UV excision repair protein RAD23

Overview
NameUV excision repair protein RAD23
Smed IDSMED30020884
Length (bp)874
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 UV excision repair protein RAD23 (SMED30020884) t-SNE clustered cells

Violin plots show distribution of expression levels for UV excision repair protein RAD23 (SMED30020884) 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 UV excision repair protein RAD23 (SMED30020884) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for UV excision repair protein RAD23 (SMED30020884) 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.
Sort Descending | Sort Ascending | Only Non-Zero Values | Tile/Chart | Reset

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




SMED30020884

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



PAGE Curations: 8

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30020884SMESG000077827.1 SmedASXL_005930SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
epidermisSMED30020884SMESG000077827.1 dd_Smed_v4_10053_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30020884SMESG000077827.1 dd_Smed_v4_10053_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30020884SMESG000077827.1 dd_Smed_v4_10053_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30020884SMESG000077827.1 dd_Smed_v4_10053_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017
whole organism asexual adult single-cell RNA-sequencing evidence
neoblastSMED30020884SMESG000077827.1 SMED_20631_V2_1GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30020884SMESG000077827.1 SMED_20631_V2_1GPL14150PMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30020884SMESG000077827.1 SmWIOct06_029267GPL14150_gene_modelsPMID:22385657
Wagner et al., 2012
whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Homology
BLAST of UV excision repair protein RAD23 vs. Planmine SMEST
Match: SMESG000077827.1 (SMESG000077827.1)

HSP 1 Score: 396.741 bits (1018), Expect = 7.658e-141
Identity = 227/228 (99.56%), Postives = 228/228 (100.00%), Query Frame = 1
Query:  145 DIDSEKSVGYLKSKIEKEYGSEYPADRLKLILKGKVLSDEQIINTLLYAEKSQILLMIVRDMNHSDKNNCSNSKKADSTLKHVSKSESDESPVNLAXXXXXXXXXXXXXXXFFINLPEDSDLDGIMNILKEHMQTDPNIVKCVVEDDYSDSDMSSILSNIEFDQNLSDDTNESDESLDEDGTREILTQNDLDNIERISSMGFNKEQVIEAYLASGKNMEAAVTFLLNK 828
            DIDSEKSVGYLKSKIEKEYGSEYPADRLKLILKGKVLSDEQIINTLLYAEKSQILLMIVRDMNHSDKNNCSNSKKADSTLKHVSKSESDESPVNLAETIEIEDGDETETVEFFINLPEDSDLDGIMNILKEHMQTDPNIVKCVVEDDYSDSDMSSILSNIEFDQNLSDDTNESDESLDE+GTREILTQNDLDNIERISSMGFNKEQVIEAYLASGKNMEAAVTFLLNK
Sbjct:   16 DIDSEKSVGYLKSKIEKEYGSEYPADRLKLILKGKVLSDEQIINTLLYAEKSQILLMIVRDMNHSDKNNCSNSKKADSTLKHVSKSESDESPVNLAETIEIEDGDETETVEFFINLPEDSDLDGIMNILKEHMQTDPNIVKCVVEDDYSDSDMSSILSNIEFDQNLSDDTNESDESLDEEGTREILTQNDLDNIERISSMGFNKEQVIEAYLASGKNMEAAVTFLLNK 243          
BLAST of UV excision repair protein RAD23 vs. Planmine SMEST
Match: SMESG000007293.1 (SMESG000007293.1)

HSP 1 Score: 50.8322 bits (120), Expect = 4.329e-7
Identity = 30/97 (30.93%), Postives = 52/97 (53.61%), Query Frame = 1
Query:  145 DIDSEKSVGYLKSKIEKEYGSEYPADRLKLILKGKVLSDEQIINTLLYAEKSQILLMIVRDMNHS----DKNNCSNSKKADSTLKHVSKSESDESPV 423
            ++D + +V  LK KIEK  G+ YP  +LKLI  GK++ D++++      EKS I++M+++    S     K     +K +  T+  V K + +  P 
Sbjct:   16 EVDDDDTVLALKEKIEKCEGNGYPVPQLKLICSGKIMDDDKLLKEYKLTEKSFIVVMVMKSTVCSTEVESKGEVDTAKTSSQTVAEVPKEKGENKPC 112          
The following BLAST results are available for this feature:
BLAST of UV excision repair protein RAD23 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 UV excision repair protein RAD23 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 UV excision repair protein RAD23 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 UV excision repair protein RAD23 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 UV excision repair protein RAD23 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 UV excision repair protein RAD23 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 UV excision repair protein RAD23 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 UV excision repair protein RAD23 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 UV excision repair protein RAD23 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 UV excision repair protein RAD23 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 UV excision repair protein RAD23 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 UV excision repair protein RAD23 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 UV excision repair protein RAD23 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 UV excision repair protein RAD23 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000077827.17.658e-14199.56SMESG000077827.1[more]
SMESG000007293.14.329e-730.93SMESG000007293.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30020884 ID=SMED30020884|Name=UV excision repair protein RAD23|organism=Schmidtea mediterranea sexual|type=transcript|length=874bp
TTTTAATTCTTCATTATTTTATTTATTTAATAATTTTTTAAATCGGCAAA
ATTAGCTTGTTTAAATAATGGAGTTGTGATAAATTTAATTTATAGCATTA
TGCAATTAACTTTTAAAACTCTTAAGAAAAAAGTTTTCAAGGTAGACATT
GATAGTGAAAAATCTGTGGGCTATTTAAAATCAAAAATAGAAAAGGAATA
TGGATCGGAATATCCTGCTGATCGTCTTAAATTAATTTTGAAAGGGAAAG
TATTATCTGATGAACAAATAATTAACACTCTTCTGTATGCAGAGAAAAGT
CAAATTTTGTTGATGATTGTCAGAGATATGAATCATTCTGATAAAAATAA
TTGTTCTAATTCGAAAAAAGCAGATTCTACGTTAAAACATGTTTCTAAAT
CTGAATCAGACGAATCTCCTGTTAATCTAGCTGAAACGATTGAGATTGAA
GATGGAGATGAAACTGAAACCGTTGAGTTTTTTATTAATTTGCCCGAAGA
TAGTGATTTAGATGGAATAATGAATATTCTTAAAGAACATATGCAAACTG
ACCCAAATATTGTAAAATGTGTCGTAGAAGACGATTACAGTGATTCAGAT
ATGTCTTCTATTTTATCAAATATAGAATTTGATCAGAACTTATCTGATGA
CACCAATGAGTCCGATGAATCTTTGGATGAAGATGGGACACGAGAAATTT
TAACCCAAAATGACTTAGATAATATCGAACGAATCTCATCAATGGGATTT
AATAAAGAACAAGTCATAGAAGCGTATTTAGCATCGGGGAAAAATATGGA
AGCAGCTGTTACATTTCTGTTGAATAAATGAAATTTTGTATATTTATGCT
TTAAATAAAATTATAAAATTCCCG
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protein sequence of SMED30020884-orf-1

