SMED30014642

Overview
NameSMED30014642
Smed IDSMED30014642
Length (bp)1249
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ 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



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 SMED30014642 (SMED30014642) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30014642 (SMED30014642) 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.
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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



SMED30014642

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30014642SMESG000019979.1 SmedASXL_004258SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30014642SMESG000019979.1 dd_Smed_v4_12619_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30014642SMESG000074134.1 SMESG000072420.1 SMESG000070400.1 SMESG000069427.1 SMESG000054630.1 SMESG000054168.1 SMESG000052400.1 SMESG000051773.1 SMESG000051558.1 SMESG000051017.1 SMESG000032351.1 SMESG000030698.1 SMESG000029834.1 SMESG000023200.1 SMESG000021127.1 SMESG000019979.1 SMESG000006691.1 Contig36445newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30014642SMESG000074134.1 SMESG000072420.1 SMESG000070400.1 SMESG000069427.1 SMESG000054630.1 SMESG000054168.1 SMESG000052400.1 SMESG000051773.1 SMESG000051558.1 SMESG000051017.1 SMESG000032351.1 SMESG000030698.1 SMESG000029834.1 SMESG000023200.1 SMESG000021127.1 SMESG000019979.1 SMESG000006691.1 Contig36445uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
epidermisSMED30014642SMESG000019979.1 dd_Smed_v4_12619_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
dorsal region of the epidermisSMED30014642SMESG000019979.1 dd_Smed_v4_12619_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
Alignments
SMED30014642 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.011443:2235..5154 -6066
Homology
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BLAST of SMED30014642 vs. Planmine SMEST
Match: SMESG000019979.1 (SMESG000019979.1)

HSP 1 Score: 328.946 bits (842), Expect = 7.772e-110
Identity = 174/230 (75.65%), Postives = 174/230 (75.65%), Query Frame = 2 
Query:  470 HSERKFDLSKKQIVNNYHINGTVNLKIGIESDLSVTSEIKKKKGPCEFCQFLFEKFKEIIKTKNILGKMAESKSTICLLYRAPIGKNCRIFFQNKVRSILSSILYLTDSLKFCQ*FQYWGEEVSANPSEVVNGKVYIXXXXXXXXXXXXXDIWGRSLLLHQIFHSLYLLSTESPISSFTDLPVNPEMIPPGDNLNKTSENSQIEPTPNNSYKPTDNSHNEPAPDNANEPH 1159
            HSERKFDLSKKQIVNNYHINGTVNLKIGIESDLSVTSEIKKKKGPCEFCQFLFEKFKEIIKTKNILGKMAESKSTICLLYRAPIGKNCRIFFQNKVRSILSSI                     ANPSEVVN                                   LLSTESPISSFTDLPVNPEMIPPGDNLNKTSENSQIEPTPNNSYKPTDNSHNEPAPDNANEPH
Sbjct:   53 HSERKFDLSKKQIVNNYHINGTVNLKIGIESDLSVTSEIKKKKGPCEFCQFLFEKFKEIIKTKNILGKMAESKSTICLLYRAPIGKNCRIFFQNKVRSILSSIF--------------------ANPSEVVND----------------------------------LLSTESPISSFTDLPVNPEMIPPGDNLNKTSENSQIEPTPNNSYKPTDNSHNEPAPDNANEPH 228
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BLAST of SMED30014642 vs. Planmine SMEST
Match: SMESG000019979.1 (SMESG000019979.1)

