SMED30012333

Overview
NameSMED30012333
Smed IDSMED30012333
Length (bp)244
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



SMED30012333

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
head regionSMED30012333 SmedASXL_031116SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
prepharyngeal regionSMED30012333 SmedASXL_031116SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30012333 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.014914:2686..3385 -1202
Homology
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BLAST of SMED30012333 vs. TrEMBL
Match: E3CTJ3 (Pedal peptide prohormone like-2 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 73.559 bits (179), Expect = 3.561e-15
Identity = 43/80 (53.75%), Postives = 55/80 (68.75%), Query Frame = 3 
Query:    6 IFLFSMTIAFVAVILNSFKS-SAVDIRQSRYIDKMGDDLLKPSVVYKIGKELLKRSYFDKIGSDLLKRSYIDKIGSDLLR 242
            I + SM I  +   ++  KS    +I++ RY DK+G DLLK S   KIG +LLKRSY DKIGSDLLKR Y DKIGS++L+
Sbjct:    6 ILISSMMITIILSTVDLSKSREHGEIKRFRYFDKIGSDLLKRSYFDKIGNDLLKRSYMDKIGSDLLKRRYFDKIGSEMLK 85

HSP 2 Score: 72.7886 bits (177), Expect = 7.565e-15
Identity = 38/61 (62.30%), Postives = 47/61 (77.05%), Query Frame = 3 
Query:   57 FKSSAVDIRQSRYIDKMGDDLLKPSVVYKIGKELLKRSYFDKIGSDLLKRSYIDKIGSDLL 239
            F     D+ +  Y DK+G+DLLK S + KIG +LLKR YFDKIGS++LKRSY+DKIGSDLL
Sbjct:   37 FDKIGSDLLKRSYFDKIGNDLLKRSYMDKIGSDLLKRRYFDKIGSEMLKRSYMDKIGSDLL 97
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BLAST of SMED30012333 vs. Planmine SMEST
Match: SMESG000059626.1 (SMESG000059626.1)

HSP 1 Score: 154.066 bits (388), Expect = 1.111e-50
Identity = 80/80 (100.00%), Postives = 80/80 (100.00%), Query Frame = 3 
Query:    3 KIFLFSMTIAFVAVILNSFKSSAVDIRQSRYIDKMGDDLLKPSVVYKIGKELLKRSYFDKIGSDLLKRSYIDKIGSDLLR 242
            KIFLFSMTIAFVAVILNSFKSSAVDIRQSRYIDKMGDDLLKPSVVYKIGKELLKRSYFDKIGSDLLKRSYIDKIGSDLLR
Sbjct:    4 KIFLFSMTIAFVAVILNSFKSSAVDIRQSRYIDKMGDDLLKPSVVYKIGKELLKRSYFDKIGSDLLKRSYIDKIGSDLLR 83
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BLAST of SMED30012333 vs. Planmine SMEST
Match: SMESG000059588.1 (SMESG000059588.1)

HSP 1 Score: 73.559 bits (179), Expect = 9.904e-19
Identity = 43/80 (53.75%), Postives = 55/80 (68.75%), Query Frame = 3 
Query:    6 IFLFSMTIAFVAVILNSFKS-SAVDIRQSRYIDKMGDDLLKPSVVYKIGKELLKRSYFDKIGSDLLKRSYIDKIGSDLLR 242
            I + SM I  +   ++  KS    +I++ RY DK+G DLLK S   KIG +LLKRSY DKIGSDLLKR Y DKIGS++L+
Sbjct:    6 ILISSMMITIILSTVDLSKSREHGEIKRFRYFDKIGSDLLKRSYFDKIGNDLLKRSYMDKIGSDLLKRRYFDKIGSEMLK 85

HSP 2 Score: 72.7886 bits (177), Expect = 2.104e-18
Identity = 38/61 (62.30%), Postives = 47/61 (77.05%), Query Frame = 3 
Query:   57 FKSSAVDIRQSRYIDKMGDDLLKPSVVYKIGKELLKRSYFDKIGSDLLKRSYIDKIGSDLL 239
            F     D+ +  Y DK+G+DLLK S + KIG +LLKR YFDKIGS++LKRSY+DKIGSDLL
Sbjct:   37 FDKIGSDLLKRSYFDKIGNDLLKRSYMDKIGSDLLKRRYFDKIGSEMLKRSYMDKIGSDLL 97
[Close]
BLAST of SMED30012333 vs. Planmine SMEST
Match: SMESG000035027.1 (SMESG000035027.1)

HSP 1 Score: 43.5134 bits (101), Expect = 1.320e-6
Identity = 36/84 (42.86%), Postives = 46/84 (54.76%), Query Frame = 3 
Query:   12 LFSMTIAFVAVILNSF-KSSAVDIRQSR---YIDKMGDDLLKPSVVY-KIGKELLKRS-YFDKIGSDLLKR-SYIDKIGSDLLR 242
            L  +T   V+V    F + S+ D+R+ +   Y D +G  LLK    Y  IG  LLKRS Y+D IG  LLKR S  D IG  LL+
Sbjct:    6 LLILTFVLVSVEFGDFYRVSSSDLRRFKKYSYYDSIGSGLLKRGAYYDPIGGGLLKRSSYYDPIGGGLLKRDSNYDPIGGGLLK 89
The following BLAST results are available for this feature:
BLAST of SMED30012333 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 SMED30012333 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 SMED30012333 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 SMED30012333 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 SMED30012333 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 SMED30012333 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 SMED30012333 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 SMED30012333 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
E3CTJ33.561e-1553.75Pedal peptide prohormone like-2 OS=Schmidtea medit... [more]
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BLAST of SMED30012333 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 SMED30012333 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 SMED30012333 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 SMED30012333 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 SMED30012333 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 SMED30012333 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000059626.11.111e-50100.00SMESG000059626.1[more]
SMESG000059588.19.904e-1953.75SMESG000059588.1[more]
SMESG000035027.11.320e-642.86SMESG000035027.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30012333 ID=SMED30012333|Name=SMED30012333|organism=Schmidtea mediterranea sexual|type=transcript|length=244bp
AAAAAATATTTTTATTTTCTATGACAATTGCATTTGTCGCGGTGATTTTG
AATTCTTTCAAGTCATCTGCAGTAGATATAAGGCAGTCAAGGTATATTGA
CAAAATGGGTGACGATCTACTCAAACCATCTGTAGTTTACAAAATCGGAA
AAGAGCTGCTTAAAAGATCTTATTTTGATAAAATTGGAAGTGATCTATTA
AAGCGATCATATATAGACAAAATCGGAAGTGATTTGCTAAGGCG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: biological process
TermDefinition
GO:0007218neuropeptide signaling pathway
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..23
score: 0.652