Ubiquitin-like protein

Overview
NameUbiquitin-like protein
Smed IDSMED30005782
Length (bp)584
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




SMED30005782

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
neuronSMED30005782SMESG000036610.1 dd_Smed_v4_5328_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30005782SMESG000036610.1 dd_Smed_v4_5328_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
anterior region of the whole animalSMED30005782SMESG000036610.1 dd_Smed_v4_5328_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
whole organism asexual adult single-cell RNA-sequencing evidence
headSMED30005782SMESG000036610.1 dd_Smed_v6_5328_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
headSMED30005782SMESG000036610.1 OX_Smed_1.0.21290ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
BLAST of Ubiquitin-like protein vs. Planmine SMEST
Match: SMESG000036610.1 (SMESG000036610.1)

HSP 1 Score: 108.612 bits (270), Expect = 7.340e-36
Identity = 65/86 (75.58%), Postives = 67/86 (77.91%), Query Frame = 2
Query:    5 METTADSXXXXXXXXXXVSGKXGTLEVGGEKXLXHXXCEYIFNNWPXDWDEKPDXNILXLXYHGRFLNFDMKLKDXNLPXGLVVXH 262
            METTADSLLMVNLKLLLVSGK  T+E      +    CEYIFNNWP DWDEKPD NIL L YHGRFLNFDMKLKD NLP GLVV H
Sbjct:    1 METTADSLLMVNLKLLLVSGKSCTIEFASLTTVSEI-CEYIFNNWPNDWDEKPDDNILRLIYHGRFLNFDMKLKDLNLPDGLVVMH 85          

HSP 2 Score: 59.6918 bits (143), Expect = 7.340e-36
Identity = 28/33 (84.85%), Postives = 28/33 (84.85%), Query Frame = 3
Query:  267 IFRKSXPQPGTQXDXKKSKXPSHSWFRSCCCIC 365
            IFRKS PQPGTQ D KKSK PSHS FRSCCCIC
Sbjct:   87 IFRKSIPQPGTQEDVKKSKSPSHSCFRSCCCIC 119          
BLAST of Ubiquitin-like protein vs. Planmine SMEST
Match: SMESG000054551.1 (SMESG000054551.1)

HSP 1 Score: 56.6102 bits (135), Expect = 1.026e-10
Identity = 24/54 (44.44%), Postives = 33/54 (61.11%), Query Frame = 2
Query:  116 CEYIFNNWPXDWDEKPDXNILXLXYHGRFLNFDMKLKDXNLPXGLVVXHXDIQE 277
            C +I+NNWP +W +KPD NIL L Y GRF   D  L++ N+     V H  ++E
Sbjct:   29 CNHIYNNWPEEWTDKPDQNILRLIYQGRFFMDDTTLENMNIASETTVIHLVMRE 82          
The following BLAST results are available for this feature:
BLAST of Ubiquitin-like 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 Ubiquitin-like 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 Ubiquitin-like 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 Ubiquitin-like 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 Ubiquitin-like 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 Ubiquitin-like 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 Ubiquitin-like 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 Ubiquitin-like protein 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 Ubiquitin-like 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 Ubiquitin-like 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 Ubiquitin-like 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 Ubiquitin-like 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 Ubiquitin-like 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 Ubiquitin-like protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000036610.17.340e-3675.58SMESG000036610.1[more]
SMESG000054551.11.026e-1044.44SMESG000054551.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30005782 ID=SMED30005782|Name=Ubiquitin-like protein|organism=Schmidtea mediterranea sexual|type=transcript|length=584bp
ACATATGGAAACAACTGCAGACAGTCTTTTGATGGTGAACTTAAAACTTC
TTCTGGTTAGTGGAAAAAGNGGGACTCTTGAAGTGGGCGGGGAAAAACNC
CTNTNTCATANTATNTGTGAATATATTTTTAATAATTGGCCCAANGATTG
GGATGAAAAACCTGATGANAATATTTTAANATTAATNTATCATGGTAGAT
TTCTAAATTTTGATATGAAATTAAAAGATCNCAATTTACCTGANGGTCTC
GTAGTAANGCACTNAGATATTCAGGAAAAGCNTTCCTCAACCTGGCACNC
AANAAGACNNTAAGAAGAGCAAGNCTCCCAGTCATTCTTGGTTCAGGTCT
TGCTGTTGCATATGCTANANTTTTGAAANACNGCAACAGCTAAAACNACT
GTNTGANANGAACCCAACTNGATATCCTATCGCATACTGCACAANNGCAT
CTNATCATNGACNNACAAATNTTTTTNTGNNGCCGATACACANNCTGTCA
CCANTTAATTAATTAATATNTACCANTCACNTACCAACCCGCCCATTCGN
ATTTCTTGAAATCNCNTCNACCNTCCGNACATCA
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protein sequence of SMED30005782-orf-1

>SMED30005782-orf-1 ID=SMED30005782-orf-1|Name=SMED30005782-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=104bp
HMETTADSLLMVNLKLLLVSGKXGTLEVGGEKXXXHXXCEYIFNNWPXDW
DEKPDXNILXLXYHGRFLNFDMKLKDXNLPXGLVVXHXDIQEKXSSTWHX
XRX*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0005886plasma membrane
GO:0016020membrane
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000101muscle cell
PLANA:0000140anterior region of the whole animal
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR039540UBL3-like_ubiquitin_dom
IPR040015UBL3-like
IPR000626Ubiquitin-like_dom
IPR029071Ubiquitin-like_domsf
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableGENE3DG3DSA:3.10.20.90coord: 1..96
e-value: 3.8E-24
score: 86.5
NoneNo IPR availablePANTHERPTHR13169:SF0UBIQUITIN-LIKE PROTEIN 3coord: 11..100
NoneNo IPR availableCDDcd17048Ubl_UBL3coord: 19..90
e-value: 1.27693E-21
score: 78.9596
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..21
score: 0.484
IPR039540UBL3-like, ubiquitin domainPFAMPF13881Rad60-SLD_2coord: 11..100
e-value: 1.3E-16
score: 60.6
IPR040015UBL3-likePANTHERPTHR13169UBIQUITIN-LIKE PROTEIN 3 HCG-1 PROTEINcoord: 11..100
IPR000626Ubiquitin-like domainPROSITEPS50053UBIQUITIN_2coord: 12..85
score: 9.417
IPR029071Ubiquitin-like domain superfamilySUPERFAMILYSSF54236Ubiquitin-likecoord: 11..96