SMED30013926

Overview
NameSMED30013926
Smed IDSMED30013926
Length (bp)338
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 SMED30013926 (SMED30013926) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30013926 (SMED30013926) 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 SMED30013926 (SMED30013926) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30013926 (SMED30013926) 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



SMED30013926

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
X1 cellSMED30013926 SmedASXL_004243SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
prepharyngeal regionSMED30013926 dd_Smed_v6_13871_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30013926 OX_Smed_1.0.14361ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30013926 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.007895:8601..9025 +1657
v31.005423:8414..8838 +1657
Homology
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BLAST of SMED30013926 vs. Ensembl Human
Match: SFR1 (SWI5 dependent homologous recombination repair protein 1 [Source:HGNC Symbol;Acc:HGNC:29574])

HSP 1 Score: 44.2838 bits (103), Expect = 9.699e-6
Identity = 26/77 (33.77%), Postives = 50/77 (64.94%), Query Frame = 2 
Query:   77 LLNSIKTKEDIIRRIEMINQLKNKSDFKDMKSLIDKWKLNCRTSILMLYEYMR--SRNDPKLSITELLDKLSVEENL 301
            L+  ++ KED++RR++++   ++K+D   ++ LI KW+ +C  S L+LYE     S  + KLS+T+L+D   +++ L
Sbjct:  159 LVKQVQEKEDLLRRLKLVKMYRSKNDLSQLQLLIKKWR-SC--SQLLLYELQSAVSEENKKLSLTQLIDHYGLDDKL 232
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BLAST of SMED30013926 vs. Ensembl Human
Match: SFR1 (SWI5 dependent homologous recombination repair protein 1 [Source:HGNC Symbol;Acc:HGNC:29574])

HSP 1 Score: 43.8986 bits (102), Expect = 9.985e-6
Identity = 26/77 (33.77%), Postives = 50/77 (64.94%), Query Frame = 2 
Query:   77 LLNSIKTKEDIIRRIEMINQLKNKSDFKDMKSLIDKWKLNCRTSILMLYEYMR--SRNDPKLSITELLDKLSVEENL 301
            L+  ++ KED++RR++++   ++K+D   ++ LI KW+ +C  S L+LYE     S  + KLS+T+L+D   +++ L
Sbjct:  146 LVKQVQEKEDLLRRLKLVKMYRSKNDLSQLQLLIKKWR-SC--SQLLLYELQSAVSEENKKLSLTQLIDHYGLDDKL 219
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BLAST of SMED30013926 vs. UniProt/SwissProt
Match: sp|E1BXS0|SFR1_CHICK (Swi5-dependent recombination DNA repair protein 1 homolog OS=Gallus gallus OX=9031 GN=SFR1 PE=3 SV=1)

HSP 1 Score: 46.2098 bits (108), Expect = 7.628e-6
Identity = 23/77 (29.87%), Postives = 52/77 (67.53%), Query Frame = 2 
Query:   77 LLNSIKTKEDIIRRIEMINQLKNKSDFKDMKSLIDKWKLNCRTSILMLYEYMR--SRNDPKLSITELLDKLSVEENL 301
            L+  +K KE+++RR++++   ++K++  ++++LI KW+    ++ LMLYE     S +  K+S+++L+D   +E++L
Sbjct:  136 LMKQVKEKEELLRRLKLVKMYRSKNNLSELQALIVKWR---SSTQLMLYELQAAFSADGKKVSLSQLIDTFGLEDHL 209
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BLAST of SMED30013926 vs. TrEMBL
Match: K1Q2M0 (RFT1-like protein OS=Crassostrea gigas OX=29159 GN=CGI_10013565 PE=4 SV=1)

HSP 1 Score: 57.3806 bits (137), Expect = 3.647e-7
Identity = 31/99 (31.31%), Postives = 56/99 (56.57%), Query Frame = 2 
Query:   35 ARSKTVSGDNKNKELLNSIKTKEDIIRRIEMINQLKNKSDFKDMKSLIDKWKLNCRTSILMLYEYMRSRNDPKLSITELLDKLSVEENL----REDLNF 319
            A S+T   D + ++L  SIK KED++R++ ++   +NK D   M+ LI KW    +  ++ L   M    +P+  +TEL+D L ++ ++    +ED +F
Sbjct:  784 ADSETQEQDKRRQQLQASIKEKEDVLRKLRLVQFYENKHDLGKMEELIRKWYQVSQEGLVDLLNLM---PEPRPELTELIDHLGIDHSMIGYNKEDQSF 879
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BLAST of SMED30013926 vs. TrEMBL
Match: W4Z9H8 (Uncharacterized protein OS=Strongylocentrotus purpuratus OX=7668 PE=4 SV=1)

HSP 1 Score: 52.373 bits (124), Expect = 2.222e-6
Identity = 25/86 (29.07%), Postives = 53/86 (61.63%), Query Frame = 2 
Query:   44 KTVSGDNKNKELLNSIKTKEDIIRRIEMINQLKNKSDFKDMKSLIDKWKLNCRTSILMLYEYMRSRNDPKLSITELLDKLSVEENL 301
            K +  D   KEL   +  KE+  R+++++   ++K+D + +++LI+KW+  C+TSIL LY   +   +PK S+ + ++   ++++L
Sbjct:   14 KIIEADLNRKELTRQVAEKEETCRKLKLVKMYRSKNDLEALQNLIEKWREGCQTSILRLY---KKHPEPKPSLGDFINSCRLDKDL 96
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BLAST of SMED30013926 vs. Ensembl Nematostella
Match: EDO45407 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7RT67])

