SMED30028688

Overview
NameSMED30028688
Smed IDSMED30028688
Length (bp)2053
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 SMED30028688 (SMED30028688) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30028688 (SMED30028688) 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 SMED30028688 (SMED30028688) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30028688 (SMED30028688) 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



SMED30028688

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30028688SMESG000042109.1 dd_Smed_v4_26059_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30028688SMESG000042109.1 dd_Smed_v4_26059_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30028688SMESG000042109.1 dd_Smed_v6_26059_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
body wall musculatureSMED30028688SMESG000042109.1 dd_Smed_v4_26059_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30028688 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.009938:3373..5343 -8117
Homology
[Close]
BLAST of SMED30028688 vs. TrEMBL
Match: A0A504Z448 (Uncharacterized protein (Fragment) OS=Fasciola gigantica OX=46835 GN=FGIG_11484 PE=4 SV=1)

HSP 1 Score: 70.8626 bits (172), Expect = 5.051e-10
Identity = 30/88 (34.09%), Postives = 56/88 (63.64%), Query Frame = 1 
Query:  784 NERRNENMNVPMEQFIDPEFSLIQVRCRMSVKLSLSYLLVWAVGAFALIFSEPSLWHLFTMVCALQSLYINISFIFTRPVLMTIHNWN 1047
            +ERR        + F+      +  R  +++KL+L+Y LVW +   A+ ++  +LWH+FT++C+LQ++Y+ ++ +F+RPVL  IH W+
Sbjct:  136 SERR--------DAFLLAHLPHLDARLWITIKLALTYCLVWTIAFIAIFYASVALWHVFTLLCSLQAIYVTVNSVFSRPVLDLIHQWH 215
[Close]
BLAST of SMED30028688 vs. TrEMBL
Match: A0A2H1BYI7 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_008391 PE=4 SV=1)

HSP 1 Score: 70.8626 bits (172), Expect = 1.194e-9
Identity = 30/88 (34.09%), Postives = 56/88 (63.64%), Query Frame = 1 
Query:  784 NERRNENMNVPMEQFIDPEFSLIQVRCRMSVKLSLSYLLVWAVGAFALIFSEPSLWHLFTMVCALQSLYINISFIFTRPVLMTIHNWN 1047
            +ERR        + F+      +  R  +++KL+L+Y LVW +   A+ ++  +LWH+FT++C+LQ++Y+ ++ +F+RPVL  IH W+
Sbjct:  136 SERR--------DAFLLAHLPHLDARLWITIKLALTYCLVWTIAFIAIFYASVALWHVFTLLCSLQAIYVTVNSVFSRPVLDLIHQWH 215
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BLAST of SMED30028688 vs. TrEMBL
Match: A0A183AGH7 (Uncharacterized protein OS=Echinostoma caproni OX=27848 GN=ECPE_LOCUS6061 PE=4 SV=1)

HSP 1 Score: 68.1662 bits (165), Expect = 1.148e-8
Identity = 27/76 (35.53%), Postives = 51/76 (67.11%), Query Frame = 1 
Query:  820 EQFIDPEFSLIQVRCRMSVKLSLSYLLVWAVGAFALIFSEPSLWHLFTMVCALQSLYINISFIFTRPVLMTIHNWN 1047
            + F+      +  R  ++VKL+ +Y L+W +   A+ ++  +LWH+FT++C+LQ++Y+ ++ IF+RPVL  IH W+
Sbjct:  145 DGFLLAHLPHLNARLWITVKLAATYCLIWTMAFLAIFYASVALWHVFTLLCSLQAIYVTVNSIFSRPVLDLIHQWH 220
[Close]
BLAST of SMED30028688 vs. TrEMBL
Match: A0A183Q6S8 (Uncharacterized protein OS=Schistosoma mattheei OX=31246 GN=SMTD_LOCUS22314 PE=4 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 6.104e-6
Identity = 26/65 (40.00%), Postives = 45/65 (69.23%), Query Frame = 1 
Query:  850 IQVRCRMSVKLSLSYLLVWAVGAFALIFSEPSLWHLFTMVCALQSLYINISFIFTRPVLMTIHNW 1044
            I  R  +++K ++++ LVW +   ALI +  S+WH+FT++ +LQ++YI ++  FTRPVL  I+ W
Sbjct:   92 ISARFWITLKFTMTHSLVWLIAFIALIQASTSIWHVFTLLYSLQAIYITVNCTFTRPVLDLIYQW 156
[Close]
BLAST of SMED30028688 vs. Planmine SMEST
Match: SMESG000042109.1 (SMESG000042109.1)

