SMED30011254

Overview
NameSMED30011254
Smed IDSMED30011254
Length (bp)929
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 SMED30011254 (SMED30011254) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30011254 (SMED30011254) 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.
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




SMED30011254

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
testis primordiumSMED30011254SMESG000028716.1 Contig1932_SE3GPL10652PMID:20844018
Wang et al., 2010
whole organism juvenile cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Homology
BLAST of SMED30011254 vs. TrEMBL
Match: A0A1I8G026 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 73.1738 bits (178), Expect = 1.932e-10
Identity = 32/71 (45.07%), Postives = 53/71 (74.65%), Query Frame = 2
Query:  347 NTDIESIIKKPMPNRLRHLEPLHNPPLLTREKLIRKLKSAEEKRKQILEIKRYSHSRPKTVSAEQLQNSQN 559
            N+DI+ I++KP+P RLRHLEPL + P+++ E+L  KL+ AEEKR+++LE +R+S    K+ +  +L  +Q+
Sbjct:  580 NSDIDKILRKPLPPRLRHLEPLDSVPVMSPEQLAEKLRKAEEKRERMLEKRRHSKVTKKSKARRELLKAQD 650          
BLAST of SMED30011254 vs. TrEMBL
Match: A0A1I8G547 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 67.781 bits (164), Expect = 4.380e-9
Identity = 32/71 (45.07%), Postives = 53/71 (74.65%), Query Frame = 2
Query:  347 NTDIESIIKKPMPNRLRHLEPLHNPPLLTREKLIRKLKSAEEKRKQILEIKRYSHSRPKTVSAEQLQNSQN 559
            N+DI+ I++KP+P RLRHLEPL + P+++ E+L  KL+ AEEKR+++LE +R+S    K+ +  +L  +Q+
Sbjct:   88 NSDIDKILRKPLPPRLRHLEPLDSVPVMSPEQLAEKLRKAEEKRERMLEKRRHSKVTKKSKARRELLKAQD 158          
BLAST of SMED30011254 vs. TrEMBL
Match: A0A1I8H8U6 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 67.3958 bits (163), Expect = 6.077e-9
Identity = 32/71 (45.07%), Postives = 53/71 (74.65%), Query Frame = 2
Query:  347 NTDIESIIKKPMPNRLRHLEPLHNPPLLTREKLIRKLKSAEEKRKQILEIKRYSHSRPKTVSAEQLQNSQN 559
            N+DI+ I++KP+P RLRHLEPL + P+++ E+L  KL+ AEEKR+++LE +R+S    K+ +  +L  +Q+
Sbjct:   88 NSDIDKILRKPLPPRLRHLEPLDSVPVMSPEQLAEKLRKAEEKRERMLEKRRHSKVTKKSKARRELLKAQD 158          
BLAST of SMED30011254 vs. TrEMBL
Match: A0A267H4A1 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig033735g2 PE=4 SV=1)

HSP 1 Score: 67.0106 bits (162), Expect = 8.602e-9
Identity = 29/54 (53.70%), Postives = 45/54 (83.33%), Query Frame = 2
Query:  347 NTDIESIIKKPMPNRLRHLEPLHNPPLLTREKLIRKLKSAEEKRKQILEIKRYS 508
            N+DI+ I++KP+P RLRHLEPL + P+++ E+L  KL+ AEEKR+++LE +R+S
Sbjct:   99 NSDIDKILRKPLPPRLRHLEPLDSVPVMSPEQLAEKLRKAEEKRERMLEKRRHS 152          
BLAST of SMED30011254 vs. TrEMBL
Match: A0A1I8IX26 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 67.0106 bits (162), Expect = 1.070e-8
Identity = 32/71 (45.07%), Postives = 53/71 (74.65%), Query Frame = 2
Query:  347 NTDIESIIKKPMPNRLRHLEPLHNPPLLTREKLIRKLKSAEEKRKQILEIKRYSHSRPKTVSAEQLQNSQN 559
            N+DI+ I++KP+P RLRHLEPL + P+++ E+L  KL+ AEEKR+++LE +R+S    K+ +  +L  +Q+
Sbjct:  139 NSDIDKILRKPLPPRLRHLEPLDSVPVMSPEQLAEKLRKAEEKRERMLEKRRHSKVTKKSKARRELLKAQD 209          
BLAST of SMED30011254 vs. Planmine SMEST
Match: SMESG000028716.1 (SMESG000028716.1)

