SMED30027739

Overview
NameSMED30027739
Smed IDSMED30027739
Length (bp)410
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 SMED30027739 (SMED30027739) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30027739 (SMED30027739) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top

 

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



SMED30027739

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30027739 SmedASXL_018881SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30027739 SmedASXL_018881SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30027739 dd_Smed_v4_496_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30027739 dd_Smed_v4_496_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30027739 dd_Smed_v4_496_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30027739 dd_Smed_v6_496_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30027739 OX_Smed_1.0.15300ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30027739 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.025791:10550..10917 +1822
v31.005192:34948..35316 -1819
Homology
[Close]
BLAST of SMED30027739 vs. Planmine SMEST
Match: SMESG000067657.1 (SMESG000067657.1)

HSP 1 Score: 156.377 bits (394), Expect = 1.214e-50
Identity = 79/79 (100.00%), Postives = 79/79 (100.00%), Query Frame = -3 
Query:  172 LSLVMKYFIVFIGLIVVAKCEECVDRDNDCASKTVKGCNNEDMLNKCAKSCHICGDCGDSRLDCALLKERGDCDRMDDQ 408
            LSLVMKYFIVFIGLIVVAKCEECVDRDNDCASKTVKGCNNEDMLNKCAKSCHICGDCGDSRLDCALLKERGDCDRMDDQ
Sbjct:    4 LSLVMKYFIVFIGLIVVAKCEECVDRDNDCASKTVKGCNNEDMLNKCAKSCHICGDCGDSRLDCALLKERGDCDRMDDQ 82
[Close]
BLAST of SMED30027739 vs. Planmine SMEST
Match: SMESG000067661.1 (SMESG000067661.1)

HSP 1 Score: 109.383 bits (272), Expect = 3.576e-32
Identity = 52/75 (69.33%), Postives = 62/75 (82.67%), Query Frame = -3 
Query:  172 MKYFIVFIGLIVVAKCEECVDRDNDCASKTVKGCNNEDMLNKCAKSCHICGDCGDSRLDCALLKERGDCDRMDDQ 396
            MK FI F+GL+VVA CE+C+D  +DCASKT + C NED+L KC KSCH+CGDC DSR DCA LKERGDCD+MDD+
Sbjct:    1 MKLFIFFLGLVVVAMCEDCLDSGDDCASKTGEDCTNEDVLTKCPKSCHLCGDCADSRPDCAFLKERGDCDKMDDR 75
[Close]
BLAST of SMED30027739 vs. Planmine SMEST
Match: SMESG000067668.1 (SMESG000067668.1)

HSP 1 Score: 108.612 bits (270), Expect = 7.716e-32
Identity = 52/75 (69.33%), Postives = 62/75 (82.67%), Query Frame = -3 
Query:  172 MKYFIVFIGLIVVAKCEECVDRDNDCASKTVKGCNNEDMLNKCAKSCHICGDCGDSRLDCALLKERGDCDRMDDQ 396
            MK FI F+GLIVVA CE+C+D  +DCASKT + C NE++L KC KSCH+CGDC DSR DCA LKERGDCD+MDD+
Sbjct:    1 MKLFIFFLGLIVVAMCEDCLDSGDDCASKTGEDCTNEEVLTKCPKSCHLCGDCADSRPDCAFLKERGDCDKMDDR 75
[Close]
BLAST of SMED30027739 vs. Planmine SMEST
Match: SMESG000067659.1 (SMESG000067659.1)

HSP 1 Score: 107.842 bits (268), Expect = 1.809e-31
Identity = 52/75 (69.33%), Postives = 60/75 (80.00%), Query Frame = -3 
Query:  172 MKYFIVFIGLIVVAKCEECVDRDNDCASKTVKGCNNEDMLNKCAKSCHICGDCGDSRLDCALLKERGDCDRMDDQ 396
            MK FI F+GLIVVA CE+C+D  +DCASKT + C NED+  KC KSCH CGDC DSR DCA LKERGDCD+MDD+
Sbjct:    1 MKLFIFFLGLIVVAMCEDCLDSGDDCASKTGEDCTNEDVYTKCPKSCHFCGDCADSRPDCAFLKERGDCDKMDDR 75
[Close]
BLAST of SMED30027739 vs. Planmine SMEST
Match: SMESG000079865.1 (SMESG000079865.1)

HSP 1 Score: 100.908 bits (250), Expect = 7.506e-29
Identity = 49/75 (65.33%), Postives = 59/75 (78.67%), Query Frame = -3 
Query:  172 MKYFIVFIGLIVVAKCEECVDRDNDCASKTVKGCNNEDMLNKCAKSCHICGDCGDSRLDCALLKERGDCDRMDDQ 396
            MK FIV +GLIVVAKCE+C+D  +DCASKT + C +E++  KC KSCH CGDC DSR DC  LKERGDC+ MDD+
Sbjct:    1 MKLFIVLLGLIVVAKCEDCLDSGDDCASKTGEDCTSEEVYTKCPKSCHFCGDCADSRPDCDFLKERGDCELMDDR 75
The following BLAST results are available for this feature:
BLAST of SMED30027739 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 SMED30027739 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 SMED30027739 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 SMED30027739 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 SMED30027739 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 SMED30027739 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 SMED30027739 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 SMED30027739 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 SMED30027739 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 SMED30027739 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 SMED30027739 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 SMED30027739 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 SMED30027739 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 SMED30027739 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000067657.11.214e-50100.00SMESG000067657.1[more]
SMESG000067661.13.576e-3269.33SMESG000067661.1[more]
SMESG000067668.17.716e-3269.33SMESG000067668.1[more]
SMESG000067659.11.809e-3169.33SMESG000067659.1[more]
SMESG000079865.17.506e-2965.33SMESG000079865.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027739 ID=SMED30027739|Name=SMED30027739|organism=Schmidtea mediterranea sexual|type=transcript|length=410bp
TTTTTTTTTTTGTTTTTTTTTTTTTTNTTTTTTTTTTTTTTTTTTAACAT
TTTTGAAGAATTTATTAAATTTGAAGCATAAAATATTTTTTTAATTGTAA
AACATCTTAAAGATCTTCACAGAAATTTTAATTTTAGTTTAGGTACATTT
TCCACAAGTTTTTCTGCAAATTTGGTCGTCCATTCTGTCACAGTCACCAC
GTTCTTTTAGTAAAGCACAGTCAAGGCGGCTGTCTCCGCAATCTCCACAA
ATGTGACAGGATTTGGCGCATTTATTCAACATGTCTTCATTATTGCAACC
CTTTACAGTTTTTGATGCACAATCATTGTCCCTGTCAACGCATTCTTCAC
ATTTTGCGACAACAATCAAACCAATAAAAACAATGAAATATTTCATGACC
AACGAAAGAG
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0000420parapharyngeal region
PLANA:0003117parapharyngeal cell
Vocabulary: INTERPRO
TermDefinition
IPR003582ShKT_dom
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR003582ShKT domainSMARTSM00254ShkT_1coord: 56..89
e-value: 3.3E-4
score: 30.0
coord: 22..55
e-value: 0.0037
score: 26.5
IPR003582ShKT domainPFAMPF01549ShKcoord: 22..54
e-value: 2.2E-5
score: 24.9
coord: 57..88
e-value: 4.0E-4
score: 20.9
IPR003582ShKT domainPROSITEPS51670SHKTcoord: 57..88
score: 6.705
IPR003582ShKT domainPROSITEPS51670SHKTcoord: 23..54
score: 8.15
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..20
score: 0.813