SMED30012466

Overview
NameSMED30012466
Smed IDSMED30012466
Length (bp)1574
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 SMED30012466 (SMED30012466) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30012466 (SMED30012466) 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




SMED30012466

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
parenchymaSMED30012466h1SMcG0005928 dd_Smed_v4_81237_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30012466 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.005792:19657..24747 +7729
Homology
BLAST of SMED30012466 vs. Planmine SMEST
Match: SMESG000047021.1 (SMESG000047021.1)

HSP 1 Score: 645.58 bits (1664), Expect = 0.000e+0
Identity = 400/400 (100.00%), Postives = 400/400 (100.00%), Query Frame = -3
Query:   49 MNEKEFIEMSSKLSKNLGIVSQYILILMPFICKFIVKTIKEIKKQNTEFACKNAMKSGFWNEEMEIFGNCLDKLRDRDLNNNAANEMCNKRLYSEDDECQAIEEIMNALDRNKLNTRFLKSKESFSTLIDEWASEIAKSRKEKVEKNNFDEILKDPISYYGDNYNFESKRQNAKVNKIKNVIEEMLKNAEKSDALYRYFESLYSTFTDENKIFKVVLKDLEENKMKSPIYPIIFPAENIEIHRTDSNESSVNSVDLKETIPVHSSFIEKYDLNPSIDMDEFPSNGPEXXXXXXXXXXXXXXXXXXXXIEKPLVKQVSTLTXXXXXXXXXXXXXXKNDKPLVKHVSLPKNKLVINXXXXXXXXXXXXXXXEFSNLKNQIXXXXXXXXXXXXXXKIDLSQRI 1248
            MNEKEFIEMSSKLSKNLGIVSQYILILMPFICKFIVKTIKEIKKQNTEFACKNAMKSGFWNEEMEIFGNCLDKLRDRDLNNNAANEMCNKRLYSEDDECQAIEEIMNALDRNKLNTRFLKSKESFSTLIDEWASEIAKSRKEKVEKNNFDEILKDPISYYGDNYNFESKRQNAKVNKIKNVIEEMLKNAEKSDALYRYFESLYSTFTDENKIFKVVLKDLEENKMKSPIYPIIFPAENIEIHRTDSNESSVNSVDLKETIPVHSSFIEKYDLNPSIDMDEFPSNGPELSTLTLKKSKIKSVSLPSSKIEKPLVKQVSTLTSKKSKDKSVSIPSSKNDKPLVKHVSLPKNKLVINKPEKKLEMFKKKEVEEFSNLKNQILKKREAKLKKEKYKKIDLSQRI
Sbjct:    1 MNEKEFIEMSSKLSKNLGIVSQYILILMPFICKFIVKTIKEIKKQNTEFACKNAMKSGFWNEEMEIFGNCLDKLRDRDLNNNAANEMCNKRLYSEDDECQAIEEIMNALDRNKLNTRFLKSKESFSTLIDEWASEIAKSRKEKVEKNNFDEILKDPISYYGDNYNFESKRQNAKVNKIKNVIEEMLKNAEKSDALYRYFESLYSTFTDENKIFKVVLKDLEENKMKSPIYPIIFPAENIEIHRTDSNESSVNSVDLKETIPVHSSFIEKYDLNPSIDMDEFPSNGPELSTLTLKKSKIKSVSLPSSKIEKPLVKQVSTLTSKKSKDKSVSIPSSKNDKPLVKHVSLPKNKLVINKPEKKLEMFKKKEVEEFSNLKNQILKKREAKLKKEKYKKIDLSQRI 400          
BLAST of SMED30012466 vs. Planmine SMEST
Match: SMESG000031070.1 (SMESG000031070.1)

