DNA-binding protein RFX5

Overview
NameDNA-binding protein RFX5
Smed IDSMED30025755
Length (bp)624
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 DNA-binding protein RFX5 (SMED30025755) t-SNE clustered cells

Violin plots show distribution of expression levels for DNA-binding protein RFX5 (SMED30025755) 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 DNA-binding protein RFX5 (SMED30025755) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for DNA-binding protein RFX5 (SMED30025755) 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



SMED30025755

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



PAGE Curations: 17

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30025755SMESG000072002.1 Contig142newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30025755SMESG000072002.1 Contig142uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30025755SMESG000065727.1 Contig142newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30025755SMESG000065727.1 Contig142uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
head regionSMED30025755SMESG000072002.1 SmedASXL_061538SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30025755SMESG000072002.1 dd_Smed_v4_6108_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30025755SMESG000072002.1 dd_Smed_v4_6108_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30025755SMESG000072002.1 dd_Smed_v4_6108_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30025755SMESG000072002.1 dd_Smed_v4_6108_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30025755SMESG000072002.1 dd_Smed_v4_6108_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30025755SMESG000072002.1 dd_Smed_v4_6108_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
neoblastSMED30025755SMESG000072002.1 dd_Smed_v4_6108_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30025755SMESG000072002.1 dd_Smed_v6_6108_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
reproductive organSMED30025755SMESG000072002.1 Contig12273newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30025755SMESG000072002.1 Contig12273uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
epidermisSMED30025755SMESG000072002.1 dd_Smed_v4_6108_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
ventral epidermisSMED30025755SMESG000072002.1 dd_Smed_v4_6108_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of DNA-binding protein RFX5 vs. TrEMBL
Match: A0A1I8JDU2 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig012361g1 PE=4 SV=1)

HSP 1 Score: 191.43 bits (485), Expect = 1.269e-58
Identity = 94/165 (56.97%), Postives = 115/165 (69.70%), Query Frame = 3 
Query:   75 ARDAYSKYS----HQSDKVMIPEHNYPMGERKSLCYEGAAWYVPSERRWENYHEHRCLPTLARRDAIDFQREEDYMAFVRKRDRPRAPNLTSYIPNEIP-EVKWNGHRRIDTCAPPHGQFKSGTKFPMWDGPGYYGYYHEALDRHSAGEFRTLPALRRYPGYPVC 554
            AR+ YSKYS        K++ P +NY  G  KS  Y+GA WYVPSERRW+ YHE+  LP+ +RRDAIDFQ E+D++ F + RDRPRAP LTSYIP E P ++K  G+RR D+  P H QF +  +FP W G GYYGYYHEALD H  G  +TLPAL RYPGYP+ 
Sbjct:    3 ARNCYSKYSTDPAFTGPKIVTPPNNYLSGNGKSEVYQGAGWYVPSERRWQRYHEYTALPSSSRRDAIDFQSEDDFVQFRQARDRPRAPMLTSYIPGEKPADLKLTGYRREDSVVPEHSQFSTYERFPRWQGSGYYGYYHEALDLHDGGRMKTLPALPRYPGYPLV 167
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BLAST of DNA-binding protein RFX5 vs. TrEMBL
Match: A0A267FNG8 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig032686g1 PE=4 SV=1)

