RING-type domain-containing protein

Overview
NameRING-type domain-containing protein
Smed IDSMED30013773
Length (bp)1629
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 RING-type domain-containing protein (SMED30013773) t-SNE clustered cells

Violin plots show distribution of expression levels for RING-type domain-containing protein (SMED30013773) 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 RING-type domain-containing protein (SMED30013773) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for RING-type domain-containing protein (SMED30013773) 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



SMED30013773

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
whole organismSMED30013773h1SMcG0014614 Contig13588uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
whole organismSMED30013773h1SMcG0014614 Contig13588newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of RING-type domain-containing protein vs. Planmine SMEST
Match: SMESG000009171.1 (SMESG000009171.1)

HSP 1 Score: 451.44 bits (1160), Expect = 8.068e-158
Identity = 273/274 (99.64%), Postives = 273/274 (99.64%), Query Frame = 3 
Query:   54 MSLTSRISNLKDGFLKRKVLCKDILNISFTKFMKMIDECNIWSIDIAMKTKSQNKMNFFVIPSSVNGLFWRIRARIEFKKLDIESGNIIKVRXXXXXXXXXXXXXXXXXXYMNEYDNIGLQYSMLVTRVDVNNIRRXXXXXXXXXXXXXXXXICLNQPLDVILPCGHGYCSKCTKEWXXXXXXXXXXXXXWEVLQVANHYCWPNIHSNTSTVESDSMISHVYNGGKFSCPECRIECSSDSELWNMLDRPKSGDCNSEMNKALENLIENLNCKRK 875
            MSLTSRISNLKDGFLKRKVLCKDILNISFTKFMKMIDECNIWSIDIAMKTKSQNKMNFFVIPSSVNGLFWRIRARIEF KLDIESGNIIKVRLLKLHQFLLLHQQIQLIIYMNEYDNIGLQYSMLVTRVDVNNIRRLSTSSDTLTTESTECSICLNQPLDVILPCGHGYCSKCTKEWSNSSSNMNFSASNWEVLQVANHYCWPNIHSNTSTVESDSMISHVYNGGKFSCPECRIECSSDSELWNMLDRPKSGDCNSEMNKALENLIENLNCKRK
Sbjct:    1 MSLTSRISNLKDGFLKRKVLCKDILNISFTKFMKMIDECNIWSIDIAMKTKSQNKMNFFVIPSSVNGLFWRIRARIEFNKLDIESGNIIKVRLLKLHQFLLLHQQIQLIIYMNEYDNIGLQYSMLVTRVDVNNIRRLSTSSDTLTTESTECSICLNQPLDVILPCGHGYCSKCTKEWSNSSSNMNFSASNWEVLQVANHYCWPNIHSNTSTVESDSMISHVYNGGKFSCPECRIECSSDSELWNMLDRPKSGDCNSEMNKALENLIENLNCKRK 274
The following BLAST results are available for this feature:
BLAST of RING-type domain-containing 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 RING-type domain-containing 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 RING-type domain-containing 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 RING-type domain-containing 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 RING-type domain-containing 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 RING-type domain-containing 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 RING-type domain-containing 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 RING-type domain-containing 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 RING-type domain-containing 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 RING-type domain-containing 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 RING-type domain-containing 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 RING-type domain-containing 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 RING-type domain-containing 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 RING-type domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000009171.18.068e-15899.64SMESG000009171.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013773 ID=SMED30013773|Name=RING-type domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=1629bp
GTTAATTTTAAAACTTTTTAATTGTGATAAGTGAAACAATTTTTCTCATT
AAAATGAGTTTAACTAGTCGCATCAGTAATTTGAAAGACGGATTTTTAAA
ACGTAAAGTCCTATGTAAAGATATTTTAAATATTTCTTTTACAAAATTCA
TGAAGATGATTGATGAATGCAATATATGGTCTATTGATATAGCCATGAAA
ACCAAATCTCAAAATAAAATGAATTTTTTCGTCATACCGTCATCTGTTAA
TGGTTTATTTTGGCGAATAAGAGCTAGAATAGAATTTAAAAAATTGGATA
TTGAAAGTGGAAATATTATAAAAGTTCGATTATTAAAATTGCATCAATTT
CTTTTGTTGCATCAACAAATCCAATTGATAATTTATATGAATGAATATGA
CAATATTGGATTACAGTATTCTATGTTAGTTACAAGAGTTGATGTAAACA
ATATCCGTCGATTATCAACATCATCTGACACATTGACTACTGAGTCGACT
GAATGCTCTATTTGTCTCAATCAACCACTGGATGTGATATTACCCTGTGG
TCATGGATATTGTTCGAAATGCACAAAAGAATGGAGTAATTCAAGTAGTA
ATATGAACTTTTCCGCTTCGAATTGGGAAGTATTACAAGTGGCAAATCAT
TATTGTTGGCCTAACATCCATTCCAACACGTCAACGGTTGAATCAGACTC
CATGATAAGTCATGTATATAATGGAGGTAAATTCAGTTGTCCTGAGTGTC
GAATAGAGTGCTCATCAGACAGTGAATTGTGGAACATGCTTGATAGGCCG
AAATCCGGTGACTGTAATTCAGAAATGAATAAAGCATTGGAAAATTTGAT
AGAGAACTTGAATTGCAAGAGAAAATAAATCCATTCCATATTTCATTGTA
CTTTTCCGAATAGTAAATTGTTTTAATAACAAAAGATTCTTATTTTAATG
AATTTTATTATTGATGCTGGTTCTGTGAATATTCGGTTTATCGATTATTT
TATTATTGATTTGATCTCTGTCATCGGAATATTTGGTTTGTAAACGAATT
ATCGGCAATTCATTGATTATTTTTTCATGTTAGAAAATTTCCTTATTTTT
TGGCAATTTTAATAAAAATATCCATTTAGAATGTTTAGGTTACTTTTTAG
CAAGATATTGAGATGAGTTTTTGAATTAACTGTTTTTGATAAAAATTCTA
AATTCAGTAAAAATAGTGTTTATCGGTGAGGGTAAAGGTTTGTCGATTCG
TGTTTGAATGGCTGTTTACGGGTAAAACTCATCGAAATCTTTGAATAGAC
AAGGAGACAATTATGTTAAATTTACGGCTACATATTAATAAATTGATAAT
ACGTTATTGCTTGATATTTATTAGAATAAGTCAATTAGAATATGGGTTTT
GTTGTGTACATTCATAGGGGCAAATGTCTTTAAGGGATAAATTTCGTTTT
TTAGTTAATATGTTATTTATTTAGCTATTTAATGACATGTAATATTTTTA
TTATGATCTTTTCAATTTGTTGACGCAAAAGATAGAAAATGGAAAGTAAA
AAGAAACGACATTTTATTGTAGAAATTGCAATATTGATTTGTTCCGTGAC
TTATTTTGTAATAAATCACGCTTATTAAA
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protein sequence of SMED30013773-orf-1

