SMED30026893

Overview
NameSMED30026893
Smed IDSMED30026893
Length (bp)1126
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 SMED30026893 (SMED30026893) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30026893 (SMED30026893) 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 SMED30026893 (SMED30026893) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30026893 (SMED30026893) 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




SMED30026893

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



PAGE Curations: 1

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30026893h1SMcG0014041 SmedASXL_009522SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015
FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30026893 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.000794:71807..72934 +5596
Homology
BLAST of SMED30026893 vs. TrEMBL
Match: A0A1I8GZZ1 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 78.1814 bits (191), Expect = 2.021e-12
Identity = 69/284 (24.30%), Postives = 125/284 (44.01%), Query Frame = 1
Query:   52 YYDLNISESSKPSDILRYLRLGYTRLAFNRI---IDVKEGCXXXXXXXXXXXXXXXXXXXXXRRIAIPDFSFLINEEVKETALKLNTEVKLFSRLTLIASDHMQLSSFMREYGQLIKKYDVLACDARCSEVLNHMMEKVSFELLTFDLNSPVTILSHKIFKQCRD---RNVAVEINLSAALTSNAGRMNSVKFIHDL--GLYRCPSIITVTSGARSNLLIRNHLSLRCILSTMGLN-DKILKEINNNADKAINKGLARKHTIYGSAAIIQLNKIPGVVSVQVTN 876
            YYDLN+ +  + + + R   LGY+ LAF  +   I V                   + S+   R+     +F    EV+ET LK                      S+ R++ + ++ YD+LA   +    L+   E +  +L+  DL SP        F+  R    R + +E++L   L S   R+ +   + +L       P  + ++SGA +   +R+   +  + +++G+  DK    ++ N + A+   L R+ T +G+ AI Q+ K+PGV SVQ+ +
Sbjct:    9 YYDLNLLDRQE-AMVARSQNLGYSHLAFASVHTNIKVPPPPPSPLPTAAGSSGSGSVWSRTGSRVCRLTLAF--GPEVQETELK----------------------SYFRQHAKELEAYDLLAVLPKSQSALHACAETLPVDLIACDLGSPKLETFWSDFRDIRTAVRRGIKIEVSLQPMLHSQQSRILAATLLFELLTSARLSPDGLVLSSGALNQWDLRDPFGVCALAASLGVPPDKTRACLSANCESAVEHALVRRKTAHGALAIAQIAKLPGVSSVQLAD 267          
BLAST of SMED30026893 vs. TrEMBL
Match: A0A1I8G0Y9 (Uncharacterized protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 78.1814 bits (191), Expect = 2.464e-12
Identity = 69/284 (24.30%), Postives = 125/284 (44.01%), Query Frame = 1
Query:   52 YYDLNISESSKPSDILRYLRLGYTRLAFNRI---IDVKEGCXXXXXXXXXXXXXXXXXXXXXRRIAIPDFSFLINEEVKETALKLNTEVKLFSRLTLIASDHMQLSSFMREYGQLIKKYDVLACDARCSEVLNHMMEKVSFELLTFDLNSPVTILSHKIFKQCRD---RNVAVEINLSAALTSNAGRMNSVKFIHDL--GLYRCPSIITVTSGARSNLLIRNHLSLRCILSTMGLN-DKILKEINNNADKAINKGLARKHTIYGSAAIIQLNKIPGVVSVQVTN 876
            YYDLN+ +  + + + R   LGY+ LAF  +   I V                   + S+   R+     +F    EV+ET LK                      S+ R++ + ++ YD+LA   +    L+   E +  +L+  DL SP        F+  R    R + +E++L   L S   R+ +   + +L       P  + ++SGA +   +R+   +  + +++G+  DK    ++ N + A+   L R+ T +G+ AI Q+ K+PGV SVQ+ +
Sbjct:    9 YYDLNLLDRQE-AMVARSQNLGYSHLAFASVHTNIKVPPPPPSPLPTAAGSSGSGSVWSRTGSRVCRLTLAF--GPEVQETELK----------------------SYFRQHAKELEAYDLLAVLPKSQSALHACAETLPVDLIACDLGSPKLETFWSDFRDIRTAVRRGIKIEVSLQPMLHSQQSRILAATLLFELLTSARLSPDGLVLSSGALNQWDLRDPFGVCALAASLGVPPDKTRACLSANCESAVEHALVRRKTAHGALAIAQIAKLPGVSSVQLAD 267          
BLAST of SMED30026893 vs. TrEMBL
Match: A0A267FCV9 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig013535g1 PE=4 SV=1)

