SMED30018024

Overview
NameSMED30018024
Smed IDSMED30018024
Length (bp)320
Neoblast Clusters

Zeng et. al., 2018



 

 

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



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



SMED30018024

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 systemSMED30018024h1SMcG0021492 dd_Smed_v4_12583_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30018024h1SMcG0021492 dd_Smed_v4_12583_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30018024h1SMcG0021492 dd_Smed_v4_12583_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30018024h1SMcG0021492 dd_Smed_v6_12583_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
SMED30018024 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006513:1280..1656 +1569
Homology
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BLAST of SMED30018024 vs. Ensembl Xenopus
Match: arrb2 (arrestin beta 2 [Source:NCBI gene;Acc:100101741])

HSP 1 Score: 45.4394 bits (106), Expect = 2.898e-6
Identity = 27/72 (37.50%), Postives = 41/72 (56.94%), Query Frame = 2 
Query:   47 ISMSSDIQLELPFNLTHPNPEEDLT--VNTYDGLD--IFKNSLTFTDNYEPISSQAEQDDDLIFVDFARLKL 250
            +S   D+ +ELPF L HP P E+++  ++ Y   D  +  N + F  N+        QDDD++F DFARL+L
Sbjct:  276 VSRGGDVAVELPFVLMHPKPPENISRPLSEYPQTDAPVDTNLIEFDTNF-------AQDDDIVFEDFARLRL 340
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BLAST of SMED30018024 vs. Ensembl Cavefish
Match: arrb2b (arrestin, beta 2b [Source:ZFIN;Acc:ZDB-GENE-040426-1332])

HSP 1 Score: 45.0542 bits (105), Expect = 2.709e-6
Identity = 24/68 (35.29%), Postives = 33/68 (48.53%), Query Frame = 2 
Query:   47 ISMSSDIQLELPFNLTHPNPEEDLTVNTYDGLDIFKNSLTFTDNYEPISSQAEQDDDLIFVDFARLKL 250
            +S   D+ +ELPF L HP P E  +     G+        +  N+        QDDD +F DFARL+L
Sbjct:  323 VSRGGDVSVELPFVLMHPKPSEQPSSRPQSGM--------YATNF-------SQDDDFVFEDFARLRL 375
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BLAST of SMED30018024 vs. Ensembl Nematostella
Match: EDO27814 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7T880])

HSP 1 Score: 44.669 bits (104), Expect = 2.320e-7
Identity = 27/76 (35.53%), Postives = 38/76 (50.00%), Query Frame = 2 
Query:   47 ISMSSDIQLELPFNLTHPNPEEDLTVNTYDGLDIFKNSLTFTDN----YEPISSQAEQDDDLIFVDFARLKLDVKD 262
            ++   D+ LELPF L+HP P ED T           N     D+    ++    + + +DDLIF DFARL+L   D
Sbjct:   18 VAYGGDLTLELPFMLSHPKPCEDPTPPPTPAKQPSNNEQAAVDHNLIDFDTDGPEQDNNDDLIFEDFARLRLKGSD 93
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BLAST of SMED30018024 vs. Ensembl Medaka
Match: arrb2a (arrestin beta 2 [Source:NCBI gene;Acc:101159286])

HSP 1 Score: 43.5134 bits (101), Expect = 8.631e-6
Identity = 23/68 (33.82%), Postives = 32/68 (47.06%), Query Frame = 2 
Query:   47 ISMSSDIQLELPFNLTHPNPEEDLTVNTYDGLDIFKNSLTFTDNYEPISSQAEQDDDLIFVDFARLKL 250
            +S   D+ +ELPF L HP P E        G    +   +  +     +    QDDD +F DFARL+L
Sbjct:  330 VSRGGDVSVELPFILMHPKPVEPPLSRPQSGRSTRRRHYSGLELVSMETDHVSQDDDFVFEDFARLRL 397
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BLAST of SMED30018024 vs. Planmine SMEST
Match: SMESG000078454.1 (SMESG000078454.1)

