Myb_DNA-bind_5 domain-containing protein

Overview
NameMyb_DNA-bind_5 domain-containing protein
Smed IDSMED30019120
Length (bp)1124
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 Myb_DNA-bind_5 domain-containing protein (SMED30019120) t-SNE clustered cells

Violin plots show distribution of expression levels for Myb_DNA-bind_5 domain-containing protein (SMED30019120) 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 Myb_DNA-bind_5 domain-containing protein (SMED30019120) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for Myb_DNA-bind_5 domain-containing protein (SMED30019120) 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




SMED30019120

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



PAGE Curations: 11

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
Smed sexual biotypeSMED30019120h1SMcG0009288 Contig41541uc_Smed_v2PMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30019120h1SMcG0009288 Contig41541newmark_estsPMID:29674431
Fincher et al., 2018
FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
nervous systemSMED30019120h1SMcG0009288 dd_Smed_v4_4675_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30019120h1SMcG0009288 dd_Smed_v4_4675_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parapharyngeal regionSMED30019120h1SMcG0009288 dd_Smed_v4_4675_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30019120h1SMcG0009288 dd_Smed_v4_4675_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30019120h1SMcG0009288 dd_Smed_v4_4675_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30019120h1SMcG0009288 dd_Smed_v4_4675_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30019120h1SMcG0009288 dd_Smed_v6_4675_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
cholinergic neuronSMED30019120h1SMcG0009288 dd_Smed_v6_4675_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30019120h1SMcG0009288 dd_Smed_v4_4675_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
BLAST of Myb_DNA-bind_5 domain-containing protein vs. TrEMBL
Match: A0A183QQP9 (Myb_DNA-bind_5 domain-containing protein OS=Schistosoma rodhaini OX=6188 PE=4 SV=1)

HSP 1 Score: 84.7297 bits (208), Expect = 4.218e-14
Identity = 80/263 (30.42%), Postives = 121/263 (46.01%), Query Frame = 1
Query:  316 RADNFPXXXXXXXXXXXXCRSEIILSLSPSSHRLKKSAWEEVTAIMG---IYFQKRTPEQVKKKWENLLTKTRRKVRQGLMNTS-SWSHLNDMVWNFLIENR---ETKYLFG--PGRF---------SRASELSNLLGVSVASESKTEHHNSMESW-SICSPIEQALINENLKNLGETIETMKDDSVDSKDEQDLIDKSCKNDFESFVISDPVNSVPFSPLLSQMSKSSQEEVLTMWKSEHTMRMKVLAMQHEAAFIQLKLMK 1047
            RA+ F ++E+++MLKE++ R  I+LSLSPS++RLK+ AWEEV   M     +  +RT +QVKKKWENL++KT+RKVR G +     W+  N  V  FL ++      +YL    P  F         +  + + N   V  AS+      +  ES+ S  SP  Q+ IN  L +  E+  T                                            S+  Q+E+    K EH +RM +L +Q +   +Q+ L K
Sbjct:  125 RAETFVIDEVKVMLKEIEARKHILLSLSPSTNRLKRRAWEEVAVCMANRWPHAPRRTADQVKKKWENLVSKTKRKVRAGHITPELDWNETNAAVMQFLTQHSPPVRLRYLTSTTPSLFNLEENDVDMTNITNVQNTTTVEGASDVGNITGSVHESFLSSFSPFNQSFINFGLPSTAESFYTT------------------------------------------FSRDIQKELYLQLKQEHELRMDILRLQKQTWLLQMNLFK 345          
BLAST of Myb_DNA-bind_5 domain-containing protein vs. TrEMBL
Match: G4VL31 (Myb_DNA-bind_5 domain-containing protein OS=Schistosoma mansoni OX=6183 GN=Smp_009300 PE=4 SV=1)