HSP 1 Score: 707.212 bits (1824), Expect = 0.000e+0
Identity = 349/350 (99.71%), Postives = 349/350 (99.71%), Query Frame = 1 
Query:   61 MLNESSHPINATDNFQSSSISHVCFGITIVCHLVHLGIIICIRDLKFLYGLAITLSLLTNTIGFIILIVSCSTRIAISKDQIISSTWPEITTESLFLSAVSWNLIAILQVALLTKFTVFLPTRKFSITNYHPRLFTQLFLKIVYFILEVSFAIGFPLFFGIWRGISRSATKTSFPIYDSKYHEIECSLSQSKTLFEMFLTPLLIIIFLQSIGGIGLLIVLRSKHRMLYSMENGIVDETQQTNERRNENMNVPMEQFIDPEFSLIQVRCRMSVKLSLSYLLVWAVGAFALIFSEPSLWHLFTMVCALQSLYINISFIFTRPVLMTIHNWNYRGPSNPFNIRPSLNHIHFDR 1110
            MLNESSHPINATDNFQSSSISHVCFGITIVCHLVHLGIIICIRDLKFLYGLAITLSLLTNTIGFIILIVSCSTRIAISKDQIISSTWPEITTESLFLSAVSWNLIAILQVALLTKFTVFLPTRKFSITNYHPRLFTQLFLKIVYFILEVSFAIGFPLFFGIWRGISRSATKTSFPIYDSKYHEIECSLSQSKTLFEMFLTPLLIIIFLQSIGGIGLLIVLRSKHRMLYSMENGIVDETQQTNER NENMNVPMEQFIDPEFSLIQVRCRMSVKLSLSYLLVWAVGAFALIFSEPSLWHLFTMVCALQSLYINISFIFTRPVLMTIHNWNYRGPSNPFNIRPSLNHIHFDR
Sbjct:    1 MLNESSHPINATDNFQSSSISHVCFGITIVCHLVHLGIIICIRDLKFLYGLAITLSLLTNTIGFIILIVSCSTRIAISKDQIISSTWPEITTESLFLSAVSWNLIAILQVALLTKFTVFLPTRKFSITNYHPRLFTQLFLKIVYFILEVSFAIGFPLFFGIWRGISRSATKTSFPIYDSKYHEIECSLSQSKTLFEMFLTPLLIIIFLQSIGGIGLLIVLRSKHRMLYSMENGIVDETQQTNERHNENMNVPMEQFIDPEFSLIQVRCRMSVKLSLSYLLVWAVGAFALIFSEPSLWHLFTMVCALQSLYINISFIFTRPVLMTIHNWNYRGPSNPFNIRPSLNHIHFDR 350
[Close]
BLAST of SMED30028688 vs. Planmine SMEST
Match: SMESG000011191.1 (SMESG000011191.1)

HSP 1 Score: 111.694 bits (278), Expect = 9.785e-27
Identity = 89/320 (27.81%), Postives = 141/320 (44.06%), Query Frame = 1 
Query:   88 NATDNFQSSSISHVCFGITIVCHLVHLGIIICIRDLKFLYGLAITLSLLTNTIGFIILIVSCSTRI-----AISKDQIISSTWPEITTESLFLSAVSWNLIAILQVALLTKFTVFLPTRKFSITNYHPRLF--TQLFLKIVYFILEVSFAIGFPLFFGIWRGISRSATKTSFPIYDSKYHEIECSLSQSKTLFEMFLTPLLIIIFLQSIGGIGLLIVLRSKHRMLYSMENGIVDETQQTNERRNENMNVPMEQFIDPEFSLIQVRCRMSVKLSLSYLLVWAVGAFALIFSEPSLWHLFTMVCALQSLYINISFIFTRPVL 1026
            N T+ FQ S++S VCF + I+    H   + CIR ++ LYG  I  +L   T  +I  + SCS  I     A   + I   +  E  ++  F+S++ WNL A  Q+ L+          +   T    +LF   Q F   +   +       F  +   W  ++         I D+  HEIECS + S      F  P    IF   +  + +L+++                 T + N+ R + + +   Q I   +        M  KL  +YL++W  GA A     P LWH+FT+ C+LQ+L+I ++FIF+RPVL
Sbjct:   20 NLTNQFQPSAVSKVCFAVAILTMSTHCLFVTCIRHIRMLYGSFILTNLYMMTFSYIFFMTSCSMDIKTIQYAFQYNWINKRSIMESISQFSFVSSIYWNLAASCQICLVI--------YRGCHTESTYKLFDCVQYFWGTIMSFVMPGLCCYFKFYLDNWLDLNPK-------IVDNLKHEIECSFNSSVNTDIFFYLP----IFTGMMITVAILVIIY----------------TMRCNKSREDRIIMFQNQEISARYG-------MCCKLVFTYLVIWVTGAAATHIISPPLWHVFTLCCSLQTLFIAVNFIFSRPVL 297
[Close]
BLAST of SMED30028688 vs. Planmine SMEST
Match: SMESG000043863.1 (SMESG000043863.1)

