SMED30015658

Overview
NameSMED30015658
Smed IDSMED30015658
Length (bp)1530
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 SMED30015658 (SMED30015658) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30015658 (SMED30015658) 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



SMED30015658

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 cellSMED30015658 SmedASXL_075661SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30015658 SmedASXL_075661SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
parenchymaSMED30015658 dd_Smed_v4_17687_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
Homology
[Close]
BLAST of SMED30015658 vs. TrEMBL
Match: A0A4C1XLJ2 (Uncharacterized protein OS=Eumeta variegata OX=151549 GN=EVAR_59718_1 PE=4 SV=1)

HSP 1 Score: 90.5077 bits (223), Expect = 7.829e-18
Identity = 47/119 (39.50%), Postives = 69/119 (57.98%), Query Frame = -3 
Query: 1178 IIVKLSEKIKNNLRFSLTLDEWTSSRTNKYVNIILHSAPDPYEKSYNLGL------CTATKLLKVVTDHLDSFKVNYEQHIVVTTRDDASLMVKCGKECLASYQLCLNHGLHLAVCDTL 1516
            +I K    + +  RFSL++DEWTS R  +Y N+ L+       + +NLGL      C A +  K+V D L  F++++E+HIV TT D  ++M K G+E  +   LCLNH +HL V DT 
Sbjct:    1 MIQKFKNLVASGTRFSLSVDEWTSVRNRRYFNLCLYVEDG---EVFNLGLIYIPGKCGAEETKKMVEDTLKRFQLDFEKHIVATTSDGPNVMKKFGRESPSEMILCLNHAIHLGVVDTF 116
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BLAST of SMED30015658 vs. TrEMBL
Match: E2BHG7 (Uncharacterized protein (Fragment) OS=Harpegnathos saltator OX=610380 GN=EAI_00742 PE=4 SV=1)

HSP 1 Score: 88.1965 bits (217), Expect = 2.285e-16
Identity = 50/128 (39.06%), Postives = 70/128 (54.69%), Query Frame = -3 
Query: 1160 KEKIIVKLSEKIKNNLRFSLTLDEWTSSRTNKYVNIILHSAPDPYEKSYNLGL------CTATKLLKVVTDHLDSFKVNYEQHIVVTTRDDASLMVKCGKECLASYQLCLNHGLHLAVCDTL*EKIKQ 1525
            K ++I       ++  R SLT+DEWTS +  KY NI +H     +   YNLGL      C  T+  K V   L  F++N++ HIV  T D  ++M K G+E      LCLNH +HL+V DT  EKI++
Sbjct:   38 KNEMIAHFKNLYESGARLSLTIDEWTSLQNRKYFNICVHYIDGKF---YNLGLVYIPGKCGVTETKKNVETSLQEFELNFKNHIVAVTSDGPNIMKKFGRESTCEIILCLNHAIHLSVFDTFSEKIEK 162
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BLAST of SMED30015658 vs. TrEMBL
Match: A0A087TB62 (Uncharacterized protein (Fragment) OS=Stegodyphus mimosarum OX=407821 GN=X975_12308 PE=4 SV=1)

HSP 1 Score: 90.1225 bits (222), Expect = 1.495e-15
Identity = 53/126 (42.06%), Postives = 77/126 (61.11%), Query Frame = -3 
Query: 1178 MKEKIIVKLSEKIKNNLRFSLTLDEWTSSRTNKYVNIILHSAPDPYEKSYNLGL------CTATKLL---KVVTDHLDSFKVNYEQHIVVTTRDDASLMVKCGKECLASYQLCLNHGLHLAVCDTL 1528
            +K+KI   + + I  +  FS+T+DEWTS    +++NI LH+A    +KS +LGL      C A K     ++V +HL+SF ++++  IV  T D AS+M+K GKE  A YQ CL H LHLAV  T+
Sbjct:    4 VKQKIKNDIKKDIAESKEFSITMDEWTSIGNRRFLNISLHNA---CQKSIDLGLVRIFGSCNAKKKKKKRELVEEHLESFGLSFKHDIVSNTGDGASVMIKFGKESPAFYQTCLAHALHLAVTKTV 126
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BLAST of SMED30015658 vs. TrEMBL
Match: A0A1J1ITF6 (CLUMA_CG015396, isoform A (Fragment) OS=Clunio marinus OX=568069 GN=CLUMA_CG015396 PE=4 SV=1)

