Tetraspanin

Overview
NameTetraspanin
Smed IDSMED30030260
Length (bp)813
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 Tetraspanin (SMED30030260) t-SNE clustered cells

Violin plots show distribution of expression levels for Tetraspanin (SMED30030260) 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 Tetraspanin (SMED30030260) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Tetraspanin (SMED30030260) 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



SMED30030260

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 regionSMED30030260SMESG000023404.1 dd_Smed_v4_6528_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30030260SMESG000023404.1 dd_Smed_v4_6528_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Category 4 cellSMED30030260SMESG000023404.1 dd_Smed_v4_6528_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of Tetraspanin vs. Planmine SMEST
Match: SMESG000023404.1 (SMESG000023404.1)

HSP 1 Score: 236.498 bits (602), Expect = 4.403e-78
Identity = 222/225 (98.67%), Postives = 224/225 (99.56%), Query Frame = 3 
Query:   69 MNKMKISLKTVKDILFXXXXXXXXXXXXXXXXXXXGFDFLKRYRLIFEDKYSLTLQXXXXXXXXXXXXXXXXYFGVVRESRCLLLIHTLSMFVLILSEFVXXXXXXXXXXXXXXXXXXXLWTAYEKYNSSQDYRNSIDSFQTSLKCCGFNNTIIFNSTIAXXXXXXXXXXXXXNVYSKNCPNVLSSIIQGEXXXXXXXXXXXXXXXXXXXFLSCALARQVDIYDE 743
            MNKMKISLKTVKDILFSIN IFFIIGLIILIISG+GF+FLKRYRLIFEDKYSLTLQLCIILGISIILASLLGYFGVVRESRCLLLIHTLSMFVLILSEFVILFILSIQKSKIIIDIQNILWTAYEKYNSSQDYRNSIDSFQTSLKCCGFNNTIIFNSTIASSCCMRSRSCSISNVYSKNCPNVLSSIIQGEIYVSIVLIVILILVDTLSVFLSCALARQVDIYDE
Sbjct:    1 MNKMKISLKTVKDILFSINFIFFIIGLIILIISGIGFNFLKRYRLIFEDKYSLTLQLCIILGISIILASLLGYFGVVRESRCLLLIHTLSMFVLILSEFVILFILSIQKSKIIIDIQNILWTAYEKYNSSQDYRNSIDSFQTSLKCCGFNNTIIFNSTIASSCCMRSRSCSISNVYSKNCPNVLSSIIQGEIYVSIVLIVILILVDTLSVFLSCALARQVDIYDE 225
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BLAST of Tetraspanin vs. Planmine SMEST
Match: SMESG000023404.1 (SMESG000023404.1)

