SMED30007361

Overview
NameSMED30007361
Smed IDSMED30007361
Length (bp)1020
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 SMED30007361 (SMED30007361) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30007361 (SMED30007361) 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 SMED30007361 (SMED30007361) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30007361 (SMED30007361) 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



SMED30007361

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



PAGE Curations: 9

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermisSMED30007361SMESG000063825.1 dd_Smed_v4_569_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30007361SMESG000063825.1 dd_Smed_v4_569_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30007361SMESG000063825.1 dd_Smed_v4_569_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30007361SMESG000063825.1 dd_Smed_v4_569_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30007361SMESG000063825.1 dd_Smed_v4_569_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007361SMESG000063825.1 Contig45476newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30007361SMESG000063825.1 Contig45476uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
secretory systemSMED30007361SMESG000063825.1 dd_Smed_v6_569_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30007361SMESG000063825.1 dd_Smed_v4_569_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30007361 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000320:163351..165771 -3989
Homology
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BLAST of SMED30007361 vs. Ensembl Human
Match: SELENOS (selenoprotein S [Source:HGNC Symbol;Acc:HGNC:30396])

HSP 1 Score: 50.447 bits (119), Expect = 5.675e-7
Identity = 42/146 (28.77%), Postives = 74/146 (50.68%), Query Frame = 3 
Query:   33 MILDLLSEYGWYLVILIGIGYYLWQRYSSQITNTKEDK-----KQIYSDQVFVRNQALERAREKMQQKMNEDASIXXXXXXXXXXXXXXXXXXXWEKFNKVLGCKSNTKGKDPQDRIDPSQSHNKKKERLRE-----SYNPLMGDS 440
            M+  LL+ YGWY+V    + Y ++Q+ S+++   ++ +       +  D V  R +AL  AR KMQ+++N       EK+K+ E+  + ++I+ W+   +    K N K    +D   PS S   K++  R+      YNPL G+ 
Sbjct:    2 MVGSLLATYGWYIVFSCILLYVVFQKLSARLRALRQRQLDRAAAAVEPDVVVKRQEALAAARLKMQEELNAQVEKHKEKLKQLEEEKRRQKIEMWDSMQEGKSYKGNAKKPQEEDSPGPSTSSVLKRKSDRKPLRGGGYNPLSGEG 147
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BLAST of SMED30007361 vs. Ensembl Human
Match: SELENOS (selenoprotein S [Source:HGNC Symbol;Acc:HGNC:30396])

HSP 1 Score: 48.521 bits (114), Expect = 3.274e-6
Identity = 41/150 (27.33%), Postives = 75/150 (50.00%), Query Frame = 3 
Query:   21 YKNYMILDLLSEYGWYLVILIGIGYYLWQRYSSQITNTKEDK-----KQIYSDQVFVRNQALERAREKMQQKMNEDASIXXXXXXXXXXXXXXXXXXXWEKFNKVLGCKSNTKGKDPQDRIDPSQSHNKKKERLRE-----SYNPLMGDS 440
            + +  +  LL+ YGWY+V    + Y ++Q+ S+++   ++ +       +  D V  R +AL  AR KMQ+++N       EK+K+ E+  + ++I+ W+   +    K N K    +D   PS S   K++  R+      YNPL G+ 
Sbjct:   21 FLHTTVGSLLATYGWYIVFSCILLYVVFQKLSARLRALRQRQLDRAAAAVEPDVVVKRQEALAAARLKMQEELNAQVEKHKEKLKQLEEEKRRQKIEMWDSMQEGKSYKGNAKKPQEEDSPGPSTSSVLKRKSDRKPLRGGGYNPLSGEG 170
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BLAST of SMED30007361 vs. Ensembl Human
Match: SELENOS (selenoprotein S [Source:HGNC Symbol;Acc:HGNC:30396])

