SMED30007436

Overview
NameSMED30007436
Smed IDSMED30007436
Length (bp)1597
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 SMED30007436 (SMED30007436) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30007436 (SMED30007436) 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.
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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



SMED30007436

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



PAGE Curations: 2

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
X1 cellSMED30007436 SmedASXL_013109SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
X2 cellSMED30007436 SmedASXL_013109SmedAsxl_ww_GCZZ01PMID:26114597
Zhu et al., 2015		FACS sorted cell population asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of SMED30007436 vs. Planmine SMEST
Match: SMESG000074893.1 (SMESG000074893.1)

HSP 1 Score: 172.555 bits (436), Expect = 4.097e-51
Identity = 95/145 (65.52%), Postives = 110/145 (75.86%), Query Frame = -1 
Query:  107 PKRQSTNKYSLSKYRKFRGMESISTTTPEM*PQFSEEISMAEIDLTTEENITMPV*NLSTYLKWAIEAFL*ISKENIISMDNVTMKRIQPTLEYGPMLKCRPSRKRKASLDMNVGEDNVTISGVMYEKEESIHIYKHGSE*VGIK 541
            PK     KYSLS+YRK RG+ES STT  E+ PQF EE +M EIDLT EENI M   N ST LKWA E FL  +KE II M  V ++RIQPTLEYGPM KCRPSRKRKAS +++V EDN+TI+ V+YE++ESIHIYKHGSE V IK
Sbjct:   23 PKISHPEKYSLSEYRKLRGIESTSTTR-EICPQFPEETTMTEIDLTVEENI-MKFENFSTLLKWATETFLEEAKEIIIPMVIVKIERIQPTLEYGPMPKCRPSRKRKASSNIDVVEDNITINEVVYERKESIHIYKHGSERVEIK 165
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BLAST of SMED30007436 vs. Planmine SMEST
Match: SMESG000031866.1 (SMESG000031866.1)

HSP 1 Score: 123.635 bits (309), Expect = 1.576e-49
Identity = 60/90 (66.67%), Postives = 68/90 (75.56%), Query Frame = -3 
Query:  849 DSILLPISEDMLKKKMSLIGKEMDL*EIPDRILFFDAKYGASETGKIIPLAVAIMNYHVKAVMNAYIISRGRIRHFNLRIHGIMEVSTSN 1118
            DS LLPISED++KKKMS I KEM L EI D+ LF DA+YG SETGK+IPL VAIMNYH   V N Y+    RIRHFNLR+HGI E S+ N
Sbjct:  537 DSTLLPISEDIVKKKMSFIRKEMGLEEIRDKKLFVDAEYGTSETGKMIPLTVAIMNYHGGVVKNTYLTPGRRIRHFNLRVHGITETSSRN 626

HSP 2 Score: 85.1149 bits (209), Expect = 1.576e-49
Identity = 37/75 (49.33%), Postives = 57/75 (76.00%), Query Frame = -2 
Query: 1129 IKLAMDEEYYLHIIKETLEIRNANNQVWWELKTFTPWKVQKEAVSKIIRAANEEAVIVLEIRTKIEVNEVSKAHP 1353
            I+++  E+ Y+HI++ T+E+ N  NQ+W ELK  T WK+Q+E+V+K +RAANEE +I +E RT+ + +EV KAHP
Sbjct:  458 IQISRREKGYVHIMRRTIEVLNGENQLWMELKKLTSWKIQRESVTKTMRAANEEVIIAIESRTESKAHEVPKAHP 532

HSP 3 Score: 28.1054 bits (61), Expect = 1.576e-49
Identity = 15/35 (42.86%), Postives = 20/35 (57.14%), Query Frame = -1 
Query: 1427 WSKYHGRDPLMTFIQGYRKI--ILYSKSTESITTY 1525
            WSK+ G+D  MT    YR+I  +  SKS  +I  Y
Sbjct:  397 WSKFRGQDRYMTVTPNYREITQVKDSKSIPNIPNY 431
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BLAST of SMED30007436 vs. Planmine SMEST
Match: SMESG000034928.1 (SMESG000034928.1)

