SMED30002190

Overview
NameSMED30002190
Smed IDSMED30002190
Length (bp)542
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 SMED30002190 (SMED30002190) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30002190 (SMED30002190) 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



SMED30002190

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30002190h1SMcG0015055 SmedASXL_064638SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30002190h1SMcG0015055 SmedASXL_007827SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30002190 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002457:34480..35021 +2647
Homology
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BLAST of SMED30002190 vs. Planmine SMEST
Match: SMESG000011555.1 (SMESG000011555.1)

HSP 1 Score: 328.176 bits (840), Expect = 1.735e-114
Identity = 179/180 (99.44%), Postives = 180/180 (100.00%), Query Frame = 2 
Query:    2 ERMIAVVFPLKAREWCTKSRALTLSVFLFIPASIKNFMTFLTLELKTFFIVGADNNTLTEIRQCISKTKYFYYENLVRPFLSLTLYYFVTAAIIFITNGVISLAMKSRLKSMRYITQEAVKADSGXXXXXXXXXXXXXXXFIGILYLVFLTPSMTIWTTINMFTYYQVEISGEMIDFLFS 541
            ERMIAVVFPLKAREWCTKSRALTLS+FLFIPASIKNFMTFLTLELKTFFIVGADNNTLTEIRQCISKTKYFYYENLVRPFLSLTLYYFVTAAIIFITNGVISLAMKSRLKSMRYITQEAVKADSGKSQKTQSKSLLKMSLFIGILYLVFLTPSMTIWTTINMFTYYQVEISGEMIDFLFS
Sbjct:  106 ERMIAVVFPLKAREWCTKSRALTLSLFLFIPASIKNFMTFLTLELKTFFIVGADNNTLTEIRQCISKTKYFYYENLVRPFLSLTLYYFVTAAIIFITNGVISLAMKSRLKSMRYITQEAVKADSGKSQKTQSKSLLKMSLFIGILYLVFLTPSMTIWTTINMFTYYQVEISGEMIDFLFS 285
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BLAST of SMED30002190 vs. Planmine SMEST
Match: SMESG000011554.1 (SMESG000011554.1)

HSP 1 Score: 161.77 bits (408), Expect = 5.645e-49
Identity = 94/183 (51.37%), Postives = 132/183 (72.13%), Query Frame = 2 
Query:    2 ERMIAVVFPLKAREWCTKSRALTLSVFLFIPASIKNFMTFLTLELKTFFIVGAD---NNTLTEIRQCISKTKYFYYENLVRPFLSLTLYYFVTAAIIFITNGVISLAMKSRLKSMRYITQEAVKADSGXXXXXXXXXXXXXXXFIGILYLVFLTPSMTIWTTINMFTYYQVEISGEMIDFLFS 541
            ER IAVV+PLK + W TKS+A+  +  LFIP+ +KNFM F++LELK   I   D   N + +EI+ C  K +YF YEN+VRP +SL  +YF+TA  IF+TN +IS  M+ RLK+MR   ++ +   S  SQ  QSKSLLKMSLF+GIL+LVF TPS++IWTT+++FT+Y V+I+  ++ FL++
Sbjct:  124 ERFIAVVYPLKLKSWSTKSKAILFTFLLFIPSCLKNFMAFVSLELKV--ITSKDEVGNQSSSEIKFCRGKKEYFLYENVVRPMISLIGFYFLTALAIFVTNAIISCRMRERLKTMR---EDTIGISSSNSQVKQSKSLLKMSLFVGILFLVFFTPSISIWTTMSLFTFYNVDINPNLMGFLYA 301
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BLAST of SMED30002190 vs. Planmine SMEST
Match: SMESG000079761.1 (SMESG000079761.1)

HSP 1 Score: 74.7146 bits (182), Expect = 4.493e-16
Identity = 58/185 (31.35%), Postives = 97/185 (52.43%), Query Frame = 2 
Query:    2 ERMIAVVFPLKAREWCTKSRALTLSVFLFIPASIKNFMTFLTLELKTFFIVGADNNTLTEIRQCISKTKYFYYENLVRPFLSLTLYYFVTAAIIFITNGVISLAMKSRLKSMRYITQEAVK-----ADSGXXXXXXXXXXXXXXXFIGILYLVFLTPSMTIWTTINMFTYYQVEISGEMIDFLFS 541
            +R++AVVFP++   W ++  ++ + + +F  + IKNF  F TL      +V   N T    R C ++ ++ +YE  +RPF+SL +YY +   I+ I   VI L M    K +  +T    +      +    +   SKSL +MS+ I IL+++ L+PS+ IWT I   +Y+   I  E I  L+ 
Sbjct:  107 DRLVAVVFPIQNTTWKSQKNSIVILIVVFSLSLIKNFPIFFTLS-----VVTNTNGT----RFCDTRERFAFYERKIRPFISLMMYYLIPTIIMTICTVVIILKMNRVAKKLDVMTNPKRRISMEINNVNFIRPHYSKSLTQMSIAINILFVLLLSPSIFIWTII---SYWPASIQSEKISILYD 279
[Close]
BLAST of SMED30002190 vs. Planmine SMEST
Match: SMESG000079764.1 (SMESG000079764.1)