HSP 1 Score: 183.726 bits (465), Expect = 1.271e-55
Identity = 92/165 (55.76%), Postives = 113/165 (68.48%), Query Frame = 3 
Query:   75 ARDAYSKYS----HQSDKVMIPEHNYPMGERKSLCYEGAAWYVPSERRWENYHEHRCLPTLARRDAIDFQREEDYMAFVRKRDRPRAPNLTSYIPNEIP-EVKWNGHRRIDTCAPPHGQFKSGTKFPMWDGPGYYGYYHEALDRHSAGEFRTLPALRRYPGYPVC 554
            AR+ YSKYS        K++ P +NY  G  KS  Y+GA WYVPSERRW+ YHE+  LP+ +RRDAIDFQ E+D++ F + RDRPRAP LTSYIP E P ++K  G+RR D+  P H QF +  +FP W G GYYGYYHEALD H  G  +TLP   RYPGYP+ 
Sbjct:    3 ARNCYSKYSTDPAFTGPKIVTPPNNYLSGNGKSEVYQGAGWYVPSERRWQRYHEYTALPSSSRRDAIDFQSEDDFVQFRQARDRPRAPMLTSYIPGEKPADLKLTGYRREDSVVPEHSQFSTYERFPRWQGSGYYGYYHEALDLHDGGRMKTLP---RYPGYPLV 164
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BLAST of DNA-binding protein RFX5 vs. TrEMBL
Match: A0A183A7D3 (Uncharacterized protein OS=Echinostoma caproni OX=27848 GN=ECPE_LOCUS2868 PE=4 SV=1)

HSP 1 Score: 155.992 bits (393), Expect = 9.702e-45
Identity = 85/169 (50.30%), Postives = 114/169 (67.46%), Query Frame = 3 
Query:   69 AMARDAYSKYSHQSD---KVMIPEHNYPMGERKSLCYEGAAWYVPSERRWENYHEHRCLPTLARRDAIDFQREEDYMAFVRKRDRPRAPNLTSYIPNEIPEVKWNGHRRI------DTCAPPHGQFKSGTKFPMWDGPGYYGYYHEALDRHSAGEFRTLPALRRYPGYP 548
              A+D+YSK   Q+D   ++ IPE+NY  GERK+  YEG+ WY+PSERRWE+Y +H  LP L+RRDAIDF  E+D++ F++KRD P+   +T++IP+  P VKWNGH+RI      +TC     Q+ + T+ P+WDGPGYYGYY E LDR   GE R   A +   GYP
Sbjct:    2 TAAKDSYSKL--QTDDPIRIAIPEYNYRQGERKTALYEGSGWYIPSERRWESYDQHHELPRLSRRDAIDFANEKDFVNFLKKRDVPKWKKITAHIPSCPPSVKWNGHQRIAHNELENTC-----QYHTETR-PLWDGPGYYGYYQEILDRLRKGECRRF-ARQGNIGYP 161
[Close]
BLAST of DNA-binding protein RFX5 vs. TrEMBL
Match: A0A4E0RU64 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_004628 PE=4 SV=1)

HSP 1 Score: 144.436 bits (363), Expect = 3.670e-40
Identity = 71/154 (46.10%), Postives = 102/154 (66.23%), Query Frame = 3 
Query:   69 AMARDAYSKYSHQS-DKVMIPEHNYPMGERKSLCYEGAAWYVPSERRWENYHEHRCLPTLARRDAIDFQREEDYMAFVRKRDRPRAPNLTSYIPNEIPEVKWNGHRRIDTCAPPHGQFKSGTKF-----PMWDGPGYYGYYHEALDRHSAGEFR 512
              A+D YSK   ++ + + IPE+NY  GERK+  Y G+ WY+P ERRWE+Y +HR LP L R DAI+FQ E +++ ++++RD P+   +T++IP+  P  KWNGH+RI     P+ +F++  +F     P WDGPGYYGYY E LDR   G+ R
Sbjct:    2 TAAKDTYSKLQKENPNMINIPEYNYRQGERKTSLYNGSGWYIPCERRWESYDQHRELPRLTRPDAIEFQNESEFVNYLKRRDVPKWKKITAHIPSGPPYPKWNGHQRI-----PNNEFENTCQFNPAKEPTWDGPGYYGYYQEILDRLQRGQCR 150
[Close]
BLAST of DNA-binding protein RFX5 vs. TrEMBL
Match: A0A2H1CD44 (Uncharacterized protein OS=Fasciola hepatica OX=6192 GN=D915_07510 PE=4 SV=1)