HSP 1 Score: 142.895 bits (359), Expect = 4.445e-42
Identity = 70/70 (100.00%), Postives = 70/70 (100.00%), Query Frame = 2 
Query:   56 SSDIQLELPFNLTHPNPEEDLTVNTYDGLDIFKNSLTFTDNYEPISSQAEQDDDLIFVDFARLKLDVKDF 265
            SSDIQLELPFNLTHPNPEEDLTVNTYDGLDIFKNSLTFTDNYEPISSQAEQDDDLIFVDFARLKLDVKDF
Sbjct:  351 SSDIQLELPFNLTHPNPEEDLTVNTYDGLDIFKNSLTFTDNYEPISSQAEQDDDLIFVDFARLKLDVKDF 420
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BLAST of SMED30018024 vs. Planmine SMEST
Match: SMESG000006894.1 (SMESG000006894.1)

HSP 1 Score: 46.2098 bits (108), Expect = 6.566e-7
Identity = 31/75 (41.33%), Postives = 41/75 (54.67%), Query Frame = 2 
Query:   56 SSDIQLELPFNLTHPNPEEDLTV--------NTYD--GLDIFKNSLTFTDNYEPISSQAEQDDDLIFVDFARLKL 250
            +SDIQLE+PF LTHPNP+ D  +        N  D  G+D   N L F           +Q+++ IF DFARL+L
Sbjct:  341 TSDIQLEIPFILTHPNPDSDFRIPNSVSNDLNPLDSNGIDTDFNKLQF-----------KQEEEFIFEDFARLRL 404
[Close]
BLAST of SMED30018024 vs. Planmine SMEST
Match: SMESG000006894.1 (SMESG000006894.1)