HSP 1 Score: 48.521 bits (114), Expect = 3.274e-6
Identity = 41/150 (27.33%), Postives = 75/150 (50.00%), Query Frame = 3 
Query:   21 YKNYMILDLLSEYGWYLVILIGIGYYLWQRYSSQITNTKEDK-----KQIYSDQVFVRNQALERAREKMQQKMNEDASIXXXXXXXXXXXXXXXXXXXWEKFNKVLGCKSNTKGKDPQDRIDPSQSHNKKKERLRE-----SYNPLMGDS 440
            + +  +  LL+ YGWY+V    + Y ++Q+ S+++   ++ +       +  D V  R +AL  AR KMQ+++N       EK+K+ E+  + ++I+ W+   +    K N K    +D   PS S   K++  R+      YNPL G+ 
Sbjct:   21 FLHTTVGSLLATYGWYIVFSCILLYVVFQKLSARLRALRQRQLDRAAAAVEPDVVVKRQEALAAARLKMQEELNAQVEKHKEKLKQLEEEKRRQKIEMWDSMQEGKSYKGNAKKPQEEDSPGPSTSSVLKRKSDRKPLRGGGYNPLSGEG 170
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BLAST of SMED30007361 vs. Ensembl Human
Match: SELENOS (selenoprotein S [Source:HGNC Symbol;Acc:HGNC:30396])

HSP 1 Score: 47.7506 bits (112), Expect = 8.255e-6
Identity = 41/143 (28.67%), Postives = 72/143 (50.35%), Query Frame = 3 
Query:   42 DLLSEYGWYLVILIGIGYYLWQRYSSQITNTKEDK-----KQIYSDQVFVRNQALERAREKMQQKMNEDASIXXXXXXXXXXXXXXXXXXXWEKFNKVLGCKSNTKGKDPQDRIDPSQSHNKKKERLRE-----SYNPLMGDS 440
             LL+ YGWY+V    + Y ++Q+ S+++   ++ +       +  D V  R +AL  AR KMQ+++N       EK+K+ E+  + ++I+ W+   +    K N K    +D   PS S   K++  R+      YNPL G+ 
Sbjct:   68 SLLATYGWYIVFSCILLYVVFQKLSARLRALRQRQLDRAAAAVEPDVVVKRQEALAAARLKMQEELNAQVEKHKEKLKQLEEEKRRQKIEMWDSMQEGKSYKGNAKKPQEEDSPGPSTSSVLKRKSDRKPLRGGGYNPLSGEG 210
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BLAST of SMED30007361 vs. Ensembl Xenopus
Match: vimp (selenoprotein S [Source:NCBI gene;Acc:496967])

HSP 1 Score: 46.9802 bits (110), Expect = 9.533e-6
Identity = 37/141 (26.24%), Postives = 69/141 (48.94%), Query Frame = 3 
Query:   45 LLSEYGWYLVILIGIGYYLWQRYSSQITNTKEDKKQIYS--DQVFVRNQALERAREKMQQKMNEDASIXXXXXXXXXXXXXXXXXXXWEKFNKVLGCKSNTK-GKDPQDRIDPSQSHNKKKER-----LRES-YNPLMGDS 440
            +LS YGWY+++   + Y L Q+     T          +  D++  R +A+  AR +MQ+++N  A +  +K  + ++  ++  I+ W++  +    K   + G++P      S +   K+E+     LR S YNPL GD 
Sbjct:   30 VLSSYGWYILLGCILIYLLIQKLPQNFTRAGTSNHSTVTDPDEIVRRQEAVTAARLRMQEELNAQAELYKQKQVQLQEEKRQRNIETWDRMKEGKSSKVACRLGQEPSPSTSTSAATKPKQEKQERKTLRGSGYNPLTGDG 170
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BLAST of SMED30007361 vs. TrEMBL
Match: A0A0B7B5N6 (Uncharacterized protein OS=Arion vulgaris OX=1028688 GN=ORF159059 PE=4 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 2.236e-7
Identity = 43/138 (31.16%), Postives = 79/138 (57.25%), Query Frame = 3 
Query:   36 ILDLLSEYGWYLVILIGIGYYLWQRYSSQITNTKEDK-----KQIYSDQVFVRNQALERAREKMQQKMNEDASIXXXXXXXXXXXXXXXXXXXWEKFNKVLGCKSNTKGKDPQDRIDPSQSHNKKKERLRESYNPLMG 434
            ++D+L  YGW+++ +I    YL  +    +    + +     K++ S     R +A+ERAR KMQ +++E+A    E+ K KE+  + +++++WE+  +  G +S TK   P++R  P+   +K K+ L+  YNPLMG
Sbjct:   21 VIDVLQLYGWFILFVIIAVLYLGSKVRPWLDQLSQQRDINSYKKMDSGVAQSRLEAMERARLKMQAQLDEEAKRFAERQKAKEEEKRNQRLEDWERHCQGKGYRSKTKA--PEERPTPALVKSKAKKPLKPEYNPLMG 156
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BLAST of SMED30007361 vs. Planmine SMEST
Match: SMESG000063825.1 (SMESG000063825.1)

