SMED30013083

Overview
NameSMED30013083
Smed IDSMED30013083
Length (bp)1170
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 SMED30013083 (SMED30013083) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30013083 (SMED30013083) 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 SMED30013083 (SMED30013083) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30013083 (SMED30013083) 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




SMED30013083

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
protonephridiaSMED30013083 dd_Smed_v4_11991_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30013083 dd_Smed_v4_11991_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
Alignments
SMED30013083 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000523:5050..6219 +5823
Homology
BLAST of SMED30013083 vs. TrEMBL
Match: G4VFR1 (Uncharacterized protein OS=Schistosoma mansoni OX=6183 GN=Smp_144350 PE=4 SV=1)

HSP 1 Score: 183.341 bits (464), Expect = 7.337e-52
Identity = 82/153 (53.59%), Postives = 110/153 (71.90%), Query Frame = 1
Query:  703 PVVIVNPQEKKEIFVGGNENVRLPFWAYRKCLTCIRGKPNELSSRLCLRLLQAKFGRKYMLSHNYNGSGDKVPIDRQIMSSILVQAKMQFPDQEDFQNNPAKFAMFRDYINNAFRVVAYRHRKGIQSNTPFWDQNGEPIADLDPP-SWIADNI 1158
            PVV++NP E +EIF+GG ++V LP WAY KCLT +RG+P+EL  RLCLRLLQ+ F   Y+++HNYNGSG K PID  +MS++L QA++QF     F   P      RDY+NNAFRV+A+R RKG +  +PFW++ GEPI DL+ P  W+ + I
Sbjct:   97 PVVVLNPDEPREIFIGGVQSVALPLWAYCKCLTMVRGEPHELGPRLCLRLLQSLFSLHYLVTHNYNGSGGKAPIDPIVMSAVLRQAQLQF-GSGYFFTEPMALGKLRDYLNNAFRVMAFRQRKGERVRSPFWNEKGEPIHDLEAPKEWLLNVI 248          
BLAST of SMED30013083 vs. TrEMBL
Match: A0A183PXD5 (Uncharacterized protein OS=Schistosoma mattheei OX=31246 GN=SMTD_LOCUS19021 PE=4 SV=1)

HSP 1 Score: 183.341 bits (464), Expect = 2.995e-51
Identity = 80/145 (55.17%), Postives = 106/145 (73.10%), Query Frame = 1
Query:  703 PVVIVNPQEKKEIFVGGNENVRLPFWAYRKCLTCIRGKPNELSSRLCLRLLQAKFGRKYMLSHNYNGSGDKVPIDRQIMSSILVQAKMQFPDQEDFQNNPAKFAMFRDYINNAFRVVAYRHRKGIQSNTPFWDQNGEPIADLDPP 1137
            PVV++NP E +EIF+GG ++V LP WAY KCLT +RG+P+EL  RLCLRLLQ+ F   Y+++HNYNGSG K PID  +MS++L QA++QF     F   P      RDY+NNAFRV+A+R RKG +  +PFW++ GEPI DL+ P
Sbjct:  105 PVVVLNPDEPREIFIGGVQSVALPLWAYCKCLTMVRGEPHELGPRLCLRLLQSLFSLHYLVTHNYNGSGGKAPIDPIVMSAVLRQAQLQF-GSGYFFTEPMALGKLRDYLNNAFRVMAFRQRKGERVRSPFWNEKGEPIHDLEAP 248          
BLAST of SMED30013083 vs. TrEMBL
Match: A0A095CBW8 (Uncharacterized protein OS=Schistosoma haematobium OX=6185 GN=MS3_08494 PE=4 SV=1)

HSP 1 Score: 183.341 bits (464), Expect = 3.620e-51
Identity = 80/145 (55.17%), Postives = 106/145 (73.10%), Query Frame = 1
Query:  703 PVVIVNPQEKKEIFVGGNENVRLPFWAYRKCLTCIRGKPNELSSRLCLRLLQAKFGRKYMLSHNYNGSGDKVPIDRQIMSSILVQAKMQFPDQEDFQNNPAKFAMFRDYINNAFRVVAYRHRKGIQSNTPFWDQNGEPIADLDPP 1137
            PVV++NP E +EIF+GG ++V LP WAY KCLT +RG+P+EL  RLCLRLLQ+ F   Y+++HNYNGSG K PID  +MS++L QA++QF     F   P      RDY+NNAFRV+A+R RKG +  +PFW++ GEPI DL+ P
Sbjct:  103 PVVVLNPDEPREIFIGGVQSVALPLWAYCKCLTMVRGEPHELGPRLCLRLLQSLFSLHYLVTHNYNGSGGKAPIDPIVMSAVLRQAQLQF-GSGYFFTEPMALGKLRDYLNNAFRVMAFRQRKGERVRSPFWNEKGEPIHDLEAP 246          
BLAST of SMED30013083 vs. TrEMBL
Match: A0A183M5B3 (Uncharacterized protein OS=Schistosoma margrebowiei OX=48269 GN=SMRZ_LOCUS11238 PE=4 SV=1)

