SMED30016736

Overview
NameSMED30016736
Smed IDSMED30016736
Length (bp)387
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30016736 (SMED30016736) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30016736 (SMED30016736) in cells (dots) of each of the 12 neoblast clusters.

 

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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



SMED30016736

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
reproductive organSMED30016736SMESG000019723.1 Contig17025newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30016736SMESG000019723.1 Contig17025uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of SMED30016736 vs. TrEMBL
Match: A0A2G8LCX0 (Integrase catalytic domain-containing protein OS=Stichopus japonicus OX=307972 GN=BSL78_04960 PE=4 SV=1)

HSP 1 Score: 128.257 bits (321), Expect = 2.500e-33
Identity = 69/127 (54.33%), Postives = 84/127 (66.14%), Query Frame = -3 
Query:   17 PFLTKQGRRNVRKGRYLCLFTCLESREVHLELAHRLGTDFFIRALLIFISRRGQPEYIISVNGRNVVGALKEVREL--NIDNYRVQRELSKG--NTRWIFNQPSAPHFGGGLEYMIKAAKRALVSEL 385
            PFLTKQGR  ++  RYLCLFTC+++R VHLE+A  L TD FI  L  F SRRG P  I S NG N VGA  E  +L   ID  +V+R+ SK   N +W+ N P APHFGG  E MIK+AKRA+ + L
Sbjct:  121 PFLTKQGRGKIKTKRYLCLFTCMKTRAVHLEMAFGLDTDSFINCLYRFTSRRGIPSEIRSDNGTNFVGARNEFIKLFDTIDKAKVERDTSKKGINWKWVLNPPLAPHFGGIHESMIKSAKRAIYAIL 247
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BLAST of SMED30016736 vs. TrEMBL
Match: A0A2B4RV04 (Integrase catalytic domain-containing protein OS=Stylophora pistillata OX=50429 GN=AWC38_SpisGene14531 PE=4 SV=1)

HSP 1 Score: 130.954 bits (328), Expect = 1.249e-32
Identity = 65/122 (53.28%), Postives = 80/122 (65.57%), Query Frame = -3 
Query:   29 PFLTKQGRRNVRKGRYLCLFTCLESREVHLELAHRLGTDFFIRALLIFISRRGQPEYIISVNGRNVVGALKEVREL--NIDNYRVQRELSKGN-TRWIFNQPSAPHFGGGLEYMIKAAKRAL 385
            PFLTK GR   R  RYLCLFTCL +R VHLE+++ L TD FI       SRRG P Y+IS NG N VG  +E+REL   +D  R+ +E SK +   W FN PSAPHFGG  E +IK+AK+ +
Sbjct:  541 PFLTKHGRGRTRAKRYLCLFTCLTTRAVHLEMSYSLDTDSFINTFTRMTSRRGTPTYVISDNGTNFVGTERELRELVEALDTDRITQETSKYHPIDWTFNPPSAPHFGGVFEALIKSAKKVI 662
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BLAST of SMED30016736 vs. TrEMBL
Match: A0A2G8KB92 (Integrase catalytic domain-containing protein OS=Stichopus japonicus OX=307972 GN=BSL78_17882 PE=4 SV=1)

HSP 1 Score: 120.168 bits (300), Expect = 1.091e-30
Identity = 62/121 (51.24%), Postives = 79/121 (65.29%), Query Frame = -3 
Query:   29 PFLTKQGRRNVRKGRYLCLFTCLESREVHLELAHRLGTDFFIRALLIFISRRGQPEYIISVNGRNVVGALKEVREL--NIDNYRVQRELSKGNTRWIFNQPSAPHFGGGLEYMIKAAKRAL 385
            PFL KQGR  ++  RYLC FTCL SR VHLE+A+ L TD F+ AL   I+RRG P  +IS NG N  GA K++REL   +D  ++ R  +    +W FN P +PHFGG  E MIK AK+A+
Sbjct:   26 PFLAKQGRGRIKLKRYLCFFTCLSSRAVHLEMAYGLDTDSFLNALNRMINRRGVPVEMISDNGTNFKGAEKKLRELVDRMDKDKMTRSTANQMIKWHFNPPLSPHFGGVHETMIKGAKKAI 146
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BLAST of SMED30016736 vs. TrEMBL
Match: A0A2G8L9D8 (Integrase catalytic domain-containing protein OS=Stichopus japonicus OX=307972 GN=BSL78_06265 PE=4 SV=1)

HSP 1 Score: 120.939 bits (302), Expect = 1.544e-29
Identity = 61/120 (50.83%), Postives = 81/120 (67.50%), Query Frame = -3 
Query:   17 QGRRNVRKGRYLCLFTCLESREVHLELAHRLGTDFFIRALLIFISRRGQPEYIISVNGRNVVGALKEVRELN--IDNYRVQRELSKGNTRWIFNQPSAPHFGGGLEYMIKAAKRALVSEL 370
             G+R+    RYLCLFTCL +R VHLE+A+ L TD F+ A   F+SRRG+PE + S NG N VGA +E++EL   ID  +VQ E++ G  RW F  P +PHFGG  E +IK +KRA+ + L
Sbjct:  120 DGKRSCEDKRYLCLFTCLSTRAVHLEIAYGLDTDTFLNAFYRFVSRRGEPEEVFSDNGTNFVGASRELKELFRLIDKSKVQ-EVTAGQMRWHFLPPLSPHFGGAHEALIKTSKRAIQAVL 238
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BLAST of SMED30016736 vs. TrEMBL
Match: A0A2B4S5H1 (Integrase catalytic domain-containing protein OS=Stylophora pistillata OX=50429 GN=AWC38_SpisGene11684 PE=4 SV=1)

