SMED30026362

Overview
NameSMED30026362
Smed IDSMED30026362
Length (bp)636
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ 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



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 SMED30026362 (SMED30026362) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30026362 (SMED30026362) 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.
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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



SMED30026362

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
nervous systemSMED30026362 dd_Smed_v4_6704_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30026362 dd_Smed_v4_6704_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30026362 dd_Smed_v4_6704_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
SMED30026362 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005073:136..772 +3168
Homology
[Close]
BLAST of SMED30026362 vs. TrEMBL
Match: A0A504YWG7 (Uncharacterized protein OS=Fasciola gigantica OX=46835 GN=FGIG_11041 PE=4 SV=1)

HSP 1 Score: 73.559 bits (179), Expect = 5.985e-13
Identity = 40/115 (34.78%), Postives = 63/115 (54.78%), Query Frame = 1 
Query:  106 VATPSWGCGNLISDCS---YNGGLIAAKIFFMIGLICFLVILILEIMGFASHSYRGNATMNLVRIIFLGIASCSLILCIVIFTASSSHRWSYMCAVIAMTLGCQVLIIGLMTSSC 441
            +AT SWGCG+L   C    Y    IA  I  +IG++C  ++ IL+++G  S  +  +A     R IFL + S  L++ +++FT S  H WSY  A +      QV I+ +++S C
Sbjct:   23 LATSSWGCGSLFEGCQRGYYKDAAIAVLILLIIGVVCLAIVFILDLVGLCSDVFVVSAGYLTTRFIFLYLGSTVLLIGVLVFTGSIGHAWSYFIATVGCVFAMQVAILAILSSRC 137
[Close]
BLAST of SMED30026362 vs. TrEMBL
Match: A0A4E0RN06 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_000104 PE=4 SV=1)

HSP 1 Score: 73.559 bits (179), Expect = 5.985e-13
Identity = 40/115 (34.78%), Postives = 63/115 (54.78%), Query Frame = 1 
Query:  106 VATPSWGCGNLISDCS---YNGGLIAAKIFFMIGLICFLVILILEIMGFASHSYRGNATMNLVRIIFLGIASCSLILCIVIFTASSSHRWSYMCAVIAMTLGCQVLIIGLMTSSC 441
            +AT SWGCG+L   C    Y    IA  I  +IG++C  ++ IL+++G  S  +  +A     R IFL + S  L++ +++FT S  H WSY  A +      QV I+ +++S C
Sbjct:   23 LATSSWGCGSLFEGCQRGYYKDAAIAVLILLIIGVVCLAIVFILDLVGLCSDVFVVSAGYLTTRFIFLYLGSTVLLIGVLVFTGSIGHAWSYFIATVGCVFAMQVAILAILSSRC 137
[Close]
BLAST of SMED30026362 vs. TrEMBL
Match: A0A183AUP5 (Uncharacterized protein OS=Echinostoma caproni OX=27848 GN=ECPE_LOCUS10680 PE=4 SV=1)

HSP 1 Score: 72.0182 bits (175), Expect = 2.263e-12
Identity = 40/115 (34.78%), Postives = 62/115 (53.91%), Query Frame = 1 
Query:  106 VATPSWGCGNLISDCS---YNGGLIAAKIFFMIGLICFLVILILEIMGFASHSYRGNATMNLVRIIFLGIASCSLILCIVIFTASSSHRWSYMCAVIAMTLGCQVLIIGLMTSSC 441
            +AT SW CG L  +C    +    IA  I  +IG++C  ++ IL+++G  S  +  +A     R IFL + S  L++ I++FT S  H WSY  A +      QV I+ +M+S C
Sbjct:   23 LATSSWSCGGLFDNCQRGYHKDAAIAVLILLLIGVVCLAIVFILDLVGLCSDVFVVSAGYITTRFIFLYLGSTVLLIGILVFTGSIGHAWSYFLATVGCVFAMQVAILAIMSSRC 137
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BLAST of SMED30026362 vs. TrEMBL
Match: A0A3P7P2W1 (Uncharacterized protein OS=Dibothriocephalus latus OX=60516 GN=DILT_LOCUS8117 PE=4 SV=1)

HSP 1 Score: 71.633 bits (174), Expect = 2.557e-12
Identity = 39/118 (33.05%), Postives = 65/118 (55.08%), Query Frame = 1 
Query:  106 VATPSWGCGNLISDCSYNGG-----LIAAKIFFMIGLICFLVILILEIMGFASHSYRGNATMNLVRIIFLGIASCSLILCIVIFTASSSHRWSYMCAVIAMTLGCQVLIIGLMTSSCT 444
            +ATP+W C +L  DC   G      +I+     +IGL+C  V+ IL+++   S    G A +    +++LG A   L++ ++++TA + + WSY  AV +   G  V I+G+M S CT
Sbjct:   22 LATPNWDCVSLFEDCIEEGANERVAMISVAALLVIGLVCLTVVFILDVLYLRSKQLSGVAQVARFCLLYLGAAM--LLVAVIVYTAQTHNHWSYFLAVASAAFGLTVAILGVMASRCT 137
[Close]
BLAST of SMED30026362 vs. TrEMBL
Match: H2KRD2 (Uncharacterized protein OS=Clonorchis sinensis OX=79923 GN=CLF_106005 PE=4 SV=1)