HSP 1 Score: 82.4185 bits (202), Expect = 1.177e-14
Identity = 46/116 (39.66%), Postives = 69/116 (59.48%), Query Frame = -3 
Query: 1160 NNLRFSLTLDEWTSSRTNKYVNIILHSAPDPYEKSYNLGL-------CTATKLLKVVTDHLDSFKVNYEQHIVVTTRDDASLMVKCGKECLASYQLCLNHGLHLAVCDTL*EKIKQ 1486
             + RFSLTLDEWT     +Y+++ LH      E +YNLG+       CTA  + ++VT  L+   ++  +HIV +T D A +M+K G+     +Q C+NHG+HLAV D L +K K+
Sbjct:   59 RDARFSLTLDEWTDLTGRRYLHVNLHD----LEGTYNLGIIPVPTGHCTADVISQLVTSKLEEVGLSLTKHIVSSTTDGAKVMLKYGRITHIGFQACINHGIHLAVTDVLYKKKKK 170
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BLAST of SMED30015658 vs. TrEMBL
Match: A0A4C1ZMV9 (Uncharacterized protein OS=Eumeta variegata OX=151549 GN=EVAR_21761_1 PE=4 SV=1)

HSP 1 Score: 83.9593 bits (206), Expect = 1.446e-14
Identity = 48/127 (37.80%), Postives = 71/127 (55.91%), Query Frame = -3 
Query: 1166 MKEKIIVKLSEKIKNNLRFSLTLDEWTSSRTNKYVNIILHSAPDPYEKSYNLGLC------TATKLLKVVTDHLDSFKVNYEQHIVVTTRDDASLMVKCGKECLASYQLCLNHGLHLAVCDTL*EKI 1528
            ++ K++ +LS+  +   RFSLT DEWTSS   +Y+NI  H+  +     +NLGL        AT  ++ +   L  F+++ ++ IV  T D AS+MVK G    A  QLC  HGL L + D L +KI
Sbjct:   88 LRMKVVNELSQLKETGHRFSLTFDEWTSSSNRRYLNINAHTYANDRALFWNLGLTRIFGSMPATVCVETLRKKLKKFEIDLDEDIVAITTDGASVMVKTGSLVPAFQQLCYAHGLQLGILDVLYKKI 214
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BLAST of SMED30015658 vs. Planmine SMEST
Match: SMESG000068156.1 (SMESG000068156.1)

HSP 1 Score: 105.531 bits (262), Expect = 1.639e-24
Identity = 59/124 (47.58%), Postives = 78/124 (62.90%), Query Frame = -3 
Query: 1178 MKEKIIVKL-SEKIKNNLRFSLTLDEWTSSRTNKYVNIILHSAPDPYEKSYNLGL------CTATKLLKVVTDHLDSFKVNYEQHIVVTTRDDASLMVKCGKECLASYQLCLNHGLHLAVCDTL 1528
            +K+ I +K   E IK   +FS+TLDE  SSR N+Y+NI +H   D   K +NLGL      C A K+L +VTDHL  F +++E   + T  D AS+MVK G+E  A  QLCLNHGLHLAV + +
Sbjct:   10 LKKNIFIKFFDEAIKKGQKFSITLDECLSSRQNRYMNINVH---DKTGKVFNLGLIRIIGSCNARKILSIVTDHLKIFHLSFENADMATINDGASVMVKYGRESPAEVQLCLNHGLHLAVYEAI 130
[Close]
BLAST of SMED30015658 vs. Planmine SMEST
Match: SMESG000004539.1 (SMESG000004539.1)

HSP 1 Score: 103.605 bits (257), Expect = 2.882e-23
Identity = 55/113 (48.67%), Postives = 71/113 (62.83%), Query Frame = -3 
Query: 1184 LSEKIKNNLRFSLTLDEWTSSRTNKYVNIILHSAPDPYEKSYNLGL------CTATKLLKVVTDHLDSFKVNYEQHIVVTTRDDASLMVKCGKECLASYQLCLNHGLHLAVCD 1504
              E IK   +FS+TLDE  SSR ++Y+NI +H   D   K +NLGL      CT  K+  +VTDHL  F +++E  +V TT D  S+MVK G+E  A  QLCLNHGLHL VC+
Sbjct:   87 FDEAIKKGQKFSITLDELVSSRQHRYMNINVH---DKTGKVFNLGLIRIIGSCTTRKIPSIVTDHLKVFHLSFENDVVATTNDGTSVMVKYGRESPAEVQLCLNHGLHLDVCN 196
[Close]
BLAST of SMED30015658 vs. Planmine SMEST
Match: SMESG000046976.1 (SMESG000046976.1)