HSP 1 Score: 182.956 bits (463), Expect = 3.810e-51
Identity = 80/145 (55.17%), Postives = 106/145 (73.10%), Query Frame = 1
Query:  703 PVVIVNPQEKKEIFVGGNENVRLPFWAYRKCLTCIRGKPNELSSRLCLRLLQAKFGRKYMLSHNYNGSGDKVPIDRQIMSSILVQAKMQFPDQEDFQNNPAKFAMFRDYINNAFRVVAYRHRKGIQSNTPFWDQNGEPIADLDPP 1137
            PVV++NP E +EIF+GG ++V LP WAY KCLT +RG+P+EL  RLCLRLLQ+ F   Y+++HNYNGSG K PID  +MS++L QA++QF     F   P      RDY+NNAFRV+A+R RKG +  +PFW++ GEPI DL+ P
Sbjct:  103 PVVVLNPDEPREIFIGGVQSVALPLWAYCKCLTMVRGEPHELGPRLCLRLLQSLFSLHYLVTHNYNGSGGKAPIDPIVMSAVLRQAQLQF-GSGYFFTEPMALGKLRDYLNNAFRVMAFRQRKGERVRSPFWNEKGEPIHDLEAP 246          
BLAST of SMED30013083 vs. TrEMBL
Match: G7YEM1 (Uncharacterized protein OS=Clonorchis sinensis OX=79923 GN=CLF_106053 PE=4 SV=1)

HSP 1 Score: 179.874 bits (455), Expect = 1.737e-50
Identity = 79/154 (51.30%), Postives = 108/154 (70.13%), Query Frame = 1
Query:  694 ILEPVVIVNPQEKKEIFVGGNENVRLPFWAYRKCLTCIRGKPNELSSRLCLRLLQAKFGRKYMLSHNYNGSGDKVPIDRQIMSSILVQAKMQFPDQEDFQNNPAKFAMFRDYINNAFRVVAYRHRKGIQSNTPFWDQNGEPIADLDPPSWIADN 1155
            I  P+VI+NP+E +EIF+GG  +V LP WAY+KCLT +RG+P+EL  RLCLRLLQ+ F   Y+++HNYNGSG K PID  +M ++L QA++QF     F   P      RDY+NNAFRV+A+R RKG +  +PFW++ GEP+  L+ P   A+ 
Sbjct:   67 IGNPIVILNPKEPREIFIGGIPSVPLPLWAYKKCLTMVRGEPHELGPRLCLRLLQSLFSLHYLVTHNYNGSGGKAPIDPIVMGAVLRQAQIQF-GSGYFFTEPMALGKLRDYLNNAFRVMAFRQRKGERVRSPFWNEQGEPVHGLEAPVEFAET 219          
BLAST of SMED30013083 vs. Planmine SMEST
Match: SMESG000062614.1 (SMESG000062614.1)