HSP 1 Score: 71.633 bits (174), Expect = 3.722e-12
Identity = 37/116 (31.90%), Postives = 63/116 (54.31%), Query Frame = 1 
Query:  106 VATPSWGCGNLISDC---SYNGGLIAAKIFFMIGLICFLVILILEIMGFASHSYRGNATMNLVRIIFLGIASCSLILCIVIFTASSSHRWSYMCAVIAMTLGCQVLIIGLMTSSCT 444
            +AT  WGCG+L   C    Y   +IA  I  +IG+ C  ++ +L+++   S   R  +     R++ L I S +L++ I++FT    + WSY  A +   LG QV I+ +++S C+
Sbjct:   24 LATSHWGCGSLFVSCQNADYKDAVIAVIILLLIGVACIAIVFLLDLISLCSDELRSKSGYITARLVLLYIGSAALLIGILVFTGKVGYAWSYFAATVGCVLGIQVAILAVISSRCS 139
[Close]
BLAST of SMED30026362 vs. Planmine SMEST
Match: SMESG000012166.1 (SMESG000012166.1)

HSP 1 Score: 148.288 bits (373), Expect = 1.817e-45
Identity = 91/152 (59.87%), Postives = 119/152 (78.29%), Query Frame = 1 
Query:   43 MNTANXXXXXXXXXXXXXXXXVATPSWGCGNLISDCSYNGGLIAAKIFFMIGLICFLVILILEIMGFASHSYRGNATMNLVRIIFLGIASCSLILCIVIFTASSSHRWSYMCAVIAMTLGCQVLIIGLMTSSCTLIXXXXXXXXXSNVVVSH 498
            MNT+NLSLGLII+TFILL+I++ATP W CGNL++DC+  G  IA KIFFM+GL+   V+LILEI+G  S +YRGN+++NL R+I LGI  CSL++C+++FT+   H WSYM  VIA+TLG QVLIIG+MTSSCT+ TR+R        VV+H
Sbjct:    1 MNTSNLSLGLIISTFILLVIAIATPYWNCGNLLTDCN-EGKDIAVKIFFMLGLVSIAVVLILEILGIVSITYRGNSSINLARLILLGIGICSLLICVLVFTSIRGHNWSYMLTVIALTLGLQVLIIGMMTSSCTVTTRSRGHVIVRETVVTH 151
[Close]
BLAST of SMED30026362 vs. Planmine SMEST
Match: SMESG000012170.1 (SMESG000012170.1)

HSP 1 Score: 137.887 bits (346), Expect = 2.189e-41
Identity = 81/133 (60.90%), Postives = 110/133 (82.71%), Query Frame = 1 
Query:   43 MNTANXXXXXXXXXXXXXXXXVATPSWGCGNLISDCSYNGGLIAAKIFFMIGLICFLVILILEIMGFASHSYRGNATMNLVRIIFLGIASCSLILCIVIFTASSSHRWSYMCAVIAMTLGCQVLIIGLMTSSC 441
            MNT +LSLGLII+ F+LLII+VATP W CGN++ DC++ G  +AAKIFFM+GL+C  V+LILEI+G+A  +YR + TMNLV++I LGI+  SL++CI++F + +S++WSYM AV+ MTLG QV IIGLM+SSC
Sbjct:    1 MNTLSLSLGLIISMFVLLIIAVATPYWHCGNILLDCNHYGTWVAAKIFFMLGLVCCAVVLILEILGYACLNYRSHGTMNLVKLILLGISVGSLLICILLFNSVTSNQWSYMLAVVGMTLGLQVFIIGLMSSSC 133
[Close]
BLAST of SMED30026362 vs. Planmine SMEST
Match: SMESG000012168.1 (SMESG000012168.1)