HSP 1 Score: 81.2629 bits (199), Expect = 1.362e-16
Identity = 40/74 (54.05%), Postives = 49/74 (66.22%), Query Frame = -3 
Query: 1178 YNLGL------CTATKLLKVVTDHLDSFKVNYEQHIVVTTRDDASLMVKCGKECLASYQLCLNHGLHLAVCDTL 1381
            +NLGL      C A KLL +VTDHL  F +++E  +V    D AS+MVK G+E  A  QLCLNHGLHLAVC+T 
Sbjct:   11 FNLGLIRIIGSCNARKLLSIVTDHLKIFHLSFENDVVANINDGASVMVKYGRESKAEVQLCLNHGLHLAVCNTF 84
[Close]
BLAST of SMED30015658 vs. Planmine SMEST
Match: SMESG000018816.1 (SMESG000018816.1)

HSP 1 Score: 67.781 bits (164), Expect = 6.802e-13
Identity = 37/104 (35.58%), Postives = 59/104 (56.73%), Query Frame = -3 
Query: 1169 LDEWTSSRTNKYVNIILHSAPDPYEKSYNLGLC------TATKLLKVVTDHLDSFKVNYEQHIVVTTRDDASLMVKCGKECLASYQLCLNHGLHLAVCDTL*EK 1462
            ++EWTS++  +Y NI LH A   +    NLGL        + K  +VV +HL  F ++++ +IV  T + A++ +K G E    +QLCL H  +LAV D + +K
Sbjct:    1 MNEWTSTKMRRYFNINLHDASGKFN---NLGLARINGSFNSEKFQQVVRNHLLQFGISFDIYIVACTTNGAAVNIKFGGERTTEFQLCLAHSAYLAVIDIICDK 101
[Close]
BLAST of SMED30015658 vs. Planmine SMEST
Match: SMESG000065760.1 (SMESG000065760.1)

