SMED30017016

Overview
NameSMED30017016
Smed IDSMED30017016
Length (bp)2598
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 SMED30017016 (SMED30017016) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30017016 (SMED30017016) 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 SMED30017016 (SMED30017016) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30017016 (SMED30017016) 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



SMED30017016

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 regionSMED30017016 SmedASXL_069889SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30017016 vs. TrEMBL
Match: T1FBF8 (Uncharacterized protein OS=Helobdella robusta OX=6412 GN=20206157 PE=4 SV=1)

HSP 1 Score: 107.842 bits (268), Expect = 4.248e-22
Identity = 63/159 (39.62%), Postives = 92/159 (57.86%), Query Frame = -1 
Query: 1003 MVRKGKLSTKKVAQVLHI*KYDNYNVPNPSTPDVYKAIYKESGLLIEHLKETLKTYE*YLRFDDKNFNG-EKEVVLIKNRNKEIRFAVL------TATVFKAIKSTLMKYKLWPQVKMIICDTTNTNSGSKNGIITQFQKYCKEVHGYSSQ-YIGCQHY 1455
            +V+ GKLS ++ A V  I       +  PS   VY+A+Y+E+  +++ L  TL      L FD K     E +VVL++N  KE+R AVL        T+  AI+ TL  Y LW  +KMI+ DTTN N+GSK+G++ + QK   + HG S+  +IGCQH+
Sbjct:  204 LVQSGKLSVRRAAIVSTILNKSGVKITTPSQSGVYRAVYREANKVMKTLMNTLCNSSWCLHFDGKIIKKKEHQVVLLRNEVKEVRLAVLVLPDGKATTIASAIQKTLDDYNLWAAIKMIVSDTTNVNTGSKSGVVVRLQKLFVQ-HGESAPVFIGCQHH 361

HSP 2 Score: 28.4906 bits (62), Expect = 4.248e-22
Identity = 11/17 (64.71%), Postives = 12/17 (70.59%), Query Frame = -2 
Query:  900 AIHGGILV*FLHCWYSY 950
            A+  GIL  FLHCW SY
Sbjct:  379 AMPDGILEQFLHCWLSY 395
[Close]
BLAST of SMED30017016 vs. TrEMBL
Match: R7TD63 (Uncharacterized protein OS=Capitella teleta OX=283909 GN=CAPTEDRAFT_195363 PE=4 SV=1)

HSP 1 Score: 102.064 bits (253), Expect = 1.020e-20
Identity = 59/176 (33.52%), Postives = 95/176 (53.98%), Query Frame = -1 
Query: 1003 PSSKALP*QHYP------MVRKGKLSTKKVAQVLHI*KYDNYNVPNPSTPDVYKAIYKESGLLIEHLKETLKTYE*YLRFDDKNFNG-EKEVVLIKNRNKEIRFAVL------TATVFKAIKSTLMKYKLWPQVKMIICDTTNTNSGSKNGIITQFQKYCKEVHGYSSQYIGCQHY 1491
            PS+     +H P      +V   KLST   A+V      +   +P PS P ++KAIYK +  + +HL  TL   +  L FD K+F+G E + V++KN  +EI+ AVL       AT+ + +K  L ++ LW  V MII + T+ N+G + G++ + QK  + +     ++I CQH+
Sbjct:  164 PSASPGKREHNPTGVARRLVTGAKLSTHGAARVCRQLSGEGKALPAPSQPAIHKAIYKRAAEVKQHLVNTLHQEKWSLHFDGKHFDGLEHQGVVLKNEEREIKLAVLRLKDGKAATIVQGLKGVLEEFNLWGSVLMIIANITSVNTGKEKGVVIRLQKMFESLGHPRPRFISCQHH 339

HSP 2 Score: 29.6462 bits (65), Expect = 1.020e-20
Identity = 23/76 (30.26%), Postives = 38/76 (50.00%), Query Frame = -2 
Query: 1515 DIMNIQGNWPSGEDKQFY*L*LYSNGSTVYATAKEVS---IHSF*KERCFQEATTSF---PGIKSTNEQSATSSEE 1724
            D+  + G W + ED++ + L + + G   Y+T K  S   IH   K R   EA++S    P   + +  S+ +SEE
Sbjct:   83 DVTKLNGQWLNKEDEKLFKLQIETKGQVGYSTGKPASPLTIHPS-KRRKPAEASSSAQDCPKWDTVSCDSSDTSEE 157
[Close]
BLAST of SMED30017016 vs. TrEMBL
Match: T1FCQ4 (Uncharacterized protein OS=Helobdella robusta OX=6412 GN=20206603 PE=4 SV=1)

