SMED30017202

Overview
NameSMED30017202
Smed IDSMED30017202
Length (bp)1354
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ Neoblast 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 SMED30017202 (SMED30017202) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30017202 (SMED30017202) in cells (dots) of each of the 12 neoblast clusters.

 

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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



SMED30017202

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
X2 cellSMED30017202 SmedASXL_074439SmedAsxl_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
SMED30017202 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.004218:43575..44929 +6476
v31.007133:12042..13396 -6422
v31.000788:82758..84077 +4632
v31.005258:6819..8194 -4519
v31.015534:9524..10690 +4472
v31.000187:201539..202890 +4129
Homology
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BLAST of SMED30017202 vs. Planmine SMEST
Match: SMESG000044259.1 (SMESG000044259.1)

HSP 1 Score: 245.358 bits (625), Expect = 2.857e-80
Identity = 147/150 (98.00%), Postives = 148/150 (98.67%), Query Frame = 3 
Query:  555 MAQQIDIIPAYPLPANAENSVTNNESSALTGGASHSXXXXXXXXXXXXXXXXXXXXXXXMLQANLRSNKDTELRELSDLMMTEYTTSRHDDELDVIYAPRQPEFSHPVPTSAQITTTTNGHSAESPINIQIATSSRTIPDGEISSTGRSS 1004
            MAQQIDIIPAYPLPANAENSVTNNESSALTGGASHSNANHRHKPNRNR RRQRRRAENA+LQANLRSNKDTELRELSDLMMTEYTTSRHDDELDVIYAPRQPEFSHPVPTSAQIT TTNGHSAESPINIQIATSSRTIPDGEISSTGRSS
Sbjct:    1 MAQQIDIIPAYPLPANAENSVTNNESSALTGGASHSNANHRHKPNRNRSRRQRRRAENALLQANLRSNKDTELRELSDLMMTEYTTSRHDDELDVIYAPRQPEFSHPVPTSAQITITTNGHSAESPINIQIATSSRTIPDGEISSTGRSS 150
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BLAST of SMED30017202 vs. Planmine SMEST
Match: SMESG000003019.1 (SMESG000003019.1)

HSP 1 Score: 244.588 bits (623), Expect = 5.228e-77
Identity = 174/332 (52.41%), Postives = 213/332 (64.16%), Query Frame = 3 
Query:  144 WKTNVSHLLNQICSFLFSLRTDHINFLRNLSYAEIKHDFTANSKNCASSVCRGCGTIC*EARAG*FTLREKYKKLKGT*WSPEATKELYKKIT*LSHAPDYLIIENRSHRITISKQSPALHQVFTEKELQARLPSRNMAQQIDIIPAYPLPANAENSVTNNESSALTGGASHSXXXXXXXXXXXXXXXXXXXXXXXMLQANLRSNKDTELRELSDLMMTEYTTSRHDDELDVIYAPRQPEFSHPVPTSAQITTTTNGHSAESPINIQIATSSRTIPDGEISSTGRSS*QIISVIEPTVPRDHIANHFRQADSHPTPRLPKRRCLPVDIDGEE 1139
            ++  +S L+     F+ S R    NF   L Y    ++   + +N  SSVC G  T   +     F LREKY+KLKG    PEA KELYK+IT LS A D LIIE RS R  ISKQ   L Q+FTEKELQARLPSRN+AQQI IIPA+     AE S  N++S A     S +  N RHKPNRNRRRRQRRRAENA+LQANLRS+   ELR++ D +  E++  R+DD+LD+IYAP QPEFSH  P  AQ+T    GH  E PI I IAT+ R+I D ++ S+GRSS QIISV+EPT PR    +   QA+ H     PKR+CL VDIDG+E
Sbjct:   45 YRVILSVLVRIFGFFVQSTR----NFSWKLLYIFNNNELATHPQNYISSVCYGYDTTTRKLERENFILREKYEKLKGL---PEAIKELYKEITLLSRASDDLIIETRSQRSKISKQIAVLRQIFTEKELQARLPSRNLAQQIIIIPAHHQSIIAEKSSINHDSIAPVDRISQA--NRRHKPNRNRRRRQRRRAENALLQANLRSDGRPELRKVLDFVFIEHSAPRYDDDLDIIYAPIQPEFSHLAP--AQLTINATGH--ELPIKIHIATTFRSILDEDVESSGRSSPQIISVVEPTTPRGQRVDSSPQAEPHTILLCPKRQCLSVDIDGDE 363
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BLAST of SMED30017202 vs. Planmine SMEST
Match: SMESG000047104.1 (SMESG000047104.1)