HSP 1 Score: 119.013 bits (297), Expect = 9.771e-47
Identity = 72/189 (38.10%), Postives = 105/189 (55.56%), Query Frame = -1 
Query:  248 KILVSHNLHAEPQYLGIWIEKLHGIRDLAAAQVLNNMRVTRKGDWFNLQTVVREICGEETQIWIHSAL-DVKRICNVYQTVENQWVDDIPMPKRQSTNKYSLSKYRKFRGMESISTTTPEM*PQFSEEISMAEIDLTTEENITMPV*NLSTYLKWAIEAFL*ISKENIISMDNVTMKRIQPTLEYGPML 811
            KIL+ H+LHAE QYL +WI+ LHGIRDLA AQ L  + + R+G++F L+TVV+E+ G++  + IHSAL DV+ I                  ++Q + KYSL +YRK     S S T               EIDLT  E++       +  LKWA E  + I ++++  + N  + RIQP  E+GP++
Sbjct: 1294 KILIDHDLHAEIQYLKLWIDHLHGIRDLATAQALEKIGMFRRGEFFKLKTVVQEMFGDQMWVAIHSALEDVRNI------------------RKQPSRKYSLEEYRKLHNSTSTSMTG-----------ITEEIDLTAAEDMETDGETQTVQLKWATEESIEIIEKSLGLIINEPIHRIQPIFEHGPII 1453

HSP 2 Score: 88.1965 bits (217), Expect = 9.771e-47
Identity = 39/83 (46.99%), Postives = 60/83 (72.29%), Query Frame = -3 
Query:  810 KEMDL*EIPDRILFFDAKYGASETGKIIPLAVAIMNYHVKAVMNAYIISRGRIRHFNLRIHGIMEVSTSNLKDQHEEMADIQK 1058
            KEM+  EI  +ILF DA+YG+S++ +++PL+ AIMNY+ K + + Y+  RG + HFN +IHGI EV++ N  DQ+  M ++QK
Sbjct: 1207 KEMNQEEIRSKILFIDAEYGSSKSKQMVPLSTAIMNYYGKTIKDVYLTPRGNLWHFNSQIHGITEVASRNQYDQYAIMKEVQK 1289
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BLAST of SMED30007436 vs. Planmine SMEST
Match: SMESG000013248.1 (SMESG000013248.1)

HSP 1 Score: 100.523 bits (249), Expect = 4.865e-44
Identity = 49/102 (48.04%), Postives = 74/102 (72.55%), Query Frame = -3 
Query:  804 LLPISEDMLKKKMSLIGKEMDL*EIPDRILFFDAKYGASETGKIIPLAVAIMNYHVKAVMNAYIISRGRIRHFNLRIHGIMEVSTSNLKDQHEEMADIQKDT 1109
            LLPISE+MLK+K+  I K + + EI ++ILF DA+YG SE  ++I L+VAIM+Y+ + + + YI +R ++++FN  IHGI E ++ N +DQ+EEM  IQ  T
Sbjct:   40 LLPISEEMLKRKLLFIRKRLTIDEIREKILFMDAEYGISEAHEMIQLSVAIMDYYGRVIEDVYITTRIKLQYFNASIHGITERNSPNQQDQYEEMKSIQNLT 141

HSP 2 Score: 97.0561 bits (240), Expect = 4.865e-44
Identity = 75/230 (32.61%), Postives = 111/230 (48.26%), Query Frame = -1 
Query:  122 KILVSHNLHAEPQYLGIWIEKLHGIRDLAAAQVLNNMRVTRKGDWFNLQTVVREICGEETQIWIHSALDVKRICNVYQTVENQWVDDIPMPKRQSTNKYSLSKYRKFRGMESISTTTPEM*PQFSEEISMAEIDLTTEENITMPV*NLSTYLKWAIEAFL*ISKENIISMDNVTMKRIQPTLEYGPMLKCRPSRKRKASLDMNVGEDNVTISGVMYEKEESIHIYKHGSE 811
            KIL+ H+L AE +YL IW+  L+GIRD AAAQ+                                               E QW+DD+       + KY LS+Y+  R     ST+     P+  EE  + E+ +  E N T+P       LKWA E  + + +E    +++  + ++Q TLEYGPMLK +P RKRK  +   +GED + I+  M++KEE++H YK G+E
Sbjct:  144 KILIGHDLQAERKYLKIWVNHLYGIRDFAAAQM-----------------------------------------------EQQWIDDVDWKTINPSRKYLLSEYKTMRA----STSKD---PESEEECEIVEMQM--EVNKTIPE------LKWATEETIEMPEEGFDEIEDAKIIKLQITLEYGPMLKEKPIRKRK--IISEIGEDTMGINWKMFKKEETVHRYKCGNE 309
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BLAST of SMED30007436 vs. Planmine SMEST
Match: SMESG000017494.1 (SMESG000017494.1)

