RING-type domain-containing protein

Overview
NameRING-type domain-containing protein
Smed IDSMED30031123
Length (bp)1179
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 (SMED30031123) t-SNE clustered cells

Violin plots show distribution of expression levels for RING-type domain-containing protein (SMED30031123) 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 (SMED30031123) 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 (SMED30031123) 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




SMED30031123

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parenchymal cellSMED30031123h1SMcG0010277 dd_Smed_v4_4338_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior sideSMED30031123h1SMcG0010277 dd_Smed_v4_4338_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
posterior muscle cellSMED30031123h1SMcG0010277 dd_Smed_v4_4338_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 RING-type domain-containing protein vs. Planmine SMEST
Match: SMESG000064076.1 (SMESG000064076.1)

HSP 1 Score: 442.965 bits (1138), Expect = 6.236e-157
Identity = 251/263 (95.44%), Postives = 255/263 (96.96%), Query Frame = 3
Query:  336 LDNIVITEEPSTSSITRVTTNSLSRKFHSFSCTGDRSVNLYRKSSLNELETIYFGLSRNETLDAGSRKELSTQSHNLSMLEIQTPRNFSIESSDIDKNRILYEDLFNFIQNFSIYDSQFLYHIRKSICSESIGILSEMNGFRKDLLIFSSLFYYFSNHSICNIEQLLSQFWEINDKRLQDGKFLRMXXXXXXXXXXXXXXXXXXXKVRTKRNLICAECGENSVSVLYLPCGHIIMCSECHGKLKFNKCKQCSCTIDEFHNVYF 1124
            L  +   ++PSTSSIT VTTNSLSRKFHSFSCTGDRSVNLYRKSSLNELETIYFGLSRNETLDAGS KELSTQSHNLSMLEIQTPRNFSIESSDIDKNRILYEDLFNFIQNFSIYDSQFLYHIRKSICSESIGILSEMNGFRKDLLIFSSLFYYFSNHSICNIEQLLSQFWEINDKRLQDGKFLRMIESNSRELNEL+ENISEILKVRTKRNLICAECGENSVSVLYLPCGHIIMCSECH KLKFNKCKQCSCTIDEFHNVYF
Sbjct:    9 LSKLSRKKKPSTSSITTVTTNSLSRKFHSFSCTGDRSVNLYRKSSLNELETIYFGLSRNETLDAGSSKELSTQSHNLSMLEIQTPRNFSIESSDIDKNRILYEDLFNFIQNFSIYDSQFLYHIRKSICSESIGILSEMNGFRKDLLIFSSLFYYFSNHSICNIEQLLSQFWEINDKRLQDGKFLRMIESNSRELNELKENISEILKVRTKRNLICAECGENSVSVLYLPCGHIIMCSECHRKLKFNKCKQCSCTIDEFHNVYF 271          
BLAST of RING-type domain-containing protein vs. Planmine SMEST
Match: SMESG000067789.1 (SMESG000067789.1)

HSP 1 Score: 75.0998 bits (183), Expect = 2.012e-15
Identity = 62/203 (30.54%), Postives = 103/203 (50.74%), Query Frame = 3
Query:  513 ETLDAGSRKELSTQSHNLSMLEIQTPRNFSIESSDIDKNRILYEDLFNFIQNFSIYDSQFLYHIRKSICSESIGILSEMNGFRKDLLIFSSLFYYFSNHSICNIEQLLSQFWEINDKRLQDGKFLRMXXXXXXXXXXXXXXXXXXXKVRTKRNLICAECGENSVSVLYLPCGHIIMCSECHGKLKFNKCKQCSCTIDEFHNVY 1121
            + L   S  E S ++ N +++  Q P    IE             + +FI  +  +  + + +I K   + SI  L ++  + K +L  SS   Y     + N + L   FW+  + RL + ++ R+ +   R+ + +E+ ++E L    KR L C+ C EN VSVLYLPCGH+I+CS+C  K    KC+ CS  I+E+H +Y
Sbjct:   20 KNLSKKSENENSVKTKNKTIISEQKPSMEFIE---------FKSTVEDFINTYDTFTDKEIINILKIFKNPSIEYLIDIFNYDKCILKLSSYLMYLDKTGMDN-DSLNEYFWDCMELRL-NPEYSRLFKEWIRKSDFIEDKLTEKLNDVKKRYLTCSICKENQVSVLYLPCGHVIVCSKCQDK-NNRKCQACSAPINEYHAIY 210          
BLAST of RING-type domain-containing protein vs. Planmine SMEST
Match: SMESG000032006.1 (SMESG000032006.1)

