XenopsinB

Overview
NameXenopsinB
Smed IDSMED30000266
Length (bp)869
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 XenopsinB (SMED30000266) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for XenopsinB (SMED30000266) 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




SMED30000266

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
nervous systemSMED30000266SMESG000065997.1 dd_Smed_v4_18799_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30000266SMESG000065997.1 dd_Smed_v4_18799_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30000266SMESG000065997.1 dd_Smed_v4_18799_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30000266SMESG000065997.1 dd_Smed_v4_18799_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of XenopsinB vs. TrEMBL
Match: A0A2D3VLV4 (Xenopsin (Fragment) OS=Prosthiostomum siphunculus OX=983679 PE=2 SV=1)

HSP 1 Score: 67.0106 bits (162), Expect = 1.644e-9
Identity = 35/95 (36.84%), Postives = 55/95 (57.89%), Query Frame = 2
Query:   86 AYMISWTPYAICSFQAFINKPLSNLLKNLAELCAKSSYVWDSLIYCWTLSEINNL---LFQYCCLPFRKIQQGKMFSTIDQSIDNSETLTPVSKK 361
            +Y+ SWTPYAIC+F  F+N P ++ L   + L AK+SY+WDS+IY W L E+  +   + +  C   +  Q  +M    D+   NS  L P+ ++
Sbjct:  108 SYLASWTPYAICAFLMFLNPPPNHTLLVASILLAKASYIWDSIIYTWALPELRTIWMGILRKACFRPKPNQASEM----DEITMNSLPLAPIIRR 198          
BLAST of XenopsinB vs. TrEMBL
Match: A0A2D3VR06 (XenopsinB (Fragment) OS=Stylochus ellipticus OX=1385436 PE=2 SV=1)

HSP 1 Score: 64.3142 bits (155), Expect = 1.772e-8
Identity = 25/55 (45.45%), Postives = 39/55 (70.91%), Query Frame = 2
Query:   83 AAYMISWTPYAICSFQAFINKPLSNLLKNLAELCAKSSYVWDSLIYCWTLSEINN 247
             +++ISW+PYA+C+   F+  P S+ +  ++ + AKSSY+WDS+IY W L EI N
Sbjct:  114 GSFIISWSPYAVCALLMFLGHPPSSFILVISVILAKSSYIWDSMIYTWALPEIRN 168          
BLAST of XenopsinB vs. TrEMBL
Match: A0A2D3VCG0 (XenopsinB2 (Fragment) OS=Prostheceraeus vittatus OX=107736 PE=2 SV=1)

HSP 1 Score: 61.2326 bits (147), Expect = 5.426e-7
Identity = 25/56 (44.64%), Postives = 41/56 (73.21%), Query Frame = 2
Query:   83 AAYMISWTPYAICSFQAFINKPLSNLLKNLAELCAKSSYVWDSLIYCWTLSEINNL 250
             +Y++SWTPYAIC+   F++ P +++L   + + AK+SY+WDS+IY W L E+ N+
Sbjct:  260 VSYLVSWTPYAICATLMFLDYPPNHMLLVSSIILAKASYIWDSIIYTWALPELKNV 315          
BLAST of XenopsinB vs. Planmine SMEST
Match: SMESG000065997.1 (SMESG000065997.1)

