SMED30015748

Overview
NameSMED30015748
Smed IDSMED30015748
Length (bp)3034
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 SMED30015748 (SMED30015748) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30015748 (SMED30015748) in cells (dots) of each of the 12 neoblast clusters.

 

back to top

 

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 SMED30015748 (SMED30015748) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30015748 (SMED30015748) in cells (dots) of each of the 10 clusters of sub-leathally irradiated X1 and X2 cells.

 

back to top

 

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

 

back to top
Anatomical Expression

PAGE et. al., 2020



SMED30015748

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



PAGE Curations: 7

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30015748SMESG000036160.1 SmedASXL_017103SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
pharynxSMED30015748SMESG000036160.1 dd_Smed_v4_14291_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30015748SMESG000036160.1 dd_Smed_v4_14291_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30015748SMESG000036160.1 dd_Smed_v4_14291_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30015748SMESG000036160.1 dd_Smed_v4_14291_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30015748SMESG000036160.1 dd_Smed_v6_14291_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
epidermisSMED30015748SMESG000036160.1 dd_Smed_v4_14291_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
Alignments
SMED30015748 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006342:19098..25849 +13572
Homology
[Close]
BLAST of SMED30015748 vs. Planmine SMEST
Match: SMESG000036160.1 (SMESG000036160.1)

HSP 1 Score: 318.161 bits (814), Expect = 7.372e-95
Identity = 195/210 (92.86%), Postives = 197/210 (93.81%), Query Frame = 1 
Query:  139 MESERKLWGIYLNLIFFDNPLDQISKYRSSTNDSRLNGTYLCVENIIHCXXXXXXXXXXXXAIFSRTLTVTEKDSLERIERIPFFELCRQSLEIQEVKSLEFQKINDTFTKECCRLENELKLLNDINKEKENQCLEYKREIFXXXXXXXXXXXXXXSMQEEKLEMTKSTQNIFEKIDEENIILKNEINRQKAIIDDLKHFKESHEHLNKS 768
            M+SERKLW             DQISKYRSSTNDSRLNGTYLCVENIIHCLELFENVVEFLEAIFSRTLTVTEKDSLERIERIP+FELCRQSLEIQEVKSLEFQKINDTFTKECCRLENELKLLNDINKEKENQCLEYKREIFQNLQNINQIQREIQSMQEEKLEMTKSTQNIFEKIDEENIILKNEINRQKAIIDDLKHFKESHEHLNKS
Sbjct:    1 MQSERKLW-------------DQISKYRSSTNDSRLNGTYLCVENIIHCLELFENVVEFLEAIFSRTLTVTEKDSLERIERIPYFELCRQSLEIQEVKSLEFQKINDTFTKECCRLENELKLLNDINKEKENQCLEYKREIFQNLQNINQIQREIQSMQEEKLEMTKSTQNIFEKIDEENIILKNEINRQKAIIDDLKHFKESHEHLNKS 197
[Close]
BLAST of SMED30015748 vs. Planmine SMEST
Match: SMESG000036160.1 (SMESG000036160.1)

HSP 1 Score: 308.916 bits (790), Expect = 2.156e-91
Identity = 187/225 (83.11%), Postives = 191/225 (84.89%), Query Frame = 1 
Query:  139 MESERKLWGIYLNLIFFDNPLDQISKYRSSTNDSRLNGTYLCVENIIHCXX---------------XXXXXXXXXXAIFSRTLTVTEKDSLERIERIPFFELCRQSLEIQEVKSLEFQKINDTFTKECCRLENELKLLNDINKEKENQCLEYKREIFXXXXXXXXXXXXXXSMQEEKLEMTKSTQNIFEKIDEENIILKNEINRQKAIIDDLKHFKESHEHLNKS 768
            M+SERKLW             DQISKYRSSTNDSRLNGTYLCVENIIHCLE               + E   +  EAIFSRTLTVTEKDSLERIERIP+FELCRQSLEIQEVKSLEFQKINDTFTKECCRLENELKLLNDINKEKENQCLEYKREIFQNLQNINQIQREIQSMQEEKLEMTKSTQNIFEKIDEENIILKNEINRQKAIIDDLKHFKESHEHLNKS
Sbjct:    1 MQSERKLW-------------DQISKYRSSTNDSRLNGTYLCVENIIHCLELFENVVEFLGIFKEIMKEIKDDLTEAIFSRTLTVTEKDSLERIERIPYFELCRQSLEIQEVKSLEFQKINDTFTKECCRLENELKLLNDINKEKENQCLEYKREIFQNLQNINQIQREIQSMQEEKLEMTKSTQNIFEKIDEENIILKNEINRQKAIIDDLKHFKESHEHLNKS 212
[Close]
BLAST of SMED30015748 vs. Planmine SMEST
Match: SMESG000077219.1 (SMESG000077219.1)