HSP 1 Score: 71.2478 bits (173), Expect = 2.594e-14
Identity = 52/162 (32.10%), Postives = 84/162 (51.85%), Query Frame = 3
Query:  645 DLFNFIQNFSIYDSQFLYHIRKSICSESIGILSEMNGFRKDLLIFSSLFYYFSNHSICNIEQLLSQFWEINDKRLQD--GKFLRMXXXXXXXXXXXXXXXXXXXKVRTKRNLICAECGENSVSVLYLPCGHIIMCSECHGKLKFNKCKQCSCTIDEFHNVYF 1124
            ++F+F++N+ I   + +  I KS  +E + IL E  G+ + +L  +S      N    ++E++   FW+  + RL    GK ++    N   +    + IS  L   +K  L C  C  N VS+LYLPCG I++CSEC+      KC+ C   +DE H +YF
Sbjct:   28 EIFDFLENYEILPLKTVQRIVKSFANEYVEILHEKFGYEQSVLKLASCVISI-NQIDESLERMNEIFWDCMNLRLDKSCGKIIKSWMLNIDRIVLDLKKISNKL---SKEYLTCCACQLNPVSILYLPCGDIVICSECYND-SVVKCQGCQRHVDEMHKIYF 184          
BLAST of RING-type domain-containing protein vs. Planmine SMEST
Match: SMESG000067788.1 (SMESG000067788.1)

HSP 1 Score: 69.3218 bits (168), Expect = 1.998e-13
Identity = 50/154 (32.47%), Postives = 73/154 (47.40%), Query Frame = 3
Query:  663 QNFSIYDSQFLYHIRKSICSESIGILSEMNGFRKDLLIFSSLFYYFSNHSICNIEQLLSQFWEINDKRLQDGKFLRMXXXXXXXXXXXXXXXXXXXKVRTKRNLICAECGENSVSVLYLPCGHIIMCSECHGKLKFNKCKQCSCTIDEFHNVYF 1124
            +N++  +S+ L  I K   + SI    E  G+ K +L   S F    N    N E L   FW   +    DG    M E                 K R K+ L C  C +NSVS+LYLPCGH++MC++C+ ++    C+ C  +I+EFH +Y 
Sbjct:   74 RNYAKLNSKILLEILKLFKNSSIKFCHETFGYNKKILKLCS-FLMERNKVNINHENLNDYFWSFMNLSQLDGIEKEMCEIV---------------KERNKQLLTCMGCQKNSVSILYLPCGHVVMCNKCY-QISTKHCQACGSSIEEFHVIYI 210          
BLAST of RING-type domain-containing protein vs. Planmine SMEST
Match: SMESG000031926.1 (SMESG000031926.1)

