BED-type domain-containing protein

Overview
NameBED-type domain-containing protein
Smed IDSMED30009896
Length (bp)571
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 BED-type domain-containing protein (SMED30009896) t-SNE clustered cells

Violin plots show distribution of expression levels for BED-type domain-containing protein (SMED30009896) in cells (dots) of each of the 12 neoblast clusters.

 

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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



SMED30009896

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
X1 cellSMED30009896 SmedASXL_018417SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30009896 SmedASXL_018417SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of BED-type domain-containing protein vs. TrEMBL
Match: A0A4C1ZDZ7 (Uncharacterized protein OS=Eumeta variegata OX=151549 GN=EVAR_99875_1 PE=4 SV=1)

HSP 1 Score: 80.8777 bits (198), Expect = 2.392e-14
Identity = 46/102 (45.10%), Postives = 66/102 (64.71%), Query Frame = 3 
Query:  168 ELEDADSEKSNTIMDFVKFSSLDEIILKLAAVDEISIRAITRSEFIRESILNRGYKLPKNETDVL*LIYDPFEEK---MIIELS*NIKNKLRFSLTLNEWIT 464
            E +  + E    I ++V   SL EII +LAA D + I AIT S+FIRESI  RGYK+PKNETD++ ++ D +EEK   +I      I + +RFSL+++EW +
Sbjct:  214 ESKKTEQEIEPEITEYVTKKSLSEIISRLAAEDGLFISAITNSKFIRESITQRGYKMPKNETDIMKIVLDYYEEKKDEIIENFKDFIASGVRFSLSVDEWTS 315
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BLAST of BED-type domain-containing protein vs. TrEMBL
Match: A0A0P4VX07 (BED-type domain-containing protein OS=Scylla olivacea OX=85551 PE=4 SV=1)

HSP 1 Score: 75.8702 bits (185), Expect = 4.668e-13
Identity = 48/150 (32.00%), Postives = 83/150 (55.33%), Query Frame = 3 
Query:   60 NKCNTCKKIIGIVDSSTTSLFKHLK-------TYDIHPNLDIRELEDADSEKSNTIMD-----FVKFSSLDEIILKLAAVDEISIRAITRSEFIRESILNRGYKLPKNETDVL*LIYDPF---EEKMIIELS*NIKNKLRFSLTLNEWIT 464
            ++C  C+ +I     ST+ + +HLK       T ++    D    +D    K N++         K  + +EI+ KLAAVD  SI AI +SEFI+ S+L RGYKLP++ T V+ L++  +   +E++I +++      +RF L+L+E+ +
Sbjct:   28 SRCKKCRAVIKCRGWSTSGMIRHLKSKHSIEKTENLKRPSDRSHDKDTSEVKRNSVQQKMTDLLKKEETKEEIVGKLAAVDGFSINAIAKSEFIKTSMLARGYKLPQSPTLVMDLVHKQYNVAKERVIFDINKRKNVGVRFGLSLDEYTS 177
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BLAST of BED-type domain-containing protein vs. TrEMBL
Match: A0A0N7Z9Z3 (BED-type domain-containing protein OS=Scylla olivacea OX=85551 PE=4 SV=1)

HSP 1 Score: 74.3294 bits (181), Expect = 3.571e-12
Identity = 49/151 (32.45%), Postives = 83/151 (54.97%), Query Frame = 3 
Query:   57 PNKCNTCKKIIGIVDSSTTSLFKHLK-------TYDIHPNLDIRELEDADSEKSNTIMD-----FVKFSSLDEIILKLAAVDEISIRAITRSEFIRESILNRGYKLPKNETDVL*LI---YDPFEEKMIIELS*NIKNKLRFSLTLNEWIT 464
             ++C  C+ +I     ST+ + +HLK       T ++    D    +D    K N++         K  + +EI+ KLAAVD  SI AI +SEFI+ S+L RGYKLP++ T V+ L+   Y+  +E++I +++      +RF L+L+E+ +
Sbjct:   27 SSRCKKCRAVIKCRGWSTSGMIRHLKSKHSIEKTENLKRPSDRSHDKDTSEVKRNSVQQKMTDLLKKEETKEEIVGKLAAVDGFSINAIAKSEFIKTSMLARGYKLPQSPTLVMDLVHKQYNVAKERVIFDINKRKNVGVRFGLSLDEYTS 177
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BLAST of BED-type domain-containing protein vs. TrEMBL
Match: B0W9I7 (Predicted protein OS=Culex quinquefasciatus OX=7176 GN=6035136 PE=4 SV=1)