HSP 1 Score: 77.0258 bits (188), Expect = 5.074e-12
Identity = 52/194 (26.80%), Postives = 97/194 (50.00%), Query Frame = 1
Query:  322 RLTLIASDHMQ---LSSFMREYGQLIKKYDVLACDARCSEVLNHMMEKVSFELLTFDLNSPVTILSHKIFKQCRD---RNVAVEINLSAALTSNAGRMNSVKFIHDL--GLYRCPSIITVTSGARSNLLIRNHLSLRCILSTMGLN-DKILKEINNNADKAINKGLARKHTIYGSAAIIQLNKIPGVVSVQVTN 876
            RLTL     +Q   L S+ R++ + ++ YD+LA   +    L+   E +  +L+  DL SP        F+  R    R + +E++L   L S   R+ +   + +L       P  + ++SGA +   +R+   +  + +++G+  DK    ++ N + A+   L R+ T +G+ AI Q+ K+PGV SVQ+ +
Sbjct:   64 RLTLAFGPEVQETELKSYFRQHAKELEAYDLLAVLPKSQSALHACAETLPVDLIACDLGSPKLETFWSDFRDIRTAVRRGIKIEVSLQPMLHSQQSRILAATLLFELLTSARLSPDGLVLSSGALNQWDLRDPFGVCALAASLGVPPDKTRACLSANCESAVEHALVRRKTAHGALAIAQIAKLPGVSSVQLAD 257          
BLAST of SMED30026893 vs. TrEMBL
Match: A0A267FZD3 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig013535g4 PE=4 SV=1)

HSP 1 Score: 76.6406 bits (187), Expect = 6.290e-12
Identity = 52/194 (26.80%), Postives = 97/194 (50.00%), Query Frame = 1
Query:  322 RLTLIASDHMQ---LSSFMREYGQLIKKYDVLACDARCSEVLNHMMEKVSFELLTFDLNSPVTILSHKIFKQCRD---RNVAVEINLSAALTSNAGRMNSVKFIHDL--GLYRCPSIITVTSGARSNLLIRNHLSLRCILSTMGLN-DKILKEINNNADKAINKGLARKHTIYGSAAIIQLNKIPGVVSVQVTN 876
            RLTL     +Q   L S+ R++ + ++ YD+LA   +    L+   E +  +L+  DL SP        F+  R    R + +E++L   L S   R+ +   + +L       P  + ++SGA +   +R+   +  + +++G+  DK    ++ N + A+   L R+ T +G+ AI Q+ K+PGV SVQ+ +
Sbjct:   61 RLTLAFGPEVQETELKSYFRQHAKELEAYDLLAVLPKSQSALHACAETLPVDLIACDLGSPKLETFWSDFRDIRTAVRRGIKIEVSLQPMLHSQQSRILAATLLFELLTSARLSPDGLVLSSGALNQWDLRDPFGVCALAASLGVPPDKTRACLSANCESAVEHALVRRKTAHGALAIAQIAKLPGVSSVQLAD 254          
BLAST of SMED30026893 vs. TrEMBL
Match: H2KRR0 (Ribonuclease P/MRP protein subunit RPP1 OS=Clonorchis sinensis OX=79923 GN=CLF_106902 PE=4 SV=1)