HSP 1 Score: 144.821 bits (364), Expect = 4.308e-40
Identity = 71/152 (46.71%), Postives = 102/152 (67.11%), Query Frame = 3 
Query:   75 ARDAYSKYSHQS-DKVMIPEHNYPMGERKSLCYEGAAWYVPSERRWENYHEHRCLPTLARRDAIDFQREEDYMAFVRKRDRPRAPNLTSYIPNEIPEVKWNGHRRIDTCAPPHGQFKSGTKF-----PMWDGPGYYGYYHEALDRHSAGEFR 512
            A+D YSK   ++ + + IPE+NY  GERK+  Y G+ WY+P ERRWE+Y +HR LP L R DAI+FQ E +++ ++++RD P+   +T++IP+  P  KWNGH+RI     P+ +F++  +F     P WDGPGYYGYY E LDR   G+ R
Sbjct:   20 AKDTYSKLQKENPNMINIPEYNYRQGERKTSLYNGSGWYIPCERRWESYDQHRELPRLTRPDAIEFQNESEFVNYLKRRDVPKWKKITAHIPSGPPYPKWNGHQRI-----PNNEFENTCQFNPAKEPTWDGPGYYGYYQEILDRLQRGQCR 166
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BLAST of DNA-binding protein RFX5 vs. Planmine SMEST
Match: SMESG000072002.1 (SMESG000072002.1)

HSP 1 Score: 340.887 bits (873), Expect = 2.447e-121
Identity = 162/162 (100.00%), Postives = 162/162 (100.00%), Query Frame = 3 
Query:   72 MARDAYSKYSHQSDKVMIPEHNYPMGERKSLCYEGAAWYVPSERRWENYHEHRCLPTLARRDAIDFQREEDYMAFVRKRDRPRAPNLTSYIPNEIPEVKWNGHRRIDTCAPPHGQFKSGTKFPMWDGPGYYGYYHEALDRHSAGEFRTLPALRRYPGYPVCR 557
            MARDAYSKYSHQSDKVMIPEHNYPMGERKSLCYEGAAWYVPSERRWENYHEHRCLPTLARRDAIDFQREEDYMAFVRKRDRPRAPNLTSYIPNEIPEVKWNGHRRIDTCAPPHGQFKSGTKFPMWDGPGYYGYYHEALDRHSAGEFRTLPALRRYPGYPVCR
Sbjct:    1 MARDAYSKYSHQSDKVMIPEHNYPMGERKSLCYEGAAWYVPSERRWENYHEHRCLPTLARRDAIDFQREEDYMAFVRKRDRPRAPNLTSYIPNEIPEVKWNGHRRIDTCAPPHGQFKSGTKFPMWDGPGYYGYYHEALDRHSAGEFRTLPALRRYPGYPVCR 162
[Close]
BLAST of DNA-binding protein RFX5 vs. Planmine SMEST
Match: SMESG000072002.1 (SMESG000072002.1)