HSP 1 Score: 68.5514 bits (166), Expect = 3.855e-12
Identity = 30/67 (44.78%), Postives = 49/67 (73.13%), Query Frame = 1 
Query:  850 IQVRCRMSVKLSLSYLLVWAVGAFALIFSEPSLWHLFTMVCALQSLYINISFIFTRPVLMTIHNWNY 1050
            ++ R  M +KL L+  L+W +  FA+ F+  S+WH+FT+ C+LQS+++ ISFIF+RPVL  +HN ++
Sbjct:  230 MKSRHFMHIKLVLTNTLIWTIAFFAVEFNITSMWHIFTLSCSLQSIFLAISFIFSRPVLDVLHNGDH 296
The following BLAST results are available for this feature:
BLAST of SMED30028688 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 SMED30028688 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 SMED30028688 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 SMED30028688 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 SMED30028688 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 SMED30028688 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 SMED30028688 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 SMED30028688 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 4
Match NameE-valueIdentityDescription
A0A504Z4485.051e-1034.09Uncharacterized protein (Fragment) OS=Fasciola gig... [more]
A0A2H1BYI71.194e-934.09Uncharacterized protein OS=Fasciola hepatica OX=61... [more]
A0A183AGH71.148e-835.53Uncharacterized protein OS=Echinostoma caproni OX=... [more]
A0A183Q6S86.104e-640.00Uncharacterized protein OS=Schistosoma mattheei OX... [more]
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BLAST of SMED30028688 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 SMED30028688 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 SMED30028688 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 SMED30028688 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 SMED30028688 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 SMED30028688 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000042109.10.000e+099.71SMESG000042109.1[more]
SMESG000011191.19.785e-2727.81SMESG000011191.1[more]
SMESG000043863.13.855e-1244.78SMESG000043863.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028688 ID=SMED30028688|Name=SMED30028688|organism=Schmidtea mediterranea sexual|type=transcript|length=2053bp
ATCCTAAGTTTTTCAACTTACTCGCATACAATTTTGTATTAGTGTATCTG
TTATGGGAAAATGTTAAATGAGAGTTCTCATCCGATTAACGCCACGGATA
ATTTCCAATCCTCATCAATTAGTCATGTTTGTTTTGGAATCACAATTGTT
TGTCATTTGGTGCATTTGGGAATTATTATTTGTATCAGAGATCTGAAATT
CCTGTATGGACTAGCAATAACTCTTAGTTTATTGACAAATACAATTGGCT
TCATCATTCTCATTGTGAGCTGTTCCACGAGAATAGCAATTTCTAAAGAT
CAGATAATTTCATCCACGTGGCCGGAAATCACGACAGAATCATTGTTCTT
ATCCGCAGTCTCCTGGAATTTAATCGCGATTTTGCAAGTGGCTTTATTGA
CAAAATTCACAGTCTTTCTTCCAACCAGAAAATTCTCCATTACCAATTAC
CATCCTCGATTATTTACACAATTGTTTCTAAAGATTGTCTACTTTATTCT
TGAAGTGTCTTTCGCGATTGGATTTCCATTGTTTTTTGGAATTTGGAGAG
GAATTTCGAGATCTGCAACGAAAACTTCGTTTCCAATTTATGATTCAAAA
TATCACGAAATTGAGTGCAGTCTCAGTCAAAGCAAAACTTTATTTGAAAT
GTTTCTTACACCATTGTTGATTATTATATTTTTACAGTCGATTGGTGGCA
TTGGTCTGTTAATAGTTTTGAGATCAAAGCATCGAATGCTTTATTCCATG
GAAAATGGAATTGTAGATGAAACCCAACAGACAAATGAAAGACGCAACGA
GAACATGAATGTTCCTATGGAACAATTTATAGATCCAGAATTCAGTTTGA
TACAAGTTCGTTGTAGAATGAGTGTTAAATTGAGTTTGTCGTATTTATTA
GTTTGGGCTGTGGGAGCATTTGCTCTTATATTTTCGGAGCCATCTTTATG
GCATTTATTTACCATGGTTTGTGCTTTACAAAGTCTTTATATAAACATAA
GTTTCATTTTTACTAGACCAGTTCTTATGACAATACATAACTGGAATTAT
CGGGGCCCTTCTAATCCATTTAATATTAGACCTTCTTTAAATCACATTCA
CTTTGACAGATAATTTTATATTAGTTGTTTTGATGAAAATTTCTTTGCAT
TATTTTTTATTTTTAAAGTATAAATAATTATGATTGGGTTAATTTTATAT
ATATTATAAATATTTTTAAATCGAATTATGGTTTCATAAATTTGTTTGTA
CTTAGGAAGGAGAAAGCATTTTGTAGCACATTTTTTAATTGAAACTTTTA
ATTCAAGAACACAAACATTGTGTTTTAAACAAGTCGGTTATTATTTAAAG
CTTAGAATTATGAACTTCATCTTATTTCTTGTAAGGATCTCTCTTATTTA
AAAATAAGATAGTTTAAATGCTATAAGAGCGATCAGTTAGTTGAAATAAC
TTTTATGTTAAATTTGTATATTAAGATGTATTAAAAAACATAATATTATA
GTAAATTATATTAAAGTATTTTTAAATTAAATGAATTATATTGGTGACCG
ATAACTATATCAATATTAATAATTTCCACACCTCAGTTGTTTGAATTTTC
AGATTTAAACTGAATTTGTATTTCGTAATTAAATAATAAATGTTAGAAGA
AAATTTGAAATTTATTGCGTCTAACAGGTCGCAGTTCTAAAGTCCCATTG
TCCCGTTTTTAATGATGTAAAAAAGCAGTAAATTATTGATGTAGAATAAT
AATTAGATTATTAAAAGTTATGAAAAATAACATAATAATGAGTGGGAAAA
CGATTATGGATTTATGCTTAAAAGAAGATATATATTCCTGACAAATTAAT
TGATTTATTAAAACAAAAATGCTGAAAATTTCGTTTAGCTCCAAAAATCA
ACACAGAAAACACATACATATAATTTGAGTGGTTAGTTAACTTTATTAGT
ATTAAAATTTATTAGATTTATCATTTTTCATAAATTGTATCATATATTAT
CTTATATATAAAAGTCTAAATATGTTTGTTTGTTTGCCACATTTTAAATT
GTT
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protein sequence of SMED30028688-orf-1