HSP 1 Score: 120.553 bits (301), Expect = 5.826e-34
Identity = 78/78 (100.00%), Postives = 78/78 (100.00%), Query Frame = 3 
Query:  210 MQQKMNEDASIXXXXXXXXXXXXXXXXXXXWEKFNKVLGCKSNTKGKDPQDRIDPSQSHNKKKERLRESYNPLMGDSC 443
            MQQKMNEDASIKLEKMKEKEKRLKEEQIKEWEKFNKVLGCKSNTKGKDPQDRIDPSQSHNKKKERLRESYNPLMGDSC
Sbjct:    1 MQQKMNEDASIKLEKMKEKEKRLKEEQIKEWEKFNKVLGCKSNTKGKDPQDRIDPSQSHNKKKERLRESYNPLMGDSC 78
[Close]
BLAST of SMED30007361 vs. Planmine SMEST
Match: SMESG000063825.1 (SMESG000063825.1)

HSP 1 Score: 112.849 bits (281), Expect = 4.396e-31
Identity = 74/74 (100.00%), Postives = 74/74 (100.00%), Query Frame = 3 
Query:  222 MNEDASIXXXXXXXXXXXXXXXXXXXWEKFNKVLGCKSNTKGKDPQDRIDPSQSHNKKKERLRESYNPLMGDSC 443
            MNEDASIKLEKMKEKEKRLKEEQIKEWEKFNKVLGCKSNTKGKDPQDRIDPSQSHNKKKERLRESYNPLMGDSC
Sbjct:    1 MNEDASIKLEKMKEKEKRLKEEQIKEWEKFNKVLGCKSNTKGKDPQDRIDPSQSHNKKKERLRESYNPLMGDSC 74
The following BLAST results are available for this feature:
BLAST of SMED30007361 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 4
Match NameE-valueIdentityDescription
SELENOS5.675e-728.77selenoprotein S [Source:HGNC Symbol;Acc:HGNC:30396... [more]
SELENOS3.274e-627.33selenoprotein S [Source:HGNC Symbol;Acc:HGNC:30396... [more]
SELENOS3.274e-627.33selenoprotein S [Source:HGNC Symbol;Acc:HGNC:30396... [more]
SELENOS8.255e-628.67selenoprotein S [Source:HGNC Symbol;Acc:HGNC:30396... [more]
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BLAST of SMED30007361 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 SMED30007361 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 SMED30007361 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 SMED30007361 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 1
Match NameE-valueIdentityDescription
vimp9.533e-626.24selenoprotein S [Source:NCBI gene;Acc:496967][more]
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BLAST of SMED30007361 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 SMED30007361 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 SMED30007361 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A0B7B5N62.236e-731.16Uncharacterized protein OS=Arion vulgaris OX=10286... [more]
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BLAST of SMED30007361 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 SMED30007361 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 SMED30007361 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 SMED30007361 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 SMED30007361 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 SMED30007361 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000063825.15.826e-34100.00SMESG000063825.1[more]
