SMED30004177

Overview
NameSMED30004177
Smed IDSMED30004177
Length (bp)407
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 SMED30004177 (SMED30004177) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30004177 (SMED30004177) 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




SMED30004177

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
gutSMED30004177SMESG000077853.1 dd_Smed_v4_5429_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30004177SMESG000077853.1 dd_Smed_v4_5429_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
medial muscle cellSMED30004177SMESG000077853.1 dd_Smed_v4_5429_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30004177 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000896:10529..14010 -1256
Homology
BLAST of SMED30004177 vs. Planmine SMEST
Match: SMESG000077853.1 (SMESG000077853.1)

HSP 1 Score: 214.927 bits (546), Expect = 7.609e-73
Identity = 110/143 (76.92%), Postives = 111/143 (77.62%), Query Frame = 2
Query:   32 MSNSFRNQLSVVVDSNYLPTDEEVYTYSSNFDYQRKSEKDVQH-------------------------------RSCFEAKVENWHEKNEYSTRTRTNPNMISRKDYEKMVRNPSGNWKCRRCTILNPNSISTCECGSTRPNH 367
            +SNSFRNQLSVVVDSNYLPTDEEVYTYSSNFDYQRKSEKDVQH                                SCFEAKVENWHEKNEYSTRTRTNPNMISRKDYEKMVRNPSGNWKCRRCTILNPNSISTCECGSTRPNH
Sbjct:   14 LSNSFRNQLSVVVDSNYLPTDEEVYTYSSNFDYQRKSEKDVQHPLHTSVRNTHSNSSCDFHYHQTIGYNRSKSDGSCFEAKVENWHEKNEYSTRTRTNPNMISRKDYEKMVRNPSGNWKCRRCTILNPNSISTCECGSTRPNH 156          
BLAST of SMED30004177 vs. Planmine SMEST
Match: SMESG000077853.1 (SMESG000077853.1)

HSP 1 Score: 213.001 bits (541), Expect = 3.453e-72
Identity = 110/142 (77.46%), Postives = 110/142 (77.46%), Query Frame = 2
Query:   35 SNSFRNQLSVVVDSNYLPTDEEVYTYSSNFDYQRKSEKDVQH-------------------------------RSCFEAKVENWHEKNEYSTRTRTNPNMISRKDYEKMVRNPSGNWKCRRCTILNPNSISTCECGSTRPNH 367
            SNSFRNQLSVVVDSNYLPTDEEVYTYSSNFDYQRKSEKDVQH                                SCFEAKVENWHEKNEYSTRTRTNPNMISRKDYEKMVRNPSGNWKCRRCTILNPNSISTCECGSTRPNH
Sbjct:    9 SNSFRNQLSVVVDSNYLPTDEEVYTYSSNFDYQRKSEKDVQHPLHTSVRNTHSNSSCDFHYHQTIGYNRSKSDGSCFEAKVENWHEKNEYSTRTRTNPNMISRKDYEKMVRNPSGNWKCRRCTILNPNSISTCECGSTRPNH 150          
BLAST of SMED30004177 vs. Planmine SMEST
Match: SMESG000077853.1 (SMESG000077853.1)

HSP 1 Score: 150.599 bits (379), Expect = 8.625e-47
Identity = 68/68 (100.00%), Postives = 68/68 (100.00%), Query Frame = 2
Query:  164 SCFEAKVENWHEKNEYSTRTRTNPNMISRKDYEKMVRNPSGNWKCRRCTILNPNSISTCECGSTRPNH 367
            SCFEAKVENWHEKNEYSTRTRTNPNMISRKDYEKMVRNPSGNWKCRRCTILNPNSISTCECGSTRPNH
Sbjct:  146 SCFEAKVENWHEKNEYSTRTRTNPNMISRKDYEKMVRNPSGNWKCRRCTILNPNSISTCECGSTRPNH 213          

HSP 2 Score: 87.8113 bits (216), Expect = 2.563e-22
Identity = 42/42 (100.00%), Postives = 42/42 (100.00%), Query Frame = 2
Query:   35 SNSFRNQLSVVVDSNYLPTDEEVYTYSSNFDYQRKSEKDVQH 160
            SNSFRNQLSVVVDSNYLPTDEEVYTYSSNFDYQRKSEKDVQH
Sbjct:    9 SNSFRNQLSVVVDSNYLPTDEEVYTYSSNFDYQRKSEKDVQH 50          
BLAST of SMED30004177 vs. Planmine SMEST
Match: SMESG000077853.1 (SMESG000077853.1)

