MER

Overview
NameMER (AHJ60960.1)
Smed IDSMED30013435
Length (bp)1336
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 MER (SMED30013435) t-SNE clustered cells

Violin plots show distribution of expression levels for MER (SMED30013435) 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 MER (SMED30013435) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for MER (SMED30013435) 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




SMED30013435

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
epidermisSMED30013435h1SMcG0022544 dd_Smed_v4_2243_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30013435h1SMcG0022544 dd_Smed_v4_2243_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30013435h1SMcG0022544 dd_Smed_v4_2243_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30013435h1SMcG0022544 dd_Smed_v4_2243_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
whole organismSMED30013435h1SMcG0022545 mersmed_ncbi_20240424PMID:24523458
Lin et al., 2014
whole organism asexual adult colorimetric in situ hybridization evidence
whole organismSMED30013435h1SMcG0022544 mersmed_ncbi_20240424PMID:24523458
Lin et al., 2014
whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Homology
BLAST of MER vs. TrEMBL
Match: W8E6B9 (MER OS=Schmidtea mediterranea OX=79327 GN=mer PE=2 SV=1)

HSP 1 Score: 680.633 bits (1755), Expect = 0.000e+0
Identity = 379/392 (96.68%), Postives = 380/392 (96.94%), Query Frame = 2
Query:   83 MEECAKDTNQNHIEIXXXXXXXXXXXXXXXTSIFQRKPNRKRNKSEPCLPGTNENNPKEGSEKRLSLNNDDKSKEKPDENGENQISSASFRPVSKAPFFVNDFTAELKKSLLQRSKMVEEGQTSEGIIQIEMTRSNYSVSDEEKQEEIERKTFEEKVALFESQISGGSVHNSLKRDSGENRLENEESELDETAEKSMNYNNDDVTQEMALEFSESDNRAIDDASCKLSSXXXXXXXXXXXXXXXXXXXXXGEGNAQNISLRISDSDKIIQADSNEGNSKMGNNSDGILNYEITEIAVTENQNQEVPTAMEDGEINCVKNKLENVEIVDTQNEEIVENGAILDEIKTEINADNNCQSCLVTESQGSQSCLTEASAAHGNLLNETDSVQLTNDT 1258
            MEECAKDTNQNHIEIKPKKSGFFRRFKRRFTSIFQRKPNRKRNKSEPCLPGTNENN KEGSEKRLSLNNDDKSKEKPDENGENQISSASFRPVSKAPFFVNDFTAELKKSLLQRSKMVEEGQTSEGIIQIEMTRSNYSVSDEEKQEEIERKTFEEKVALFESQISGGSVHNSLKRDSGENRLENEESELDETAEKSMNYNNDDVTQEMALEFSESDNRAIDDASCKLSS      AA AAADDDDNDNDDGEGNAQNISLRISDSDKIIQ DSNEGNSKMGNNSDGI NYEITEIAVTENQNQE PT MEDGEINCV+NKLENVEIVDTQNEEIVENGAILDEIKTEINADNNCQSCLVTESQGSQSCLTEASAAHGNLLNETDSVQLTNDT
Sbjct:    1 MEECAKDTNQNHIEIKPKKSGFFRRFKRRFTSIFQRKPNRKRNKSEPCLPGTNENNLKEGSEKRLSLNNDDKSKEKPDENGENQISSASFRPVSKAPFFVNDFTAELKKSLLQRSKMVEEGQTSEGIIQIEMTRSNYSVSDEEKQEEIERKTFEEKVALFESQISGGSVHNSLKRDSGENRLENEESELDETAEKSMNYNNDDVTQEMALEFSESDNRAIDDASCKLSS----NNAAAAAADDDDNDNDDGEGNAQNISLRISDSDKIIQVDSNEGNSKMGNNSDGIPNYEITEIAVTENQNQEEPTVMEDGEINCVENKLENVEIVDTQNEEIVENGAILDEIKTEINADNNCQSCLVTESQGSQSCLTEASAAHGNLLNETDSVQLTNDT 388          
BLAST of MER vs. Planmine SMEST
Match: SMESG000016263.1 (SMESG000016263.1)