HSP 1 Score: 83.9593 bits (206), Expect = 6.146e-14
Identity = 80/263 (30.42%), Postives = 121/263 (46.01%), Query Frame = 1
Query:  316 RADNFPXXXXXXXXXXXXCRSEIILSLSPSSHRLKKSAWEEVTAIMG---IYFQKRTPEQVKKKWENLLTKTRRKVRQGLMNTS-SWSHLNDMVWNFLIENR---ETKYLFG--PGRF---------SRASELSNLLGVSVASESKTEHHNSMESW-SICSPIEQALINENLKNLGETIETMKDDSVDSKDEQDLIDKSCKNDFESFVISDPVNSVPFSPLLSQMSKSSQEEVLTMWKSEHTMRMKVLAMQHEAAFIQLKLMK 1047
            RA+ F ++E+++MLKE++ R  I+LSLSPS++RLK+ AWEEV   M     +  +RT +QVKKKWENL++KT+RKVR G +     W+  N  V  FL ++      +YL    P  F         +  + + N   V  AS+      +  ES+ S  SP  Q+ IN  L +  E+  T                                            S+  Q+E+    K EH +RM +L +Q +   +Q+ L K
Sbjct:  120 RAETFVIDEVKVMLKEIEARKHILLSLSPSTNRLKRRAWEEVAVCMANRWPHAPRRTADQVKKKWENLVSKTKRKVRAGHITPELDWNETNAAVMQFLTQHSPPVRLRYLTSTTPSLFNLEENDVDMTNITNVQNTTTVEGASDVGNITGSVHESFLSSFSPFNQSFINFGLPSTTESFYTT------------------------------------------FSRDIQKELYLQLKQEHELRMDILRLQKQTWLLQMNLFK 340          
BLAST of Myb_DNA-bind_5 domain-containing protein vs. TrEMBL
Match: A0A5J4NY51 (Myb_DNA-bind_5 domain-containing protein OS=Paragonimus westermani OX=34504 GN=DEA37_0008145 PE=4 SV=1)

HSP 1 Score: 80.1073 bits (196), Expect = 1.147e-12
Identity = 52/115 (45.22%), Postives = 76/115 (66.09%), Query Frame = 1
Query:  274 LLSIPSQMIDVHKSRADNFPXXXXXXXXXXXXCRSEIILSLSPSSHRLKKSAWEEVTAIMGI---YFQKRTPEQVKKKWENLLTKTRRKVRQGLMNTS-SWSHLNDMVWNFLIEN 606
            +L+ PS      K RA++F +EE+ +ML E+  R +I+LSLSPS++RLK+ AWEEV   M     +  +RT +QVKKKWENL++KT+RK+R G M     W+  N +V  FL ++
Sbjct:   81 ILAAPS------KQRAESFLIEEVRVMLHEIGLRKQILLSLSPSTNRLKRRAWEEVAGSMAARWPHSPRRTADQVKKKWENLVSKTKRKLRAGHMTPEFDWNETNAIVMEFLTQH 189          
BLAST of Myb_DNA-bind_5 domain-containing protein vs. TrEMBL
Match: A0A183TL21 (Myb_DNA-bind_5 domain-containing protein OS=Schistocephalus solidus OX=70667 GN=SSLN_LOCUS17169 PE=4 SV=1)

HSP 1 Score: 76.6406 bits (187), Expect = 7.562e-12
Identity = 53/113 (46.90%), Postives = 77/113 (68.14%), Query Frame = 1
Query:  271 ELLSIPSQMIDVHKSRADNFPXXXXXXXXXXXXCRSEIILSLSPSSHRLKKSAWEEVTAIMGIYF---QKRTPEQVKKKWENLLTKTRRKVRQGLMNTS-SWSHLNDMVWNFL 597
            E+ SI S M    K RA++F LEEI +ML+E++ R  I+LS+SP+S++LK+ AWEEV   M + +    +RT +Q+KKKWENL++KT+RK+R G M     W+  N +V  FL
Sbjct:  112 EMASIISPMT---KRRAESFVLEEIRVMLQEIERRKHILLSVSPASNKLKRRAWEEVANCMALRWPQETRRTGDQIKKKWENLVSKTKRKIRDGHMTPDLDWNETNTLVMQFL 221          
BLAST of Myb_DNA-bind_5 domain-containing protein vs. TrEMBL
Match: C7TXV2 (Leucine-rich repeat-containing protein (LRR) OS=Schistosoma japonicum OX=6182 PE=2 SV=1)

