SMED30013673

Overview
NameSMED30013673
Smed IDSMED30013673
Length (bp)512
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 SMED30013673 (SMED30013673) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30013673 (SMED30013673) 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



SMED30013673

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



PAGE Curations: 12

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30013673h1SMcG0019976 SmedASXL_004241SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
tail regionSMED30013673h1SMcG0019976 SmedASXL_004241SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
tail regionSMED30013673h1SMcG0019976 SmedASXL_074705SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
gutSMED30013673h1SMcG0019976 dd_Smed_v4_42_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30013673h1SMcG0019976 dd_Smed_v4_42_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30013673h1SMcG0019976 dd_Smed_v4_19_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013673h1SMcG0019976 Contig51562uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30013673h1SMcG0019976 Contig51562newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
body wall musculatureSMED30013673h1SMcG0019976 dd_Smed_v4_19_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30013673h1SMcG0019977 SMED_00329_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30013673h1SMcG0019977 SMED_15231_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30013673h1SMcG0019976 SMED_15231_V2_1GPL14150PMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30013673 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.013637:7282..8473 +1693
v31.016296:9519..11580 +1672
v31.015535:7546..9515 -1299
Homology
[Close]
BLAST of SMED30013673 vs. Planmine SMEST
Match: SMESG000035325.1 (SMESG000035325.1)

HSP 1 Score: 228.024 bits (580), Expect = 1.190e-77
Identity = 111/121 (91.74%), Postives = 113/121 (93.39%), Query Frame = 2 
Query:   62 MISFMILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNKVEIILEQLKEIVQRQGVHTPFRQRNRYPQRERSSMFIG 424
            MISFMILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNK+EIILEQLKEIVQR G H PF+QR  Y QR RSSMF G
Sbjct:    1 MISFMILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNKMEIILEQLKEIVQRHGSHAPFKQRGYYHQRGRSSMFAG 121
[Close]
BLAST of SMED30013673 vs. Planmine SMEST
Match: SMESG000035327.1 (SMESG000035327.1)

HSP 1 Score: 223.787 bits (569), Expect = 6.720e-76
Identity = 109/121 (90.08%), Postives = 112/121 (92.56%), Query Frame = 2 
Query:   62 MISFMILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNKVEIILEQLKEIVQRQGVHTPFRQRNRYPQRERSSMFIG 424
            MISFMILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLE IS+EIAREPENLPYLL+SHEIVNILNRMDGFVRNKVEIILEQLKEIVQR G H PF+QR  Y QR RSSMF G
Sbjct:    1 MISFMILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLETISVEIAREPENLPYLLHSHEIVNILNRMDGFVRNKVEIILEQLKEIVQRHGSHAPFKQRGYYHQRGRSSMFAG 121
[Close]
BLAST of SMED30013673 vs. Planmine SMEST
Match: SMESG000035325.1 (SMESG000035325.1)

HSP 1 Score: 220.32 bits (560), Expect = 1.265e-74
Identity = 107/118 (90.68%), Postives = 109/118 (92.37%), Query Frame = 2 
Query:   74 MILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNKVEIILEQLKEIVQRQGVHTPFRQRNRYPQRERSSMFIGM 427
            MILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNK+EIILEQLKEIVQR G H PF+QR  Y QR RSSMF G 
Sbjct:    1 MILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNKMEIILEQLKEIVQRHGSHAPFKQRGYYHQRGRSSMFAGF 118
[Close]
BLAST of SMED30013673 vs. Planmine SMEST
Match: SMESG000035327.1 (SMESG000035327.1)

HSP 1 Score: 216.083 bits (549), Expect = 6.681e-73
Identity = 105/118 (88.98%), Postives = 108/118 (91.53%), Query Frame = 2 
Query:   74 MILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNKVEIILEQLKEIVQRQGVHTPFRQRNRYPQRERSSMFIGM 427
            MILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLE IS+EIAREPENLPYLL+SHEIVNILNRMDGFVRNKVEIILEQLKEIVQR G H PF+QR  Y QR RSSMF G 
Sbjct:    1 MILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLETISVEIAREPENLPYLLHSHEIVNILNRMDGFVRNKVEIILEQLKEIVQRHGSHAPFKQRGYYHQRGRSSMFAGF 118
[Close]
BLAST of SMED30013673 vs. Planmine SMEST
Match: SMESG000035325.1 (SMESG000035325.1)

HSP 1 Score: 205.297 bits (521), Expect = 7.163e-69
Identity = 99/110 (90.00%), Postives = 101/110 (91.82%), Query Frame = 2 
Query:   98 MVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNKVEIILEQLKEIVQRQGVHTPFRQRNRYPQRERSSMFIGM 427
            MVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNK+EIILEQLKEIVQR G H PF+QR  Y QR RSSMF G 
Sbjct:    1 MVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNKMEIILEQLKEIVQRHGSHAPFKQRGYYHQRGRSSMFAGF 110
The following BLAST results are available for this feature:
BLAST of SMED30013673 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 SMED30013673 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 SMED30013673 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 SMED30013673 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 SMED30013673 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 SMED30013673 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 SMED30013673 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 SMED30013673 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 SMED30013673 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 SMED30013673 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 SMED30013673 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 SMED30013673 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 SMED30013673 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 SMED30013673 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000035325.11.190e-7791.74SMESG000035325.1[more]
SMESG000035327.16.720e-7690.08SMESG000035327.1[more]
SMESG000035325.11.265e-7490.68SMESG000035325.1[more]
SMESG000035327.16.681e-7388.98SMESG000035327.1[more]
SMESG000035325.17.163e-6990.00SMESG000035325.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013673 ID=SMED30013673|Name=SMED30013673|organism=Schmidtea mediterranea sexual|type=transcript|length=512bp
AAATCGTATAAATATTGGCATAAATTTTCAATGAAAATATATAACAATAA
ACATTTCTAAAATGATTTCGTTTATGATTCTTGCAATTTCGTTGTCAATG
GTTTCGTGCACTTATATTCCTGAATGGAGGACTTATGGCGTTTCTGAAAC
ATTTTCTGGTCCAACAGGAAGATCAATGAAATTAGTTAAAATTCTCTTGG
AAAAAATTTCTATGGAAATCGCGAGAGAACCGGAAAATCTTCCATATTTA
CTCTATAGCCATGAAATAGTTAATATTTTGAACAGAATGGACGGATTTGT
TAGAAACAAAGTGGAAATAATACTTGAACAATTAAAAGAGATTGTCCAAA
GACAAGGAGTCCATACACCGTTCAGACAAAGAAATCGTTATCCACAAAGA
GAACGATCTTCAATGTTTATAGGAATGTAAATTTCGAAACAAAGAAACAT
TTCAAAACCGGTCAAAATATTTATTTGTGCAATCAATAAAATTTATTTGC
GTTAAAAAAAAA
back to top

protein sequence of SMED30013673-orf-1

>SMED30013673-orf-1 ID=SMED30013673-orf-1|Name=SMED30013673-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=123bp
MISFMILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKIS
MEIAREPENLPYLLYSHEIVNILNRMDGFVRNKVEIILEQLKEIVQRQGV
HTPFRQRNRYPQRERSSMFIGM*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000421tail
PLANA:0000429neoblast
PLANA:0002075pigment cell
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..16
score: 0.788