HSP 1 Score: 701.049 bits (1808), Expect = 0.000e+0
Identity = 392/392 (100.00%), Postives = 392/392 (100.00%), Query Frame = 2
Query:   83 MEECAKDTNQNHIEIXXXXXXXXXXXXXXXTSIFQRKPNRKRNKSEPCLPGTNENNPKEGSEKRLSLNNDDKSKEKPDENGENQISSASFRPVSKAPFFVNDFTAELKKSLLQRSKMVEEGQTSEGIIQIEMTRSNYSVSDEEKQEEIERKTFEEKVALFESQISGGSVHNSLKRDSGENRLENEESELDETAEKSMNYNNDDVTQEMALEFSESDNRAIDDASCKLSSXXXXXXXXXXXXXXXXXXXXXGEGNAQNISLRISDSDKIIQADSNEGNSKMGNNSDGILNYEITEIAVTENQNQEVPTAMEDGEINCVKNKLENVEIVDTQNEEIVENGAILDEIKTEINADNNCQSCLVTESQGSQSCLTEASAAHGNLLNETDSVQLTNDT 1258
            MEECAKDTNQNHIEIKPKKSGFFRRFKRRFTSIFQRKPNRKRNKSEPCLPGTNENNPKEGSEKRLSLNNDDKSKEKPDENGENQISSASFRPVSKAPFFVNDFTAELKKSLLQRSKMVEEGQTSEGIIQIEMTRSNYSVSDEEKQEEIERKTFEEKVALFESQISGGSVHNSLKRDSGENRLENEESELDETAEKSMNYNNDDVTQEMALEFSESDNRAIDDASCKLSSNNAAAAAAVAAADDDDNDNDDGEGNAQNISLRISDSDKIIQADSNEGNSKMGNNSDGILNYEITEIAVTENQNQEVPTAMEDGEINCVKNKLENVEIVDTQNEEIVENGAILDEIKTEINADNNCQSCLVTESQGSQSCLTEASAAHGNLLNETDSVQLTNDT
Sbjct:    1 MEECAKDTNQNHIEIKPKKSGFFRRFKRRFTSIFQRKPNRKRNKSEPCLPGTNENNPKEGSEKRLSLNNDDKSKEKPDENGENQISSASFRPVSKAPFFVNDFTAELKKSLLQRSKMVEEGQTSEGIIQIEMTRSNYSVSDEEKQEEIERKTFEEKVALFESQISGGSVHNSLKRDSGENRLENEESELDETAEKSMNYNNDDVTQEMALEFSESDNRAIDDASCKLSSNNAAAAAAVAAADDDDNDNDDGEGNAQNISLRISDSDKIIQADSNEGNSKMGNNSDGILNYEITEIAVTENQNQEVPTAMEDGEINCVKNKLENVEIVDTQNEEIVENGAILDEIKTEINADNNCQSCLVTESQGSQSCLTEASAAHGNLLNETDSVQLTNDT 392          
The following BLAST results are available for this feature:
BLAST of MER 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 MER 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 MER 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 MER 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 MER 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 MER 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 MER 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 MER vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
W8E6B90.000e+096.68MER OS=Schmidtea mediterranea OX=79327 GN=mer PE=2... [more]
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BLAST of MER 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 MER 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 MER 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 MER 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 MER 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 MER vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000016263.10.000e+0100.00SMESG000016263.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30013435
