SMED30017612

Overview
NameSMED30017612
Smed IDSMED30017612
Length (bp)561
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 SMED30017612 (SMED30017612) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30017612 (SMED30017612) 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 SMED30017612 (SMED30017612) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30017612 (SMED30017612) 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



SMED30017612

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
parapharyngeal regionSMED30017612 SmedASXL_080486SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30017612 dd_Smed_v4_5456_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30017612 dd_Smed_v6_5456_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30017612 dd_Smed_v4_5456_0_1dd_Smed_v4PMID:30962434
Cote et al., 2019		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30017612 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000038:177438..178045 +2712
Homology
[Close]
BLAST of SMED30017612 vs. TrEMBL
Match: A0A1I8HGJ1 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 53.1434 bits (126), Expect = 5.829e-6
Identity = 29/74 (39.19%), Postives = 41/74 (55.41%), Query Frame = 3 
Query:  234 SAQTISCYTCFGCPVPFVTAGITKFSNCTSCLKMTALNIVTKSCNPGACGANIDITGVSTSCCNTNLCDVGQRF 455
            +A+ ISCYTC GC V F+++ +T  S C  C K     +  +SC P +C    D  G    CC+ NLC+ G+R 
Sbjct:    3 TAEAISCYTCTGCSVSFMSSEVTTVSGCNYCAKTVYPGLAIRSCLP-SCSQASDSFGNVPYCCDGNLCNSGERL 75
[Close]
BLAST of SMED30017612 vs. TrEMBL
Match: A0A267GJI2 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig025981g2 PE=4 SV=1)

HSP 1 Score: 53.1434 bits (126), Expect = 5.962e-6
Identity = 29/74 (39.19%), Postives = 41/74 (55.41%), Query Frame = 3 
Query:  234 SAQTISCYTCFGCPVPFVTAGITKFSNCTSCLKMTALNIVTKSCNPGACGANIDITGVSTSCCNTNLCDVGQRF 455
            +A+ ISCYTC GC V F+++ +T  S C  C K     +  +SC P +C    D  G    CC+ NLC+ G+R 
Sbjct:    4 TAEAISCYTCTGCSVSFMSSEVTTVSGCNYCAKTVYPGLAIRSCLP-SCSQASDSFGNVPYCCDGNLCNSGERL 76
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BLAST of SMED30017612 vs. Planmine SMEST
Match: SMESG000007344.1 (SMESG000007344.1)

HSP 1 Score: 189.119 bits (479), Expect = 2.297e-62
Identity = 94/97 (96.91%), Postives = 95/97 (97.94%), Query Frame = 3 
Query:  225 QQNSAQTISCYTCFGCPVPFVTAGITKFSNCTSCLKMTALNIVTKSCNPGACGANIDITGVSTSCCNTNLCDVGQRFTVQRAGIVIAMMLAIGKNLL 515
            QQNSAQTISCYTCFGCPVPFVTAGIT FSNCTSCLKMT LNIVTKSCNPGACGANIDITGVSTSCCNTNLC+VGQRFTVQRAGIVIAMMLAIGKNLL
Sbjct:   17 QQNSAQTISCYTCFGCPVPFVTAGITTFSNCTSCLKMTTLNIVTKSCNPGACGANIDITGVSTSCCNTNLCNVGQRFTVQRAGIVIAMMLAIGKNLL 113
[Close]
BLAST of SMED30017612 vs. Planmine SMEST
Match: SMESG000028039.1 (SMESG000028039.1)

HSP 1 Score: 75.0998 bits (183), Expect = 1.114e-17
Identity = 40/97 (41.24%), Postives = 55/97 (56.70%), Query Frame = 3 
Query:  225 QQNSAQTISCYTCFGCPVPFVTAGITKFSNCTSCLKMTALNIVTKSCNPGACGANIDITGVSTSCCNTNLCDVGQRFTVQRAGIVIAMMLAIGKNLL 515
             QN  QTI+CYTC GCP PFV +     +NCTSC   T  +I+TK+    A  ++  + G S +CCNTNLC+ G   T    G +   ++   KN+L
Sbjct:   17 HQNYGQTINCYTCVGCPNPFVASSAIVITNCTSCYTTTLYSIITKT-CSLASCSSASVLGASVACCNTNLCNKGHWLTASTGGFISVALMVTMKNML 112
[Close]
BLAST of SMED30017612 vs. Planmine SMEST
Match: SMESG000007197.1 (SMESG000007197.1)

HSP 1 Score: 56.9954 bits (136), Expect = 9.744e-11
Identity = 34/98 (34.69%), Postives = 51/98 (52.04%), Query Frame = 3 
Query:  225 QQNSAQTISCYTCFGCPVPFVTAGITKFSNCTSCLKMTALNIVTKSCNPGACGANIDITGVS-TSCCNTNLCDVGQRFTVQRAGIVIAMMLAIGKNLL 515
               +AQT SCY C  C  PFV +  T+ + CT+C   T   IVTK+C   +       TG++  +CC TNLC++  RFT  +  +    + ++G N  
Sbjct:   17 SYTAAQTFSCYNCANCTTPFVASSATQSTGCTACSTTTVTGIVTKACATASLPCVAINTGLAVVACCTTNLCNLATRFTAFKTLLFGLPIFSLGINYF 114
[Close]
BLAST of SMED30017612 vs. Planmine SMEST
Match: SMESG000031234.1 (SMESG000031234.1)