HSP 1 Score: 236.498 bits (602), Expect = 9.279e-77
Identity = 143/150 (95.33%), Postives = 146/150 (97.33%), Query Frame = 3 
Query:  555 MAQQIDIIPAYPLPANAENSVTNNESSALTGGASHSXXXXXXXXXXXXXXXXXXXXXXXMLQANLRSNKDTELRELSDLMMTEYTTSRHDDELDVIYAPRQPEFSHPVPTSAQITTTTNGHSAESPINIQIATSSRTIPDGEISSTGRSS 1004
            MAQQIDIIPAYPLPANAENSVTNNE+SALTGGASHSN NHRHKPNRNRRRRQRRRAENA+LQANLRSNKDTELRELSDLMMTEYTTS+HDDELDVIYA RQPEFSHPVPTSAQIT TTNG SAESPINIQIATSSRTIPDGEISSTGRSS
Sbjct:    1 MAQQIDIIPAYPLPANAENSVTNNENSALTGGASHSNENHRHKPNRNRRRRQRRRAENALLQANLRSNKDTELRELSDLMMTEYTTSKHDDELDVIYATRQPEFSHPVPTSAQITITTNGRSAESPINIQIATSSRTIPDGEISSTGRSS 150
[Close]
BLAST of SMED30017202 vs. Planmine SMEST
Match: SMESG000000887.1 (SMESG000000887.1)

HSP 1 Score: 225.328 bits (573), Expect = 5.867e-71
Identity = 148/217 (68.20%), Postives = 169/217 (77.88%), Query Frame = 3 
Query:  456 ENRSHRITISKQSPALHQVFTEKELQARLPSRNMAQQIDIIPAYPLPANAENSVTNNESSALTGGASHSXXXXXXXXXXXXXXXXXXXXXXXMLQANLRSNKDTELRELSDLMMTEYTTSRHDDELDVIYAPRQPEFSHPVPTSAQITTTTNGHSAESPINIQIATSSRTIPDGEISSTGRSS*QIISVIEPTVPRDHIANHFRQADSHPTPRLPKR 1106
            + RS RITIS+QS +L Q+FTEKELQARLPSRN+AQ IDIIPA  LP N  NS  NN+ S L  GASH NAN R+KPNRNR RRQR RAENA+LQA LRSN+D++LRE+SD M+ E+T   HD ELDVIY P Q  FSHPVPT AQIT TTNGHSAESPINI IAT+   IPDGE SS+GRSS QIIS+++ TVPR+  AN FRQ D H T + PKR
Sbjct:   41 KERSQRITISEQSASLRQIFTEKELQARLPSRNLAQHIDIIPANHLPINTGNSAMNNDDSVLADGASHPNANRRNKPNRNRHRRQRCRAENALLQAKLRSNRDSKLREISDPMVMEHTAYGHDGELDVIYGPIQSAFSHPVPTPAQITITTNGHSAESPINIYIATAFYAIPDGERSSSGRSSPQIISIVDSTVPRNQRANLFRQIDFHTTSQFPKR 257
[Close]
BLAST of SMED30017202 vs. Planmine SMEST
Match: SMESG000046646.1 (SMESG000046646.1)

