TCEN protein

Overview
NameTCEN protein
Smed IDSMED30006806
Length (bp)335
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast Population

▻ 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



 

Neoblast Population

 

t-SNE plot shows two-dimensional representation of global gene expression relationships among all neoblasts (n = 7,088 after filter). Cluster identity was assigned based on the top 10 marker genes of each cluster (Table S2), followed by inspection of RNA in situ hybridization patterns. Neoblast groups, Nb.


Expression of TCEN protein (SMED30006806) t-SNE clustered cells

Violin plots show distribution of expression levels for TCEN protein (SMED30006806) in cells (dots) of each of the 12 neoblast clusters.

 

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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 TCEN protein (SMED30006806) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for TCEN protein (SMED30006806) 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



SMED30006806

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
prepharyngeal regionSMED30006806 SmedASXL_003539SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30006806 SmedASXL_003539SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
parenchymaSMED30006806 dd_Smed_v4_53_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30006806 dd_Smed_v6_53_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
parapharyngeal regionSMED30006806 EU082822.1smed_ncbi_20240424PMID:21282632
Almuedo-Castillo et al., 2011		whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30006806 TCENsmed_ncbi_20240424PMID:21282632
Almuedo-Castillo et al., 2011		whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30006806 EU082822.1smed_ncbi_20240424PMID:18287199
Iglesias et al., 2008		whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal regionSMED30006806 EU082822smed_ncbi_20240424PMID:18287199
Iglesias et al., 2008		whole organism asexual adult colorimetric in situ hybridization evidence
body wall musculatureSMED30006806 dd_Smed_v4_53_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
prepharyngeal cellSMED30006806 EU082822.1smed_ncbi_20240424PMID:20422023
Felix et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
parapharyngeal cellSMED30006806 EU082822.1smed_ncbi_20240424PMID:20422023
Felix et al., 2010		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of TCEN protein vs. TrEMBL
Match: B1NTA3 (TCEN protein OS=Schmidtea mediterranea OX=79327 GN=tcen PE=2 SV=1)

HSP 1 Score: 99.3673 bits (246), Expect = 3.419e-25
Identity = 61/61 (100.00%), Postives = 61/61 (100.00%), Query Frame = 3 
Query:    6 MFKXXXXXXXXXXXIEEGYSLNFKSIQCLAKSASCAKDCPKLNSDCFVKCGEVYKKCKQDG 188
            MFKLALFLVVFVAVIEEGYSLNFKSIQCLAKSASCAKDCPKLNSDCFVKCGEVYKKCKQDG
Sbjct:    1 MFKLALFLVVFVAVIEEGYSLNFKSIQCLAKSASCAKDCPKLNSDCFVKCGEVYKKCKQDG 61
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BLAST of TCEN protein vs. TrEMBL
Match: O97433 (Uncharacterized protein OS=Girardia tigrina OX=6162 GN=tcen49 PE=4 SV=1)

HSP 1 Score: 76.6406 bits (187), Expect = 3.346e-16
Identity = 45/61 (73.77%), Postives = 53/61 (86.89%), Query Frame = 3 
Query:    6 MFKXXXXXXXXXXXIEEGYSLNFKSIQCLAKSASCAKDCPKLNSDCFVKCGEVYKKCKQDG 188
            M+K ALFLV+FVAV +EG+SLN KS++CLAKS SCAK CPKLNSDCFV+CG VYK CKQ+ 
Sbjct:    1 MYKAALFLVIFVAVFQEGFSLNLKSMKCLAKSISCAKSCPKLNSDCFVECGAVYKTCKQEA 61
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BLAST of TCEN protein vs. Planmine SMEST
Match: SMESG000030595.1 (SMESG000030595.1)

HSP 1 Score: 43.5134 bits (101), Expect = 1.950e-6
Identity = 20/44 (45.45%), Postives = 29/44 (65.91%), Query Frame = 3 
Query:   48 IEEGYSLNFKSIQCLAKSASCAKDCPKLNSDCFVKCGEVYKKCK 179
            ++EG S  F SI C+ +S  CAK C K+N +C  +C +V+K CK
Sbjct:   49 VQEGSSFVFGSISCVVESVKCAKKCSKVNMECAQQCLQVFKDCK 92
The following BLAST results are available for this feature:
BLAST of TCEN protein 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 TCEN protein 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 TCEN protein 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 TCEN protein 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 TCEN protein 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 TCEN protein 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 TCEN protein 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 TCEN protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
B1NTA33.419e-25100.00TCEN protein OS=Schmidtea mediterranea OX=79327 GN... [more]
O974333.346e-1673.77Uncharacterized protein OS=Girardia tigrina OX=616... [more]
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BLAST of TCEN protein 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 TCEN protein 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 TCEN protein 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 TCEN protein 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 TCEN protein 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 TCEN protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000030595.11.950e-645.45SMESG000030595.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006806 ID=SMED30006806|Name=TCEN protein|organism=Schmidtea mediterranea sexual|type=transcript|length=335bp
AAAAAATGTTTAAATTGGCTTTATTTCTTGTGGTATTCGTCGCCGTCATT
GAGGAGGGATATTCTCTCAATTTCAAATCCATTCAATGCCTTGCCAAATC
CGCATCATGTGCCAAAGATTGCCCAAAATTGAATTCAGATTGCTTTGTCA
AATGCGGAGAAGTCTATAAGAAATGTAAACAAGATGGAAAAGAAACTGAA
AAAGAGAAAGAAAAAGAGTGAATAACAGTAAAAAAAATAAAATTAAAACA
AAACAAAATATTTTAAATATTTAAAAGCAATTGTTTTAACAAATACATTT
TAAATGTGAGCTAAAAAAAAAAAAAAAAAATGCGA
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Aliases
The feature 'TCEN protein' has the following synonyms
Synonym
TCEN
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000240body wall musculature
PLANA:0000420parapharyngeal region
PLANA:0003117parapharyngeal cell
PLANA:0003118prepharyngeal 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..21
score: 0.767