HSP 1 Score: 73.1738 bits (178), Expect = 9.793e-11
Identity = 58/209 (27.75%), Postives = 99/209 (47.37%), Query Frame = 1
Query:  310 KLFSRLTLIASDHMQLSSFMREYGQLIKKYDVLACDARCSEVLNHMMEKV-SFELLTFDLNSPVTI-LSHKIFKQCRDRNVAVEINLSAAL---TSNAGRMNSVKFIHDLGLYRCPS----IITVTSGARSNLLIRNHLSLRCILSTMGLNDKILKE--INNNADKAINKGLARKHTIYGSAAIIQLNKIPGVVSVQVTNKPDDLTNSP 903
            +LF RL L+ S+      F RE+G+ + ++D+++     SE L    E+  +F+L+  DL+S V   LS K +   + R + +E  L   L   +S     +++ F     L  C S     I ++SGA     +R  L++  IL ++GL  K L    + +     +  GL R  T +G+A +++L   P VVS+       +   SP
Sbjct:  104 RLFKRLNLVCSEPSLAGLFFREFGETLNRFDIVSMCPSSSEALVFAYEQPDTFDLIAIDLDSQVDFRLSSKQYSLIQTRGLRLEFKLGPLLRPGSSGTTARSNLAFHFSSMLAGCRSSFSKCIVISSGATMGWEVRRPLAVVSILQSLGLQPKELAHHALTSGPCAVLTHGLTRSRTAHGAAVMLKLLSNPSVVSIGEAQDASEPCESP 312          
BLAST of SMED30026893 vs. Ensembl Yeast
Match: RPP1 (Subunit of both RNase MRP and nuclear RNase P; RNase MRP cleaves pre-rRNA, while nuclear RNase P cleaves tRNA precursors to generate mature 5' ends and facilitates turnover of nuclear RNAs; relocalizes to the cytosol in response to hypoxia [Source:SGD;Acc:S000001104])