HSP 1 Score: 64.3142 bits (155), Expect = 2.513e-12
Identity = 55/183 (30.05%), Postives = 95/183 (51.91%), Query Frame = 2 
Query:    2 ERMIAVVFPLKAREWCTKSRALTLSVFLFIPASIKNFMTFLTLELKTFFIVGADNNTLTEIRQCISKTKYFYYENLVRPFLSLTLYYFVTAAIIFITNGVISLAMK---SRLKSMRYITQEAVKADSGXXXXXXXXXXXXXXXFIGILYLVFLTPSMTIWTTINMFTYYQVEISGEMIDFLFS 541
            +R++AVV+P +   W +    L + + +F  + +KNF  F TL         + N T     +C ++T +  YE+ VRP +SL LYY +    + +   +I   M+    ++++M    + +V AD    +   SKSL KMS+ I IL+ V +TPS+TIWT ++    Y  +I+ + I   + 
Sbjct:  101 DRLVAVVYPHQNSFWKSNKNTLFVLIVIFALSLLKNFPVFFTL--------ASINGT-----RCAARTSFEIYEDSVRPIISLILYYLIPTITMTVCTVMILKEMRKIVGKIRAMSNPNRNSVSAD--YMKNHYSKSLTKMSIAINILFFVLITPSITIWTLMS----YAKDINADAIALCYD 264
[Close]
BLAST of SMED30002190 vs. Planmine SMEST
Match: SMESG000079764.1 (SMESG000079764.1)

HSP 1 Score: 63.929 bits (154), Expect = 2.687e-12
Identity = 55/183 (30.05%), Postives = 95/183 (51.91%), Query Frame = 2 
Query:    2 ERMIAVVFPLKAREWCTKSRALTLSVFLFIPASIKNFMTFLTLELKTFFIVGADNNTLTEIRQCISKTKYFYYENLVRPFLSLTLYYFVTAAIIFITNGVISLAMK---SRLKSMRYITQEAVKADSGXXXXXXXXXXXXXXXFIGILYLVFLTPSMTIWTTINMFTYYQVEISGEMIDFLFS 541
            +R++AVV+P +   W +    L + + +F  + +KNF  F TL         + N T     +C ++T +  YE+ VRP +SL LYY +    + +   +I   M+    ++++M    + +V AD    +   SKSL KMS+ I IL+ V +TPS+TIWT ++    Y  +I+ + I   + 
Sbjct:  108 DRLVAVVYPHQNSFWKSNKNTLFVLIVIFALSLLKNFPVFFTL--------ASINGT-----RCAARTSFEIYEDSVRPIISLILYYLIPTITMTVCTVMILKEMRKIVGKIRAMSNPNRNSVSAD--YMKNHYSKSLTKMSIAINILFFVLITPSITIWTLMS----YAKDINADAIALCYD 271
The following BLAST results are available for this feature:
BLAST of SMED30002190 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 SMED30002190 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 SMED30002190 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 SMED30002190 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 SMED30002190 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 SMED30002190 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 SMED30002190 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 SMED30002190 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 SMED30002190 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 SMED30002190 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 SMED30002190 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 SMED30002190 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 SMED30002190 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 SMED30002190 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000011555.11.735e-11499.44SMESG000011555.1[more]
SMESG000011554.15.645e-4951.37SMESG000011554.1[more]
SMESG000079761.14.493e-1631.35SMESG000079761.1[more]
SMESG000079764.12.513e-1230.05SMESG000079764.1[more]
SMESG000079764.12.687e-1230.05SMESG000079764.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002190 ID=SMED30002190|Name=SMED30002190|organism=Schmidtea mediterranea sexual|type=transcript|length=542bp
GGAACGAATGATTGCGGTTGTGTTTCCATTGAAAGCGAGAGAATGGTGCA
CGAAATCGAGAGCTTTGACATTATCGGTATTTCTTTTCATTCCTGCTAGC
ATCAAAAACTTCATGACCTTTCTTACGTTGGAGCTGAAAACCTTTTTTAT
TGTTGGCGCTGATAACAATACTCTAACTGAGATTAGACAATGTATTTCGA
AGACAAAATACTTTTATTATGAAAACTTAGTGAGGCCTTTTTTAAGCTTA
ACTTTGTATTATTTTGTCACAGCCGCTATTATTTTTATTACAAATGGAGT
TATTTCACTTGCAATGAAATCAAGACTCAAGTCAATGAGGTACATCACTC
AAGAAGCTGTCAAAGCTGATTCCGGGAAATCTCAAAAGACTCAGTCGAAA
AGTTTACTAAAGATGTCTCTCTTCATTGGTATTTTGTATCTAGTATTTCT
CACCCCCTCAATGACCATTTGGACAACCATCAATATGTTTACTTACTATC
AAGTAGAGATTAGTGGAGAAATGATTGACTTTCTATTTTCTG
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protein sequence of SMED30002190-orf-1

>SMED30002190-orf-1 ID=SMED30002190-orf-1|Name=SMED30002190-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=180bp
ERMIAVVFPLKAREWCTKSRALTLSVFLFIPASIKNFMTFLTLELKTFFI
VGADNNTLTEIRQCISKTKYFYYENLVRPFLSLTLYYFVTAAIIFITNGV
ISLAMKSRLKSMRYITQEAVKADSGKSQKTQSKSLLKMSLFIGILYLVFL
TPSMTIWTTINMFTYYQVEISGEMIDFLFS
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000420parapharyngeal region
Vocabulary: INTERPRO
TermDefinition
IPR017452GPCR_Rhodpsn_7TM
Vocabulary: cellular component
TermDefinition
GO:0016021integral component of membrane