HSP 1 Score: 42.743 bits (99), Expect = 5.239e-6
Identity = 26/80 (32.50%), Postives = 45/80 (56.25%), Query Frame = 2 
Query:   62 NKNKELLNSIKTKEDIIRRIEMINQLKNKSDFKDMKSLIDKWKLNCRTSILMLYEYMRSRNDPKLSITELLDKLSVEENL 301
            NKN  LL  I  +ED +R+++M+   + K+D  D++ LIDKW+   + +   L   ++    PK+   ELLD+  ++  L
Sbjct:  100 NKNG-LLRQIAEREDKLRKLKMVKMYRTKNDLTDLQKLIDKWRNVSQEAAERLLTKIKKEPSPKMK--ELLDQFQIDYKL 176
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BLAST of SMED30013926 vs. Planmine SMEST
Match: SMESG000039442.1 (SMESG000039442.1)

HSP 1 Score: 199.904 bits (507), Expect = 4.547e-68
Identity = 102/102 (100.00%), Postives = 102/102 (100.00%), Query Frame = 2 
Query:   17 MYRRSLARSKTVSGDNKNKELLNSIKTKEDIIRRIEMINQLKNKSDFKDMKSLIDKWKLNCRTSILMLYEYMRSRNDPKLSITELLDKLSVEENLREDLNFE 322
            MYRRSLARSKTVSGDNKNKELLNSIKTKEDIIRRIEMINQLKNKSDFKDMKSLIDKWKLNCRTSILMLYEYMRSRNDPKLSITELLDKLSVEENLREDLNFE
Sbjct:    1 MYRRSLARSKTVSGDNKNKELLNSIKTKEDIIRRIEMINQLKNKSDFKDMKSLIDKWKLNCRTSILMLYEYMRSRNDPKLSITELLDKLSVEENLREDLNFE 102
The following BLAST results are available for this feature:
BLAST of SMED30013926 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 2
Match NameE-valueIdentityDescription
SFR19.699e-633.77SWI5 dependent homologous recombination repair pro... [more]
SFR19.985e-633.77SWI5 dependent homologous recombination repair pro... [more]
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BLAST of SMED30013926 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 SMED30013926 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 SMED30013926 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 SMED30013926 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 SMED30013926 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 SMED30013926 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|E1BXS0|SFR1_CHICK7.628e-629.87Swi5-dependent recombination DNA repair protein 1 ... [more]
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BLAST of SMED30013926 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
K1Q2M03.647e-731.31RFT1-like protein OS=Crassostrea gigas OX=29159 GN... [more]
W4Z9H82.222e-629.07Uncharacterized protein OS=Strongylocentrotus purp... [more]
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BLAST of SMED30013926 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 SMED30013926 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 SMED30013926 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 SMED30013926 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO454075.239e-632.50Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of SMED30013926 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 SMED30013926 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000039442.14.547e-68100.00SMESG000039442.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013926 ID=SMED30013926|Name=SMED30013926|organism=Schmidtea mediterranea sexual|type=transcript|length=338bp
GACCTTCAGTTAAATCATGTATAGAAGAAGTTTGGCCAGAAGTAAAACAG
TCAGTGGGGACAATAAAAATAAAGAATTGTTAAACTCAATTAAAACCAAA
GAAGATATAATAAGACGTATTGAGATGATAAATCAACTTAAAAATAAAAG
TGACTTTAAAGATATGAAGTCCTTAATTGATAAATGGAAATTAAATTGCC
GCACATCTATTTTAATGCTTTATGAGTACATGCGCTCGAGAAATGATCCA
AAACTGTCTATTACTGAATTATTGGATAAGCTGTCTGTAGAAGAAAATTT
ACGTGAAGATCTTAACTTTGAATAACTTTGAAAAATAA
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protein sequence of SMED30013926-orf-1

>SMED30013926-orf-1 ID=SMED30013926-orf-1|Name=SMED30013926-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=103bp
MYRRSLARSKTVSGDNKNKELLNSIKTKEDIIRRIEMINQLKNKSDFKDM
KSLIDKWKLNCRTSILMLYEYMRSRNDPKLSITELLDKLSVEENLREDLN
FE*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000418head
PLANA:0000419prepharyngeal region
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR042429SFR1
IPR018468SFR1/Mei5
Vocabulary: biological process
TermDefinition
GO:0000724double-strand break repair via homologous recombination
GO:0006281DNA repair
GO:0006351transcription, DNA-templated
GO:0006355regulation of transcription, DNA-templated
GO:0006974cellular response to DNA damage stimulus
GO:0045893positive regulation of transcription, DNA-templated
GO:0071391cellular response to estrogen stimulus
Vocabulary: cellular component
TermDefinition
GO:0005634nucleus
GO:0032798Swi5-Sfr1 complex
Vocabulary: molecular function
TermDefinition
GO:0030374ligand-dependent nuclear receptor transcription coactivator activity
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR018468SFR1/Mei5 familyPFAMPF10376Mei5coord: 20..95
e-value: 6.0E-8
score: 32.8
IPR042429Swi5-dependent recombination DNA repair protein 1 homologPANTHERPTHR28643FAMILY NOT NAMEDcoord: 16..95