HSP 1 Score: 46.595 bits (109), Expect = 2.824e-6
Identity = 42/145 (28.97%), Postives = 65/145 (44.83%), Query Frame = 1
Query:  301 TEVKLFSRLTLIASDHMQLSSFMREYGQLIKKYDVLACDARCSEVLNHMMEKVSFELLTFDLNSPV-TILSHKIFKQCRDRNVAVEINLSAALTSNAGRMNSVKFIHDLGLYRCPSIITVTSGARSNLLIRNHLSLRCILSTMGL 732
            T +KL+SR+TLI  D  +  S  +    + + +D++A      + L      +  +LLTF   S + T L HK    C +R V +EI    AL     R   V  +  +        I + SGA S L  RN L +  ++  +GL
Sbjct:   76 TGLKLYSRITLIIDDPSKGQSLSK----ISQAFDIVAALPISEKGLTLSTTNLDIDLLTFQYGSRLPTFLKHKSICSCVNRGVKLEIVYGYALRDVQARRQFVSNVRSVIRSSRSRGIVIGSGAMSPLECRNILGVTSLIKNLGL 216          
The following BLAST results are available for this feature:
BLAST of SMED30026893 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 SMED30026893 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 SMED30026893 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 SMED30026893 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 SMED30026893 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 SMED30026893 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 SMED30026893 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 SMED30026893 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A1I8GZZ12.021e-1224.30Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A1I8G0Y92.464e-1224.30Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267FCV95.074e-1226.80Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A267FZD36.290e-1226.80Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
H2KRR09.793e-1127.75Ribonuclease P/MRP protein subunit RPP1 OS=Clonorc... [more]
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BLAST of SMED30026893 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 SMED30026893 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 SMED30026893 vs. Ensembl Yeast
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Yeast e!Fungi46)
Total hits: 1
Match NameE-valueIdentityDescription
RPP12.824e-628.97Subunit of both RNase MRP and nuclear RNase P; RNa... [more]
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BLAST of SMED30026893 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 SMED30026893 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 SMED30026893 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 0
Match NameE-valueIdentityDescription
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30026893 ID=SMED30026893|Name=SMED30026893|organism=Schmidtea mediterranea sexual|type=transcript|length=1126bp
CCTGATTAAAATTTTGTAAAATTAAATTTTTACTTTTTAGAAATGAAATT
TTATTATGATTTGAATATATCAGAATCGTCAAAACCTTCAGATATTTTAC
GTTATTTACGACTTGGATATACAAGGCTTGCCTTTAATAGAATAATTGAC
GTGAAAGAAGGTTGCTTATTAGACGAAGACAAAAAGCAATCTAAAGAAGA
AAAAACAAAATTAAAATCAAAATTAGAAAGACGTATTGCAATTCCAGATT
TTAGCTTTTTAATTAATGAAGAAGTTAAAGAAACTGCGTTAAAATTGAAT
ACTGAAGTAAAATTATTTTCTAGATTAACTTTGATTGCGTCTGATCATAT
GCAATTGTCATCCTTCATGCGAGAATACGGTCAACTTATTAAAAAATATG
ACGTTTTGGCATGTGATGCGCGATGCAGTGAAGTTTTGAATCATATGATG
GAGAAGGTCTCATTTGAATTGTTGACGTTCGATCTTAATTCACCGGTTAC
AATACTTTCTCATAAAATTTTTAAACAGTGCCGAGATAGAAATGTTGCCG
TAGAAATTAATCTCTCTGCTGCTTTAACCAGTAACGCGGGTCGAATGAAT
TCAGTAAAATTTATTCATGACTTGGGGTTGTACAGGTGTCCATCAATTAT
AACAGTGACATCAGGTGCCAGATCCAATCTATTAATAAGAAACCATCTTA
GTTTGAGGTGTATTTTGTCAACAATGGGATTGAATGATAAAATCCTCAAA
GAAATTAATAATAACGCAGATAAAGCTATTAACAAAGGTCTGGCAAGAAA
GCATACCATTTATGGTAGCGCAGCAATTATCCAATTGAACAAAATTCCAG
GCGTTGTCTCAGTACAAGTTACTAACAAGCCAGATGATCTGACGAATTCA
CCAAAGAAAAAGAAATTAAAACTTTAAATTAAAATAAAATTTCAACGGGA
ATTTTATTAATTGATAACATTTCTATTCGAAATAGACTCGATCGAATCCG
ATTCATGTAACAGCAAAATTTCACAGCACTGAATGATCTGTAAATAAATG
TTGATATTAATTTATGCTTTTTATAATTAAAAATAAATGTGAAATACATT
GTAAATCAGCAAATAATGAGAGAGGC
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protein sequence of SMED30026893-orf-1

>SMED30026893-orf-1 ID=SMED30026893-orf-1|Name=SMED30026893-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=295bp
MKFYYDLNISESSKPSDILRYLRLGYTRLAFNRIIDVKEGCLLDEDKKQS
KEEKTKLKSKLERRIAIPDFSFLINEEVKETALKLNTEVKLFSRLTLIAS
DHMQLSSFMREYGQLIKKYDVLACDARCSEVLNHMMEKVSFELLTFDLNS
PVTILSHKIFKQCRDRNVAVEINLSAALTSNAGRMNSVKFIHDLGLYRCP
SIITVTSGARSNLLIRNHLSLRCILSTMGLNDKILKEINNNADKAINKGL
ARKHTIYGSAAIIQLNKIPGVVSVQVTNKPDDLTNSPKKKKLKL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000099neuron
PLANA:0002032epidermal cell
PLANA:0002109X1 cell
Vocabulary: INTERPRO
TermDefinition
IPR002738RNase_P_p30
IPR016195Pol/histidinol_Pase-like
Vocabulary: biological process
TermDefinition
GO:0008033tRNA processing
GO:0090501RNA phosphodiester bond hydrolysis
Vocabulary: molecular function
TermDefinition
GO:0004540ribonuclease activity
GO:0003824catalytic activity
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 4..26