HSP 1 Score: 77.0258 bits (188), Expect = 1.328e-11
Identity = 48/100 (48.00%), Postives = 70/100 (70.00%), Query Frame = 1
Query:  316 RADNFPXXXXXXXXXXXXCRSEIILSLSPSSHRLKKSAWEEVTAIMG---IYFQKRTPEQVKKKWENLLTKTRRKVRQGLMNTS-SWSHLNDMVWNFLIE 603
            RA++F ++E+++MLKE++ R  I+LSLSPS++RLK+ AWEEV   M     +  +RT +QVKKKWENL++KT+RKVR G +     W+  N  V  FL +
Sbjct:  122 RAESFVIDEVKVMLKEIEARKHILLSLSPSTNRLKRRAWEEVAVCMANRWPHAPRRTADQVKKKWENLVSKTKRKVRAGHVTPELDWNETNAAVMQFLTQ 221          
BLAST of Myb_DNA-bind_5 domain-containing protein vs. Planmine SMEST
Match: SMESG000029917.1 (SMESG000029917.1)

HSP 1 Score: 555.058 bits (1429), Expect = 0.000e+0
Identity = 282/284 (99.30%), Postives = 284/284 (100.00%), Query Frame = 1
Query:  238 MEICSPNQFNDELLSIPSQMIDVHKSRADNFPXXXXXXXXXXXXCRSEIILSLSPSSHRLKKSAWEEVTAIMGIYFQKRTPEQVKKKWENLLTKTRRKVRQGLMNTSSWSHLNDMVWNFLIENRETKYLFGPGRFSRASELSNLLGVSVASESKTEHHNSMESWSICSPIEQALINENLKNLGETIETMKDDSVDSKDEQDLIDKSCKNDFESFVISDPVNSVPFSPLLSQMSKSSQEEVLTMWKSEHTMRMKVLAMQHEAAFIQLKLMKIQLEKATGIRYDNK 1089
            MEICSPNQFNDELLSIPSQMIDVHKSRADNFPLEEIELMLKEMKCRSEIILSLSPSSHRLKKSAWEEVTAIMGIYFQKRTPEQVKKKWENLLTKTRRKVRQGLMNTSSWSHLNDMVWNFLIENRETKYLFGPGRFSRASELSNLLGVSVASESKTEHHNS+ESWSICSPIEQALINENLKNLGETIETMKDDSVDSKDEQDL+DKSCKNDFESFVISDPVNSVPFSPLLSQMSKSSQEEVLTMWKSEHTMRMKVLAMQHEAAFIQLKLMKIQLEKATGIRYDNK
Sbjct:    1 MEICSPNQFNDELLSIPSQMIDVHKSRADNFPLEEIELMLKEMKCRSEIILSLSPSSHRLKKSAWEEVTAIMGIYFQKRTPEQVKKKWENLLTKTRRKVRQGLMNTSSWSHLNDMVWNFLIENRETKYLFGPGRFSRASELSNLLGVSVASESKTEHHNSIESWSICSPIEQALINENLKNLGETIETMKDDSVDSKDEQDLMDKSCKNDFESFVISDPVNSVPFSPLLSQMSKSSQEEVLTMWKSEHTMRMKVLAMQHEAAFIQLKLMKIQLEKATGIRYDNK 284          
The following BLAST results are available for this feature:
BLAST of Myb_DNA-bind_5 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 Myb_DNA-bind_5 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 Myb_DNA-bind_5 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 Myb_DNA-bind_5 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 Myb_DNA-bind_5 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 Myb_DNA-bind_5 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 Myb_DNA-bind_5 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 Myb_DNA-bind_5 domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A183QQP94.218e-1430.42Myb_DNA-bind_5 domain-containing protein OS=Schist... [more]
G4VL316.146e-1430.42Myb_DNA-bind_5 domain-containing protein OS=Schist... [more]
A0A5J4NY511.147e-1245.22Myb_DNA-bind_5 domain-containing protein OS=Parago... [more]
A0A183TL217.562e-1246.90Myb_DNA-bind_5 domain-containing protein OS=Schist... [more]
C7TXV21.328e-1148.00Leucine-rich repeat-containing protein (LRR) OS=Sc... [more]
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BLAST of Myb_DNA-bind_5 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 Myb_DNA-bind_5 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 Myb_DNA-bind_5 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 Myb_DNA-bind_5 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 Myb_DNA-bind_5 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 Myb_DNA-bind_5 domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000029917.10.000e+099.30SMESG000029917.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30019120 ID=SMED30019120|Name=Myb_DNA-bind_5 domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=1124bp
GCATCGGGTGATACGTGAATGGGTGTAGCGTGTGTGTGCATGGCAGATAA
TACATGCTGTACAACACTCTACTCTAAGTCATGGATTTACACACTTCAAC
TGAAGAGAGACAGGCATAGAGAGAGAGAGTAACATAAGAGAGATTATTGA
TTACAAAGTAACAGTAGTGTAAGAGAGTTACAAATCTTTATACATAATAG
TTTAGAATAAATATTTACAAAAATAAATTTTAAAATTATGGAAATCTGCT
CTCCGAATCAATTCAACGACGAGCTTCTATCGATTCCATCTCAAATGATT
GATGTCCACAAGTCGAGAGCCGACAATTTCCCACTAGAAGAAATCGAATT
GATGCTGAAAGAAATGAAATGTCGCAGTGAAATAATTCTTTCTCTCTCTC
CGTCTTCGCATCGATTGAAAAAGTCCGCTTGGGAAGAAGTCACAGCAATA
ATGGGGATCTATTTCCAGAAACGAACCCCAGAACAAGTGAAAAAGAAATG
GGAAAATCTTCTGACGAAAACCAGACGAAAAGTCCGTCAAGGCTTAATGA
ACACGAGTTCTTGGAGCCATCTGAATGATATGGTTTGGAATTTTTTGATT
GAAAATCGAGAAACGAAATATTTATTTGGGCCTGGACGATTTTCTCGAGC
AAGTGAGTTGTCTAATTTGTTGGGAGTTTCAGTTGCTTCGGAATCGAAAA
CAGAACACCATAATTCCATGGAGTCCTGGTCTATTTGTTCTCCTATTGAA
CAGGCGTTAATAAATGAAAACTTGAAGAATCTTGGCGAAACAATTGAAAC
AATGAAGGATGATTCGGTGGATTCAAAAGACGAGCAAGACTTAATTGATA
AATCCTGTAAAAATGATTTTGAATCGTTTGTAATTTCAGATCCAGTGAAT
TCGGTTCCATTCTCTCCGCTGTTGTCACAAATGAGTAAATCTTCCCAGGA
AGAAGTTCTGACTATGTGGAAATCCGAACATACCATGAGAATGAAAGTAT
TGGCAATGCAACACGAGGCAGCATTTATTCAATTGAAACTCATGAAAATA
CAGCTTGAGAAAGCAACAGGAATCAGATATGATAATAAATAATATTTGCT
TTATTTTTCTCTTTGTGTTTCACA
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protein sequence of SMED30019120-orf-1

>SMED30019120-orf-1 ID=SMED30019120-orf-1|Name=SMED30019120-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=285bp
MEICSPNQFNDELLSIPSQMIDVHKSRADNFPLEEIELMLKEMKCRSEII
LSLSPSSHRLKKSAWEEVTAIMGIYFQKRTPEQVKKKWENLLTKTRRKVR
QGLMNTSSWSHLNDMVWNFLIENRETKYLFGPGRFSRASELSNLLGVSVA
SESKTEHHNSMESWSICSPIEQALINENLKNLGETIETMKDDSVDSKDEQ
DLIDKSCKNDFESFVISDPVNSVPFSPLLSQMSKSSQEEVLTMWKSEHTM
RMKVLAMQHEAAFIQLKLMKIQLEKATGIRYDNK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000099neuron
PLANA:0000418head
PLANA:0000463cholinergic neuron
PLANA:0003117parapharyngeal cell
Vocabulary: INTERPRO
TermDefinition
IPR028002Myb_DNA-bind_5
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
Vocabulary: biological process
TermDefinition
GO:0006915apoptotic process
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR028002Myb/SANT-like DNA-binding domainPFAMPF13873Myb_DNA-bind_5coord: 27..100
e-value: 2.1E-9
score: 37.3