>SMED30020884-orf-1 ID=SMED30020884-orf-1|Name=SMED30020884-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=244bp
MQLTFKTLKKKVFKVDIDSEKSVGYLKSKIEKEYGSEYPADRLKLILKGK
VLSDEQIINTLLYAEKSQILLMIVRDMNHSDKNNCSNSKKADSTLKHVSK
SESDESPVNLAETIEIEDGDETETVEFFINLPEDSDLDGIMNILKEHMQT
DPNIVKCVVEDDYSDSDMSSILSNIEFDQNLSDDTNESDESLDEDGTREI
LTQNDLDNIERISSMGFNKEQVIEAYLASGKNMEAAVTFLLNK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: cellular component
TermDefinition
GO:0042025host cell nucleus
GO:0005634nucleus
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000429neoblast
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR004806Rad23
IPR015940UBA
IPR000626Ubiquitin-like_dom
IPR009060UBA-like_sf
IPR029071Ubiquitin-like_domsf
Vocabulary: biological process
TermDefinition
GO:0006289nucleotide-excision repair
GO:0043161proteasome-mediated ubiquitin-dependent protein catabolic process
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
GO:0003684damaged DNA binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR004806UV excision repair protein Rad23PRINTSPR01839RAD23PROTEINcoord: 216..230
score: 43.03
coord: 199..215
score: 27.01
coord: 143..165
score: 16.8
coord: 231..243
score: 34.94
IPR015940Ubiquitin-associated domainSMARTSM00165uba_6coord: 205..242
e-value: 6.4E-7
score: 39.0
IPR015940Ubiquitin-associated domainPFAMPF00627UBAcoord: 205..240
e-value: 3.2E-9
score: 36.5
IPR015940Ubiquitin-associated domainPROSITEPS50030UBAcoord: 191..243
score: 14.089
IPR000626Ubiquitin-like domainSMARTSM00213ubq_7coord: 1..74
e-value: 3.2E-11
score: 53.3
IPR000626Ubiquitin-like domainPFAMPF00240ubiquitincoord: 3..73
e-value: 5.3E-13
score: 48.5
IPR000626Ubiquitin-like domainPROSITEPS50053UBIQUITIN_2coord: 1..73
score: 16.015
NoneNo IPR availableGENE3DG3DSA:3.10.20.90coord: 1..78
e-value: 1.9E-14
score: 55.2
NoneNo IPR availableGENE3DG3DSA:1.10.8.10coord: 200..243
e-value: 9.9E-14
score: 53.1
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 82..108
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 176..196
NoneNo IPR availablePANTHERPTHR10621UV EXCISION REPAIR PROTEIN RAD23coord: 1..104
NoneNo IPR availablePANTHERPTHR10621:SF0AT15685P-RELATEDcoord: 113..241
NoneNo IPR availablePANTHERPTHR10621:SF0AT15685P-RELATEDcoord: 1..104
NoneNo IPR availablePANTHERPTHR10621UV EXCISION REPAIR PROTEIN RAD23coord: 113..241
NoneNo IPR availableCDDcd14281UBA2_Rad23_likecoord: 205..241
e-value: 2.38926E-9
score: 49.4319
NoneNo IPR availableCDDcd01805Ubl_Rad23coord: 1..73
e-value: 4.78366E-17
score: 71.049
IPR009060UBA-like superfamilySUPERFAMILYSSF46934UBA-likecoord: 191..242
IPR029071Ubiquitin-like domain superfamilySUPERFAMILYSSF54236Ubiquitin-likecoord: 1..73