HSP 1 Score: 229.565 bits (584), Expect = 1.652e-75
Identity = 219/222 (98.65%), Postives = 221/222 (99.55%), Query Frame = 3 
Query:   78 MKISLKTVKDILFXXXXXXXXXXXXXXXXXXXGFDFLKRYRLIFEDKYSLTLQXXXXXXXXXXXXXXXXYFGVVRESRCLLLIHTLSMFVLILSEFVXXXXXXXXXXXXXXXXXXXLWTAYEKYNSSQDYRNSIDSFQTSLKCCGFNNTIIFNSTIAXXXXXXXXXXXXXNVYSKNCPNVLSSIIQGEXXXXXXXXXXXXXXXXXXXFLSCALARQVDIYDE 743
            MKISLKTVKDILFSIN IFFIIGLIILIISG+GF+FLKRYRLIFEDKYSLTLQLCIILGISIILASLLGYFGVVRESRCLLLIHTLSMFVLILSEFVILFILSIQKSKIIIDIQNILWTAYEKYNSSQDYRNSIDSFQTSLKCCGFNNTIIFNSTIASSCCMRSRSCSISNVYSKNCPNVLSSIIQGEIYVSIVLIVILILVDTLSVFLSCALARQVDIYDE
Sbjct:    1 MKISLKTVKDILFSINFIFFIIGLIILIISGIGFNFLKRYRLIFEDKYSLTLQLCIILGISIILASLLGYFGVVRESRCLLLIHTLSMFVLILSEFVILFILSIQKSKIIIDIQNILWTAYEKYNSSQDYRNSIDSFQTSLKCCGFNNTIIFNSTIASSCCMRSRSCSISNVYSKNCPNVLSSIIQGEIYVSIVLIVILILVDTLSVFLSCALARQVDIYDE 222
The following BLAST results are available for this feature:
BLAST of Tetraspanin 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 Tetraspanin 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 Tetraspanin 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 Tetraspanin 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 Tetraspanin 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 Tetraspanin 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 Tetraspanin 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 Tetraspanin 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 Tetraspanin 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 Tetraspanin 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 Tetraspanin 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 Tetraspanin 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 Tetraspanin 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 Tetraspanin vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000023404.14.403e-7898.67SMESG000023404.1[more]
SMESG000023404.11.652e-7598.65SMESG000023404.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30030260 ID=SMED30030260|Name=Tetraspanin|organism=Schmidtea mediterranea sexual|type=transcript|length=813bp
ATAATTTTAGTCTTCCAAATTAAGACTTATATATTTATATGTACTGTCAT
TTAGCTAATAAAATATGAATGAATAAAATGAAAATATCTTTGAAAACTGT
TAAAGATATTTTATTTTCAATTAATGTTATATTTTTCATAATTGGCTTGA
TCATACTTATTATCAGTGGTGTTGGATTCGATTTCTTAAAAAGATACCGC
TTGATTTTTGAAGATAAATATTCGTTAACTTTGCAACTATGTATAATATT
AGGTATTTCAATTATTCTTGCCTCGCTTTTAGGCTATTTTGGAGTTGTCA
GAGAATCTAGATGCTTACTTTTAATCCACACTTTATCAATGTTCGTTCTC
ATTCTAAGTGAATTTGTTATACTTTTCATATTATCAATTCAAAAATCAAA
AATAATTATTGACATTCAAAATATACTTTGGACAGCTTATGAAAAATATA
ACAGTTCTCAGGATTACAGGAATTCAATAGATTCTTTTCAAACATCACTA
AAATGCTGTGGTTTCAACAACACAATTATTTTCAATAGCACAATTGCTTC
GAGCTGCTGTATGCGGAGTAGATCTTGCTCAATATCAAACGTTTATAGCA
AAAATTGTCCAAACGTTTTATCCAGCATTATACAGGGAGAAATTTATGTT
TCGATTGTTCTAATTGTAATATTAATATTGGTTGATACTCTTAGCGTATT
TTTATCATGCGCTTTGGCCAGACAAGTTGATATTTATGACGAGTTAAAAT
GATATATTTATAAAAAATATCTATTATTGCTTTTAAAGTAAATATTTTTT
TTGTTTAAACAAA
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protein sequence of SMED30030260-orf-1

>SMED30030260-orf-1 ID=SMED30030260-orf-1|Name=SMED30030260-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=228bp
MNKMKISLKTVKDILFSINVIFFIIGLIILIISGVGFDFLKRYRLIFEDK
YSLTLQLCIILGISIILASLLGYFGVVRESRCLLLIHTLSMFVLILSEFV
ILFILSIQKSKIIIDIQNILWTAYEKYNSSQDYRNSIDSFQTSLKCCGFN
NTIIFNSTIASSCCMRSRSCSISNVYSKNCPNVLSSIIQGEIYVSIVLIV
ILILVDTLSVFLSCALARQVDIYDELK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000018Category 4 cell
PLANA:0000034epidermis
PLANA:0003117parapharyngeal cell
Vocabulary: INTERPRO
TermDefinition
IPR000301Tetraspanin
IPR018499Tetraspanin/Peripherin
IPR028977CD81_LEL
IPR008952Tetraspanin_EC2_sf
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR000301TetraspaninPRINTSPR00259TMFOURcoord: 78..106
score: 21.28
coord: 194..220
score: 16.0
coord: 13..36
score: 27.13
coord: 51..77
score: 22.22
IPR000301TetraspaninPIRSFPIRSF002419Tetraspanincoord: 2..225
e-value: 1.6E-30
score: 103.7
IPR008952Tetraspanin, EC2 domain superfamilyGENE3DG3DSA:1.10.1450.10coord: 106..187
e-value: 6.3E-11
score: 43.9
IPR008952Tetraspanin, EC2 domain superfamilySUPERFAMILYSSF48652Tetraspanincoord: 108..190
IPR018499Tetraspanin/PeripherinPFAMPF00335Tetraspanincoord: 11..219
e-value: 2.3E-27
score: 96.2
NoneNo IPR availablePANTHERPTHR19282:SF39LEUKOCYTE SURFACE ANTIGEN CD53coord: 7..218
NoneNo IPR availablePANTHERPTHR19282TETRASPANINcoord: 7..218
NoneNo IPR availableCDDcd03127tetraspanin_LELcoord: 107..189
e-value: 2.79069E-11
score: 55.9735
NoneNo IPR availableTMHMMTMhelixcoord: 83..105
NoneNo IPR availableTMHMMTMhelixcoord: 20..39
NoneNo IPR availableTMHMMTMhelixcoord: 192..214
NoneNo IPR availableTMHMMTMhelixcoord: 54..76