SMED30024594

Overview
NameSMED30024594
Smed IDSMED30024594
Length (bp)339
Neoblast Clusters

Zeng et. al., 2018




 



 

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




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




SMED30024594

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
parenchymal cellSMED30024594SMESG000074421.1 dd_Smed_v4_10813_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
epidermal cellSMED30024594SMESG000074421.1 dd_Smed_v4_10813_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
epidermisSMED30024594SMESG000074421.1 dd_Smed_v4_10813_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
Homology
BLAST of SMED30024594 vs. Planmine SMEST
Match: SMESG000050479.1 (SMESG000050479.1)

HSP 1 Score: 48.521 bits (114), Expect = 8.420e-11
Identity = 24/49 (48.98%), Postives = 36/49 (73.47%), Query Frame = 1
Query:  193 TKKYINV*KFYKGSGLEILDHDMILNKL*DVLSAPQWIIITNFQKNEKF 339
             KK IN+ KF KG+G+ ILDHD+ +NKL D+L++PQ++ +   +KN K 
Sbjct: 2418 AKKNINICKFDKGNGIVILDHDVYVNKLNDLLNSPQFVKLPKGRKNGKL 2466          

HSP 2 Score: 33.4982 bits (75), Expect = 8.420e-11
Identity = 17/31 (54.84%), Postives = 23/31 (74.19%), Query Frame = 2
Query:   98 NCLKSLMSLSTIEYVDKNKK*IIMDNLLIKN 190
            N +KS +S ST+EY+DKNKK  I D + +KN
Sbjct: 2386 NYVKSSLSASTMEYIDKNKKQNIRDFMTLKN 2416          
BLAST of SMED30024594 vs. Planmine SMEST
Match: SMESG000050479.1 (SMESG000050479.1)

HSP 1 Score: 48.521 bits (114), Expect = 8.937e-11
Identity = 24/49 (48.98%), Postives = 36/49 (73.47%), Query Frame = 1
Query:  193 TKKYINV*KFYKGSGLEILDHDMILNKL*DVLSAPQWIIITNFQKNEKF 339
             KK IN+ KF KG+G+ ILDHD+ +NKL D+L++PQ++ +   +KN K 
Sbjct: 1461 AKKNINICKFDKGNGIVILDHDVYVNKLNDLLNSPQFVKLPKGRKNGKL 1509          

HSP 2 Score: 33.4982 bits (75), Expect = 8.937e-11
Identity = 17/31 (54.84%), Postives = 23/31 (74.19%), Query Frame = 2
Query:   98 NCLKSLMSLSTIEYVDKNKK*IIMDNLLIKN 190
            N +KS +S ST+EY+DKNKK  I D + +KN
Sbjct: 1429 NYVKSSLSASTMEYIDKNKKQNIRDFMTLKN 1459          
BLAST of SMED30024594 vs. Planmine SMEST
Match: SMESG000050479.1 (SMESG000050479.1)

HSP 1 Score: 48.521 bits (114), Expect = 9.763e-11
Identity = 24/49 (48.98%), Postives = 36/49 (73.47%), Query Frame = 1
Query:  193 TKKYINV*KFYKGSGLEILDHDMILNKL*DVLSAPQWIIITNFQKNEKF 339
             KK IN+ KF KG+G+ ILDHD+ +NKL D+L++PQ++ +   +KN K 
Sbjct: 1527 AKKNINICKFDKGNGIVILDHDVYVNKLNDLLNSPQFVKLPKGRKNGKL 1575          

HSP 2 Score: 33.113 bits (74), Expect = 9.763e-11
Identity = 17/31 (54.84%), Postives = 23/31 (74.19%), Query Frame = 2
Query:   98 NCLKSLMSLSTIEYVDKNKK*IIMDNLLIKN 190
            N +KS +S ST+EY+DKNKK  I D + +KN
Sbjct: 1495 NYVKSSLSASTMEYIDKNKKQNIRDFMTLKN 1525          
BLAST of SMED30024594 vs. Planmine SMEST
Match: SMESG000081574.1 (SMESG000081574.1)

