. Planmine SMEST
Match: SMESG000022623.1 (SMESG000022623.1)

HSP 1 Score: 88.1965 bits (217), Expect = 3.849e-23
Identity = 46/80 (57.50%), Postives = 58/80 (72.50%), Query Frame = 3
Query: 1548 QRELKFNKNGTRKTFEDELRDSDDEVIFIKQESGPKLVKTVKIEPQEATTFQEELMKCNLRTRQK*KSDINKEKEKVTEK 1787
            Q ELKFN+NGTR+TFEDELRDSDDE+IF+++E  PKL +TVK+EPQE TT Q+  M+C          DI K+ E V E+
Sbjct:  217 QIELKFNRNGTRRTFEDELRDSDDEIIFVREEKKPKLTETVKLEPQEPTTSQQ--MEC----------DIEKQHENVCER 284          

HSP 2 Score: 40.0466 bits (92), Expect = 3.849e-23
Identity = 16/39 (41.03%), Postives = 29/39 (74.36%), Query Frame = 1
Query: 1435 KQFRKVVKWNSETLSDNKEYLLSQVQGSIKENMYIKPSR 1551
            KQ+ +VVKW+S+  + +KE ++SQ Q   +E+ Y++PS+
Sbjct:  179 KQWEEVVKWDSDAFNGSKEQIISQAQEDNEEDAYMEPSQ 217          
BLAST of SMED30009524 vs. Planmine SMEST
Match: SMESG000022623.1 (SMESG000022623.1)

HSP 1 Score: 87.8113 bits (216), Expect = 5.710e-23
Identity = 46/80 (57.50%), Postives = 58/80 (72.50%), Query Frame = 3
Query: 1548 QRELKFNKNGTRKTFEDELRDSDDEVIFIKQESGPKLVKTVKIEPQEATTFQEELMKCNLRTRQK*KSDINKEKEKVTEK 1787
            Q ELKFN+NGTR+TFEDELRDSDDE+IF+++E  PKL +TVK+EPQE TT Q+  M+C          DI K+ E V E+
Sbjct:  224 QIELKFNRNGTRRTFEDELRDSDDEIIFVREEKKPKLTETVKLEPQEPTTSQQ--MEC----------DIEKQHENVCER 291          