HSP 1 Score: 438.728 bits (1127), Expect = 3.132e-157
Identity = 229/229 (100.00%), Postives = 229/229 (100.00%), Query Frame = 2
Query:   95 MGCSPSTFRKVDANNSANVQAXXXXXXXXXXXXLSKHTSSCYSTKDEIETLLKESPLPISVENEINKEPKSLAYDIKINNGDHFNTDIESIIKKPMPNRLRHLEPLHNPPLLTREKLIRKLKSAEEKRKQILEIKRYSHSRPKTVSAEQLQNSQNNIEDQQIYENDIALKRLKINSSRNLQKFKGKDLRKLNIMTSIHHNDNRINILKSASCSDIDEEYFCSYDSLNQT 781
            MGCSPSTFRKVDANNSANVQATTIVKSTTETSTLSKHTSSCYSTKDEIETLLKESPLPISVENEINKEPKSLAYDIKINNGDHFNTDIESIIKKPMPNRLRHLEPLHNPPLLTREKLIRKLKSAEEKRKQILEIKRYSHSRPKTVSAEQLQNSQNNIEDQQIYENDIALKRLKINSSRNLQKFKGKDLRKLNIMTSIHHNDNRINILKSASCSDIDEEYFCSYDSLNQT
Sbjct:    1 MGCSPSTFRKVDANNSANVQATTIVKSTTETSTLSKHTSSCYSTKDEIETLLKESPLPISVENEINKEPKSLAYDIKINNGDHFNTDIESIIKKPMPNRLRHLEPLHNPPLLTREKLIRKLKSAEEKRKQILEIKRYSHSRPKTVSAEQLQNSQNNIEDQQIYENDIALKRLKINSSRNLQKFKGKDLRKLNIMTSIHHNDNRINILKSASCSDIDEEYFCSYDSLNQT 229          
BLAST of SMED30011254 vs. Planmine SMEST
Match: SMESG000028716.1 (SMESG000028716.1)

HSP 1 Score: 409.838 bits (1052), Expect = 6.143e-146
Identity = 216/220 (98.18%), Postives = 217/220 (98.64%), Query Frame = 2
Query:   95 MGCSPSTFRKVDANNSANVQAXXXXXXXXXXXXLSKHTSSCYSTKDEIETLLKESPLPISVENEINKEPKSLAYDIKINNGDHFNTDIESIIKKPMPNRLRHLEPLHNPPLLTREKLIRKLKSAEEKRKQILEIKRYSHSRPKTVSAEQLQNSQNNIEDQQIYENDIALKRLKINSSRNLQKFKGKDLRKLNIMTSIHHNDNRINILKSASCSDIDEEYF 754
            MGCSPSTFRKVDANNSANVQATTIVKSTTETSTLSKHTSSCYSTKDEIETLLKESPLPISVENEINKEPKSLAYDIKINNGDHFNTDIESIIKKPMPNRLRHLEPLHNPPLLTREKLIRKLKSAEEKRKQILEIKRYSHSRPKTVSAEQLQNSQNNIEDQQIYENDIALKRLKINSSRNLQKFKGKDLRKLNIMTSIHHNDNRINILKSASCSD +  YF
Sbjct:    1 MGCSPSTFRKVDANNSANVQATTIVKSTTETSTLSKHTSSCYSTKDEIETLLKESPLPISVENEINKEPKSLAYDIKINNGDHFNTDIESIIKKPMPNRLRHLEPLHNPPLLTREKLIRKLKSAEEKRKQILEIKRYSHSRPKTVSAEQLQNSQNNIEDQQIYENDIALKRLKINSSRNLQKFKGKDLRKLNIMTSIHHNDNRINILKSASCSDSESIYF 220          
BLAST of SMED30011254 vs. Planmine SMEST
Match: SMESG000028716.1 (SMESG000028716.1)

