SMED30002221

Overview
NameSMED30002221
Smed IDSMED30002221
Length (bp)621
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



SMED30002221

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30002221 SmedASXL_007531SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30002221 dd_Smed_v4_3733_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30002221 dd_Smed_v4_3733_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30002221 dd_Smed_v4_3733_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30002221 dd_3733dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult fluorescence in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30002221 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.002457:17489..18160 +2745
Homology
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BLAST of SMED30002221 vs. Planmine SMEST
Match: SMESG000011558.1 (SMESG000011558.1)

HSP 1 Score: 184.882 bits (468), Expect = 9.824e-61
Identity = 89/89 (100.00%), Postives = 89/89 (100.00%), Query Frame = 1 
Query:  238 MKTNVPLFVLIISIALYRVTNALGAMKRVERREWNLLDALNNRSPLFNELFGHQEIHDGKRSQGLQRYTPAFFLMDRAIDPVRFQRSLK 504
            MKTNVPLFVLIISIALYRVTNALGAMKRVERREWNLLDALNNRSPLFNELFGHQEIHDGKRSQGLQRYTPAFFLMDRAIDPVRFQRSLK
Sbjct:    1 MKTNVPLFVLIISIALYRVTNALGAMKRVERREWNLLDALNNRSPLFNELFGHQEIHDGKRSQGLQRYTPAFFLMDRAIDPVRFQRSLK 89
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BLAST of SMED30002221 vs. Planmine SMEST
Match: SMESG000036246.1 (SMESG000036246.1)

HSP 1 Score: 60.8474 bits (146), Expect = 3.400e-12
Identity = 28/84 (33.33%), Postives = 49/84 (58.33%), Query Frame = 1 
Query:  244 TNVPLFVLIISIALYRVTNALGAMKRVERREWNLLDALNNRSPLFNELFGHQEIHDGKRS------QGLQRYTPAFFLMDRAID 477
            T++ +F +I+ +           +KR ++ +W   + ++ R+P FNEL+GHQ+IHDGKRS      +   + +P FFL+D  +D
Sbjct:   11 TSLFIFSMILVLINLIFAETTDPLKRFKQEDWEKFNIISRRNPYFNELYGHQQIHDGKRSWMNKETKKTVKDSPEFFLLDHVLD 94
The following BLAST results are available for this feature:
BLAST of SMED30002221 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 SMED30002221 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 SMED30002221 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 SMED30002221 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 SMED30002221 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 SMED30002221 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 SMED30002221 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 SMED30002221 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 SMED30002221 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 SMED30002221 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 SMED30002221 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 SMED30002221 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 SMED30002221 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 SMED30002221 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000011558.19.824e-61100.00SMESG000011558.1[more]
SMESG000036246.13.400e-1233.33SMESG000036246.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30002221 ID=SMED30002221|Name=SMED30002221|organism=Schmidtea mediterranea sexual|type=transcript|length=621bp
ATTCTTAAACCTAAATCTTAATCAATATCTCATTATTATCTCAGACGAAA
ATTAATTAAATTTAGATTCGATGGAGAATAAGTTTTGAGCAAATAGACAT
TGTCCTGATCTTGATAACAGTTGGCGTTATTTGTGAGAACTAGCCATGTT
TTTGATTGTAAATGAATTATTAATCGGATATTTCCAGAATATAAATCATN
NNANNNTNNNANNNNNTNAAAATAATCAGTTTGAAACATGAAAACTAATG
TTCCATTATTCGTTTTAATTATTTCAATAGCTTTATATCGAGTAACAAAT
GCATTGGGAGCGATGAAACGGGTCGAGAGACGAGAATGGAATTTGCTTGA
CGCATTAAACAACAGAAGTCCACTTTTCAATGAACTATTTGGTCATCAGG
AAATACATGATGGCAAACGTTCGCAGGGTTTACAACGATATACACCAGCT
TTCTTTTTAATGGACCGTGCTATTGATCCAGTTCGATTTCAACGATCTTT
GAAATAAAAGGCCAAACAATTACANAATCNNTANTTNNTNNNNNATNNNA
TAGATNNNNNAANNTNTGNNTNAGANTNANNANAAAATAAAATAGATCAA
CAAACTTTGTAAGATAAACAT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000070intestinal phagocyte
PLANA:0000099neuron
PLANA:0000420parapharyngeal region
PLANA:0002089reproductive organ
Vocabulary: INTERPRO
TermDefinition
IPR000299FERM_domain
Vocabulary: cellular component
TermDefinition
GO:0005856cytoskeleton
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-TMSignalP-TMcoord: 1..22
score: 0.589
NoneNo IPR availableTMHMMTMhelixcoord: 5..22