HSP 2 Score: 40.0466 bits (92), Expect = 5.710e-23
Identity = 16/39 (41.03%), Postives = 29/39 (74.36%), Query Frame = 1
Query: 1435 KQFRKVVKWNSETLSDNKEYLLSQVQGSIKENMYIKPSR 1551
            KQ+ +VVKW+S+  + +KE ++SQ Q   +E+ Y++PS+
Sbjct:  186 KQWEEVVKWDSDAFNGSKEQIISQAQEDNEEDAYMEPSQ 224          
The following BLAST results are available for this feature:
BLAST of SMED30009524 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 SMED30009524 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 SMED30009524 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 SMED30009524 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 SMED30009524 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 SMED30009524 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 SMED30009524 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 SMED30009524 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 SMED30009524 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 SMED30009524 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 SMED30009524 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 SMED30009524 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 SMED30009524 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 SMED30009524 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000005270.12.834e-5835.71SMESG000005270.1[more]
SMESG000044899.14.088e-2651.14SMESG000044899.1[more]
SMESG000027806.11.724e-2534.87SMESG000027806.1[more]
SMESG000022623.13.849e-2357.50SMESG000022623.1[more]
SMESG000022623.15.710e-2357.50SMESG000022623.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009524 ID=SMED30009524|Name=SMED30009524|organism=Schmidtea mediterranea sexual|type=transcript|length=2177bp
GATCTCGGTGATTTTTGCTAATTAAATTTTTTTTTTGATAATGATTTTTT
ATTTTTCCAATAAGGATATTTTTTAGTTGGATATTTAGAATCATTCATTA
TTTAGCATTTGATATTATTTATTTTCTATTTATTATTGCTTTGATTTTTT
TAAATTTTGAGATCATTTCAATTTTTTATAATTAATAAATCAAATAAGCA
TGTCAATGATTTCATTAAAAGAAAGCGCCATTGAAGCACTCGTTTTTCGA
CATTTCTACAGATTTTCTGTCATCAGGCAAAATCCACCAAAACAATATGG
ATTTAATTTATTTACAAATTATTATTATTTTTCTTATATATAGAAAAAAG
AGAACGCTATATTTACTGTATGCTCCACAAACATTACAGCAGTTTTTACA
AAAACCTAAAGTACAACAAATGTAAAGATGGAAACTCTATAATAGTCCGC
AGTTTTCCCAATCAGGTATGCATTCCAAATGAGATGAAGGTCGAGATCGA
GGAAAGGGAATTACATTTAATAAAATTCAATGAAGCTCAGAGAGTGAAAT
TACATGAATTGATTGGAGCTTACGACAGATACCCTAATGCCGATGAAGCA
GTTAAGAAAAAAAGGAAAATGCCACATCGAATACTATTTCACATAACAAA
AACAGAGTTGTCAATTTGTCAACAAAAATATCATTATAACAACCAATATG
TGCACTGCAGTTACAAAAACAATAAATAATGATCGAAGCGTCCCAAATAA
TTTCAATGATATGATCATACAAATGAACAATTTTCCCAGCGTCATCGCAA
TTAAAATACTATACGTACCAACATCCCAAACCCATTTCAGCCACTACAAA
CCATACAATCAAATATTCAAATGCATGAAAATTTCATTAAGGAAAAAATG
TCATTCACCCATAAAGATCTATCAACAGATAAAAGATTCAGCATATTATG
TTCATAGACGTGAATTTAGTAAGTAATTCAAACGACAGTATGAGACCTGT
AGATGTCAACATTAGAAACTTTAAAGGAGTAACAGTTTATGACAAAAAAT
CACATCCAGAACAAAGATCACACATCCTTAAAAAACAATGGTCAACCGAG
AAAATATCATCGGAAATAAAGACGAATATCAAGCGCTAATAAACATCCAG
AAACTGCTGTGAAAAAATAATAATTGGTTTCGATATCAGTAAATTGAAAG
CACTTACCTTAAATCTGTACAATGTAATAGGGGTACGGGAAATTTCAGAA
GATACATTCATGTGCTCATTCGCAATGAACGTCGCCCCACATAAAATCAA
ATTTTGTCTATCAAGTCATTTAGCACCGTAAATGGTATAAAGACAAAATC
ATCAATGAAACATTACAGAAACCCGAACCTTTCTCTACAACAATAAACAC
TATGATAGTAAAAGTTATTTATGGAATAACAGAAAAGCAGTTTAGAAAAG
TTGTCAAATGGAACTCGGAAACCTTAAGTGACAATAAGGAATATTTATTA
TCACAAGTTCAAGGTAGCATCAAAGAAAACATGTACATCAAACCATCCAG
AGAGAACTAAAATTCAACAAAAATGGCACCAGGAAAACCTTTGAGGACGA
ATTACGGGATAGTGACGATGAAGTCATTTTCATAAAGCAAGAAAGTGGAC
CGAAGCTTGTGAAAACAGTCAAAATTGAGCCACAAGAAGCCACGACATTC
CAAGAAGAGCTAATGAAGTGCAATCTCAGAACCAGACAGAAATAGAAGAG
CGATATCAATAAAGAAAAGGAGAAAGTCACTGAAAAGGATTTATGTCGTC
ATTTTGTAAGACGAATTAATGAAGGTGAAATTTTAAATCTGGCACTAGAA
AAAGGCTTCAGTAGAACAAAAATAATGATTCAGGATGTCGAAGTAGAGTT
GGTGCGCACAGAAAAAGATAATTCGGACATTATCCTAACAGCCCTGGGAA
AAATGTTGGATGATGAGGGTAAACTCATCACCACATTTATTCTCAACAAA
TATTTCAAGACATGGTCTAGAAAATACAGAGTAAATGTATATGCTAAAAG
TTGAACGTAGTCAAATCCCAATTCAAAAAAAACGAACACTCAATCCAATC
TTCAAACAAGCCTGCAATAGCTGAACAATTGTTATTATCTAGAAATGCAT
GTAACATTATTTGTGATTTAATTTTTG
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protein sequence of SMED30009524-orf-1

>SMED30009524-orf-1 ID=SMED30009524-orf-1|Name=SMED30009524-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=120bp
MLHKHYSSFYKNLKYNKCKDGNSIIVRSFPNQVCIPNEMKVEIEERELHL
IKFNEAQRVKLHELIGAYDRYPNADEAVKKKRKMPHRILFHITKTELSIC
QQKYHYNNQYVHCSYKNNK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
Vocabulary: INTERPRO
TermDefinition
IPR001912Ribosomal_S4/S9_N
Vocabulary: molecular function
TermDefinition
GO:0019843rRNA binding
Vocabulary: cellular component
TermDefinition
GO:0005622intracellular