SMESG000063825.14.396e-31100.00SMESG000063825.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007361 ID=SMED30007361|Name=SMED30007361|organism=Schmidtea mediterranea sexual|type=transcript|length=1020bp
GACGGTCTTATCGAAATCTATATAAAAATTATATGATTTTAGATTTATTG
TCAGAATACGGTTGGTATTTAGTGATTCTTATAGGGATCGGATATTATTT
ATGGCAAAGATATTCATCCCAGATTACCAATACTAAAGAAGATAAAAAAC
AAATCTATTCAGATCAAGTGTTTGTGCGAAATCAGGCGCTAGAACGAGCC
CGTGAAAAAATGCAGCAGAAAATGAATGAAGACGCATCAATCAAGCTGGA
AAAGATGAAAGAGAAAGAAAAGCGATTGAAAGAAGAACAAATAAAGGAAT
GGGAGAAATTCAATAAAGTTTTAGGCTGCAAGTCCAATACGAAGGGGAAG
GATCCACAGGACCGGATTGATCCATCACAGTCACACAACAAGAAAAAAGA
AAGATTGAGAGAGAGTTACAATCCGTTGATGGGTGACTCATGTTCGCGGT
TTCGGCCGTCGCGGTCTGCGGCGAGTGGAGGAGGATGAGGGTAATTAATC
AGTCGCCGTGTCCTCGCATGACCGAGACTGATATCCATTATTGATTTTTT
TTGTTATTCTTCTAGCTAATGACGTGGCCTGTTGAAATGGTCTAATCGCC
ATGACAGTCCACTGAGGCCGCTAGGAACCTTTTTTTGCTATTGCTTGTGG
CTAAGCGTTACCTTTGAGTGGCGGGAATAAATTATTTATTTTGTGTTTGT
GTACATTTCAACATTGTATGAATGCGGTGTTGCATGAATTGATTTGATTG
TTTGTCACTTGTGATTGGATGAATTAATTTGATTGGCTGTCATTTTATTT
GGCGTTCTGTTAGGCAAACAATGATAAACGATAACCTTGTACAAACGTCA
TTTTAAAATATTTTACTATTTTCAGGAAAGCGAATGCAAATTGTAACACA
TCCCACAATAATCATCTGACATTTTTCGATTTATTTTTATCTGCATGTTC
TTGACATCAATTCTAACTAGTATTTTATGACTGATATTCGTTCATGAAGC
AAGTGTAATTATATTTTGTA
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protein sequence of SMED30007361-orf-1

>SMED30007361-orf-1 ID=SMED30007361-orf-1|Name=SMED30007361-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=162bp
RSYRNLYKNYMILDLLSEYGWYLVILIGIGYYLWQRYSSQITNTKEDKKQ
IYSDQVFVRNQALERAREKMQQKMNEDASIKLEKMKEKEKRLKEEQIKEW
EKFNKVLGCKSNTKGKDPQDRIDPSQSHNKKKERLRESYNPLMGDSCSRF
RPSRSAASGGG*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000484secretory system
PLANA:0002032epidermal cell
PLANA:0003117parapharyngeal cell
Vocabulary: INTERPRO
TermDefinition
IPR009703Selenoprotein_S
Vocabulary: cellular component
TermDefinition
GO:0030176integral component of endoplasmic reticulum membrane
Vocabulary: biological process
TermDefinition
GO:0006886intracellular protein transport
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 52..84
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 103..128
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 98..150
NoneNo IPR availableTMHMMTMhelixcoord: 4..23
IPR009703Selenoprotein SPFAMPF06936Selenoprotein_Scoord: 3..150
e-value: 6.2E-22
score: 78.3
IPR009703Selenoprotein SPANTHERPTHR28621FAMILY NOT NAMEDcoord: 3..150