HSP 1 Score: 408.683 bits (1049), Expect = 5.573e-145
Identity = 215/220 (97.73%), Postives = 216/220 (98.18%), Query Frame = 2
Query:   95 MGCSPSTFRKVDANNSANVQAXXXXXXXXXXXXLSKHTSSCYSTKDEIETLLKESPLPISVENEINKEPKSLAYDIKINNGDHFNTDIESIIKKPMPNRLRHLEPLHNPPLLTREKLIRKLKSAEEKRKQILEIKRYSHSRPKTVSAEQLQNSQNNIEDQQIYENDIALKRLKINSSRNLQKFKGKDLRKLNIMTSIHHNDNRINILKSASCSDIDEEYF 754
            MGCSPSTFRKVDANNSANVQATTIVKSTTETSTLSKHTSSCYSTKDEIETLLKESPLPISVENEINKEPKSLAYDIKINNGDHFNTDIESIIKKPMPNRLRHLEPLHNPPLLTREKLIRKLKSAEEKRKQILEIKRYSHSRPKTVSAEQLQNSQNNIEDQQIYENDIALKRLKINSSRNLQKFKGKDLRKLNIMTSIHHNDNRINILKSASCSD  +  F
Sbjct:    1 MGCSPSTFRKVDANNSANVQATTIVKSTTETSTLSKHTSSCYSTKDEIETLLKESPLPISVENEINKEPKSLAYDIKINNGDHFNTDIESIIKKPMPNRLRHLEPLHNPPLLTREKLIRKLKSAEEKRKQILEIKRYSHSRPKTVSAEQLQNSQNNIEDQQIYENDIALKRLKINSSRNLQKFKGKDLRKLNIMTSIHHNDNRINILKSASCSDNTDASF 220          
BLAST of SMED30011254 vs. Planmine SMEST
Match: SMESG000073243.1 (SMESG000073243.1)

HSP 1 Score: 51.2174 bits (121), Expect = 3.125e-7
Identity = 35/84 (41.67%), Postives = 49/84 (58.33%), Query Frame = 2
Query:  308 LAYDIKINNGD--HFNTDIESIIKKPMPNRLRHLEPLHNPPLLTREKLIRKLKSAEEKRKQI----LEIKRYSHSRPKTVSAEQ 541
            +A+ I INN +    N DI+ I+ KP+P RL+ LEP++    LT E L +KL+ AE KR++     LE  R    R  T+ AEQ
Sbjct:   28 VAFQIDINNNETKDLNKDIDLILSKPLPKRLQRLEPINGVSKLTAEDLEKKLELAEIKRQKTFERRLEFTRKGSLRRSTI-AEQ 110          
BLAST of SMED30011254 vs. Planmine SMEST
Match: SMESG000073243.1 (SMESG000073243.1)