HSP 1 Score: 323.553 bits (828), Expect = 8.532e-108
Identity = 171/230 (74.35%), Postives = 172/230 (74.78%), Query Frame = 2 
Query:  470 HSERKFDLSKKQIVNNYHINGTVNLKIGIESDLSVTSEIKKKKGPCEFCQFLFEKFKEIIKTKNILGKMAESKSTICLLYRAPIGKNCRIFFQNKVRSILSSILYLTDSLKFCQ*FQYWGEEVSANPSEVVNGKVYIXXXXXXXXXXXXXDIWGRSLLLHQIFHSLYLLSTESPISSFTDLPVNPEMIPPGDNLNKTSENSQIEPTPNNSYKPTDNSHNEPAPDNANEPH 1159
            HSERKFDLSKKQIVNNYHINGTVNLKIGIESDLSVTSEIKKKKGPCEFCQFLFEKFKEIIKTKNILGKMAESKSTICLLYRAPIGKNCRIFFQNKVR                       +EVSANPSEVVN                                   LLSTESPISSFTDLPVNPEMIPPGDNLNKTSENSQIEPTPNNSYKPTDNSHNEPAPDNANEPH
Sbjct:   53 HSERKFDLSKKQIVNNYHINGTVNLKIGIESDLSVTSEIKKKKGPCEFCQFLFEKFKEIIKTKNILGKMAESKSTICLLYRAPIGKNCRIFFQNKVR-----------------------KEVSANPSEVVND----------------------------------LLSTESPISSFTDLPVNPEMIPPGDNLNKTSENSQIEPTPNNSYKPTDNSHNEPAPDNANEPH 225
The following BLAST results are available for this feature:
BLAST of SMED30014642 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 SMED30014642 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 SMED30014642 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 SMED30014642 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 SMED30014642 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 SMED30014642 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 SMED30014642 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 SMED30014642 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 SMED30014642 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 SMED30014642 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 SMED30014642 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 SMED30014642 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 SMED30014642 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 SMED30014642 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000019979.17.772e-11075.65SMESG000019979.1[more]
SMESG000019979.18.532e-10874.35SMESG000019979.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30014642 ID=SMED30014642|Name=SMED30014642|organism=Schmidtea mediterranea sexual|type=transcript|length=1249bp
AACGCCAATAACTATAATTACGAATATGTATCAGAGAATTTATTAATTCC
ACAAAATAATGGATTTTATCCACAAACTTATGGTGAAACTATATACAAAA
TTTAGAATCAACTACACGAATTATCCACAATATATTGTTGGTGGATTTCA
AAATAATAATTTAAGTTATAACAACAGCAACCTACAATTCAATGGAGGAA
ATCAATATATGTCTGGGAATGAACCAAATTTTGGATATGAAGTTTATTAG
ATAATTAATATTAAATTATTTCGTTTAAATGAGCTACAGAATATGCTATA
AATACAGCTTTGTTGGACTACAAATGCTATTAAGCAAATGCACTTTTTCA
ACATATTTAAGATTCTTTTTGTATTTGCGTCAATTTTCGTTCTTTGTAGC
GGGTCAAAGGTTAAAGAAAAAAAAGCATTTCAGGAGCTCGAATTCTTGGA
AAAATTCTTTTTGAAGTTTCATTCAGAAAGAAAATTTGATTTGTCAAAAA
AACAAATAGTAAACAATTACCACATCAATGGGACAGTTAATTTGAAAATC
GGAATTGAATCAGATTTGTCTGTTACATCTGAAATTAAAAAGAAAAAGGG
TCCATGTGAATTTTGTCAATTTCTTTTTGAAAAATTCAAGGAGATAATTA
AAACAAAAAATATCTTAGGTAAAATGGCCGAATCTAAATCCACCATTTGT
CTGTTGTATAGGGCTCCAATTGGCAAAAATTGCCGGATATTTTTTCAAAA
CAAAGTTCGAAGTATTTTATCCTCCATTTTGTATTTAACAGACTCCCTGA
AATTTTGCCAATAATTCCAATATTGGGGAGAAGAGGTCAGTGCAAATCCC
AGTGAGGTAGTTAATGGTAAGGTTTATATTTGAAATTTTGTTTAGTTGAA
TTTATCTTTGTTTTTACTGGACATTTGGGGAAGGTCTTTACTTCTGCATC
AGATCTTCCATTCACTTTACCTTCTGTCAACGGAATCACCAATATCATCC
TTTACGGATTTACCAGTTAATCCAGAAATGATACCACCAGGAGATAATTT
AAATAAAACTTCCGAAAATTCTCAGATTGAGCCAACTCCAAATAATTCTT
ATAAACCTACTGATAACTCACACAATGAGCCGGCTCCAGATAATGCAAAT
GAACCGCATGAAAATTCTTCTAGTGACACTTCTGATGAAAATTCAAATGA
AAATTCACAACCAAAGCCTAAACCGAAACCAAAGCCTAAACCAAAGCCT
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protein sequence of SMED30014642-orf-1

>SMED30014642-orf-1 ID=SMED30014642-orf-1|Name=SMED30014642-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=159bp
MHFFNIFKILFVFASIFVLCSGSKVKEKKAFQELEFLEKFFLKFHSERKF
DLSKKQIVNNYHINGTVNLKIGIESDLSVTSEIKKKKGPCEFCQFLFEKF
KEIIKTKNILGKMAESKSTICLLYRAPIGKNCRIFFQNKVRSILSSILYL
TDSLKFCQ*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000034epidermis
PLANA:0000054dorsal region of the epidermis
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR011001Saposin-like
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..22
score: 0.862