HSP 1 Score: 106.301 bits (264), Expect = 3.275e-20
Identity = 62/159 (38.99%), Postives = 92/159 (57.86%), Query Frame = -1 
Query: 1003 MVRKGKLSTKKVAQVLHI*KYDNYNVPNPSTPDVYKAIYKESGLLIEHLKETLKTYE*YLRFDDKNFNG-EKEVVLIKNRNKEIRFAVL------TATVFKAIKSTLMKYKLWPQVKMIICDTTNTNSGSKNGIITQFQKYCKEVHGYSSQ-YIGCQHY 1455
            +V+ GKLS ++ A V  I       +  PS   VY+A+Y+E+  +++ L  TL      + FD K     E +VVL++N  KE+R AVL        T+  AI+ TL  Y LW  +KMI+ DTTN N+GSK+G++ + QK   + HG S+  +IGCQH+
Sbjct:  114 LVQSGKLSVRRAAIVSTILNKSGVKITTPSQSGVYRAVYREASKVMKTLMNTLCNSSWCIHFDGKIIKKKEHQVVLLRNEVKEVRLAVLVLPDGKATTIASAIQKTLDDYNLWAAIKMIVSDTTNVNTGSKSGVVVRLQKLFVQ-HGESAPVFIGCQHH 271

HSP 2 Score: 54.299 bits (129), Expect = 2.391e-11
Identity = 22/43 (51.16%), Postives = 29/43 (67.44%), Query Frame = -1 
Query:  883 QHYSKYNVFPFIYFHNLPGISDSWWNSRVVFALLVFILLPKTR 1011
            +H+  +   P + F  LPGIS++ WNSR +FALL FILLP  R
Sbjct:  346 KHFKNFQKIPKVNFKALPGISNARWNSRAIFALLTFILLPDER 388

HSP 3 Score: 45.4394 bits (106), Expect = 2.391e-11
Identity = 27/78 (34.62%), Postives = 35/78 (44.87%), Query Frame = -3 
Query:  635 ELCLFIAKPWLMVWFLLDQQNLKPGMDVLKPQLQNYSNAKKCFDKHWKTEDGVIAGVERSNRCAECVIEILGNIFPYC 868
            +LC FI   W   WF  D        + L   +  Y  A +CF  HW      I   +RSN CAE  I++L +I P C
Sbjct:  393 KLCEFICGQWSDAWFS-DHYYRTEQYEFLLYAVNGYPKALRCFQTHWSQSPSSI-HTQRSNVCAERTIKVLQDIAPLC 468
[Close]
BLAST of SMED30017016 vs. TrEMBL
Match: T1EPU1 (Uncharacterized protein OS=Helobdella robusta OX=6412 GN=20198591 PE=4 SV=1)

HSP 1 Score: 99.7525 bits (247), Expect = 5.592e-18
Identity = 61/159 (38.36%), Postives = 92/159 (57.86%), Query Frame = -1 
Query: 1003 MVRKGKLSTKKVAQVLHI*KYDNYNVPNPSTPDVYKAIYKESGLLIEHLKETLKTYE*YLRFDDKNFNG-EKEVVLIKNRNKEIRFAVL------TATVFKAIKSTLMKYKLWPQVKMIICDTTNTNSGSKNGIITQFQKYCKEVHGYSSQ-YIGCQHY 1455
            +V+ GKLS ++ A V  I       + +P +  VY+A+Y+E+  +++ L  TL      L FD K     E +VVL++N  KE+R AVL        T+  AI+  L  Y LW  +KMI+ DTTN N+GSK+G++ + QK   + HG S+  +IGCQH+
Sbjct:  160 LVQSGKLSVRRAAIVSTILNKSGVKITSPQS-GVYRAVYREASKVMKTLMNTLCNSSWCLHFDGKIIKKKEHQVVLLRNEVKEVRLAVLVLPDGKATTIASAIQKKLDDYNLWAAIKMIVSDTTNVNTGSKSGVVVRLQKLFVQ-HGESAPVFIGCQHH 316
[Close]
BLAST of SMED30017016 vs. TrEMBL
Match: T1FR88 (Uncharacterized protein OS=Helobdella robusta OX=6412 GN=20211335 PE=4 SV=1)