HSP 1 Score: 671.389 bits (1731), Expect = 0.000e+0
Identity = 330/330 (100.00%), Postives = 330/330 (100.00%), Query Frame = 1
Query:  172 MNSNFGFNNGMTIQIPAFNIANDQLFLAIQTYFDNRFNELKDQIQQIQIKSEKLIVNTKKIELEIRNLKMNKYKDVNRGKNKLKYRKSLSKITKKGKVLESDVNELNPKKDCIDQNMESNEILETNSFLLGINKIEDLENKYPAELSPKNFELPLDNIIKKYLKANESKIVYKDILEPVVIVNPQEKKEIFVGGNENVRLPFWAYRKCLTCIRGKPNELSSRLCLRLLQAKFGRKYMLSHNYNGSGDKVPIDRQIMSSILVQAKMQFPDQEDFQNNPAKFAMFRDYINNAFRVVAYRHRKGIQSNTPFWDQNGEPIADLDPPSWIADNIN 1161
            MNSNFGFNNGMTIQIPAFNIANDQLFLAIQTYFDNRFNELKDQIQQIQIKSEKLIVNTKKIELEIRNLKMNKYKDVNRGKNKLKYRKSLSKITKKGKVLESDVNELNPKKDCIDQNMESNEILETNSFLLGINKIEDLENKYPAELSPKNFELPLDNIIKKYLKANESKIVYKDILEPVVIVNPQEKKEIFVGGNENVRLPFWAYRKCLTCIRGKPNELSSRLCLRLLQAKFGRKYMLSHNYNGSGDKVPIDRQIMSSILVQAKMQFPDQEDFQNNPAKFAMFRDYINNAFRVVAYRHRKGIQSNTPFWDQNGEPIADLDPPSWIADNIN
Sbjct:    1 MNSNFGFNNGMTIQIPAFNIANDQLFLAIQTYFDNRFNELKDQIQQIQIKSEKLIVNTKKIELEIRNLKMNKYKDVNRGKNKLKYRKSLSKITKKGKVLESDVNELNPKKDCIDQNMESNEILETNSFLLGINKIEDLENKYPAELSPKNFELPLDNIIKKYLKANESKIVYKDILEPVVIVNPQEKKEIFVGGNENVRLPFWAYRKCLTCIRGKPNELSSRLCLRLLQAKFGRKYMLSHNYNGSGDKVPIDRQIMSSILVQAKMQFPDQEDFQNNPAKFAMFRDYINNAFRVVAYRHRKGIQSNTPFWDQNGEPIADLDPPSWIADNIN 330          
The following BLAST results are available for this feature:
BLAST of SMED30013083 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 SMED30013083 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 SMED30013083 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 SMED30013083 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 SMED30013083 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 SMED30013083 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 SMED30013083 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 SMED30013083 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
G4VFR17.337e-5253.59Uncharacterized protein OS=Schistosoma mansoni OX=... [more]
A0A183PXD52.995e-5155.17Uncharacterized protein OS=Schistosoma mattheei OX... [more]
A0A095CBW83.620e-5155.17Uncharacterized protein OS=Schistosoma haematobium... [more]
A0A183M5B33.810e-5155.17Uncharacterized protein OS=Schistosoma margrebowie... [more]
G7YEM11.737e-5051.30Uncharacterized protein OS=Clonorchis sinensis OX=... [more]
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BLAST of SMED30013083 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 SMED30013083 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 SMED30013083 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 SMED30013083 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 SMED30013083 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 SMED30013083 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000062614.10.000e+0100.00SMESG000062614.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013083 ID=SMED30013083|Name=SMED30013083|organism=Schmidtea mediterranea sexual|type=transcript|length=1170bp
GATCTGGAATACATACATTATTTAACGTGACGCGGCGTTATCATGAATAA
TGTTTCAACGTTCTTGGTCGATAATCGATATTTGAGTGAGTATTCAGTGA
TTACTAGTCGTTTCCTAATTCAACAATAAATTCTCCAGCCGTTATTCGCA
TTAAAAACACATTATCTATCAATGAATTCGAATTTTGGATTCAATAATGG
AATGACAATTCAAATACCGGCATTCAATATAGCAAACGATCAATTGTTTC
TTGCTATTCAAACCTATTTCGATAATAGATTCAACGAATTAAAGGACCAA
ATCCAACAAATCCAAATAAAAAGTGAGAAACTAATTGTCAATACAAAGAA
AATTGAATTAGAAATCAGAAATTTAAAAATGAATAAATATAAAGATGTAA
ATAGAGGAAAAAATAAATTGAAATATCGAAAATCTTTATCGAAAATTACG
AAAAAAGGGAAAGTACTGGAATCGGATGTTAATGAATTAAATCCGAAAAA
AGATTGCATTGACCAAAATATGGAATCCAATGAAATATTGGAAACTAATT
CATTTTTGTTGGGAATTAACAAAATTGAAGACCTGGAAAATAAATATCCA
GCAGAATTATCTCCTAAAAACTTTGAATTGCCTCTTGATAATATAATTAA
AAAATATTTAAAAGCAAATGAATCTAAAATTGTTTATAAAGATATTTTAG
AACCGGTAGTTATCGTTAATCCGCAAGAGAAAAAAGAAATATTTGTAGGA
GGTAATGAAAATGTTAGATTACCCTTTTGGGCTTACAGAAAATGTTTAAC
TTGTATAAGAGGCAAACCAAATGAACTAAGTTCAAGATTATGCTTAAGAC
TCTTACAGGCCAAATTTGGAAGAAAATATATGTTGAGTCACAATTATAAT
GGGAGTGGCGATAAAGTACCAATAGACAGACAAATAATGTCATCAATTTT
GGTTCAAGCTAAAATGCAATTCCCTGATCAAGAAGATTTTCAGAATAACC
CAGCAAAATTCGCTATGTTTAGAGATTATATAAATAACGCTTTCAGAGTT
GTGGCTTATCGACACAGAAAGGGAATACAATCAAATACACCATTTTGGGA
TCAAAATGGAGAACCAATAGCTGATTTAGATCCTCCTTCATGGATAGCAG
ATAATATTAACTAAATGTGG
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protein sequence of SMED30013083-orf-1

>SMED30013083-orf-1 ID=SMED30013083-orf-1|Name=SMED30013083-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=331bp
MNSNFGFNNGMTIQIPAFNIANDQLFLAIQTYFDNRFNELKDQIQQIQIK
SEKLIVNTKKIELEIRNLKMNKYKDVNRGKNKLKYRKSLSKITKKGKVLE
SDVNELNPKKDCIDQNMESNEILETNSFLLGINKIEDLENKYPAELSPKN
FELPLDNIIKKYLKANESKIVYKDILEPVVIVNPQEKKEIFVGGNENVRL
PFWAYRKCLTCIRGKPNELSSRLCLRLLQAKFGRKYMLSHNYNGSGDKVP
IDRQIMSSILVQAKMQFPDQEDFQNNPAKFAMFRDYINNAFRVVAYRHRK
GIQSNTPFWDQNGEPIADLDPPSWIADNIN*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 37..57