HSP 1 Score: 43.1282 bits (100), Expect = 1.671e-8
Identity = 23/51 (45.10%), Postives = 35/51 (68.63%), Query Frame = 1
Query:  184 KEPTKKYINV*KFYKGSGLEILDHDMILNKL*DVLSAPQWIIITNFQKNEK 336
            K   KK IN+ KF KG+G+ I  HD+ +NKL D+L++PQ++ +   +KN K
Sbjct: 1477 KNLAKKNINICKFDKGNGIVIFYHDLYVNKLNDLLNSPQFVKLPKGRKNGK 1527          

HSP 2 Score: 30.8018 bits (68), Expect = 1.671e-8
Identity = 16/31 (51.61%), Postives = 23/31 (74.19%), Query Frame = 2
Query:   98 NCLKSLMSLSTIEYVDKNKK*IIMDNLLIKN 190
            N ++SL+S ST+EY+DK KK  I D + +KN
Sbjct: 1448 NYVRSLLSASTMEYIDKIKKQNIGDFMTLKN 1478          
BLAST of SMED30024594 vs. Planmine SMEST
Match: SMESG000081574.1 (SMESG000081574.1)

HSP 1 Score: 43.1282 bits (100), Expect = 1.683e-8
Identity = 23/51 (45.10%), Postives = 35/51 (68.63%), Query Frame = 1
Query:  184 KEPTKKYINV*KFYKGSGLEILDHDMILNKL*DVLSAPQWIIITNFQKNEK 336
            K   KK IN+ KF KG+G+ I  HD+ +NKL D+L++PQ++ +   +KN K
Sbjct: 1511 KNLAKKNINICKFDKGNGIVIFYHDLYVNKLNDLLNSPQFVKLPKGRKNGK 1561          

HSP 2 Score: 30.8018 bits (68), Expect = 1.683e-8
Identity = 16/31 (51.61%), Postives = 23/31 (74.19%), Query Frame = 2
Query:   98 NCLKSLMSLSTIEYVDKNKK*IIMDNLLIKN 190
            N ++SL+S ST+EY+DK KK  I D + +KN
Sbjct: 1482 NYVRSLLSASTMEYIDKIKKQNIGDFMTLKN 1512          
The following BLAST results are available for this feature:
BLAST of SMED30024594 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 SMED30024594 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 SMED30024594 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 SMED30024594 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 SMED30024594 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 SMED30024594 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 SMED30024594 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 SMED30024594 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 SMED30024594 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 SMED30024594 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 SMED30024594 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 SMED30024594 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 SMED30024594 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 SMED30024594 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000050479.18.420e-1148.98SMESG000050479.1[more]
SMESG000050479.18.937e-1148.98SMESG000050479.1[more]
SMESG000050479.19.763e-1148.98SMESG000050479.1[more]
SMESG000081574.11.671e-845.10SMESG000081574.1[more]
SMESG000081574.11.683e-845.10SMESG000081574.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30024594 ID=SMED30024594|Name=SMED30024594|organism=Schmidtea mediterranea sexual|type=transcript|length=339bp
TTAGAAATATGAAGAAATTTTTTTGAAATAATTGAAGTAAAAATTAAATT
GATGAAAGAAAATTATGTAATAATATAAATGAAGAATACGTAGGACTAAT
TGTTTGAAAAGTTTGATGAGTTTGAGCACAATAGAGTATGTTGATAAAAA
TAAAAAGTAAATTATTATGGATAATTTGCTAATAAAGAACCAACCAAGAA
ATACATTAATGTTTAAAAGTTCTACAAAGGAAGCGGATTGGAAATTCTTG
ACCATGATATGATTTTGAATAAATTGTAAGATGTACTGAGTGCTCCTCAG
TGGATAATAATAACTAATTTTCAGAAGAATGAAAAATTT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0002032epidermal cell
PLANA:0003116parenchymal cell