HSP 1 Score: 74.7146 bits (182), Expect = 6.793e-16
Identity = 35/48 (72.92%), Postives = 40/48 (83.33%), Query Frame = -2 
Query: 2890 ECEMKRTKGSMKTGKPIDMSFLPNLNKLNQVAKMISISTPTVERKIKS 3033
            ECEMK+ K S+KTGKPIDMSFLPNLNKL+QVAK+I IST TV R   +
Sbjct:   46 ECEMKQAKRSVKTGKPIDMSFLPNLNKLDQVAKIIHISTATVGRNFST 93
[Close]
BLAST of SMED30015748 vs. Planmine SMEST
Match: SMESG000058643.1 (SMESG000058643.1)

HSP 1 Score: 77.411 bits (189), Expect = 1.654e-14
Identity = 36/43 (83.72%), Postives = 38/43 (88.37%), Query Frame = -2 
Query: 2905 ECEMKRTKGSMKTGKPIDMSFLPNLNKLNQVAKMISISTPTVE 3033
            ECE+KR K SMKTGKPIDMSFLPNLNKL+QVAKMI IST T E
Sbjct:  347 ECEIKRAKWSMKTGKPIDMSFLPNLNKLDQVAKMIPISTATAE 389
[Close]
BLAST of SMED30015748 vs. Planmine SMEST
Match: SMESG000069985.1 (SMESG000069985.1)