HSP 1 Score: 641.343 bits (1653), Expect = 0.000e+0
Identity = 398/400 (99.50%), Postives = 399/400 (99.75%), Query Frame = -3
Query:   49 MNEKEFIEMSSKLSKNLGIVSQYILILMPFICKFIVKTIKEIKKQNTEFACKNAMKSGFWNEEMEIFGNCLDKLRDRDLNNNAANEMCNKRLYSEDDECQAIEEIMNALDRNKLNTRFLKSKESFSTLIDEWASEIAKSRKEKVEKNNFDEILKDPISYYGDNYNFESKRQNAKVNKIKNVIEEMLKNAEKSDALYRYFESLYSTFTDENKIFKVVLKDLEENKMKSPIYPIIFPAENIEIHRTDSNESSVNSVDLKETIPVHSSFIEKYDLNPSIDMDEFPSNGPEXXXXXXXXXXXXXXXXXXXXIEKPLVKQVSTLTXXXXXXXXXXXXXXKNDKPLVKHVSLPKNKLVINXXXXXXXXXXXXXXXEFSNLKNQIXXXXXXXXXXXXXXKIDLSQRI 1248
            MNEKEFIEMSSKLSKNLGIVSQYILILMPFICKFIVKTIKEIKKQNTEFACKNAMKSGFWNEEMEIFGNCLDKLRDR+LNNNAANEMCNKRLYSEDDECQAIEEIMNALDRNKLNTRFLKSKESFSTLIDEWASEIAKSRKEKVEKNNFDEILKDPISYYGDNYNFESKRQNAKVNKIKNVIEEMLKNAEKSDALYRYFESLYSTFTDENKIFKVVLKDLEENKMKSPIYPIIFPAENIEIHRTDSNESSVNSVDLKETIPVHS FIEKYDLNPSIDMDEFPSNGPELSTLTLKKSKIKSVSLPSSKIEKPLVKQVSTLTSKKSKDKSVSIPSSKNDKPLVKHVSLPKNKLVINKPEKKLEMFKKKEVEEFSNLKNQILKKREAKLKKEKYKKIDLSQRI
Sbjct:    1 MNEKEFIEMSSKLSKNLGIVSQYILILMPFICKFIVKTIKEIKKQNTEFACKNAMKSGFWNEEMEIFGNCLDKLRDRELNNNAANEMCNKRLYSEDDECQAIEEIMNALDRNKLNTRFLKSKESFSTLIDEWASEIAKSRKEKVEKNNFDEILKDPISYYGDNYNFESKRQNAKVNKIKNVIEEMLKNAEKSDALYRYFESLYSTFTDENKIFKVVLKDLEENKMKSPIYPIIFPAENIEIHRTDSNESSVNSVDLKETIPVHSPFIEKYDLNPSIDMDEFPSNGPELSTLTLKKSKIKSVSLPSSKIEKPLVKQVSTLTSKKSKDKSVSIPSSKNDKPLVKHVSLPKNKLVINKPEKKLEMFKKKEVEEFSNLKNQILKKREAKLKKEKYKKIDLSQRI 400          
BLAST of SMED30012466 vs. Planmine SMEST
Match: SMESG000047021.1 (SMESG000047021.1)

HSP 1 Score: 469.929 bits (1208), Expect = 9.831e-165
Identity = 314/314 (100.00%), Postives = 314/314 (100.00%), Query Frame = -3
Query:   49 MCNKRLYSEDDECQAIEEIMNALDRNKLNTRFLKSKESFSTLIDEWASEIAKSRKEKVEKNNFDEILKDPISYYGDNYNFESKRQNAKVNKIKNVIEEMLKNAEKSDALYRYFESLYSTFTDENKIFKVVLKDLEENKMKSPIYPIIFPAENIEIHRTDSNESSVNSVDLKETIPVHSSFIEKYDLNPSIDMDEFPSNGPEXXXXXXXXXXXXXXXXXXXXIEKPLVKQVSTLTXXXXXXXXXXXXXXKNDKPLVKHVSLPKNKLVINXXXXXXXXXXXXXXXEFSNLKNQIXXXXXXXXXXXXXXKIDLSQRI 990
            MCNKRLYSEDDECQAIEEIMNALDRNKLNTRFLKSKESFSTLIDEWASEIAKSRKEKVEKNNFDEILKDPISYYGDNYNFESKRQNAKVNKIKNVIEEMLKNAEKSDALYRYFESLYSTFTDENKIFKVVLKDLEENKMKSPIYPIIFPAENIEIHRTDSNESSVNSVDLKETIPVHSSFIEKYDLNPSIDMDEFPSNGPELSTLTLKKSKIKSVSLPSSKIEKPLVKQVSTLTSKKSKDKSVSIPSSKNDKPLVKHVSLPKNKLVINKPEKKLEMFKKKEVEEFSNLKNQILKKREAKLKKEKYKKIDLSQRI
Sbjct:    1 MCNKRLYSEDDECQAIEEIMNALDRNKLNTRFLKSKESFSTLIDEWASEIAKSRKEKVEKNNFDEILKDPISYYGDNYNFESKRQNAKVNKIKNVIEEMLKNAEKSDALYRYFESLYSTFTDENKIFKVVLKDLEENKMKSPIYPIIFPAENIEIHRTDSNESSVNSVDLKETIPVHSSFIEKYDLNPSIDMDEFPSNGPELSTLTLKKSKIKSVSLPSSKIEKPLVKQVSTLTSKKSKDKSVSIPSSKNDKPLVKHVSLPKNKLVINKPEKKLEMFKKKEVEEFSNLKNQILKKREAKLKKEKYKKIDLSQRI 314          
BLAST of SMED30012466 vs. Planmine SMEST
Match: SMESG000031070.1 (SMESG000031070.1)

HSP 1 Score: 468.389 bits (1204), Expect = 4.996e-164
Identity = 313/314 (99.68%), Postives = 313/314 (99.68%), Query Frame = -3
Query:   49 MCNKRLYSEDDECQAIEEIMNALDRNKLNTRFLKSKESFSTLIDEWASEIAKSRKEKVEKNNFDEILKDPISYYGDNYNFESKRQNAKVNKIKNVIEEMLKNAEKSDALYRYFESLYSTFTDENKIFKVVLKDLEENKMKSPIYPIIFPAENIEIHRTDSNESSVNSVDLKETIPVHSSFIEKYDLNPSIDMDEFPSNGPEXXXXXXXXXXXXXXXXXXXXIEKPLVKQVSTLTXXXXXXXXXXXXXXKNDKPLVKHVSLPKNKLVINXXXXXXXXXXXXXXXEFSNLKNQIXXXXXXXXXXXXXXKIDLSQRI 990
            MCNKRLYSEDDECQAIEEIMNALDRNKLNTRFLKSKESFSTLIDEWASEIAKSRKEKVEKNNFDEILKDPISYYGDNYNFESKRQNAKVNKIKNVIEEMLKNAEKSDALYRYFESLYSTFTDENKIFKVVLKDLEENKMKSPIYPIIFPAENIEIHRTDSNESSVNSVDLKETIPVHS FIEKYDLNPSIDMDEFPSNGPELSTLTLKKSKIKSVSLPSSKIEKPLVKQVSTLTSKKSKDKSVSIPSSKNDKPLVKHVSLPKNKLVINKPEKKLEMFKKKEVEEFSNLKNQILKKREAKLKKEKYKKIDLSQRI
Sbjct:    1 MCNKRLYSEDDECQAIEEIMNALDRNKLNTRFLKSKESFSTLIDEWASEIAKSRKEKVEKNNFDEILKDPISYYGDNYNFESKRQNAKVNKIKNVIEEMLKNAEKSDALYRYFESLYSTFTDENKIFKVVLKDLEENKMKSPIYPIIFPAENIEIHRTDSNESSVNSVDLKETIPVHSPFIEKYDLNPSIDMDEFPSNGPELSTLTLKKSKIKSVSLPSSKIEKPLVKQVSTLTSKKSKDKSVSIPSSKNDKPLVKHVSLPKNKLVINKPEKKLEMFKKKEVEEFSNLKNQILKKREAKLKKEKYKKIDLSQRI 314          
The following BLAST results are available for this feature:
BLAST of SMED30012466 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 SMED30012466 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 SMED30012466 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 SMED30012466 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 SMED30012466 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 SMED30012466 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 SMED30012466 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 SMED30012466 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 SMED30012466 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 SMED30012466 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 SMED30012466 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 SMED30012466 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 SMED30012466 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 SMED30012466 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000047021.10.000e+0100.00SMESG000047021.1[more]
SMESG000031070.10.000e+099.50SMESG000031070.1[more]
SMESG000047021.19.831e-165100.00SMESG000047021.1[more]
SMESG000031070.14.996e-16499.68SMESG000031070.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30012466 ID=SMED30012466|Name=SMED30012466|organism=Schmidtea mediterranea sexual|type=transcript|length=1574bp