HSP 1 Score: 98.2117 bits (243), Expect = 4.564e-17
Identity = 57/133 (42.86%), Postives = 79/133 (59.40%), Query Frame = -1 
Query: 1003 VPNPSTPDVYKAIYKESGLLIEHLKETLKTYE*YLRFDDKNF-NGEKEVVLIKNRNKEIRFAVLT------ATVFKAIKSTLMKYKLWPQVKMIICDTTNTNSGSKNGIITQFQKYCKEVHGYSSQYIGCQHY 1380
            +P  S   VYKA  K    L EH  ETL+  +  L FD K+  N E +VV++KN N+E++ AVL        T+FK IK+ L +YKLWP +K+II DTT+ N+G   G +T+ QK+   +      YIGCQH+
Sbjct:   91 IPTLSQSGVYKATMKAGEKLKEHFIETLRNEKWSLHFDGKHIKNTEYQVVVLKNENREVKLAVLALINGKGETIFKGIKTVLDEYKLWPAIKLIISDTTSANTGKSVGAVTRLQKHFVMLGLDKPLYIGCQHH 223
[Close]
BLAST of SMED30017016 vs. Planmine SMEST
Match: SMESG000067084.1 (SMESG000067084.1)

HSP 1 Score: 87.8113 bits (216), Expect = 5.167e-20
Identity = 38/48 (79.17%), Postives = 41/48 (85.42%), Query Frame = -1 
Query: 1003 KLWPQVKMIICDTTNTNSGSKNGIITQFQKYCKEVHGYSSQYIGCQHY 1146
            +LWPQVKMIICDTTNTNS SKNGI+TQ QKY K+ H YS QYI CQHY
Sbjct:   16 ELWPQVKMIICDTTNTNSASKNGIVTQLQKYRKQAHVYSPQYISCQHY 63
The following BLAST results are available for this feature:
BLAST of SMED30017016 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 SMED30017016 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 SMED30017016 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 SMED30017016 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 SMED30017016 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 SMED30017016 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 SMED30017016 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 SMED30017016 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
T1FBF84.248e-2239.62Uncharacterized protein OS=Helobdella robusta OX=6... [more]
R7TD631.020e-2033.52Uncharacterized protein OS=Capitella teleta OX=283... [more]
T1FCQ43.275e-2038.99Uncharacterized protein OS=Helobdella robusta OX=6... [more]
T1EPU15.592e-1838.36Uncharacterized protein OS=Helobdella robusta OX=6... [more]
T1FR884.564e-1742.86Uncharacterized protein OS=Helobdella robusta OX=6... [more]
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BLAST of SMED30017016 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 SMED30017016 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 SMED30017016 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 SMED30017016 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 SMED30017016 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 SMED30017016 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000067084.15.167e-2079.17SMESG000067084.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017016 ID=SMED30017016|Name=SMED30017016|organism=Schmidtea mediterranea sexual|type=transcript|length=2598bp
ATGTGTTCTGTTTGGTTAATATCTGGAATTATAAATTACACAACAGATTT
CTATTTTCGGATGGCCACGGAACGTTAATTTAAGAAAGTCGGAATTCAAA
TCCTAATTTTGCATGATAAAAGATTTTATATTATTTTCGTACTCTGCAGA
CTTGAACATAGTTTAACTTTAAGAGTTCTTAACCTATTTAGTGATATGCA