HSP 1 Score: 306.605 bits (784), Expect = 4.682e-108
Identity = 146/146 (100.00%), Postives = 146/146 (100.00%), Query Frame = 3 
Query:  120 MIPEHNYPMGERKSLCYEGAAWYVPSERRWENYHEHRCLPTLARRDAIDFQREEDYMAFVRKRDRPRAPNLTSYIPNEIPEVKWNGHRRIDTCAPPHGQFKSGTKFPMWDGPGYYGYYHEALDRHSAGEFRTLPALRRYPGYPVCR 557
            MIPEHNYPMGERKSLCYEGAAWYVPSERRWENYHEHRCLPTLARRDAIDFQREEDYMAFVRKRDRPRAPNLTSYIPNEIPEVKWNGHRRIDTCAPPHGQFKSGTKFPMWDGPGYYGYYHEALDRHSAGEFRTLPALRRYPGYPVCR
Sbjct:    1 MIPEHNYPMGERKSLCYEGAAWYVPSERRWENYHEHRCLPTLARRDAIDFQREEDYMAFVRKRDRPRAPNLTSYIPNEIPEVKWNGHRRIDTCAPPHGQFKSGTKFPMWDGPGYYGYYHEALDRHSAGEFRTLPALRRYPGYPVCR 146
The following BLAST results are available for this feature:
BLAST of DNA-binding protein RFX5 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 DNA-binding protein RFX5 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 DNA-binding protein RFX5 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 DNA-binding protein RFX5 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 DNA-binding protein RFX5 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 DNA-binding protein RFX5 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 DNA-binding protein RFX5 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 DNA-binding protein RFX5 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1I8JDU21.269e-5856.97Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267FNG81.271e-5555.76Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A183A7D39.702e-4550.30Uncharacterized protein OS=Echinostoma caproni OX=... [more]
A0A4E0RU643.670e-4046.10Uncharacterized protein OS=Fasciola hepatica OX=61... [more]
A0A2H1CD444.308e-4046.71Uncharacterized protein OS=Fasciola hepatica OX=61... [more]
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BLAST of DNA-binding protein RFX5 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 DNA-binding protein RFX5 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 DNA-binding protein RFX5 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 DNA-binding protein RFX5 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 DNA-binding protein RFX5 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 DNA-binding protein RFX5 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 2
Match NameE-valueIdentityDescription
SMESG000072002.12.447e-121100.00SMESG000072002.1[more]
SMESG000072002.14.682e-108100.00SMESG000072002.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30025755 ID=SMED30025755|Name=DNA-binding protein RFX5|organism=Schmidtea mediterranea sexual|type=transcript|length=624bp
CAAACTAATAGCAACAAGCTTGAATTGAAAATAATTATTTGCAAAATAAT
TAATCAACATAATTAAAAGCTATGGCAAGGGACGCTTACAGCAAGTACAG
CCACCAATCTGACAAGGTCATGATTCCTGAGCATAATTATCCGATGGGAG
AACGCAAATCATTATGTTATGAAGGCGCTGCCTGGTATGTGCCATCTGAG
CGCAGGTGGGAGAATTATCATGAACATAGGTGCTTGCCGACCTTAGCAAG
GAGAGATGCAATCGACTTCCAACGGGAAGAGGATTATATGGCATTCGTTA
GGAAGAGGGATAGGCCCAGAGCCCCAAATCTCACCTCCTACATTCCAAAT
GAAATCCCCGAGGTAAAATGGAATGGACACCGTCGCATCGATACATGCGC
CCCTCCACATGGTCAGTTCAAGTCCGGAACGAAATTCCCAATGTGGGATG
GGCCTGGCTATTACGGATATTATCATGAGGCGTTGGATAGACACAGTGCT
GGTGAGTTCCGTACGTTGCCAGCGCTCCGCCGATATCCCGGATATCCCGT
CTGCAGATTATAACTCAATGCTGCCTTATTTATTTAAATACTCTTATGTA
GCACAATAAATGTGATTTCCGTCA
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protein sequence of SMED30025755-orf-1

>SMED30025755-orf-1 ID=SMED30025755-orf-1|Name=SMED30025755-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=164bp
MARDAYSKYSHQSDKVMIPEHNYPMGERKSLCYEGAAWYVPSERRWENYH
EHRCLPTLARRDAIDFQREEDYMAFVRKRDRPRAPNLTSYIPNEIPEVKW
NGHRRIDTCAPPHGQFKSGTKFPMWDGPGYYGYYHEALDRHSAGEFRTLP
ALRRYPGYPVCRL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0003700transcription factor activity, sequence-specific DNA binding
GO:0003677DNA binding
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000020protonephridia
PLANA:0000034epidermis
PLANA:0000070intestinal phagocyte
PLANA:0000096ventral epidermis
PLANA:0000099neuron
PLANA:0000418head
PLANA:0002032epidermal cell
PLANA:0002089reproductive organ
Vocabulary: biological process
TermDefinition
GO:0006355regulation of transcription, DNA-templated