HSP 1 Score: 67.3958 bits (163), Expect = 5.129e-11
Identity = 33/48 (68.75%), Postives = 37/48 (77.08%), Query Frame = -2 
Query: 2890 ECEMKRTKGSMKTGKPIDMSFLPNLNKLNQVAKMISISTPTVERKIKS 3033
            EC+MK+TK SM TGKPI MSFLPNLNKL+QVAK I IS   VER   +
Sbjct: 1223 ECKMKQTKWSMVTGKPIFMSFLPNLNKLDQVAKTIPISIAIVERNFST 1270
The following BLAST results are available for this feature:
BLAST of SMED30015748 vs. Ensembl Human
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Human e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30015748 vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30015748 vs. Ensembl Fly
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Drosophila e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30015748 vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30015748 vs. Ensembl Xenopus
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Xenopus e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30015748 vs. Ensembl Mouse
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Mouse e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30015748 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30015748 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30015748 vs. Ensembl Cavefish
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Cavefish e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30015748 vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30015748 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30015748 vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30015748 vs. Ensembl Medaka
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Medaka e!99)
Total hits: 0
Match NameE-valueIdentityDescription
back to top
BLAST of SMED30015748 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000036160.17.372e-9592.86SMESG000036160.1[more]
SMESG000036160.12.156e-9183.11SMESG000036160.1[more]
SMESG000077219.16.793e-1672.92SMESG000077219.1[more]
SMESG000058643.11.654e-1483.72SMESG000058643.1[more]
SMESG000069985.15.129e-1168.75SMESG000069985.1[more]
back to top
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015748 ID=SMED30015748|Name=SMED30015748|organism=Schmidtea mediterranea sexual|type=transcript|length=3034bp
ATTGAGTTCACCTTGGTACTAAATTTATAACTATATAAATTTTATTTAAT
GTTTTAAAATAAAGTTATTCCAAGTTATTAATTTAGATTGAACATTGTTT
GCATATTTACTTTTCCAACTTTGTATTATTTAATTTGAATGGAGTCAGAA
AGAAAATTATGGGGTATTTATTTAAATTTAATTTTTTTTGACAATCCATT
AGATCAAATTTCCAAATACCGATCTTCAACAAATGATTCTAGATTAAACG
GAACGTATTTGTGTGTTGAAAATATTATTCATTGCCTAGAATTATTTGAA
AATGTAGTAGAATTTCTAGAAGCAATATTTAGTCGTACTTTGACTGTTAC
TGAAAAAGATAGTTTAGAAAGAATAGAGCGAATACCTTTTTTTGAATTAT
GTAGACAGTCGTTAGAAATACAAGAAGTAAAATCTTTGGAATTTCAAAAA
ATTAATGACACTTTTACGAAAGAATGTTGTCGTTTGGAAAACGAGTTAAA
GCTATTAAATGATATCAATAAAGAAAAAGAAAACCAATGCTTAGAATATA
AACGAGAAATATTTCAAAATTTACAAAATATAAATCAGATACAAAGAGAG
ATACAAAGCATGCAAGAAGAAAAACTAGAAATGACCAAAAGTACACAAAA
TATATTTGAAAAAATTGATGAAGAAAATATTATTTTAAAGAATGAAATTA
ATCGACAAAAGGCTATTATAGACGATCTGAAACATTTCAAAGAGTCACAT
GAACATTTAAATAAAAGTATATTAATAAAAGTATTTAAAAAATAAAAGTA
TATAAAAGTGTTATGATCAACAATATTTTTTACTCCGCAAACCCTGCAGT
ATGCGCGCGTTGCCCGTTTCTACACAAGCAAATTGTTTTTGTAATAATAC
ATTTTCTCACGGGTTCTGCAGGGTTCAATTGAAAATATATTTTTTTAATA
TAGTGAGTTACATTAAATTTTAATAGTGTTAAGTTTTCATTTATTAGTGT
TTATTTCTATTATTTTCTATTTGTTTTATTGTTTAACTATTAATAAATAT
TAATTAAAATTTGATCATATATCAGTTATTTGTTTATGATATTTTAGCAG
TTTATTTTAATAGTGGACGAGTCAATATTTTTGTTATAATGGATATTTAA
AGATTTGCGTTTCAATAAATTGTAAAATATTGATAAGTTGTAGCTGCAGT
TTATAGATTAAGGAAACTTATTATGTAGTTATGCTTATTAAAGATATATA
AAGAAAATAAAATTTTGCTATAGCCAAATGAATTTGCCCTACTTTGAAAA
TAAATTGTCAGATTTTAACATGATTTTATGAACAACTCTTAAAAGTGGTA
GTAATAACTCGGATAATAAGTAATCATCATAGCTTTTAACATTTTACAAT
CATCTTTAAAATAAATCATTCTCCAAAATTTATAATCTGAGTCAGTTCAG
TGACTAAAGTTTCTGATCAACTCACATTTTGCAGAAGAGAGACGAAAAGT
CTGTATCCAGGCATCCATAATTTTCTAGTACTCAAAATGCTGTTTGCAAT
AGATTCTTTTTTTCCATATACAATGAATTGAAAACTGATTCAAATGTCTG
AATGTCTATTTACAAACATAGCACTCTTGAAAAGGCCAAATTTAGTGTGA
AGTAAAAAATACAAAAGTAACATATTAATTAAATATTTGCAACAATTCAG
CCTCTGGAGAATTTACCTTATCTCCATAACCTTATAATAATGGTGATTCT
ATTGTACTTTATTGTATAAGCTAAATTATTTCAGTCACACCTGTATATTG
TTTTTATACTTAAAATTTTCAGTACTAATTTTATTTTTAAATTTAAATGT
TTATGACTATTTGTTTTTATTAACTCTGTAATTCTAAAAGTTGCGTAAAC
GAAAAATTTTAAAAACGAATTTTTTTGTGATATTTTAATTTAAAAAAATA
AATTAAGGCATTTTATGTTTTAGCAATGTATTTTATAATATGTCTCAAAA
TATAATTCATATAGAATAAAAACAGAAAAATAGAAAATAATTTTTTTAAT
TTTTTTACCGTTGGAAATCATTGGGTTAATAAATAATTAATATTAAAATT
TATAAATGTTACTTTAATTTATTATTTAATCTAAATTAAAATTTATGTGA
TTTAATATTGTTAATTTTTTACGAGGGGGGTGTCCCGGTCGGACTTGCAA
AAAATCTGAAAACCCTAACAATAAATTAATTAAATTAATAAAGGAGTCAC
GTCACATAAATTTTATTATCAATGAAAACTGTTACTTTTTTGGTTTTCGA
TTTTCCTCTTTTTTTGACATTTCATTCATTTTCATATGACAAAAATTCAA
AATTTATTTTTTATGGCATAGAGAATATTTAATGATCTTTGATGACTGAA
ATATCATAAAATTTGTTGATTTATTGTTATATAATAATAACATTTGCTAA
ATACCTGCAATATGCTTTCTGATCAGGATCATCTAAAGCAGGGTTTCTTA
ACCGGTGAGGTATACCTCCCTTGGGGAGGTATACTAATGTGTTGGGGGAG
GTATGAGATTTTGTTTATTTTTGTTATGTTTATATAAAAAATTATATTTT
ATATCAGTATGAATTAAATATGATTTTTTTTATAAATATATATTAAAATG
GTAAAAATAAAATAATATATGTAATGTTGGTATACCACTAATTATGTTTC
TTATCTTTTCTTAAAATAAATTAATTATGCTGGAGGTGAGAACATAAAAT
TAAATATTAGGTGAGGTATGAAGTAAAAAAGGTTAAGAACCCCTGCTTTA
TATAGAAATCTCTCCTCAACAACTAATTAATTTTTATCAAAACTTTGATT
GAACTCCCAGGGAGCGAGTGGAGTAATTTGTTTTTATCTAGATTTGATTT
TCCTCTCTACAGTAGGTGTTGAAATAGAAATCATCTTGGCCACTTGATTT
AGCTTGTTCAGATTGGGAAGAAAGGACATGTCGATTGGTTTTCCAGTTTT
CATACTGCCTTTAGTCCGTTTCATTTCACATTCC
back to top

protein sequence of SMED30015748-orf-1

>SMED30015748-orf-1 ID=SMED30015748-orf-1|Name=SMED30015748-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=219bp
MESERKLWGIYLNLIFFDNPLDQISKYRSSTNDSRLNGTYLCVENIIHCL
ELFENVVEFLEAIFSRTLTVTEKDSLERIERIPFFELCRQSLEIQEVKSL
EFQKINDTFTKECCRLENELKLLNDINKEKENQCLEYKREIFQNLQNINQ
IQREIQSMQEEKLEMTKSTQNIFEKIDEENIILKNEINRQKAIIDDLKHF
KESHEHLNKSILIKVFKK*
back to top
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000034epidermis
PLANA:0000099neuron
PLANA:0000418head
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 120..168