HSP 1 Score: 68.9366 bits (167), Expect = 4.182e-12
Identity = 41/116 (35.34%), Postives = 64/116 (55.17%), Query Frame = -3 
Query: 1178 KLSEKIKNNLRFSLTLDEWTSSRTNKYVNIILHSAPDPYEKSYNLGL------CTATKLLKVVTDHLDSFKVNYEQHIVVTTRDDASLMVKCGKECLASYQLCLNHGLHLAVCDTL 1507
            K ++  K+ + FS+T DEWTS    +Y+N+ LHS  D    SY LGL      C A ++  +V   L  + +   ++I+ +T+D AS+M K  +      Q C+NH +HLAV +T 
Sbjct:  137 KFTKMAKSGMCFSITTDEWTSCSGKRYLNVTLHSQED----SYKLGLIAIEGSCDAYQIHSLVEQKLMDYGIKL-RNILASTQDGASVMKKYAQLNKIENQFCINHAIHLAVVETF 247
The following BLAST results are available for this feature:
BLAST of SMED30015658 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 SMED30015658 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 SMED30015658 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 SMED30015658 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 SMED30015658 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 SMED30015658 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 SMED30015658 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 SMED30015658 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A4C1XLJ27.829e-1839.50Uncharacterized protein OS=Eumeta variegata OX=151... [more]
E2BHG72.285e-1639.06Uncharacterized protein (Fragment) OS=Harpegnathos... [more]
A0A087TB621.495e-1542.06Uncharacterized protein (Fragment) OS=Stegodyphus ... [more]
A0A1J1ITF61.177e-1439.66CLUMA_CG015396, isoform A (Fragment) OS=Clunio mar... [more]
A0A4C1ZMV91.446e-1437.80Uncharacterized protein OS=Eumeta variegata OX=151... [more]
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BLAST of SMED30015658 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 SMED30015658 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 SMED30015658 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 SMED30015658 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 SMED30015658 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 SMED30015658 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000068156.11.639e-2447.58SMESG000068156.1[more]
SMESG000004539.12.882e-2348.67SMESG000004539.1[more]
SMESG000046976.11.362e-1654.05SMESG000046976.1[more]
SMESG000018816.16.802e-1335.58SMESG000018816.1[more]
SMESG000065760.14.182e-1235.34SMESG000065760.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015658 ID=SMED30015658|Name=SMED30015658|organism=Schmidtea mediterranea sexual|type=transcript|length=1530bp
TGACGCGCTATTGAATTATTAATTGCAATAATAATGGCTGGCAAGCATCT
AAGTGAAGCAGCTAAACGACGGAAAAAAGATTTACCAAACGAACTTTAGA
AAGGATGTAAAATTGACTTATTTTTGTTACCGGCACAGACTAAATTCGAA
GAAATACAATCTGTTGCTAATGTACTTAATTTAGAAAATTTGAAGGATCC
TCAGGATGATATCAGTGGGATTGAAGTCAGTAAACTACAGATAAATACAA
ATTATCAGAGTAACGGTTTTAAAGAAAATCGTGCAAGGGGTCCTGAATTT
GAAGTTACTCCACTGCATGGAAAGAAGTAGTTACATAGAAAACTTAATTT
GCGTTAACCTATACCATTTTCATGTTGAATTTATTAACTTGTTATCCACA
CCATTAAATTTCTAAGCGCTCTGCATTCCTGTATCATGGCGTGTAGGGTT
TCTAAAAACTCGGGTTTTAAGACTCGACGACTCCGAGTCCGTTGTCTTAT
TACAAGAATCTGATAAAATAATATTATATGATTTTCAATTACACTGAAAT
TTGTGATTTAATGGTCGTGCCAAGAAATTAAAAGGACAATGTACCCAAAT
TTATTGATTAATTCATTTATTTTCAAAACTTAATAAGCTTTCAAATGAAA
TAGGTAATATAACTATTCTTCATATACTCCAATGTAATACGAACTGAATG
CAGATTCGTATCGTTTCCGATTAAAACCTCAATTGCTAATTTGGCATGTT
CAAGCGAATTCTGGAGATCTTTGAGCTCGTTAAAATTATGTGATCAATAA
TGTGTGAAAAGTTGAGATCCACTAAAGCTTCCTCGATGAATTTTTCTAGT
TTAAAAAATATAATTATCATATTAGCAAGAGAACTCCAACGAGTTTTACA
ATCTAAATATAACTCAAGATTGTGTTCCAGTTTAGCTCTGATTTTTTCTT
TTAATATCCCATTTCTGACAGAAGACAATCTAAAAAATTTAACTACTTTT
CGAACTTTCTTAACTATTTCATGGATACAATTGATTTCTCGAATACCCTC
CTCTGTTGTGGTTTCAATTTAATTATCAATGTCAGCTCCTGCTCCATTAC
AAAAAACATCTTCATTCTCATCTTCAGTTTCAGAATCAATTAGTTCCTCT
TCATTTTCACTGTTTGATTTTTTCCTATAAAGTATCACATACAGCAAGAT
GCAGTCCATGATTGAGGCACAATTGATAAGAGGCTAGACACTCCTTTCCA
CATTTCACCATCAAAGAAGCATCATCTCTTGTTGTAACAACAATATGTTG
CTCATAATTAACTTTAAACGAATCCAAATGGTCAGTAACCACTTTAAGTA
ATTTTGTTGCTGTACACAATCCAAGATTGTATGATTTTTCATATGGATCT
GGGGCACTATGGAGAATTATATTGACATATTTATTCGTTCGTGAGCTGGT
CCACTCATCGAGTGTCAAGCTAAATCTCAGGTTATTTTTAATTTTTTCTG
ATAATTTGACAATTATTTTCTCTTTCATTG
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protein sequence of SMED30015658-orf-1

>SMED30015658-orf-1 ID=SMED30015658-orf-1|Name=SMED30015658-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=118bp
MKEKIIVKLSEKIKNNLRFSLTLDEWTSSRTNKYVNIILHSAPDPYEKSY
NLGLCTATKLLKVVTDHLDSFKVNYEQHIVVTTRDDASLMVKCGKECLAS
YQLCLNHGLHLAVCDTL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002056medial muscle cell
PLANA:0002109X1 cell
PLANA:0002111X2 cell
Vocabulary: INTERPRO
TermDefinition
IPR012337RNaseH-like_sf
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding