SMED30000892

Overview
NameSMED30000892
Smed IDSMED30000892
Length (bp)997
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 SMED30000892 (SMED30000892) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30000892 (SMED30000892) 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



SMED30000892

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30000892SMESG000023665.1 Contig10100newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30000892SMESG000023665.1 Contig10100uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
oocyteSMED30000892SMESG000074427.1 SMESG000058739.1 SMESG000012243.1 Contig12659newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30000892SMESG000074427.1 SMESG000058739.1 SMESG000012243.1 Contig12659uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30000892SMESG000074427.1 SMESG000058739.1 SMESG000012243.1 Contig12659newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30000892SMESG000074427.1 SMESG000058739.1 SMESG000012243.1 Contig12659uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30000892SMESG000074427.1 SMESG000058739.1 SMESG000012243.1 Contig12659newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30000892SMESG000074427.1 SMESG000058739.1 SMESG000012243.1 Contig12659uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30000892 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.013940:6191..7172 -3255
v31.005007:7696..8529 +2593
Homology
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BLAST of SMED30000892 vs. Planmine SMEST
Match: SMESG000072856.1 (SMESG000072856.1)

HSP 1 Score: 205.682 bits (522), Expect = 2.450e-66
Identity = 100/109 (91.74%), Postives = 103/109 (94.50%), Query Frame = -2 
Query:  319 NKALYEQIIQLTKEVQQVKSTWVDPAKLKSIHQRLTTAQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQLAYRDSVNNPTPVATPSTIPSNSYRPG 645
            NK LYEQIIQLTKEVQQVKSTWVDPAKLK +HQRLT AQKGWAEE+QLNQNL  QI+GLEVALAASREGEAVTYPLIFAPSQLAYRDSVNNPTPVATPSTIPSNSYR G
Sbjct:   18 NKVLYEQIIQLTKEVQQVKSTWVDPAKLKPLHQRLTAAQKGWAEEQQLNQNLLAQIKGLEVALAASREGEAVTYPLIFAPSQLAYRDSVNNPTPVATPSTIPSNSYRLG 126
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BLAST of SMED30000892 vs. Planmine SMEST
Match: SMESG000025382.1 (SMESG000025382.1)

HSP 1 Score: 205.682 bits (522), Expect = 3.047e-66
Identity = 98/109 (89.91%), Postives = 103/109 (94.50%), Query Frame = -2 
Query:  319 NKALYEQIIQLTKEVQQVKSTWVDPAKLKSIHQRLTTAQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQLAYRDSVNNPTPVATPSTIPSNSYRPG 645
            NKALYEQIIQLTKEVQQVK TWVDPAKLKSIHQRLT AQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQLAYRDS ++ TP+ TPS +PSN+YRPG
Sbjct:   25 NKALYEQIIQLTKEVQQVKFTWVDPAKLKSIHQRLTAAQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQLAYRDSASSSTPLTTPSAVPSNNYRPG 133
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BLAST of SMED30000892 vs. Planmine SMEST
Match: SMESG000068326.1 (SMESG000068326.1)

HSP 1 Score: 205.297 bits (521), Expect = 4.360e-65
Identity = 99/109 (90.83%), Postives = 104/109 (95.41%), Query Frame = -2 
Query:  319 NKALYEQIIQLTKEVQQVKSTWVDPAKLKSIHQRLTTAQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQLAYRDSVNNPTPVATPSTIPSNSYRPG 645
            N+ALYEQIIQLTKEVQQVKSTWVDPAKLK +HQRLT AQKGWAEERQLNQNLRTQIRGLEVAL+ASREGEAVTYPLIFAPSQLAY+ S  NPTPVATPSTIPS+SYRPG
Sbjct:   18 NRALYEQIIQLTKEVQQVKSTWVDPAKLKPLHQRLTAAQKGWAEERQLNQNLRTQIRGLEVALSASREGEAVTYPLIFAPSQLAYQASTTNPTPVATPSTIPSSSYRPG 126
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BLAST of SMED30000892 vs. Planmine SMEST
Match: SMESG000006905.1 (SMESG000006905.1)

HSP 1 Score: 201.445 bits (511), Expect = 9.703e-65
Identity = 98/109 (89.91%), Postives = 103/109 (94.50%), Query Frame = -2 
Query:  319 NKALYEQIIQLTKEVQQVKSTWVDPAKLKSIHQRLTTAQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQLAYRDSVNNPTPVATPSTIPSNSYRPG 645
            NK+LYEQIIQLTKEVQQVKSTWVDPAKLKSIHQRLTTAQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPS LAYR+S NN T   TPSTIPS+++RPG
Sbjct:   18 NKSLYEQIIQLTKEVQQVKSTWVDPAKLKSIHQRLTTAQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSLLAYRNSANNSTFAVTPSTIPSSNHRPG 126
[Close]
BLAST of SMED30000892 vs. Planmine SMEST
Match: SMESG000021386.1 (SMESG000021386.1)