HSP 1 Score: 67.0106 bits (162), Expect = 8.137e-13
Identity = 56/168 (33.33%), Postives = 92/168 (54.76%), Query Frame = 3
Query:  621 DKNRILYEDLFNFIQNFSIYDSQFLYHIRKSICSESIGILSEMNGFRKDLLIFSSLFYYFSNHSICNIEQLLSQFWEINDKRLQDGKFLRMXXXXXXXXXXXXXXXXXXXKVRTKRNLICAECGENSVSVLYLPCGHIIMCSECHGKLKFNKCKQCSCTIDEFHNVYF 1124
            DK  + +  +  F+ + + +D  FL  + KS   ESI  LS++ G+   +L  SS     ++    +    L  FW   + R+  G++ ++I+     ++ L++NI++ LK  T+  L C+ C  N VSVLYLPCGHI++CS C  K    +C+ C+  IDE+H VY 
Sbjct:   35 DKWCLTFSIIEKFLSSTNGFDLIFLNKLNKSFNHESIENLSKLFGYNHAMLKLSSCVISLNDIKPTDFNTNLV-FWSCMEFRV--GQYQKLIQYFMANVDNLQQNINDKLKEATRLFLTCSCCETNQVSVLYLPCGHIVVCSSCF-KSTTRRCESCAVDIDEYHFVYL 198          
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: 5
Match NameE-valueIdentityDescription
SMESG000064076.16.236e-15795.44SMESG000064076.1[more]
SMESG000067789.12.012e-1530.54SMESG000067789.1[more]
SMESG000032006.12.594e-1432.10SMESG000032006.1[more]
SMESG000067788.11.998e-1332.47SMESG000067788.1[more]
SMESG000031926.18.137e-1333.33SMESG000031926.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30031123 ID=SMED30031123|Name=RING-type domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=1179bp
CTATGTCAAGGTCATTTTAAATAAATAACAACAGTGAATAAATTTTGTAA
TCTGACAACTACTCTTTGTACATTTCAACTTTCTACAACGGCAACTAGTT
AAAGTTAAAACTTAGTTAAAATCGAATTGAACAATCAATAAGATCAAATT
TCAAATGGATATGCACTAAATGCTTCTTCTCGCTTTGCTAGTTGGTGTAA
CATTTTAGAACAAGTTTGAATTAAATTGTTTCAGATTAAAGGCTTCATCA
TTGCAAAATGAAAAAATCTTTCAAAACTTTCTTAAGTAAATTGTCTCGAA
AGAAAAGTAAAAGATCATTGATATATAACTACAATTTAGACAATATTGTT
ATAACTGAAGAACCTTCAACAAGTTCTATCACAAGAGTAACAACCAATTC
GTTGTCGAGAAAATTTCACAGTTTCAGCTGCACCGGCGACAGATCAGTGA
ATCTCTATCGAAAGAGTTCATTAAATGAGTTGGAGACAATTTACTTTGGC
TTATCCAGAAATGAAACATTGGATGCTGGTTCCAGAAAAGAATTATCTAC
TCAAAGTCATAACCTGTCGATGTTGGAAATTCAGACTCCGAGAAACTTTT
CTATTGAATCCTCAGACATTGATAAAAATCGGATTTTGTACGAAGATTTG
TTTAATTTCATACAGAACTTTTCTATTTACGACTCCCAATTTCTTTATCA
CATTCGTAAATCCATTTGCAGTGAGTCCATTGGCATTCTTTCTGAAATGA
ACGGTTTTAGAAAAGATTTACTAATATTTTCTTCTTTATTCTATTATTTT
TCAAACCATTCAATTTGCAATATCGAACAATTGCTTTCACAATTTTGGGA
AATCAACGATAAAAGACTTCAAGACGGAAAGTTTTTAAGGATGATTGAAT
CGAATTCTCGTGAGTTGAATGAGTTGGAGGAAAATATTTCAGAAATTCTC
AAAGTTCGTACAAAACGTAATTTGATTTGTGCTGAATGTGGTGAAAATTC
TGTGTCCGTTTTGTATCTGCCCTGTGGACATATAATAATGTGCTCTGAAT
GTCATGGGAAATTAAAGTTTAATAAATGTAAACAATGTAGTTGTACGATT
GATGAATTTCATAACGTTTATTTTTAAATCTAAATTTGTAATAAAGTATT
GTGTTAATATTTCTTTGGTTTATAATGAC
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protein sequence of SMED30031123-orf-1

>SMED30031123-orf-1 ID=SMED30031123-orf-1|Name=SMED30031123-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=290bp
MKKSFKTFLSKLSRKKSKRSLIYNYNLDNIVITEEPSTSSITRVTTNSLS
RKFHSFSCTGDRSVNLYRKSSLNELETIYFGLSRNETLDAGSRKELSTQS
HNLSMLEIQTPRNFSIESSDIDKNRILYEDLFNFIQNFSIYDSQFLYHIR
KSICSESIGILSEMNGFRKDLLIFSSLFYYFSNHSICNIEQLLSQFWEIN
DKRLQDGKFLRMIESNSRELNELEENISEILKVRTKRNLICAECGENSVS
VLYLPCGHIIMCSECHGKLKFNKCKQCSCTIDEFHNVYF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell
PLANA:0000142posterior region of the whole animal
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR013083Znf_RING/FYVE/PHD
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 213..233
NoneNo IPR availablePFAMPF13920zf-C3HC4_3coord: 238..283
e-value: 7.6E-8
score: 32.1
IPR013083Zinc finger, RING/FYVE/PHD-typeGENE3DG3DSA:3.30.40.10coord: 218..289
e-value: 2.2E-9
score: 38.5