HSP 1 Score: 72.4034 bits (176), Expect = 2.376e-11
Identity = 46/155 (29.68%), Postives = 82/155 (52.90%), Query Frame = 3 
Query:   63 KCNTCKKIIGIVDSSTTSLFKHLKTYDIHPNLDIR--------ELED---------ADSEKSNTIMDFVKFSSLDEIILKLAAVDEISIRAITRSEFIRESILNRGYKLPKNETDVL*LIYDPFE---EKMIIELS*NIKNKLRFSLTLNEWITN 467
            +C  C K I     ST+ L +H    ++H N  ++        + ED         +++ K +TI  F+    ++E+  +LAA D ++I AIT S+FIR S   RGY+LP ++T V+ LI+D +E   ++ + ++   +      S+TL+EW ++
Sbjct:   17 QCKKCPKTISCKGGSTSGLLRH--GVNVH-NFRVKRRIPESVVQPEDVPSGSKQAKSNTSKQSTIEPFIHKKPMNEMFARLAAQDGLTISAITNSKFIRTSFAQRGYQLPLSKTSVMKLIHDYYEIAKQQTVQQIQDKLAELHFLSITLDEWTSS 168
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BLAST of BED-type domain-containing protein vs. TrEMBL
Match: A0A4C1Y486 (BED-type domain-containing protein OS=Eumeta variegata OX=151549 GN=EVAR_52339_1 PE=4 SV=1)

HSP 1 Score: 69.707 bits (169), Expect = 1.255e-10
Identity = 57/159 (35.85%), Postives = 80/159 (50.31%), Query Frame = 3 
Query:   63 KCNTCKKIIGIVDSSTTSLFKHLKTYDIHPNLDIRELEDADSEKSNTIMD------------------FVKF-----SSLDEIILKLAAVDEISIRAITRSEFIRESILNRGYKLPKNETDVL*LIYDPFEEKM--IIELS*NIKNK--LRFSLTLNEW 458
            +C  C K I    S+TT L +HL+   IH  + I+  E   S  +    D                   + F      SL EI+  LAA D ++IR IT+S+FIRES+  RG  LPKNE+DV+ +I   +EEK    I+   N K K   RF+L+++EW
Sbjct:   20 QCLKCPKKISTKGSNTTGLVRHLE--HIH-KISIKNTETQASTSAGYSADNRDEQPSDSKKSKSKLQKTLHFEPKNKQSLGEIVAVLAAKDGLTIRQITKSDFIRESLRLRGINLPKNESDVMKIILKYYEEKKQETIDFLSNSKQKESARFNLSVDEW 175
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BLAST of BED-type domain-containing protein vs. Planmine SMEST
Match: SMESG000024467.1 (SMESG000024467.1)

HSP 1 Score: 78.5666 bits (192), Expect = 2.856e-18
Identity = 55/135 (40.74%), Postives = 80/135 (59.26%), Query Frame = 3 
Query:   81 KIIGIVDSSTTSLFKHLKTY----DIHPNLDIRELEDADSEKSNTIMDFVKFSSLDEIILKLAAVDEISIRAITRSEFIRESILNRGYKLPKNETDVL*LIYDPFEEK---MIIELS*NIKNKLRFSLTLNEWIT 464
            KII    +STT+L  HLKT+    D+  N    + E+   ++  TI DF    +L EI+  +A +D ISIRAITR+ +IR+ +L  G+K+P NE DV+ LI+  FEEK    I E+   I +  RFS +++E  T
Sbjct:   28 KIIKCSGNSTTTLKNHLKTHGINLDVPKNPPQPQPEELPKKRQKTITDFFGPKNLKEIVSDMA-IDRISIRAITRNSYIRQPLLRDGFKMPANEFDVMKLIHYYFEEKRQLTIEEIKMKIASGNRFSTSVDEVTT 161
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BLAST of BED-type domain-containing protein vs. Planmine SMEST
Match: SMESG000077712.1 (SMESG000077712.1)

HSP 1 Score: 71.2478 bits (173), Expect = 3.575e-15
Identity = 46/148 (31.08%), Postives = 86/148 (58.11%), Query Frame = 3 
Query:   66 CNTCKKIIGIVDSSTTSLFKHLKTYDIHP-----NLDIRELEDA--------DSEKSN-TIMDFVKFSSLDEIILKLAAVDEISIRAITRSEFIRESILNRGYKLPKNETDVL*L---IYDPFEEKMIIELS*NIKNKLRFSLTLNEW 458
            CN C K +    S+TT L +HL+  ++H      NL    ++D+        D   +N TI+ F++ S+L E +  LA +D ++   I++S  IR+++ ++G+KLPKN TD++ L   +Y+   +K+I ++S      ++FS++++EW
Sbjct:   24 CNICAKTLSCKTSATTGLRRHLE--EVHGFQRTENLSTSVIKDSRDYQVDKHDRCSTNETIVKFLRQSTLSEEVTTLAVIDRLTFTQISQSRLIRQALSDKGFKLPKNPTDIMNLMMELYNDKNQKLINKISDLKLKNVKFSVSIDEW 169
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BLAST of BED-type domain-containing protein vs. Planmine SMEST
Match: SMESG000028488.1 (SMESG000028488.1)

HSP 1 Score: 67.781 bits (164), Expect = 1.602e-14
Identity = 42/102 (41.18%), Postives = 60/102 (58.82%), Query Frame = 3 
Query:  189 EKSNTIMDFVKFSSLDEIILKLAAVDEISIRAITRSEFIRESILNRGYKLPKNETDVL*LIYDPFEEKMIIELS*NIKNKL--------RFSLTLNEWITNE 470
            +K  TI+DF K  SL+  + KLAA+D  SIR I +S FIR+S+   G+K+PKNE  V+ LI   +  K        +KNKL        +FSLT++EW + +
Sbjct:    3 KKPKTILDFEKKHSLEVTVSKLAAIDGFSIRGIIQSSFIRDSMNVHGFKVPKNEMYVMKLILTDYGNKKG-----ELKNKLQSTKSAGEKFSLTMDEWTSTK 99
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BLAST of BED-type domain-containing protein vs. Planmine SMEST
Match: SMESG000047723.1 (SMESG000047723.1)

HSP 1 Score: 67.0106 bits (162), Expect = 2.833e-14
Identity = 41/87 (47.13%), Postives = 57/87 (65.52%), Query Frame = 3 
Query:  207 MDFVKFSSLDEIILKLAAVDEISIRAITRSEFIRESILNRGYKLPKNETDVL*LI---YDPFEEKMIIELS*NIKNKLRFSLTLNEW 458
            MDFVK  SL+  + KLA +   SIR ITRS+ IR+S+  RG+KLPKNET+V+ LI   Y   + ++ I+L        +FSLT++EW
Sbjct:    1 MDFVKKDSLEVTVSKLAGIG-FSIRGITRSKRIRDSMNVRGFKLPKNETNVMKLILRDYGNKKGELKIKLQNAKSAGEKFSLTMDEW 86
[Close]
BLAST of BED-type domain-containing protein vs. Planmine SMEST
Match: SMESG000078681.1 (SMESG000078681.1)

HSP 1 Score: 68.1662 bits (165), Expect = 2.916e-14
Identity = 42/141 (29.79%), Postives = 79/141 (56.03%), Query Frame = 3 
Query:   63 KCNTCKKIIGIVDSSTTSLFKHLKT-YDIHPNLDIRELEDADSEKSNT---IMDFVKFSSLDEIILKLAAVDEISIRAITRSEFIRESILNRGYKLPKNETDVL*LIYDPFEEKMII---ELS*NIKNKLRFSLTLNEWIT 464
            KC  C  ++     +T++L  HL+  +DI    D+++ E+   +++ +   +++F+K  S+ E++ K AA D  SI ++T S  IRE I  R Y +P++E+ +  LI D   EK +    + +   K+ + FS+T +EW +
Sbjct:   21 KCTMCNSVLKCAGGNTSNLANHLRAKHDI----DVKKNEEPPEKRAKSTSNMLNFIKRESVGELLAKCAAYDGFSIHSMTHSSAIREFITTRSYVMPRSESKIKKLIVDFANEKKLQFKDKFTKMAKSGMCFSITTDEWTS 157
The following BLAST results are available for this feature:
BLAST of BED-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 BED-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 BED-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 BED-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 BED-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 BED-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 BED-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 BED-type domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A4C1ZDZ72.392e-1445.10Uncharacterized protein OS=Eumeta variegata OX=151... [more]
A0A0P4VX074.668e-1332.00BED-type domain-containing protein OS=Scylla oliva... [more]
A0A0N7Z9Z33.571e-1232.45BED-type domain-containing protein OS=Scylla oliva... [more]
B0W9I72.376e-1129.68Predicted protein OS=Culex quinquefasciatus OX=717... [more]
A0A4C1Y4861.255e-1035.85BED-type domain-containing protein OS=Eumeta varie... [more]
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BLAST of BED-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 BED-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 BED-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 BED-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 BED-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 BED-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
SMESG000024467.12.856e-1840.74SMESG000024467.1[more]
SMESG000077712.13.575e-1531.08SMESG000077712.1[more]
SMESG000028488.11.602e-1441.18SMESG000028488.1[more]
SMESG000047723.12.833e-1447.13SMESG000047723.1[more]
SMESG000078681.12.916e-1429.79SMESG000078681.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30009896 ID=SMED30009896|Name=BED-type domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=571bp
CCGATTTTGGATTTTGCGTGTTGTTTCCAATCCATTTAAACAAAAGCTTG
TACTGGCCCAACAAGTGTAATACATGTAAAAAGATTATAGGTATTGTTGA
CTCAAGCACAACATCGTTATTCAAGCACCTTAAAACTTATGATATTCATC
CAAATTTAGACATACGTGAACTGGAGGATGCTGATTCGGAAAAATCAAAT
ACAATTATGGATTTTGTAAAATTTTCAAGTTTAGATGAAATTATTTTGAA
ATTGGCAGCAGTAGATGAAATATCAATAAGAGCGATTACCAGATCGGAAT
TTATACGGGAATCTATTTTAAATCGTGGATATAAGTTGCCTAAAAATGAA
ACCGATGTACTGTAATTAATATATGACCCTTTTGAAGAGAAAATGATTAT
CGAATTGTCATAAAATATTAAAAATAAACTGAGATTTAGCTTGACACTCA
ATGAGTGGATCACGAACGAAGAAATATGTCAATGCAATTATATATAGTGT
CCCAGATCCATATGAATAATCATACAATTGTTGGGTTAACAAATATAAAA
AATGGAAAATCAATAAAAACA
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protein sequence of SMED30009896-orf-1

>SMED30009896-orf-1 ID=SMED30009896-orf-1|Name=SMED30009896-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=121bp
DFGFCVLFPIHLNKSLYWPNKCNTCKKIIGIVDSSTTSLFKHLKTYDIHP
NLDIRELEDADSEKSNTIMDFVKFSSLDEIILKLAAVDEISIRAITRSEF
IRESILNRGYKLPKNETDVL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0003677DNA binding
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
PLANA:0002111X2 cell