HSP 1 Score: 50.8322 bits (120), Expect = 3.732e-7
Identity = 35/84 (41.67%), Postives = 49/84 (58.33%), Query Frame = 2
Query:  308 LAYDIKINNGD--HFNTDIESIIKKPMPNRLRHLEPLHNPPLLTREKLIRKLKSAEEKRKQI----LEIKRYSHSRPKTVSAEQ 541
            +A+ I INN +    N DI+ I+ KP+P RL+ LEP++    LT E L +KL+ AE KR++     LE  R    R  T+ AEQ
Sbjct:   21 VAFQIDINNNETKDLNKDIDLILSKPLPKRLQRLEPINGVSKLTAEDLEKKLELAEIKRQKTFERRLEFTRKGSLRRSTI-AEQ 103          
The following BLAST results are available for this feature:
BLAST of SMED30011254 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 SMED30011254 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 SMED30011254 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 SMED30011254 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 SMED30011254 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 SMED30011254 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 SMED30011254 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 SMED30011254 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1I8G0261.932e-1045.07Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8G5474.380e-945.07Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8H8U66.077e-945.07Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267H4A18.602e-953.70Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8IX261.070e-845.07Uncharacterized protein OS=Macrostomum lignano OX=... [more]
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BLAST of SMED30011254 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 SMED30011254 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 SMED30011254 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 SMED30011254 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 SMED30011254 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 SMED30011254 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000028716.13.132e-157100.00SMESG000028716.1[more]
SMESG000028716.16.143e-14698.18SMESG000028716.1[more]
SMESG000028716.15.573e-14597.73SMESG000028716.1[more]
SMESG000073243.13.125e-741.67SMESG000073243.1[more]
SMESG000073243.13.732e-741.67SMESG000073243.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011254 ID=SMED30011254|Name=SMED30011254|organism=Schmidtea mediterranea sexual|type=transcript|length=929bp
GTTTGATATTTTTTTTAACATCCAATATTTATTTCACTATTCAATGTTGA
AATATTGTTAAAATAATTTTGCTTCGCGGTAATGTAATATCTTTATGGGT
TGTTCACCTTCCACATTTCGAAAAGTTGATGCTAATAATTCAGCTAATGT
TCAAGCTACAACAATTGTAAAATCAACAACTGAAACTTCCACACTAAGCA
AACATACGAGCTCATGCTATTCAACAAAAGATGAAATAGAAACCTTACTC
AAAGAGAGTCCTTTGCCTATATCAGTGGAAAATGAAATAAACAAAGAACC
AAAATCATTGGCATACGATATAAAAATTAATAACGGTGACCATTTTAATA
CAGATATTGAATCCATAATAAAGAAACCAATGCCAAACCGTTTGAGACAT
TTAGAACCACTTCACAATCCACCGTTATTAACTCGTGAAAAACTTATTAG
AAAATTAAAGTCAGCTGAAGAAAAAAGAAAGCAGATATTGGAAATCAAAC
GATATTCGCATAGCAGACCAAAAACTGTGAGCGCTGAACAGTTGCAAAAT
TCTCAAAATAATATTGAAGATCAACAAATTTATGAAAATGATATAGCACT
TAAAAGATTAAAAATAAATTCATCACGTAATCTTCAAAAATTTAAAGGGA
AGGATTTGAGAAAATTGAATATAATGACTTCAATTCACCACAATGATAAC
CGAATTAATATTTTGAAAAGTGCTAGCTGTAGTGATATTGACGAAGAATA
CTTCTGTTCATATGATTCCCTGAATCAAACATGACCTCATCTTTATTCGG
AATGTTATGACAAATATTTTAATTGTATTATGCTTATTATAAGTAAAGTA
AATCTTTACCTTTTTAAGGTAGTAATTGAAAATTTTTCATAGTTGATAAG
TAAATAAATAAAAATGTCTTAAAAAAAAA
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protein sequence of SMED30011254-orf-1

>SMED30011254-orf-1 ID=SMED30011254-orf-1|Name=SMED30011254-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=230bp
MGCSPSTFRKVDANNSANVQATTIVKSTTETSTLSKHTSSCYSTKDEIET
LLKESPLPISVENEINKEPKSLAYDIKINNGDHFNTDIESIIKKPMPNRL
RHLEPLHNPPLLTREKLIRKLKSAEEKRKQILEIKRYSHSRPKTVSAEQL
QNSQNNIEDQQIYENDIALKRLKINSSRNLQKFKGKDLRKLNIMTSIHHN
DNRINILKSASCSDIDEEYFCSYDSLNQT*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0003304testis primordium
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 114..134