>SMED30028688-orf-1 ID=SMED30028688-orf-1|Name=SMED30028688-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=351bp
MLNESSHPINATDNFQSSSISHVCFGITIVCHLVHLGIIICIRDLKFLYG
LAITLSLLTNTIGFIILIVSCSTRIAISKDQIISSTWPEITTESLFLSAV
SWNLIAILQVALLTKFTVFLPTRKFSITNYHPRLFTQLFLKIVYFILEVS
FAIGFPLFFGIWRGISRSATKTSFPIYDSKYHEIECSLSQSKTLFEMFLT
PLLIIIFLQSIGGIGLLIVLRSKHRMLYSMENGIVDETQQTNERRNENMN
VPMEQFIDPEFSLIQVRCRMSVKLSLSYLLVWAVGAFALIFSEPSLWHLF
TMVCALQSLYINISFIFTRPVLMTIHNWNYRGPSNPFNIRPSLNHIHFDR
*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000240body wall musculature
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 274..291
NoneNo IPR availableTMHMMTMhelixcoord: 47..69
NoneNo IPR availableTMHMMTMhelixcoord: 198..220
NoneNo IPR availableTMHMMTMhelixcoord: 100..122
NoneNo IPR availableTMHMMTMhelixcoord: 20..42
NoneNo IPR availableTMHMMTMhelixcoord: 143..165
NoneNo IPR availableTMHMMTMhelixcoord: 296..318