HSP 1 Score: 115.161 bits (287), Expect = 3.997e-27
Identity = 60/125 (48.00%), Postives = 77/125 (61.60%), Query Frame = -3 
Query:   14 PFLTKQGRRNVRKGRYLCLFTCLESREVHLELAHRLGTDFFIRALLIFISRRGQPEYIISVNGRNVVGALKEVRELN-IDNYRVQRELSKGNTRWIFNQPSAPHFGGGLEYMIKAAKRALVSELN 385
            PF+TKQGR    + RYLCLFTCL +R VHLE+A  L TD F+ A     S+RG  E ++  NG N+VG   E+++L  +D  +VQ         W FN P APHF G  E MIKAAK+A+ + LN
Sbjct:  715 PFITKQGRGKTCQKRYLCLFTCLATRAVHLEVAFSLDTDSFLSAFFRMASQRGLAEDVMCDNGTNLVGGSNELKDLEALDKKQVQDATLNYRVNWHFNPPLAPHFSGEHEIMIKAAKKAIYAILN 839
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BLAST of SMED30016736 vs. Planmine SMEST
Match: SMESG000041327.1 (SMESG000041327.1)

HSP 1 Score: 144.05 bits (362), Expect = 7.563e-44
Identity = 66/119 (55.46%), Postives = 87/119 (73.11%), Query Frame = -3 
Query:   29 PFLTKQGRRNVRKGRYLCLFTCLESREVHLELAHRLGTDFFIRALLIFISRRGQPEYIISVNGRNVVGALKEVRELNIDNYRVQRELSKGNTRWIFNQPSAPHFGGGLEYMIKAAKRAL 385
            PF T QGR   R+ RY+CLFTCL++R VHLE+A+ L T+ FIRA + F+ RRG+P  I+S NG N VGA  EV+E+ +D+YR  + +S  + RWIFN P APHFGG  E +IK+AK+AL
Sbjct:   63 PFETIQGRGKTRQKRYMCLFTCLQTRAVHLEVAYALDTNAFIRAFIRFMGRRGKPLMILSDNGTNFVGATNEVQEIKVDSYRFNKFMSGNDIRWIFNPPLAPHFGGVFEALIKSAKKAL 181
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BLAST of SMED30016736 vs. Planmine SMEST
Match: SMESG000042734.1 (SMESG000042734.1)

HSP 1 Score: 140.969 bits (354), Expect = 3.669e-43
Identity = 71/103 (68.93%), Postives = 79/103 (76.70%), Query Frame = -3 
Query:   23 LFTCLESREVHLELAHRLGTDFFIRALLIFISRRGQPEYIISVNGRNVVGALKEVRELNIDNYRVQRELSKGNTRWIFNQPSAPHFGGGLEYMIKAAKRALVS 331
            ++ CLE   VHLELAH L TD  I ALL FI RRG+PE+IIS NG N VG LKE+ +  IDNYRVQRELSKGNTRWIFN  SAPHFGG  E+MIKA KRAL +
Sbjct:   18 IYVCLE---VHLELAHGLITDSVIGALLRFIGRRGKPEFIISDNGTNFVGDLKEINKFKIDNYRVQRELSKGNTRWIFNLSSAPHFGGVFEFMIKATKRALAA 117
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BLAST of SMED30016736 vs. Planmine SMEST
Match: SMESG000035628.1 (SMESG000035628.1)

HSP 1 Score: 134.42 bits (337), Expect = 9.757e-41
Identity = 62/119 (52.10%), Postives = 84/119 (70.59%), Query Frame = -3 
Query:   29 PFLTKQGRRNVRKGRYLCLFTCLESREVHLELAHRLGTDFFIRALLIFISRRGQPEYIISVNGRNVVGALKEVRELNIDNYRVQRELSKGNTRWIFNQPSAPHFGGGLEYMIKAAKRAL 385
            PF T Q R   R+ RY+CLFTCL++R VHL++A+ L TD FIRA + F+ RRG+   I+S NG N VGA  EV+ + +D Y+V + +S+ N RWIFN P AP FGG  E ++K+AK+AL
Sbjct:   26 PFQTMQVRGKARQKRYMCLFTCLQTRAVHLKVAYALDTDAFIRAFIRFMGRRGKSLMILSDNGTNFVGARNEVQRIKVDIYKVNKVMSENNIRWIFNPPLAPQFGGVFEALMKSAKKAL 144
[Close]
BLAST of SMED30016736 vs. Planmine SMEST
Match: SMESG000021221.1 (SMESG000021221.1)