HSP 1 Score: 46.2098 bits (108), Expect = 6.968e-7
Identity = 31/75 (41.33%), Postives = 41/75 (54.67%), Query Frame = 2 
Query:   56 SSDIQLELPFNLTHPNPEEDLTV--------NTYD--GLDIFKNSLTFTDNYEPISSQAEQDDDLIFVDFARLKL 250
            +SDIQLE+PF LTHPNP+ D  +        N  D  G+D   N L F           +Q+++ IF DFARL+L
Sbjct:  344 TSDIQLEIPFILTHPNPDSDFRIPNSVSNDLNPLDSNGIDTDFNKLQF-----------KQEEEFIFEDFARLRL 407
The following BLAST results are available for this feature:
BLAST of SMED30018024 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 SMED30018024 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 SMED30018024 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 SMED30018024 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 SMED30018024 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 1
Match NameE-valueIdentityDescription
arrb22.898e-637.50arrestin beta 2 [Source:NCBI gene;Acc:100101741][more]
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BLAST of SMED30018024 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 SMED30018024 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 SMED30018024 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 SMED30018024 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 1
Match NameE-valueIdentityDescription
arrb2b2.709e-635.29arrestin, beta 2b [Source:ZFIN;Acc:ZDB-GENE-040426... [more]
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BLAST of SMED30018024 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 SMED30018024 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 SMED30018024 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO278142.320e-735.53Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30018024 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 1
Match NameE-valueIdentityDescription
arrb2a8.631e-633.82arrestin beta 2 [Source:NCBI gene;Acc:101159286][more]
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BLAST of SMED30018024 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000078454.14.445e-42100.00SMESG000078454.1[more]
SMESG000006894.16.566e-741.33SMESG000006894.1[more]
SMESG000006894.16.968e-741.33SMESG000006894.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30018024 ID=SMED30018024|Name=SMED30018024|organism=Schmidtea mediterranea sexual|type=transcript|length=320bp
GTTTAAAGGAATATATAATTTTTATTTTAAATAGTTATTATTTGATATTT
CTATGAGCAGTGATATTCAATTGGAACTACCATTTAACCTCACCCATCCA
AACCCCGAAGAAGATCTCACAGTGAATACTTATGACGGATTAGATATTTT
CAAGAATTCCTTGACTTTCACTGACAATTATGAACCGATTAGTAGTCAGG
CTGAACAGGACGATGATTTAATATTCGTGGATTTCGCAAGACTGAAATTA
GATGTAAAGGACTTTGAAGAAAATAACAACAATAATAAATAACCTTTTTG
TAAATATTTTGAAATTTTCC
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR014752Arrestin_C
Vocabulary: biological process
TermDefinition
GO:0007165signal transduction
GO:0032088negative regulation of NF-kappaB transcription factor activity
GO:0032226positive regulation of synaptic transmission, dopaminergic
GO:0032691negative regulation of interleukin-1 beta production
GO:0032695negative regulation of interleukin-12 production
GO:0032715negative regulation of interleukin-6 production
GO:0032720negative regulation of tumor necrosis factor production
GO:0033138positive regulation of peptidyl-serine phosphorylation
GO:0034122negative regulation of toll-like receptor signaling pathway
GO:0034260negative regulation of GTPase activity
GO:0034392negative regulation of smooth muscle cell apoptotic process
GO:0042699follicle-stimulating hormone signaling pathway
GO:0043154negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
GO:0043161proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0045953negative regulation of natural killer cell mediated cytotoxicity
GO:0050731positive regulation of peptidyl-tyrosine phosphorylation
GO:0050965detection of temperature stimulus involved in sensory perception of pain
GO:0051897positive regulation of protein kinase B signaling
GO:0051928positive regulation of calcium ion transport
GO:0060326cell chemotaxis
GO:0060765regulation of androgen receptor signaling pathway
GO:0070374positive regulation of ERK1 and ERK2 cascade
GO:0090201negative regulation of release of cytochrome c from mitochondria
GO:2000573positive regulation of DNA biosynthetic process
GO:0001932regulation of protein phosphorylation
GO:0001933negative regulation of protein phosphorylation
GO:0001934positive regulation of protein phosphorylation
GO:0002031G-protein coupled receptor internalization
GO:0002032desensitization of G-protein coupled receptor protein signaling pathway by arrestin
GO:0002092positive regulation of receptor internalization
GO:0006366transcription from RNA polymerase II promoter
GO:0006810transport
GO:0006897endocytosis
GO:0007179transforming growth factor beta receptor signaling pathway
GO:0007186G-protein coupled receptor signaling pathway
GO:0007420brain development
GO:0007628adult walking behavior
GO:0008277regulation of G-protein coupled receptor protein signaling pathway
GO:0009968negative regulation of signal transduction
GO:0010628positive regulation of gene expression
GO:0015031protein transport
GO:0016567protein ubiquitination
GO:0030817regulation of cAMP biosynthetic process
GO:0030820regulation of cAMP catabolic process
GO:0031397negative regulation of protein ubiquitination
GO:0031398positive regulation of protein ubiquitination
GO:0031623receptor internalization
GO:2000727positive regulation of cardiac muscle cell differentiation
Vocabulary: molecular function
TermDefinition
GO:0031702type 1 angiotensin receptor binding
GO:0031748D1 dopamine receptor binding
GO:0031762follicle-stimulating hormone receptor binding
GO:0031826type 2A serotonin receptor binding
GO:0031859platelet activating factor receptor binding
GO:0032403protein complex binding
GO:0032947protein complex scaffold
GO:0043422protein kinase B binding
GO:0051019mitogen-activated protein kinase binding
GO:007188914-3-3 protein binding
GO:0001664G-protein coupled receptor binding
GO:0005102signaling receptor binding
GO:0005515protein binding
GO:0019899enzyme binding
GO:0019904protein domain specific binding
GO:0030276clathrin binding
GO:0031625ubiquitin protein ligase binding
GO:0031691alpha-1A adrenergic receptor binding
GO:0031692alpha-1B adrenergic receptor binding
GO:0031701angiotensin receptor binding
Vocabulary: cellular component
TermDefinition
GO:0043197dendritic spine
GO:0043231intracellular membrane-bounded organelle
GO:0045211postsynaptic membrane
GO:0005622intracellular
GO:0005634nucleus
GO:0005737cytoplasm
GO:0005886plasma membrane
GO:0005905clathrin-coated pit
GO:0014069postsynaptic density
GO:0016020membrane
GO:0016323basolateral plasma membrane
GO:0030139endocytic vesicle
GO:0031410cytoplasmic vesicle