HSP 1 Score: 149.828 bits (377), Expect = 2.739e-46
Identity = 68/68 (100.00%), Postives = 68/68 (100.00%), Query Frame = 2
Query:  164 SCFEAKVENWHEKNEYSTRTRTNPNMISRKDYEKMVRNPSGNWKCRRCTILNPNSISTCECGSTRPNH 367
            SCFEAKVENWHEKNEYSTRTRTNPNMISRKDYEKMVRNPSGNWKCRRCTILNPNSISTCECGSTRPNH
Sbjct:  156 SCFEAKVENWHEKNEYSTRTRTNPNMISRKDYEKMVRNPSGNWKCRRCTILNPNSISTCECGSTRPNH 223          

HSP 2 Score: 88.9669 bits (219), Expect = 1.191e-22
Identity = 42/43 (97.67%), Postives = 43/43 (100.00%), Query Frame = 2
Query:   32 MSNSFRNQLSVVVDSNYLPTDEEVYTYSSNFDYQRKSEKDVQH 160
            +SNSFRNQLSVVVDSNYLPTDEEVYTYSSNFDYQRKSEKDVQH
Sbjct:   18 LSNSFRNQLSVVVDSNYLPTDEEVYTYSSNFDYQRKSEKDVQH 60          
BLAST of SMED30004177 vs. Planmine SMEST
Match: SMESG000077853.1 (SMESG000077853.1)

HSP 1 Score: 88.1965 bits (217), Expect = 3.634e-21
Identity = 42/42 (100.00%), Postives = 42/42 (100.00%), Query Frame = 2
Query:   35 SNSFRNQLSVVVDSNYLPTDEEVYTYSSNFDYQRKSEKDVQH 160
            SNSFRNQLSVVVDSNYLPTDEEVYTYSSNFDYQRKSEKDVQH
Sbjct:  695 SNSFRNQLSVVVDSNYLPTDEEVYTYSSNFDYQRKSEKDVQH 736          
The following BLAST results are available for this feature:
BLAST of SMED30004177 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 SMED30004177 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 SMED30004177 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 SMED30004177 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 SMED30004177 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 SMED30004177 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 SMED30004177 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 SMED30004177 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 SMED30004177 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 SMED30004177 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 SMED30004177 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 SMED30004177 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 SMED30004177 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 SMED30004177 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000077853.17.609e-7376.92SMESG000077853.1[more]
SMESG000077853.13.453e-7277.46SMESG000077853.1[more]
SMESG000077853.18.625e-47100.00SMESG000077853.1[more]
SMESG000077853.12.739e-46100.00SMESG000077853.1[more]
SMESG000077853.13.634e-21100.00SMESG000077853.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004177 ID=SMED30004177|Name=SMED30004177|organism=Schmidtea mediterranea sexual|type=transcript|length=407bp
AAGGTCTTACAAACGTTTTATATAAAATTGAATGAGTAATTCTTTTCGAA
ATCAGTTATCAGTTGTCGTTGATAGTAACTATCTTCCAACTGATGAAGAA
GTATACACATATTCTTCAAATTTTGATTATCAAAGAAAATCAGAAAAAGA
TGTTCAGCATCGTTCATGCTTTGAAGCAAAAGTTGAAAATTGGCATGAAA
AAAATGAATATTCAACAAGAACAAGAACAAATCCAAATATGATTTCGAGG
AAAGACTATGAAAAGATGGTGAGAAATCCATCGGGCAACTGGAAATGCCG
ACGATGCACAATTTTAAATCCAAATTCTATATCAACATGTGAATGTGGAT
CAACTAGACCAAATCACTAAAAATGATTAATATTTTTTATATTACCTTAA
TTTTGAT
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protein sequence of SMED30004177-orf-1

>SMED30004177-orf-1 ID=SMED30004177-orf-1|Name=SMED30004177-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=113bp
MSNSFRNQLSVVVDSNYLPTDEEVYTYSSNFDYQRKSEKDVQHRSCFEAK
VENWHEKNEYSTRTRTNPNMISRKDYEKMVRNPSGNWKCRRCTILNPNSI
STCECGSTRPNH*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0002056medial muscle cell
PLANA:0003116parenchymal cell