GenBankAHJ60960.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30013435 ID=SMED30013435|Name=MER|organism=Schmidtea mediterranea sexual|type=transcript|length=1336bp
CTGAAAATATTAATTTTTTTTATTAAAATCGTTTTTAAAATTAGAAGTGC
ATTGAACATTCGGATAGTTAATTGATTAACTGATGGAGGAATGCGCTAAA
GATACAAATCAAAATCATATAGAAATTAAACCGAAGAAATCGGGATTTTT
TCGTCGTTTTAAAAGACGGTTTACTTCCATTTTTCAGCGTAAACCAAACC
GAAAACGCAACAAGTCGGAGCCGTGTTTGCCTGGAACCAATGAAAACAAT
CCCAAGGAAGGTAGCGAAAAGAGACTGTCTCTAAACAATGATGATAAATC
CAAGGAGAAACCTGATGAAAATGGCGAAAATCAAATTTCGAGTGCATCAT
TCAGACCGGTTTCCAAAGCTCCCTTTTTTGTGAATGATTTTACTGCTGAA
TTAAAGAAATCCCTTTTGCAACGCTCGAAAATGGTGGAAGAAGGTCAAAC
CTCAGAAGGGATTATCCAAATTGAAATGACACGAAGTAACTATTCAGTTT
CCGATGAAGAAAAACAAGAAGAAATTGAGAGAAAAACCTTTGAAGAAAAG
GTAGCTTTATTTGAAAGTCAAATAAGTGGTGGTAGTGTGCACAACAGCCT
GAAGCGAGACAGTGGTGAAAATAGACTTGAAAATGAAGAAAGCGAACTGG
ACGAGACAGCTGAGAAAAGTATGAATTATAATAATGATGATGTCACACAA
GAGATGGCCTTGGAATTTTCTGAATCGGACAATCGAGCTATAGATGACGC
TAGTTGTAAACTTTCCAGCAATAATGCTGCTGCTGCTGCTGCTGTTGCTG
CTGCTGATGATGATGATAATGATAATGATGATGGTGAAGGAAATGCACAA
AACATTTCTCTGAGAATTTCGGACTCTGATAAAATCATTCAAGCCGACTC
CAATGAAGGAAATTCAAAAATGGGAAATAACTCAGATGGAATCCTTAATT
ACGAGATTACAGAAATAGCTGTCACCGAAAACCAAAACCAAGAAGTACCT
ACTGCCATGGAGGACGGTGAAATTAATTGCGTTAAAAATAAGTTAGAAAA
TGTGGAAATAGTCGATACCCAGAACGAGGAAATAGTTGAAAATGGTGCAA
TATTGGATGAGATAAAAACGGAAATTAATGCTGACAATAATTGCCAAAGT
TGCTTAGTTACGGAAAGTCAAGGAAGTCAGAGCTGCTTGACAGAAGCATC
GGCAGCCCATGGCAATTTACTCAACGAAACCGATTCTGTGCAATTAACAA
ACGATACATAACTTAATAATTTTGTTAATTTAAGATTATTGAAATTAATT
TGTGTAATAAATGTATTGTTAATTTTTCAAAAAAAA
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protein sequence of SMED30013435-orf-1

>SMED30013435-orf-1 ID=SMED30013435-orf-1|Name=SMED30013435-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=393bp
MEECAKDTNQNHIEIKPKKSGFFRRFKRRFTSIFQRKPNRKRNKSEPCLP
GTNENNPKEGSEKRLSLNNDDKSKEKPDENGENQISSASFRPVSKAPFFV
NDFTAELKKSLLQRSKMVEEGQTSEGIIQIEMTRSNYSVSDEEKQEEIER
KTFEEKVALFESQISGGSVHNSLKRDSGENRLENEESELDETAEKSMNYN
NDDVTQEMALEFSESDNRAIDDASCKLSSNNAAAAAAVAAADDDDNDNDD
GEGNAQNISLRISDSDKIIQADSNEGNSKMGNNSDGILNYEITEIAVTEN
QNQEVPTAMEDGEINCVKNKLENVEIVDTQNEEIVENGAILDEIKTEINA
DNNCQSCLVTESQGSQSCLTEASAAHGNLLNETDSVQLTNDT*
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Aliases
The feature 'MER' has the following synonyms
Synonym
MER
Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000101muscle cell
PLANA:0000136whole organism
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 175..202
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 33..91
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 57..81
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 168..196