SMED30017639

Overview
NameSMED30017639
Smed IDSMED30017639
Length (bp)504
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 SMED30017639 (SMED30017639) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30017639 (SMED30017639) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

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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

 

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Anatomical Expression

PAGE et. al., 2020




SMED30017639

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



PAGE Curations: 27

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
tail regionSMED30017639h1SMcG0019977 SmedASXL_016645SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
tail regionSMED30017639h1SMcG0019977 SmedASXL_016646SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
tail regionSMED30017639h1SMcG0019977 SmedASXL_016647SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016
whole organism asexual adult RNA-sequencing evidence
gutSMED30017639h1SMcG0019977 SmedASXL_016646SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017
whole organism asexual adult colorimetric in situ hybridization evidence
pigment cellSMED30017639h1SMcG0019977 SmedASXL_016646SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017
whole organism asexual adult RNA-sequencing evidence
pigment cellSMED30017639h1SMcG0019977 SmedASXL_016647SmedAsxl_ww_GCZZ01PMID:29158443
He et al., 2017
whole organism asexual adult RNA-sequencing evidence
Smed sexual biotypeSMED30017639h1SMcG0019977 Contig16655newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30017639h1SMcG0019977 Contig16655uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30017639h1SMcG0019977 Contig26777uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30017639h1SMcG0019977 Contig26777newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30017639h1SMcG0019977 Contig26819newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30017639h1SMcG0019977 Contig26819uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30017639h1SMcG0019977 Contig52163newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30017639h1SMcG0019977 Contig52163uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
gutSMED30017639h1SMcG0019977 dd_Smed_v4_8_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30017639h1SMcG0019977 dd_Smed_v4_8_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30017639h1SMcG0019977 Contig51952newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
body wall musculatureSMED30017639h1SMcG0019977 dd_Smed_v4_8_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Category 2 cellSMED30017639h1SMcG0019977 dd_Smed_v4_8_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
neoblastSMED30017639h1SMcG0019977 SMED_00329_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30017639h1SMcG0019977 SMED_00329_V2_1GPL14150PMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30017639h1SMcG0019977 SMED_15231_V2_1GPL14150PMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30017639h1SMcG0019977 SMED_15231_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30017639h1SMcG0019977 SMED_05187_V2_1GPL14150PMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30017639h1SMcG0019977 SMED_05187_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30017639h1SMcG0019976 SMED_15231_V2_1GPL14150PMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30017639h1SMcG0019976 SMED_15231_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Alignments
SMED30017639 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.015535:451..1996 -2084
v31.016296:9042..10465 +1608
v31.015535:8521..9515 -960
v31.013637:5206..6237 -674
v31.016296:7198..7999 -667
v31.019806:1193..2160 +660
Homology
BLAST of SMED30017639 vs. Planmine SMEST
Match: SMESG000035325.1 (SMESG000035325.1)

HSP 1 Score: 252.292 bits (643), Expect = 2.608e-87
Identity = 121/122 (99.18%), Postives = 122/122 (100.00%), Query Frame = 2
Query:   62 MISFMILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNKVEIILEQLKEIVQRHGSHAPFKQRGYYHQRGRSSMFAGF 427
            MISFMILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNK+EIILEQLKEIVQRHGSHAPFKQRGYYHQRGRSSMFAGF
Sbjct:    1 MISFMILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNKMEIILEQLKEIVQRHGSHAPFKQRGYYHQRGRSSMFAGF 122          
BLAST of SMED30017639 vs. Planmine SMEST
Match: SMESG000035327.1 (SMESG000035327.1)

HSP 1 Score: 248.054 bits (632), Expect = 1.369e-85
Identity = 119/122 (97.54%), Postives = 121/122 (99.18%), Query Frame = 2
Query:   62 MISFMILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNKVEIILEQLKEIVQRHGSHAPFKQRGYYHQRGRSSMFAGF 427
            MISFMILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLE IS+EIAREPENLPYLL+SHEIVNILNRMDGFVRNKVEIILEQLKEIVQRHGSHAPFKQRGYYHQRGRSSMFAGF
Sbjct:    1 MISFMILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLETISVEIAREPENLPYLLHSHEIVNILNRMDGFVRNKVEIILEQLKEIVQRHGSHAPFKQRGYYHQRGRSSMFAGF 122          
BLAST of SMED30017639 vs. Planmine SMEST
Match: SMESG000035325.1 (SMESG000035325.1)

HSP 1 Score: 244.588 bits (623), Expect = 2.575e-84
Identity = 117/118 (99.15%), Postives = 118/118 (100.00%), Query Frame = 2
Query:   74 MILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNKVEIILEQLKEIVQRHGSHAPFKQRGYYHQRGRSSMFAGF 427
            MILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNK+EIILEQLKEIVQRHGSHAPFKQRGYYHQRGRSSMFAGF
Sbjct:    1 MILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNKMEIILEQLKEIVQRHGSHAPFKQRGYYHQRGRSSMFAGF 118          
BLAST of SMED30017639 vs. Planmine SMEST
Match: SMESG000035327.1 (SMESG000035327.1)

HSP 1 Score: 240.736 bits (613), Expect = 1.049e-82
Identity = 115/118 (97.46%), Postives = 117/118 (99.15%), Query Frame = 2
Query:   74 MILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNKVEIILEQLKEIVQRHGSHAPFKQRGYYHQRGRSSMFAGF 427
            MILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLE IS+EIAREPENLPYLL+SHEIVNILNRMDGFVRNKVEIILEQLKEIVQRHGSHAPFKQRGYYHQRGRSSMFAGF
Sbjct:    1 MILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLETISVEIAREPENLPYLLHSHEIVNILNRMDGFVRNKVEIILEQLKEIVQRHGSHAPFKQRGYYHQRGRSSMFAGF 118          
BLAST of SMED30017639 vs. Planmine SMEST
Match: SMESG000035325.1 (SMESG000035325.1)

HSP 1 Score: 229.95 bits (585), Expect = 1.204e-78
Identity = 109/110 (99.09%), Postives = 110/110 (100.00%), Query Frame = 2
Query:   98 MVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNKVEIILEQLKEIVQRHGSHAPFKQRGYYHQRGRSSMFAGF 427
            MVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNK+EIILEQLKEIVQRHGSHAPFKQRGYYHQRGRSSMFAGF
Sbjct:    1 MVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKISMEIAREPENLPYLLYSHEIVNILNRMDGFVRNKMEIILEQLKEIVQRHGSHAPFKQRGYYHQRGRSSMFAGF 110          
The following BLAST results are available for this feature:
BLAST of SMED30017639 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 SMED30017639 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 SMED30017639 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 SMED30017639 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 SMED30017639 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 SMED30017639 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 SMED30017639 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 SMED30017639 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 SMED30017639 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 SMED30017639 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 SMED30017639 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 SMED30017639 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 SMED30017639 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 SMED30017639 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000035325.12.608e-8799.18SMESG000035325.1[more]
SMESG000035327.11.369e-8597.54SMESG000035327.1[more]
SMESG000035325.12.575e-8499.15SMESG000035325.1[more]
SMESG000035327.11.049e-8297.46SMESG000035327.1[more]
SMESG000035325.11.204e-7899.09SMESG000035325.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017639 ID=SMED30017639|Name=SMED30017639|organism=Schmidtea mediterranea sexual|type=transcript|length=504bp
AAATCGTATAAATATTGGCATAAATTTTCAATGAAAATATATAACAATAA
ACATTTCTAAAATGATTTCGTTTATGATTCTTGCAATTTCGTTGTCAATG
GTTTCGTGCACTTATATTCCTGAATGGAGGACTTATGGCGTTTCTGAAAC
ATTTTCTGGTCCAACAGGAAGATCAATGAAATTAGTTAAAATTCTCTTGG
AAAAAATTTCTATGGAAATCGCGAGAGAACCGGAAAATCTTCCATATTTA
CTCTATAGCCATGAAATAGTTAATATTTTGAACAGAATGGACGGATTTGT
TAGAAACAAAGTGGAAATAATACTTGAACAATTAAAAGAGATTGTTCAAA
GACATGGAAGCCATGCCCCATTCAAACAAAGAGGATATTATCACCAAAGA
GGACGATCTTCAATGTTTGCAGGATTTTAAATTTCAAAATAAAGAAATGC
ATCAAAAACAGATGAAAATAATTTTGTGTTTAATCAATAAATTTTAATTG
CATT
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protein sequence of SMED30017639-orf-1

>SMED30017639-orf-1 ID=SMED30017639-orf-1|Name=SMED30017639-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=123bp
MISFMILAISLSMVSCTYIPEWRTYGVSETFSGPTGRSMKLVKILLEKIS
MEIAREPENLPYLLYSHEIVNILNRMDGFVRNKVEIILEQLKEIVQRHGS
HAPFKQRGYYHQRGRSSMFAGF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000028Category 2 cell
PLANA:0000240body wall musculature
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: 0.787