HSP 1 Score: 54.6842 bits (130), Expect = 6.708e-10
Identity = 34/92 (36.96%), Postives = 49/92 (53.26%), Query Frame = 3 
Query:  225 QQNSAQTISCYTCFGCPVPFV-TAGITKFSNCTSCLKMTALNIVTKSCNPGACGANIDITGVSTSCCNTNLCDVGQRFTVQRAGIVIAMMLA 497
            Q   +Q I+CY C GC  PFV ++ +T  +  +     +ALNIVTK+C    C       G +  CC+TNLC+ G  F V  A ++   +LA
Sbjct:   15 QLGHSQLINCYACVGCSNPFVISSALTATNCSSCTTTTSALNIVTKTCASITCNTITSFIGPTNICCSTNLCNTGSEFKVPIAVVIGLPVLA 106
[Close]
BLAST of SMED30017612 vs. Planmine SMEST
Match: SMESG000031270.1 (SMESG000031270.1)

HSP 1 Score: 54.6842 bits (130), Expect = 7.004e-10
Identity = 32/86 (37.21%), Postives = 45/86 (52.33%), Query Frame = 3 
Query:  225 QQNSAQTISCYTCFGCPVPFV-TAGITKFSNCTSCLKMTALNIVTKSCNPGACGANIDITGVSTSCCNTNLCDVGQRFTVQRAGIV 479
            Q    Q I+CY C GC  PFV ++ +T  +  +     +ALNIVTK+C    C       G +  CC+TNLC+ G  F V  A ++
Sbjct:   17 QLGHTQLINCYACVGCSNPFVISSALTATNCSSCTTTTSALNIVTKTCASITCNTITSYIGATNICCSTNLCNTGSEFKVPIAVVI 102
The following BLAST results are available for this feature:
BLAST of SMED30017612 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 SMED30017612 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 SMED30017612 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 SMED30017612 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 SMED30017612 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 SMED30017612 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 SMED30017612 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 SMED30017612 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 2
Match NameE-valueIdentityDescription
A0A1I8HGJ15.829e-639.19Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267GJI25.962e-639.19Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
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BLAST of SMED30017612 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 SMED30017612 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 SMED30017612 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 SMED30017612 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 SMED30017612 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 SMED30017612 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000007344.12.297e-6296.91SMESG000007344.1[more]
SMESG000028039.11.114e-1741.24SMESG000028039.1[more]
SMESG000007197.19.744e-1134.69SMESG000007197.1[more]
SMESG000031234.16.708e-1036.96SMESG000031234.1[more]
SMESG000031270.17.004e-1037.21SMESG000031270.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017612 ID=SMED30017612|Name=SMED30017612|organism=Schmidtea mediterranea sexual|type=transcript|length=561bp
CAAACTGGTATTTCTAAGTGCAAAACTTAATTAAGTGCAGTTGATAAGAT
CAACAAACATAAAATTTATACTCTCAATTGTGAGCTAGCAAACCCTTTCT
GTGTAATTTGTACTGTGATATTTGTACAAGGCTCTTTGTACATTATATAA
ACACCCAACAATAATTAGTTTTTAATATGGCTTTCAAATTTTTGTTTCTT
TTGGCTTTTGCCATTGCACATTTCCAACAGAATTCTGCCCAGACAATTAG
TTGCTATACATGCTTTGGTTGTCCTGTTCCATTTGTCACAGCGGGTATAA
CAAAGTTTTCCAACTGTACATCATGTCTTAAGATGACTGCACTTAATATC
GTTACAAAAAGTTGTAATCCTGGGGCATGTGGTGCAAATATTGATATAAC
CGGAGTTTCAACATCCTGCTGCAATACAAACCTTTGCGACGTAGGACAAC
GGTTCACGGTTCAAAGAGCAGGAATCGTCATCGCAATGATGCTTGCAATC
GGGAAAAATTTGCTTTGATATCAAACTTTTAAAATTTGATTGACAATAAA
TTTTAGTGTCA
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protein sequence of SMED30017612-orf-1

>SMED30017612-orf-1 ID=SMED30017612-orf-1|Name=SMED30017612-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=114bp
MAFKFLFLLAFAIAHFQQNSAQTISCYTCFGCPVPFVTAGITKFSNCTSC
LKMTALNIVTKSCNPGACGANIDITGVSTSCCNTNLCDVGQRFTVQRAGI
VIAMMLAIGKNLL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000418head
PLANA:0000420parapharyngeal region
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..21
score: 0.845
NoneNo IPR availableSUPERFAMILYSSF57302Snake toxin-likecoord: 24..90