HSP 1 Score: 201.83 bits (512), Expect = 1.420e-64
Identity = 98/109 (89.91%), Postives = 102/109 (93.58%), Query Frame = -2 
Query:  319 NKALYEQIIQLTKEVQQVKSTWVDPAKLKSIHQRLTTAQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQLAYRDSVNNPTPVATPSTIPSNSYRPG 645
            NKALYEQIIQLTKEVQQVKSTWV+P KLKSIHQ LT AQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQLAYRDS N+ TP+ TPS IPSN+YRPG
Sbjct:   18 NKALYEQIIQLTKEVQQVKSTWVNPTKLKSIHQSLTAAQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQLAYRDSANSSTPLVTPSAIPSNNYRPG 126
The following BLAST results are available for this feature:
BLAST of SMED30000892 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 SMED30000892 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 SMED30000892 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 SMED30000892 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 SMED30000892 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 SMED30000892 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 SMED30000892 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 SMED30000892 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 SMED30000892 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 SMED30000892 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 SMED30000892 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 SMED30000892 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 SMED30000892 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 SMED30000892 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000072856.12.450e-6691.74SMESG000072856.1[more]
SMESG000025382.13.047e-6689.91SMESG000025382.1[more]
SMESG000068326.14.360e-6590.83SMESG000068326.1[more]
SMESG000006905.19.703e-6589.91SMESG000006905.1[more]
SMESG000021386.11.420e-6489.91SMESG000021386.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000892 ID=SMED30000892|Name=SMED30000892|organism=Schmidtea mediterranea sexual|type=transcript|length=997bp
GATAGAAGACCTATGCTCGCTTTGTAGTGTCCCTTGTGTGAGAAGGTTCA
AGGTCAGATTCATGTGGATGGGAAGACGTTTACCCGATGAAACGCGAATG
CTCATGACTTTTCGACAGCAATATGTAACATTATTTATTTTTTATGACAT
ACCACTTTCAAATGATTTAACAATAATTATAATTTACATTCAATTCATAA
ACAAAACAGGGTAAATTAGACGATATTTATAAGTTAATGTAATTCATAAG
CAATATAGGACAAATCAATTGAGTTTGTTCGCCAGGCGTGCAGCTCTGCG
TCGGGCGCGTTCTTTACGCCCCGGCCTATAACTGTTCGAGGGTATTGTTG
ATGGAGTCGCCACTGGTGTTGGGTTGTTGACTGAATCTCGGTACGCCAAT
TGAGATGGGGCGAAGATAAGAGGGTAAGTCACCGCTTCTCCTTCACGACT
GGCGGCCAAGGCGACTTCCAACCCCCTTATCTGCGTCCGGAGGTTCTGAT
TTAGTTGGCGTTCCTCAGCCCAACCCTTTTGAGCAGTTGTGAGACGTTGG
TGGATGGACTTGAGTTTTGCTGGGTCCACCCAGGTGGATTTCACCTGCTG
TACCTCCTTTGTGAGCTGAATTATCTGCTCGTATAGAGCTTTGTTGGATT
GCTGGGCGCGGGATAATTCCTGTTGTAGTAATTGGGCCAGTTCCATGGCT
AATAGAAAATAATAATTTAAGGGGAGAGGTTTGCTGATAGGGCGGAATCA
TATAATTTATATTTAATCCAAACAAACTATTGAAAATAACTAAAACTCTA
AACTAATCAAAAACAAAACACAAAAATTATTTTTAATTAACATTAATCAA
ACTAATCAAAACAAAAAGGAGGACAATTAGTCCTAACTATCATTGATCAA
ATTTGAGTCTTTGTCTGCTCAGAGAAAGCCTTTCGCCACCCATTCCTCGG
GTGTATAGCCCGAGATCGACCTGGTCGGTCTCTTTGTGTTGCGGGCT
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protein sequence of SMED30000892-orf-1

>SMED30000892-orf-1 ID=SMED30000892-orf-1|Name=SMED30000892-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=144bp
MELAQLLQQELSRAQQSNKALYEQIIQLTKEVQQVKSTWVDPAKLKSIHQ
RLTTAQKGWAEERQLNQNLRTQIRGLEVALAASREGEAVTYPLIFAPSQL
AYRDSVNNPTPVATPSTIPSNSYRPGRKERARRRAARLANKLN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000074oocyte
PLANA:0000231vitelline gland
PLANA:0002089reproductive organ
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 31..53