SMED30019315

Overview
NameSMED30019315
Smed IDSMED30019315
Length (bp)471
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.
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

 

back to top
Anatomical Expression

PAGE et. al., 2020




SMED30019315

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30019315 dd_Smed_v4_2668_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30019315 dd_Smed_v4_2668_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30019315 dd_Smed_v4_2668_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30019315 dd_Smed_v4_2668_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
SMED30019315 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.001411:67490..67954 -2275
Homology
BLAST of SMED30019315 vs. Planmine SMEST
Match: SMESG000022726.1 (SMESG000022726.1)

HSP 1 Score: 93.2041 bits (230), Expect = 2.992e-33
Identity = 45/46 (97.83%), Postives = 45/46 (97.83%), Query Frame = -2
Query:  276 MPTRLTLIFVFGISYFVSTATSLTLEEAYKSPERFIKYDRSTFKIW 413
            MPTRLTLIFVFGISYFVSTATSLTLEEAYKSPERFIKYDRSTFKI 
Sbjct:    1 MPTRLTLIFVFGISYFVSTATSLTLEEAYKSPERFIKYDRSTFKIC 46          

HSP 2 Score: 65.855 bits (159), Expect = 2.992e-33
Identity = 31/32 (96.88%), Postives = 31/32 (96.88%), Query Frame = -1
Query:  139 SRNLGQRQYNFQTARIEESAAIVTNKLLVFNP 234
             RNLGQRQYNFQTARIEESAAIVTNKLLVFNP
Sbjct:   46 CRNLGQRQYNFQTARIEESAAIVTNKLLVFNP 77          
BLAST of SMED30019315 vs. Planmine SMEST
Match: SMESG000022725.1 (SMESG000022725.1)

HSP 1 Score: 51.6026 bits (122), Expect = 1.829e-9
Identity = 33/63 (52.38%), Postives = 44/63 (69.84%), Query Frame = -2
Query:  177 VSTATSLTLEEAYKSPERFIKYDRSTFKIWFHXXXXXXXXXXXLVGIWVSVNTIFKLRGSKKV 365
            ++    +TL  A K P+ +IKYD++ F+IWFHI +SL ICY+IL  IW  VN IFK+R  KKV
Sbjct:    1 MAVVKCVTLGTALKEPDIYIKYDQTPFRIWFHIGISLAICYAILGTIWSMVNLIFKIRELKKV 63          
The following BLAST results are available for this feature:
BLAST of SMED30019315 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019315 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019315 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019315 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019315 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019315 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019315 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019315 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019315 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019315 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019315 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019315 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019315 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30019315 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000022726.12.992e-3397.83SMESG000022726.1[more]
SMESG000022725.11.829e-952.38SMESG000022725.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30019315 ID=SMED30019315|Name=SMED30019315|organism=Schmidtea mediterranea sexual|type=transcript|length=471bp
TGCATTTAAATAAAAAATTCTATTAATTAAATTAACAAATTTTTGACAAT
TATAACTCTAAAAACAATTCAAATAATGATAATAACATTAACAATAATAA
TAATAATAATAATAATAATAATATTAACACAGTCGTTAAGGATTAAATAC
TAAAAGCTTATTGGTCACTATCGCCGCACTTTCTTCGATCCGCGCAGTTT
GAAAATTGTATTGACGCTGACCCAAATTCCTACTAAAATTGAGTAGCATA
TTAGGAGAGATAAAAGAATATGGAACCAAATTTTGAATGTCGATCGATCG
TATTTAATAAATCTTTCTGGTGATTTATATGCTTCTTCGAGTGTCAAAGA
TGTTGCTGTTGACACAAAATACGAAATACCGAAAACAAAAATCAATGTTA
ATCTAGTCGGCATTTTTGAATTAATAATCACTTCTAAAACTTGTAGCGAT
CTTAAATTTATAGAATCATTT
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000020protonephridia
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 64..86
NoneNo IPR availableTMHMMTMhelixcoord: 25..44