HSP 1 Score: 117.472 bits (293), Expect = 2.564e-33
Identity = 63/109 (57.80%), Postives = 91/109 (83.49%), Query Frame = 1 
Query:  115 PSWGCGNLISDCSYNGGLIAAKIFFMIGLICFLVILILEIMGFASHSYRGNATMNLVRIIFLGIASCSLILCIVIFTASSSHRWSYMCAVIAMTLGCQVLIIGLMTSSC 441
            P W CGN++SDC+Y+ GL+ AKIFF++GL+CF+V+L+LE++ F + SY GNA++NLVR+I LGIA  SL++CI+I+T++  ++WSYMC VIAMTL  Q  +IG+M+SSC
Sbjct:   25 PYWHCGNILSDCNYDAGLVVAKIFFILGLVCFVVVLVLELIQFCTISYYGNASLNLVRLIMLGIAVGSLLMCILIYTSNIVNQWSYMCTVIAMTLAVQAFVIGIMSSSC 133
[Close]
BLAST of SMED30026362 vs. Planmine SMEST
Match: SMESG000011804.1 (SMESG000011804.1)

HSP 1 Score: 55.8398 bits (133), Expect = 7.893e-10
Identity = 35/114 (30.70%), Postives = 65/114 (57.02%), Query Frame = 1 
Query:  109 ATPSWGCGNLISDCSYNGGL--IAAKIFFMIGLICFLVIL-ILEIMGFASHSYRGNATMNLVRIIFLGIASCSLILCIVIFTASSSHRWSYMCAVIAMTLGCQVLIIGLMTSSC 441
            ATP WGCG L +DC  +  +  ++  I F +G ICFL+++ +L+ +   + +   N T N VR++ L +    ++  + I  +  +  WS++ A++  TL  QV+++ L T +C
Sbjct:   24 ATPYWGCGYLYTDCIQHDKVQGLSVMILFTLG-ICFLIVVAVLDFVNCCNGTLLLNVTTNQVRLVLLFLGVGCIVSAVCIHASYRAPIWSFLMAIVGGTLLVQVIVLALNTCTC 136
The following BLAST results are available for this feature:
BLAST of SMED30026362 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 SMED30026362 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 SMED30026362 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 SMED30026362 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 SMED30026362 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 SMED30026362 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 SMED30026362 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 SMED30026362 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A504YWG75.985e-1334.78Uncharacterized protein OS=Fasciola gigantica OX=4... [more]
A0A4E0RN065.985e-1334.78Uncharacterized protein OS=Fasciola hepatica OX=61... [more]
A0A183AUP52.263e-1234.78Uncharacterized protein OS=Echinostoma caproni OX=... [more]
A0A3P7P2W12.557e-1233.05Uncharacterized protein OS=Dibothriocephalus latus... [more]
H2KRD23.722e-1231.90Uncharacterized protein OS=Clonorchis sinensis OX=... [more]
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BLAST of SMED30026362 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 SMED30026362 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 SMED30026362 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 SMED30026362 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 SMED30026362 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 SMED30026362 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000012166.11.817e-4559.87SMESG000012166.1[more]
SMESG000012170.12.189e-4160.90SMESG000012170.1[more]
SMESG000012168.12.564e-3357.80SMESG000012168.1[more]
SMESG000011804.17.893e-1030.70SMESG000011804.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026362 ID=SMED30026362|Name=SMED30026362|organism=Schmidtea mediterranea sexual|type=transcript|length=636bp
AAAAAGATCTTTTTTGGGTGATTGGATTTATTTTCCTTAAAAATGAACAC
CGCTAATTTAAGTTTAGGATTGATCATCACAACCTTCATTCTCTTAATAA
TTTCTGTGGCCACCCCTTCTTGGGGTTGTGGAAATTTAATTTCTGATTGT
AGTTACAATGGAGGCTTAATAGCGGCTAAAATTTTTTTCATGATCGGTTT
GATTTGTTTTCTAGTGATTTTGATATTAGAAATAATGGGATTTGCCAGTC
ATTCGTACCGTGGAAATGCCACCATGAATTTAGTAAGGATCATATTTTTA
GGGATCGCAAGTTGCAGTCTGATCCTGTGTATTGTCATATTCACTGCCTC
AAGCTCACATAGGTGGTCATACATGTGCGCGGTAATAGCTATGACACTTG
GGTGCCAAGTGCTGATCATTGGACTGATGACAAGCAGCTGCACACTGATA
ACAAGAACGAGAACCACGACGACGACCTCAAATGTTGTCGTTTCTCATTG
AATTTAACCAAAATTTAGTAATTTTATATTTTATTTGACAATGTATGATG
TATTCTTTAAAATTTTTCAATTTTTCTTTTAAAAATTTCAAAAAATATAC
TTTTATGAATTAAATATATAATTTCTTTATTGATTA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-TMSignalP-TMcoord: 1..28
score: 0.571
NoneNo IPR availableTMHMMTMhelixcoord: 81..103
NoneNo IPR availableTMHMMTMhelixcoord: 47..69
NoneNo IPR availableTMHMMTMhelixcoord: 5..27
NoneNo IPR availableTMHMMTMhelixcoord: 113..135