HSP 1 Score: 218.009 bits (554), Expect = 1.341e-67
Identity = 144/267 (53.93%), Postives = 181/267 (67.79%), Query Frame = 3 
Query:  339 FTLREKYKKLKGT*WSPEATKELYKKIT*LSHAPDYLIIENRSHRITISKQSPALHQVFTEKELQARLPSRNMAQQIDIIPAYPLPANAENSVTNNESSALTGGASHSXXXXXXXXXXXXXXXXXXXXXXXMLQANLRSNKDTELRELSDLMMTEYTTSRHDDELDVIYAPRQPEFSHPVPTSAQITTTTNGHSAESPINIQIATSSRTIPDGEISSTGRSS*QIISVIEPTVPRDHIANHFRQADSHPTPRLPKRRCLPVDIDGEE 1139
            FTLREKY +LK T  SPE T+E YKKI  LS A D LIIENRS RI IS +  A  Q+FTEKE QARLPSRNM Q++DIIP + LP N +N   NN  +  T   + S  N RH+PNRNRRRRQRR+AENA+LQ+NL   ++  L  +++L   +       ++L VI APRQP+FS P P  AQI  T + +SAE  IN+QI+ +SRT PD +  S+GRSS QIISVIEPT+ R   +++  +A S  T R PKR+ LPVDID E+
Sbjct:   30 FTLREKYNRLKVTWCSPEITRERYKKINRLSRARDDLIIENRSQRIMISYECAAFRQIFTEKEKQARLPSRNMTQRLDIIPVHHLPTNPKNQRDNNNKNVPTKLTTPSTVNQRHRPNRNRRRRQRRKAENALLQSNLGVRENASLESITELFWPQPIALNDGEDLGVIDAPRQPDFSQPAPIPAQINITMDNYSAEMLINMQISIASRTTPDRDAISSGRSSPQIISVIEPTINRSQRSDNLPRAPSSSTTRPPKRKYLPVDIDEED 296
The following BLAST results are available for this feature:
BLAST of SMED30017202 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 SMED30017202 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 SMED30017202 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 SMED30017202 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 SMED30017202 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 SMED30017202 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 SMED30017202 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 SMED30017202 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 0
Match NameE-valueIdentityDescription
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BLAST of SMED30017202 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 SMED30017202 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 SMED30017202 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 SMED30017202 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 SMED30017202 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 SMED30017202 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000044259.12.857e-8098.00SMESG000044259.1[more]
SMESG000003019.15.228e-7752.41SMESG000003019.1[more]
SMESG000047104.19.279e-7795.33SMESG000047104.1[more]
SMESG000000887.15.867e-7168.20SMESG000000887.1[more]
SMESG000046646.11.341e-6753.93SMESG000046646.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017202 ID=SMED30017202|Name=SMED30017202|organism=Schmidtea mediterranea sexual|type=transcript|length=1354bp
AATCAATATCATCTAAATTAATTTAAGTCTTCTTTTAAAGGGTTAAAATT
TTCTCGAAGATTATCTGCATCGATTCAACACTTTGTAACCTGAAAATTAA
CCAATCCAAGTAGAAACCGAATTCCAACTGAACCTAAATTCCGTGGAAAA
CAAATGTTTCGCATCTATTAAATCAGATTTGTAGTTTTCTTTTCTCGTTG
CGAACTGATCACATCAATTTCCTGCGAAATTTATCGTACGCTGAAATTAA
GCATGACTTTACTGCGAATTCCAAGAATTGTGCCAGCTCCGTCTGCCGTG
GCTGCGGCACAATATGTTGAGAGGCTCGAGCGGGATAATTCACCCTCCGC
GAAAAATACAAAAAGCTAAAGGGCACTTGATGGTCTCCAGAAGCTACTAA
AGAACTCTACAAAAAGATCACGTAGCTCTCTCATGCTCCCGATTATCTCA
TTATTGAGAATAGAAGTCATCGGATCACGATATCCAAGCAAAGTCCCGCA
CTCCATCAGGTCTTTACGGAGAAAGAACTCCAAGCTCGCCTACCGAGCAG
AAATATGGCACAGCAAATTGATATAATTCCAGCGTATCCCTTGCCGGCCA
ATGCAGAAAACTCGGTGACCAATAATGAAAGTAGCGCGCTCACGGGTGGC
GCCTCTCATTCGAATGCAAATCACCGGCACAAACCGAATCGAAACCGCCG
TCGACGGCAGAGACGTAGAGCCGAAAACGCCATGCTACAGGCCAATTTGA
GAAGTAATAAAGACACGGAATTAAGAGAACTCTCAGATTTGATGATGACT
GAATATACAACTTCTAGGCATGACGACGAATTAGATGTTATCTATGCTCC
TCGTCAACCGGAGTTCTCTCATCCCGTCCCCACTTCTGCTCAGATCACAA
CTACTACAAATGGCCACTCTGCCGAGTCCCCAATTAATATTCAGATAGCC
ACTTCATCTCGTACAATTCCTGATGGAGAAATATCTTCTACTGGGCGATC
GTCGTAGCAGATTATCTCGGTCATAGAACCGACGGTACCTCGAGACCATA
TTGCGAATCATTTTCGTCAAGCTGATTCCCATCCAACACCACGATTACCT
AAACGTCGATGTTTGCCCGTAGATATTGACGGGGAGGAATGAAGCACAGA
TTTCCAAATCAACGATCCAAGTACTGTTACCGAAATGACATCGACACTAA
ATCTAATTAACGTTACTATGGATCTACATTCTTTTGCTCTAGTAGACAAT
CGATACAATTTCTACTTGTGTTTTCACTTTGTATCTTATAGTTAAATTAT
TTATGCCTTGTAGCTCGAATATTTATATCTGGTAGTTAAAACATTGACAT
CTTG
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protein sequence of SMED30017202-orf-1

>SMED30017202-orf-1 ID=SMED30017202-orf-1|Name=SMED30017202-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=151bp
MAQQIDIIPAYPLPANAENSVTNNESSALTGGASHSNANHRHKPNRNRRR
RQRRRAENAMLQANLRSNKDTELRELSDLMMTEYTTSRHDDELDVIYAPR
QPEFSHPVPTSAQITTTTNGHSAESPINIQIATSSRTIPDGEISSTGRSS
*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002111X2 cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 13..32