SMED30031222

Overview
NameSMED30031222
Smed IDSMED30031222
Length (bp)853
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 SMED30031222 (SMED30031222) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30031222 (SMED30031222) 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 SMED30031222 (SMED30031222) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30031222 (SMED30031222) 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



SMED30031222

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
testisSMED30031222SMESG000022878.1 DN311062.1ncbi_smed_estsPMID:22074376
Chong et al., 2011		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
testisSMED30031222SMESG000022878.1 HO005518.1ncbi_smed_estsPMID:22074376
Chong et al., 2011		whole organism adult hermaphrodite colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30031222 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001230:5247..6280 -4144
Homology
[Close]
BLAST of SMED30031222 vs. TrEMBL
Match: A0A430Q778 (HMG box domain-containing protein (Fragment) OS=Schistosoma bovis OX=6184 GN=DC041_0002889 PE=4 SV=1)

HSP 1 Score: 54.6842 bits (130), Expect = 5.465e-6
Identity = 41/147 (27.89%), Postives = 74/147 (50.34%), Query Frame = 2 
Query:   47 FFSFIRKISKIKLDKPPASVFGMFLRLNNSKHQSGNNNKSDITNR---RSMLEKYKKLSPSEIRNLKYTLKIKNNEYMEILKVLSAVKFKDIISFAEKNGIPKRCPHSGLNLFLRENLQKTNNNPNMTTKQRFSDLVSDWKNLHKTE 478
            FF  +R+I+        ++ F  F+   +S++    + K +++N    R + + YK L   E+  LK   K    E+   +K  + V F   ++FA +NG+PK  P+SGL +F+RE L+ +   P    +  F D V  W +L +++
Sbjct:    5 FFVILRQITSTSAHNN-SNAFTNFI---HSRYHEVKSAKPELSNYDVIRKLAQLYKSLPVEEVEKLKLEAK----EHQSHVKKATKVIF---LTFAYRNGMPKSPPNSGLKVFMREKLKDSKGTPVSQMRNDFKDTVKQWMSLPESD 140

HSP 2 Score: 25.0238 bits (53), Expect = 5.465e-6
Identity = 16/42 (38.10%), Postives = 22/42 (52.38%), Query Frame = 3 
Query:  477 KLLYNERFMIEKMEHLKKMKEWANQNKIPFTNNRKRLAFYFY 602
            +L YN      K ++  K+KEWA +N I +T     LA  FY
Sbjct:  141 QLEYNNIAKDLKNDYETKLKEWATKNNIQYTKRISILADRFY 182
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BLAST of SMED30031222 vs. Planmine SMEST
Match: SMESG000022878.1 (SMESG000022878.1)

HSP 1 Score: 304.679 bits (779), Expect = 1.375e-109
Identity = 150/150 (100.00%), Postives = 150/150 (100.00%), Query Frame = 2 
Query:   35 MPQPFFSFIRKISKIKLDKPPASVFGMFLRLNNSKHQSGNNNKSDITNRRSMLEKYKKLSPSEIRNLKYTLKIKNNEYMEILKVLSAVKFKDIISFAEKNGIPKRCPHSGLNLFLRENLQKTNNNPNMTTKQRFSDLVSDWKNLHKTEIV 484
            MPQPFFSFIRKISKIKLDKPPASVFGMFLRLNNSKHQSGNNNKSDITNRRSMLEKYKKLSPSEIRNLKYTLKIKNNEYMEILKVLSAVKFKDIISFAEKNGIPKRCPHSGLNLFLRENLQKTNNNPNMTTKQRFSDLVSDWKNLHKTEIV
Sbjct:    1 MPQPFFSFIRKISKIKLDKPPASVFGMFLRLNNSKHQSGNNNKSDITNRRSMLEKYKKLSPSEIRNLKYTLKIKNNEYMEILKVLSAVKFKDIISFAEKNGIPKRCPHSGLNLFLRENLQKTNNNPNMTTKQRFSDLVSDWKNLHKTEIV 150

HSP 2 Score: 111.309 bits (277), Expect = 1.375e-109
Identity = 54/54 (100.00%), Postives = 54/54 (100.00%), Query Frame = 3 
Query:  486 YNERFMIEKMEHLKKMKEWANQNKIPFTNNRKRLAFYFYFQNHFLNKLKRKKIQ 647
            YNERFMIEKMEHLKKMKEWANQNKIPFTNNRKRLAFYFYFQNHFLNKLKRKKIQ
Sbjct:  152 YNERFMIEKMEHLKKMKEWANQNKIPFTNNRKRLAFYFYFQNHFLNKLKRKKIQ 205
[Close]
BLAST of SMED30031222 vs. Planmine SMEST
Match: SMESG000022878.1 (SMESG000022878.1)

HSP 1 Score: 251.136 bits (640), Expect = 1.597e-93
Identity = 124/124 (100.00%), Postives = 124/124 (100.00%), Query Frame = 2 
Query:  113 MFLRLNNSKHQSGNNNKSDITNRRSMLEKYKKLSPSEIRNLKYTLKIKNNEYMEILKVLSAVKFKDIISFAEKNGIPKRCPHSGLNLFLRENLQKTNNNPNMTTKQRFSDLVSDWKNLHKTEIV 484
            MFLRLNNSKHQSGNNNKSDITNRRSMLEKYKKLSPSEIRNLKYTLKIKNNEYMEILKVLSAVKFKDIISFAEKNGIPKRCPHSGLNLFLRENLQKTNNNPNMTTKQRFSDLVSDWKNLHKTEIV
Sbjct:    1 MFLRLNNSKHQSGNNNKSDITNRRSMLEKYKKLSPSEIRNLKYTLKIKNNEYMEILKVLSAVKFKDIISFAEKNGIPKRCPHSGLNLFLRENLQKTNNNPNMTTKQRFSDLVSDWKNLHKTEIV 124

HSP 2 Score: 110.923 bits (276), Expect = 1.597e-93
Identity = 54/54 (100.00%), Postives = 54/54 (100.00%), Query Frame = 3 
Query:  486 YNERFMIEKMEHLKKMKEWANQNKIPFTNNRKRLAFYFYFQNHFLNKLKRKKIQ 647
            YNERFMIEKMEHLKKMKEWANQNKIPFTNNRKRLAFYFYFQNHFLNKLKRKKIQ
Sbjct:  126 YNERFMIEKMEHLKKMKEWANQNKIPFTNNRKRLAFYFYFQNHFLNKLKRKKIQ 179
[Close]
BLAST of SMED30031222 vs. Planmine SMEST
Match: SMESG000022880.1 (SMESG000022880.1)

HSP 1 Score: 68.1662 bits (165), Expect = 1.070e-18
Identity = 42/149 (28.19%), Postives = 86/149 (57.72%), Query Frame = 2 
Query:   53 SFIRKISKIKLDKPPASVFGMFLRLNNSKHQSGNNNKSDITNRRSML----EKYKKLSPSEIRNLKYTLKIKNNEYMEILKVLSAVKFKDIISFAEKNGIPKRCPHSGLNLFLRENLQKTNNNPNMTTKQRFSDLVSDWKNLHKTEIVV 487
            + +R +SKI  +KPP S++ ++ R N  K +S     +   ++++++    +++K LS  E + L+  L+I N +Y+++  + +  K  +II FAE++G+PK+   S LN++++E        P +  + +   +V D+KNL  +E+ V
Sbjct:    8 TILRGVSKIAFEKPPNSIYFLYFRENYLKLKSETEFNNLPFDKKTLMNVVRDQFKSLSGEEKKELEEKLRIVNEDYIKMKNMEAETKESEIIKFAEEHGLPKKTVTSALNVYVQEIFANKEIYPELKIQDKLKQVVHDFKNLTDSELQV 156

HSP 2 Score: 43.5134 bits (101), Expect = 1.070e-18
Identity = 17/45 (37.78%), Postives = 29/45 (64.44%), Query Frame = 3 
Query:  483 LYNERFMIEKMEHLKKMKEWANQNKIPFTNNRKRLAFYFYFQNHF 617
            +YN++F   K ++   MKEW     +PF  NR+++AFYFY++  +
Sbjct:  156 VYNDKFSAFKTDYETLMKEWTKAKDVPFLTNRRKVAFYFYYKEKY 200
The following BLAST results are available for this feature:
BLAST of SMED30031222 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 SMED30031222 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 SMED30031222 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 SMED30031222 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 SMED30031222 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 SMED30031222 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 SMED30031222 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 SMED30031222 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
A0A430Q7785.465e-627.89HMG box domain-containing protein (Fragment) OS=Sc... [more]
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BLAST of SMED30031222 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 SMED30031222 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 SMED30031222 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 SMED30031222 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 SMED30031222 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 SMED30031222 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000022878.11.375e-109100.00SMESG000022878.1[more]
SMESG000022878.11.597e-93100.00SMESG000022878.1[more]
SMESG000022880.11.070e-1828.19SMESG000022880.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031222 ID=SMED30031222|Name=SMED30031222|organism=Schmidtea mediterranea sexual|type=transcript|length=853bp
CTTTTTTGAAATTTATTAAATATATATTGAAGCTATGCCTCAACCATTTT
TTTCATTTATAAGAAAAATTTCAAAAATTAAACTAGATAAACCTCCAGCA
TCTGTTTTTGGAATGTTTCTTCGACTAAACAACTCAAAGCACCAATCTGG
AAATAATAATAAAAGTGACATAACTAACAGGAGAAGCATGTTAGAAAAGT
ATAAAAAACTGTCACCTAGTGAAATACGGAACCTAAAATACACCTTAAAG
ATTAAAAATAATGAGTATATGGAAATATTAAAAGTCTTATCAGCAGTTAA
ATTTAAAGACATAATTTCATTTGCCGAAAAAAATGGAATACCTAAAAGAT
GTCCACATTCAGGGCTAAATTTGTTTCTACGAGAAAACTTACAAAAAACC
AATAATAATCCAAATATGACGACCAAACAACGGTTTAGTGATCTGGTTTC
CGACTGGAAAAATCTTCATAAAACTGAAATTGTTGTATAACGAACGATTT
ATGATTGAAAAAATGGAACATTTAAAAAAAATGAAAGAGTGGGCAAATCA
AAATAAAATTCCATTTACTAATAATAGAAAAAGATTAGCCTTTTATTTCT
ATTTCCAAAATCATTTTTTAAATAAATTAAAGCGAAAAAAAATCCAATAA
TTACATTGGGCATATCAGAAAGATATCGGAACAAATAGAGTTAAAACTAG
TCATTTTGTTTACCCGTAGATTGCCATTAACAATATAATTAGTCGTAATT
TAGATTTGAGAATTACGATTTGACTTATTATTTAAGGATAATATTTCAAT
TATTTTTTTTGTATATGTGATAATAAAATATAATTTAATGTTTTCAAAAA
AAA
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protein sequence of SMED30031222-orf-1

>SMED30031222-orf-1 ID=SMED30031222-orf-1|Name=SMED30031222-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=152bp
MPQPFFSFIRKISKIKLDKPPASVFGMFLRLNNSKHQSGNNNKSDITNRR
SMLEKYKKLSPSEIRNLKYTLKIKNNEYMEILKVLSAVKFKDIISFAEKN
GIPKRCPHSGLNLFLRENLQKTNNNPNMTTKQRFSDLVSDWKNLHKTEIV
V*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000208testis
Vocabulary: INTERPRO
TermDefinition
IPR009071HMG_box_dom