AAAATAAAAAATTAATTTTTATTTGTTCAATGATTTTTGTTTTAATTTTA
TTCGTTGACTAAGATCGATTTTCTTATATTTTTCTTTTTTCAGTTTAGCT
TCTCGCTTCTTTAGAATTTGATTTTTTAAATTACTAAATTCTTCCACTTC
TTTTTTTTTAAACATCTCGAGCTTTTTCTCTGGTTTATTGATAACTAATT
TATTTTTAGGTAAAGAAACATGTTTTACCAAAGGTTTGTCATTTTTCGAA
CTTGGTATACTTACTGATTTGTCTTTAGATTTTTTTGATGTCAAAGTTGA
AACTTGTTTTACCAAAGGTTTTTCAATTTTCGAACTTGGTAAACTTACTG
ATTTTATTTTAGATTTTTTTAAAGTCAAAGTTGACAATTCAGGTCCATTG
GAAGGAAATTCATCCATGTCGATGGATGGATTGAGATCATATTTTTCAAT
GAAAGAGCTGTGGACGGGAATGGTTTCTTTGAGATCCACTGAGTTTACTG
AAGATTCATTAGAATCTGTTCGATGAATTTCAATGTTTTCCGCTGGAAAT
ATTATTGGATAAATTGGTGACTTCATTTTGTTTTCCTCTAAATCCTTTAA
AACTACTTTAAAGATTTTATTTTCATCCGTAAATGTTGAATACAAAGATT
CAAAATATCTGTACAATGCATCCGATTTTTCTGCATTCTTAAGCATTTCC
TCAATAACATTCTTTATTTTATTTACTTTTGCATTCTGGCGTTTGGATTC
AAAATTATAATTATCGCCATAATAACTGATTGGATCTTTTAAAATTTCGT
CAAAATTGTTTTTTTCTACCTTTTCTTTTCGAGATTTAGCTATCTCAGAC
GCCCATTCATCAATCAATGTTGAAAAAGATTCTTTTGATTTTAAGAACCT
TGTATTTAATTTATTTCTGTCCAGGGCATTCATTATTTCTTCGATTGCTT
GACATTCGTCATCCTCGCTATATAATCGTTTATTACACATTTCGTTGGCA
GCATTATTGTTCAAATCGCGGTCTCTCAATTTATCTAAACAGTTACCAAA
GATTTCCATTTCCTCGTTCCAAAATCCCGATTTCATTGCGTTCTTGCATG
CAAATTCCGTGTTTTGTTTTTTTATTTCCTTGATGGTTTTGACAATAAAT
TTACAAATAAACGGCATCAGAATTAAAATATATTGAGATACAATTCCTAG
ATTTTTGCTGAGTTTACTGCTCATTTCAATGAATTCCTTTTCATTCATTT
TGGAAATTAATTATGGAAAAAACATTGAATTTTCAGACAAATTATTTCAA
ATCAATATAAATATTTATTTTTGTTTTTGCTCATTAAGAAATTTAACCGC
TGAAATAATGAGGACACAACTACGACGCTATGTACTCTGTAAATTTCTGA
TATTGTTTATTTGGAGTGTTATACTAAGACCTATAAATAGTTAATTAAAG
ATTAAATTAATAAAAAAGGTAATTAAAAAGCTATTAATCTGTTGGAATAG
TAAAATTTTAGATGTAAGTGAAACTCTATCCGACTCCTCGTGTTCAATAA
ACAATAAGACAAAATCCCAACAAA
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protein sequence of SMED30012466-orf-1

>SMED30012466-orf-1 ID=SMED30012466-orf-1|Name=SMED30012466-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=410bp
MNEKEFIEMSSKLSKNLGIVSQYILILMPFICKFIVKTIKEIKKQNTEFA
CKNAMKSGFWNEEMEIFGNCLDKLRDRDLNNNAANEMCNKRLYSEDDECQ
AIEEIMNALDRNKLNTRFLKSKESFSTLIDEWASEIAKSRKEKVEKNNFD
EILKDPISYYGDNYNFESKRQNAKVNKIKNVIEEMLKNAEKSDALYRYFE
SLYSTFTDENKIFKVVLKDLEENKMKSPIYPIIFPAENIEIHRTDSNESS
VNSVDLKETIPVHSSFIEKYDLNPSIDMDEFPSNGPELSTLTLKKSKIKS
VSLPSSKIEKPLVKQVSTLTSKKSKDKSVSIPSSKNDKPLVKHVSLPKNK
LVINKPEKKLEMFKKKEVEEFSNLKNQILKKREAKLKKEKYKKIDLSQRI
KLKQKSLNK*
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