CAACATTAAATCTAGAAATAAGTTCTCGTACATCCTTGCAAAATGTTATT
GAATTTCTTTATTTGGTTAATGCTGGTAAATTAAAGAAGATTATGTTTAG
TATCTTCGGCAAAACCTACAGTTAACGTTCAGAGTATGTATGCTGGGGGT
ATGACTATTTCACAACCCCCTATTACCATATGTAGAAAAGATAAGTTTGA
TAAAAAAACGTGGAAATTGTGCATCTCATGTGCTTCCTTAAAAAAAGGTG
TCCCACCAAACAAGGTTTCAAAAACCGCGACAAACCATCGAATTAACCGT
ATATTACAGAAAACACATCAAAATTTTCAAGTTTAGTAATGTAAATTGTA
CACTAGTAGTTAAAAAGTCACCGAGTTAACGATAAAGTGTCATTTGTTAG
AATAAATAGTTGGTTGATTTTTTCATCACCTTTTACAATAGGGAAATATA
TTTCCCAGTATTTCAATTACGCATTCTGCACATCTGTTACTTCTTTCCAC
ACCAGCGATGACTCCATCTTCTGTTTTCCAGTGTTTATCAAAACACTTTT
TCGCATTCGAGTAGTTTTGCAGCTGAGGCTTTAATACATCCATTCCTGGC
TTCAAATTTTGTTGGTCAAGAAGAAACCACACCATCAACCATGGTTTTGC
AATGAAGAGACACAGTTCTGTGAATTTGGCACCCGTGTTTTAGGAAGCAG
TATGAATACCAGCAGTGCAAAAACTACACGAGAATTCCACCATGAATCGC
TAATTCCTGGAAGGTTGTGGAAATAAATGAAAGGGAACACATTGTACTTA
CTATAGTGCTGACAGCCAATATATTGAGAAGAATAACCATGGACTTCTTT
GCAATATTTTTGAAATTGTGTGATGATACCATTTTTTGAGCCAGAATTAG
TGTTTGTTGTGTCACAAATAATCATTTTCACTTGTGGCCATAATTTGTAC
TTCATCAAGGTTGACTTAATAGCCTTGAATACTGTTGCAGTTAGAACTGC
GAATCGAATTTCTTTATTTCTATTCTTTATCAGCACAACTTCTTTTTCTC
CATTGAAATTTTTGTCGTCAAAGCGCAAATATCACTCATAAGTTTTGAGT
GTCTCTTTTAGATGTTCTATTAACAAACCTGATTCTTTATATATGGCCTT
GTAAACATCTGGTGTCGATGGATTGGGAACATTATAGTTATCATATTTTT
AAATATGCAGTACTTGGGCTACTTTTTTTGTTGATAATTTTCCTTTTCTT
ACCATGGGGTAGTGCTGCTACGGCAACGCTTTTGAGGAGGGAACTATAAA
GGAGTCAATCCATCTTCTTCGGATGACGTTGCGGATTGTTCATTGGTACT
TTTTATTCCTGGGAATGACGTTGTTGCTTCCTGAAAACATCTTTCTTTTT
AAAAGGAGTGAATTGAAACCTCTTTTGCCGTCGCATAAACAGTGCTACCA
TTTGAATATAATTATAGCTAATAAAACTGTTTATCTTCACCAGAGGGCCA
ATTTCCTTGTATGTTCATAATATCAAACAGCTTTCCAAATATTCAGTGGG
TCATTTTAGTTAATTGCCAGATATTATTATCACATTTTTCACTTTTCTAA
AAACCGTTAGTTTACATTGTATATAAAAAATTCAATTTTTCCAATGAATG
TAAAAGATCAGCTGCAATTGAGTTGAATCTGTCTGCACGTAATTTCAATT
CACTGCTGAGCAAAAATTTTTTTCTCACAATGTCGCATTCATTGGCCATT
TTATTTCTCTCGCTGTTTCCCAGAAACCTCGAGAATAACAGAATGCATAA
AAACTGAAAAGTCAATGCACACAAGGAGATAAGCCAATATGTGACGTTTG
AGGACTATGATTTACACCTTCCACTAAATAGCGTATATTCACTCGCACAC
ATACGCACACGTACAAGCAATTACCCCTTAAATAACGAAGATGTGTGCAT
ACTGCATACATGCCCAACTAAAAAGCTTTCCATTTGACATTCCAAAGTTC
AGTTTGGTAAGATATACGCTTTACCACCGTGAAATGCATGCATACTGTAC
TGGAAAGTCATCAAATCACACGAAATACCAACGAATGCGTTGTCTTTTTG
TCAAGTTTCAATAAAAATTAATACGGAAGTGATTTTTGTCTCAAAGTTCA
TCATTTGTGGCTATGTCATTTAATAAAGGAAAAAAAGGAAAATATGCATA
CACCTAATATACATTCACACATATGGATACGCACACATATTACGAGAGAT
CATCCTTTTTGATACGCTCGTTAATTAAATTGCCTGCTATTACTTTTTAA
GTTGCATCCAAAATCAGATCTGTTATTCAAATATAGTTATACTTTTTCCT
GTTTAAAATATCGTCCCCTTTCAACTTTAACTTATTCTTTATACCTGA
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protein sequence of SMED30017016-orf-1

>SMED30017016-orf-1 ID=SMED30017016-orf-1|Name=SMED30017016-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=107bp
MKYKLWPQVKMIICDTTNTNSGSKNGIITQFQKYCKEVHGYSSQYIGCQH
YSKYNVFPFIYFHNLPGISDSWWNSRVVFALLVFILLPKTRVPNSQNCVS
SLQNHG*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000419prepharyngeal region