HSP 1 Score: 138.658 bits (348), Expect = 2.340e-39
Identity = 63/118 (53.39%), Postives = 85/118 (72.03%), Query Frame = -3 
Query:   29 FLTKQGRRNVRKGRYLCLFTCLESREVHLELAHRLGTDFFIRALLIFISRRGQPEYIISVNGRNVVGALKEVRELNIDNYRVQRELSKGNTRWIFNQPSAPHFGGGLEYMIKAAKRAL 382
            F T QGR   R+ RY+CLFTCL++R V+LE+ + L TD FIRA + F  RRG+P  I++ NG N VG   EV+E+ +D+Y+V + +S+ N RWIFN P APHFGG  E +IK+AK+AL
Sbjct:  427 FETIQGRGKTRQKRYMCLFTCLQTRAVYLEVMYALDTDAFIRAFIRFTGRRGKPLMILADNGTNFVGTTNEVKEIKVDSYKVNKVMSENNIRWIFNPPLAPHFGGVFEALIKSAKKAL 544
[Close]
BLAST of SMED30016736 vs. Planmine SMEST
Match: SMESG000041215.1 (SMESG000041215.1)

HSP 1 Score: 136.732 bits (343), Expect = 3.098e-38
Identity = 63/119 (52.94%), Postives = 84/119 (70.59%), Query Frame = -3 
Query:   29 PFLTKQGRRNVRKGRYLCLFTCLESREVHLELAHRLGTDFFIRALLIFISRRGQPEYIISVNGRNVVGALKEVRELNIDNYRVQRELSKGNTRWIFNQPSAPHFGGGLEYMIKAAKRAL 385
            P  T QGR   R+ RY+CLFTCL++R VHLE+AH L TD FIRA + F+ RR +P  I+S NG N VGA  +V+E+ +D+YR  + +S  +  WIFN P APHFGG  E +I++AK+AL
Sbjct: 1355 PLETIQGRGKTRQKRYMCLFTCLQTRAVHLEVAHALDTDAFIRAFIRFMGRREKPLMILSDNGTNFVGATNKVQEIKVDSYRFNKFMSGNDIIWIFNPPLAPHFGGVFEALIESAKKAL 1473
The following BLAST results are available for this feature:
BLAST of SMED30016736 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 SMED30016736 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 SMED30016736 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 SMED30016736 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 SMED30016736 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 SMED30016736 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 SMED30016736 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 SMED30016736 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A2G8LCX02.500e-3354.33Integrase catalytic domain-containing protein OS=S... [more]
A0A2B4RV041.249e-3253.28Integrase catalytic domain-containing protein OS=S... [more]
A0A2G8KB921.091e-3051.24Integrase catalytic domain-containing protein OS=S... [more]
A0A2G8L9D81.544e-2950.83Integrase catalytic domain-containing protein OS=S... [more]
A0A2B4S5H13.997e-2748.00Integrase catalytic domain-containing protein OS=S... [more]
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BLAST of SMED30016736 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 SMED30016736 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 SMED30016736 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 SMED30016736 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 SMED30016736 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 SMED30016736 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000041327.17.563e-4455.46SMESG000041327.1[more]
SMESG000042734.13.669e-4368.93SMESG000042734.1[more]
SMESG000035628.19.757e-4152.10SMESG000035628.1[more]
SMESG000021221.12.340e-3953.39SMESG000021221.1[more]
SMESG000041215.13.098e-3852.94SMESG000041215.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30016736 ID=SMED30016736|Name=SMED30016736|organism=Schmidtea mediterranea sexual|type=transcript|length=387bp
CGTGCTTTTCATAATTTAATTCAGATACTAGAGCTCTTTTTGCGGCTTTG
ATCATGTATTCAAGTCCTCCGCCAAAGTGTGGTGCTGATGGTTGGTTAAA
TATCCATCTCGTATTACCTTTAGACAACTCTCTTTGTACTCGGTAATTGT
CAATATTTAATTCTCTAACCTCTTTCAGAGCTCCGACAACATTCCTGCCG
TTAACCGATATAATATACTCTGGCTGTCCTCGTCTGCTTATAAATATTAG
CAATGCCCTGATAAAGAAATCAGTACCCAATCTATGAGCCAGTTCTAAAT
GCACTTCCCGACTTTCTAAGCACGTAAACAAACATAGATATCTCCCTTTT
CTAACATTCCTTCTCCCTTGTTTTGTGAGAAAAGGCC
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protein sequence of SMED30016736-orf-1

>SMED30016736-orf-1 ID=SMED30016736-orf-1|Name=SMED30016736-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=128bp
PFLTKQGRRNVRKGRYLCLFTCLESREVHLELAHRLGTDFFIRALLIFIS
RRGQPEYIISVNGRNVVGALKEVRELNIDNYRVQRELSKGNTRWIFNQPS
APHFGGGLEYMIKAAKRALVSELNYEKH
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002089reproductive organ
Vocabulary: INTERPRO
TermDefinition
IPR012337RNaseH-like_sf
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding