SMED30006413

Overview
NameSMED30006413
Smed IDSMED30006413
Length (bp)996
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 SMED30006413 (SMED30006413) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30006413 (SMED30006413) 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.
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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



SMED30006413

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30006413 SmedASXL_004835SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30006413 dd_Smed_v4_18416_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30006413 dd_Smed_v6_18416_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30006413 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007602:19719..20714 -4971
Homology
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BLAST of SMED30006413 vs. Planmine SMEST
Match: SMESG000069778.1 (SMESG000069778.1)

HSP 1 Score: 318.161 bits (814), Expect = 2.271e-110
Identity = 155/155 (100.00%), Postives = 155/155 (100.00%), Query Frame = -1 
Query:  460 MSDFDSLFVIMRISSVSQAQNGSTTNISKVNLSEYESGIYIIFVLIFFGSGAGFYLICEFKNRWKNKLREEDQVKSFIEQRGNVQKQEKVDKIWMTENHLRQIIFLHNNNRRCSKADGGKRRMSEVRVLLSKSPRNVFSIPNRIDKKCYHAVSIS 924
            MSDFDSLFVIMRISSVSQAQNGSTTNISKVNLSEYESGIYIIFVLIFFGSGAGFYLICEFKNRWKNKLREEDQVKSFIEQRGNVQKQEKVDKIWMTENHLRQIIFLHNNNRRCSKADGGKRRMSEVRVLLSKSPRNVFSIPNRIDKKCYHAVSIS
Sbjct:    1 MSDFDSLFVIMRISSVSQAQNGSTTNISKVNLSEYESGIYIIFVLIFFGSGAGFYLICEFKNRWKNKLREEDQVKSFIEQRGNVQKQEKVDKIWMTENHLRQIIFLHNNNRRCSKADGGKRRMSEVRVLLSKSPRNVFSIPNRIDKKCYHAVSIS 155
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BLAST of SMED30006413 vs. Planmine SMEST
Match: SMESG000069780.1 (SMESG000069780.1)

HSP 1 Score: 85.5001 bits (210), Expect = 4.093e-20
Identity = 44/134 (32.84%), Postives = 77/134 (57.46%), Query Frame = -1 
Query:  475 STTNISKVNLSEYESGIYIIFVLIFFGSGAGFYLICEFKNRWKNKLREEDQVKSFIEQRGNVQKQEKVDKIWMTENHLRQIIFLHNNNRRCSKADGGKRR------MSEVRVLLSKSPRNVFSIPNRIDKKCYH 858
            ST   +     +YE+G+YII +++F+  G    ++   KN+   + REE+Q++ +I+Q+  V+KQ KVD+IW T+  LR+      N R+ S  + G R          ++ L+SKSP N++SIP ++ K  ++
Sbjct:   12 STLMAAAATSKDYEAGLYIIMIILFYCVGGALLIMSGMKNKENLRSREEEQIEYYIDQKQFVEKQAKVDQIWQTDRLLREFF----NERQQSNTENGTRNGELKSDFHSIQNLISKSPINIYSIPQKVKKNNFY 141
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BLAST of SMED30006413 vs. Planmine SMEST
Match: SMESG000069832.1 (SMESG000069832.1)

HSP 1 Score: 68.5514 bits (166), Expect = 5.108e-14
Identity = 45/121 (37.19%), Postives = 70/121 (57.85%), Query Frame = -1 
Query:  493 EYESGIYIIFVLIFFGSGAGFYLICEFKNRWKNKLREEDQVKSFIEQRGNVQKQEKVDKIWMTENHLRQIIFLHNNNRRCSKADGGKR----------RMSEVRVLLSKSPRNVFSIPNRI 825
            EY +G+YII +LIF+  G  F      K + K+KL EE+QV+ +I+QR  ++KQEKVD++W T+  LR+    +       K++ G +          R + ++ L+SKS RN FSIP  +
Sbjct:   16 EYGAGLYIIIILIFYCVGGAFLTCSGIKRKQKSKLTEEEQVEVYIQQRRVIEKQEKVDQMWQTDRMLRRNFMDYPRK----KSESGTQTETIVQKSIARSNSLKDLISKSKRNNFSIPPEV 132
The following BLAST results are available for this feature:
BLAST of SMED30006413 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 SMED30006413 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 SMED30006413 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 SMED30006413 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 SMED30006413 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 SMED30006413 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 SMED30006413 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 SMED30006413 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 SMED30006413 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 SMED30006413 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 SMED30006413 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 SMED30006413 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 SMED30006413 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 SMED30006413 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000069778.12.271e-110100.00SMESG000069778.1[more]
SMESG000069780.14.093e-2032.84SMESG000069780.1[more]
SMESG000069832.15.108e-1437.19SMESG000069832.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006413 ID=SMED30006413|Name=SMED30006413|organism=Schmidtea mediterranea sexual|type=transcript|length=996bp
ATATTATTAAAGGAAACCGAGAGGGTAAAATTTTGGAACCCGAATCACAA
GTCTAATGACCAAAAATCTGAGCTATTCCTCACTAAGTGTTGTAATAAGC
ACTGATTAATTGTGACATTCCTATTAGCTTTTTCTGTCGTGTTTATAAAG
GAGGAGAATCGGTTGCTATGGCATTGAATCAATAAATTTGTGTTCGTTAC
TATAGTTATCGGAGAACTGATGGAATCAGATCAATAATTTTTGAAATCTT
TAATCATCGACTTAATGTCTCACAACACATTATTTTAAAAATTAAAAAAC
CTTTTTAAATTTCATAAACGTAACGGTAAATTTTTAAACTTTTGAAACAC
AATGTCAGTTATAAAGATATAAATAAACATTTAATAGACGGCTATAGGAA
AATCTTACAGGTGATAGAAATCAAAAATTAGCCAAAGCTTCAAGAAAGGT
CATCATTCAGGATATGGAAACAGCATGATAACATTTCTTATCAATGCGGT
TTGGAATTGAAAAAACATTTCTTGGAGATTTAGAGAGCAAAACCCGAACT
TCACTCATTCTCCTTTTCCCGCCATCTGCTTTGGAACATCTTCTATTATT
GTTGTGAAGAAAAATGATTTGTCTAAGATGATTTTCTGTCATCCAGATCT
TGTCAACCTTTTCTTGTTTTTGTACATTTCCCCTTTGTTCGATAAAGGAC
TTAACCTGGTCTTCTTCTCTCAATTTATTTTTCCATCTGTTTTTGAATTC
ACATATCAAATAGAACCCGGCACCCGATCCGAAAAAGATCAACACGAAAA
TGATATAAATACCGGATTCGTATTCGGATAAATTTACCTTAGAAATGTTT
GTTGTTGAGCCATTTTGAGCCTGTGAAACTGAACTGATTCTCATAATGAC
AAACAATGAATCAAAATCTGACATCAATTTGATGCAATTATTTATAGAGT
TATAACAAATAATACTTGATCAACTATTCAAACAATAAAATTGGAA
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protein sequence of SMED30006413-orf-1

>SMED30006413-orf-1 ID=SMED30006413-orf-1|Name=SMED30006413-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=156bp
MSDFDSLFVIMRISSVSQAQNGSTTNISKVNLSEYESGIYIIFVLIFFGS
GAGFYLICEFKNRWKNKLREEDQVKSFIEQRGNVQKQEKVDKIWMTENHL
RQIIFLHNNNRRCSKADGGKRRMSEVRVLLSKSPRNVFSIPNRIDKKCYH
AVSIS*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000420parapharyngeal region
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 38..60