HSP 1 Score: 225.713 bits (574), Expect = 3.405e-75
Identity = 108/109 (99.08%), Postives = 109/109 (100.00%), Query Frame = 2
Query:   92 MISWTPYAICSFQAFINKPLSNLLKNLAELCAKSSYVWDSLIYCWTLSEINNLLFQYCCLPFRKIQQGKMFSTIDQSIDNSETLTPVSKKIKVAKSYLFPPLVNDRGKQ 418
            MISWTPYAICSFQAFINKPLSNLLKNLAELCAKSSYVWDSLIYCWTLSEINNLLFQYCCLPFRKI+QGKMFSTIDQSIDNSETLTPVSKKIKVAKSYLFPPLVNDRGKQ
Sbjct:    1 MISWTPYAICSFQAFINKPLSNLLKNLAELCAKSSYVWDSLIYCWTLSEINNLLFQYCCLPFRKIRQGKMFSTIDQSIDNSETLTPVSKKIKVAKSYLFPPLVNDRGKQ 109          
The following BLAST results are available for this feature:
BLAST of XenopsinB 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 XenopsinB 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 XenopsinB 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 XenopsinB 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 XenopsinB 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 XenopsinB 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 XenopsinB 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 XenopsinB vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
A0A2D3VLV41.644e-936.84Xenopsin (Fragment) OS=Prosthiostomum siphunculus ... [more]
A0A2D3VR061.772e-845.45XenopsinB (Fragment) OS=Stylochus ellipticus OX=13... [more]
A0A2D3VCG05.426e-744.64XenopsinB2 (Fragment) OS=Prostheceraeus vittatus O... [more]
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BLAST of XenopsinB 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 XenopsinB 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 XenopsinB 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 XenopsinB 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 XenopsinB 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 XenopsinB vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000065997.13.405e-7599.08SMESG000065997.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30000266 ID=SMED30000266|Name=XenopsinB|organism=Schmidtea mediterranea sexual|type=transcript|length=869bp
TATTCACAAGCATCATCAAAGGAGACATAACAATTCGTCAAATATGTCAN
ANANNANTNNANTNTTNTNANTNTNNNTNNCAGCCGCCTATATGATATCA
TGGACACCTTACGCCATTTGTTCATTTCAAGCATTTATCAACAAGCCTTT
ATCAAATCTATTAAAAAATTTGGCAGAATTATGTGCAAAATCATCATACG
TTTGGGATTCATTGATCTATTGTTGGACTTTATCAGAAATCAATAATCTG
CTATTCCAATATTGCTGCTTGCCATTTAGAAAGATCCAACAAGGGAAAAT
GTTTTCAACGATTGATCAGTCGATTGATAACTCAGAGACTTTGACCCCGG
TTTCAAAGAAAATCAAGGTGGCAAAATCGTATTTATTTCCTCCCCTTGTG
AATGATAGAGGAAAACAAAANNCAGNNNNNGNNNNNNAGNTNGNNNNNNN
NNANNNNTNNATTATTAGGACAGTCGGAAAAGGAAAAAAGAAAAAAAGTT
GTAGTTGTATGTGCGAAGAATGAATGGAAATGACGGAAAACCAAACAACA
TTGAAATTATCTCAGGTGATATCAAATAACAATCTATAAAAGGAAGTGAC
ACAAATGGAGAAATTAGAATAAAANCGGATGTAAAAGTCTTCAGTGGTGA
ATGTTTTGTGCAGTTGCGTTAGCGAAAATCAAATTAATTGTCATTGTGAT
AGACAATAAATATTGAGAATATCGAGAATTTGTCGTTAATATAGATTTAT
CCATGTTCACCAACAACCATTTTTCATTTGACGGTTTAGTGAAATCATTA
GACTGAATCATCATTTCATGTATACAAAATGCACTCGACAATTATAATTA
CAAAAGCTCAAAACTCGAA
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protein sequence of SMED30000266-orf-1

>SMED30000266-orf-1 ID=SMED30000266-orf-1|Name=SMED30000266-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=174bp
IHKHHQRRHNNSSNMSXXXXXXXXXXXAAYMISWTPYAICSFQAFINKPL
SNLLKNLAELCAKSSYVWDSLIYCWTLSEINNLLFQYCCLPFRKIQQGKM
FSTIDQSIDNSETLTPVSKKIKVAKSYLFPPLVNDRGKQXXXXXXXXXXX
XXXIIRTVGKGKKKKSCSCMCEE*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0004930G-protein coupled receptor activity
Vocabulary: biological process
TermDefinition
GO:0007186G-protein coupled receptor signaling pathway
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableGENE3DG3DSA:1.20.1070.10coord: 1..88
e-value: 2.3E-5
score: 25.3
NoneNo IPR availableCDDcd149697tmA_Opsins_type2_animalscoord: 2..48
e-value: 3.70448E-8
score: 47.586
NoneNo IPR availableSUPERFAMILYSSF81321Family A G protein-coupled receptor-likecoord: 2..73