>SMED30013773-orf-1 ID=SMED30013773-orf-1|Name=SMED30013773-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=275bp
MSLTSRISNLKDGFLKRKVLCKDILNISFTKFMKMIDECNIWSIDIAMKT
KSQNKMNFFVIPSSVNGLFWRIRARIEFKKLDIESGNIIKVRLLKLHQFL
LLHQQIQLIIYMNEYDNIGLQYSMLVTRVDVNNIRRLSTSSDTLTTESTE
CSICLNQPLDVILPCGHGYCSKCTKEWSNSSSNMNFSASNWEVLQVANHY
CWPNIHSNTSTVESDSMISHVYNGGKFSCPECRIECSSDSELWNMLDRPK
SGDCNSEMNKALENLIENLNCKRK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000136whole organism
Vocabulary: INTERPRO
TermDefinition
IPR001841Znf_RING
IPR013083Znf_RING/FYVE/PHD
IPR018957Znf_C3HC4_RING-type
Vocabulary: molecular function
TermDefinition
GO:0008270zinc ion binding
GO:0005515protein binding
GO:0046872metal ion binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 255..274
NoneNo IPR availablePANTHERPTHR12109FAMILY NOT NAMEDcoord: 16..182
NoneNo IPR availablePANTHERPTHR12109:SF3RING FINGER PROTEIN 141coord: 16..182
NoneNo IPR availableSUPERFAMILYSSF57850RING/U-boxcoord: 142..183
IPR001841Zinc finger, RING-typeSMARTSM00184ring_2coord: 151..232
e-value: 2.7E-6
score: 36.9
IPR001841Zinc finger, RING-typePROSITEPS50089ZF_RING_2coord: 151..233
score: 9.303
IPR018957Zinc finger, C3HC4 RING-typePFAMPF00097zf-C3HC4coord: 151..182
e-value: 1.5E-6
score: 27.9