HSP 1 Score: 139.428 bits (350), Expect = 1.908e-39
Identity = 71/109 (65.14%), Postives = 87/109 (79.82%), Query Frame = -1 
Query:   98 MAEIDLTTEENITMPV*NLSTYLKWAIEAFL*ISKENIISMDNVTMKRIQPTLEYGPMLKCRPSRKRKASLDMNVGEDNVTISGVMYEKEESIHIYKHGSE*VGIKMNP 424
            M +IDLTT EN+ +   N ST LKW+ E FL  +++ +I M  V ++RIQPTLEYGPM KCRPSRKRKAS ++NVGEDN+TI+ V+YE+EESIHIYKHGSE V IKMNP
Sbjct:    1 MTKIDLTTNENV-LEAENFSTELKWSTETFLEEAEKIMIPMAIVKIERIQPTLEYGPMPKCRPSRKRKASSNINVGEDNITINEVVYEREESIHIYKHGSERVEIKMNP 108
The following BLAST results are available for this feature:
BLAST of SMED30007436 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 SMED30007436 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 SMED30007436 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 SMED30007436 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 SMED30007436 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 SMED30007436 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 SMED30007436 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 SMED30007436 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 SMED30007436 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 SMED30007436 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 SMED30007436 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 SMED30007436 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 SMED30007436 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 SMED30007436 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000074893.14.097e-5165.52SMESG000074893.1[more]
SMESG000031866.11.576e-4966.67SMESG000031866.1[more]
SMESG000034928.19.771e-4738.10SMESG000034928.1[more]
SMESG000013248.14.865e-4448.04SMESG000013248.1[more]
SMESG000017494.11.908e-3965.14SMESG000017494.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30007436 ID=SMED30007436|Name=SMED30007436|organism=Schmidtea mediterranea sexual|type=transcript|length=1597bp
TTCCCAGGATTCAGCATGCCAAAATTTAAAGCAAAAAAACGAAACCAAAT
CATTTATTATTGATTCTTAATAAATTATAAATATTTTATATAAATATAGG
ATTCATTTTTATCCCCACTCACTCGGACCCATGTTTATAGATGTGAATTG
ATTCTTCCTTTTCATACATAACTCCACTTATAGTGACATTATCTTCTCCA
ACATTCATGTCCAACGAGGCTTTCCGTTTCCGACTTGGCCGGCACTTTAG
CATTGGTCCGTATTCCAATGTTGGTTGGATTCTCTTCATCGTAACATTGT
CCATTGAAATTATATTTTCTTTCGATATTTAAAGAAATGCTTCAATTGCC
CATTTTAAATAAGTGGATAAATTCTAAACCGGCATTGTTATATTTTCCTC
CGTTGTCAGATCAATTTCTGCCATCGAAATCTCTTCAGAAAATTGTGGTC
ACATTTCTGGTGTTGTCGTTGATATCGATTCCATCCCTCGAAACTTTCTA
TATTTGCTTAACGAGTATTTATTCGTTGACTGCCTTTTGGGCATTGGTAT
GTCATCTACCCATTGATTTTCTACTGTCTGATATACATTGCAAATACGTT
TGACATCCAGCGCAGAGTGGATCCAAATTTGAGTTTCTTCACCACATATT
TCTCTCACAACCGTTTGCAAATTGAACCAATCACCTTTCCTGGTTACTCT
CATGTTATTGAGGACTTGTGCTGCTGCAAGATCACGTATTCCATGTAGTT
TTTCAATCCAAATTCCCAGGTATTGGGGTTCTGCGTGTAGGTTGTGACTT
ACTAGTATCTTTCTGGATATCTGCCATCTCTTCGTGTTGATCTTTTAAAT
TACTGGTGGATACCTCCATAATCCCGTGAATCCTTAAATTGAAATGTCGG
ATTCTTCCTCTCGAAATTATATAGGCATTCATTACTGCTTTTACATGGTA
ATTCATGATGGCAACTGCCAATGGTATTATCTTTCCAGTTTCTGACGCAC
CATATTTGGCATCGAAAAATAATATTCTGTCAGGGATTTCTTAAAGATCC
ATTTCCTTTCCTATCAAAGACATTTTCTTCTTCAACATGTCTTCCGAAAT
TGGCAACAATATTGAATCTCATTCCAATTGGATGCGCTTTGGATACTTCA
TTCACTTCGATCTTTGTTCTTATCTCTAGTACTATGACCGCTTCCTCGTT
TGCTGCACGTATTATTTTTGAAACAGCTTCTTTCTGCACTTTCCACGGTG
TAAATGTTTTGAGCTCCCACCACACTTGATTATTTGCATTCCTTATTTCG
AGTGTCTCTTTGATTATGTGAAGATAATATTCCTCATCCATAGCCAATTT
AATTTTGACTTGCGGCTTATCGTAAATATTTGAATTTTCATTCTTCTGTC
GTCGATCCTTAAATAATTTGGGATTTGTAAGTTGTTATTGATTCTGTAGA
TTTGCTGTACAGTATGATTTTTCTGTATCCTTGTATAAATGTCATAAGTG
GATCTCGCCCATGGTATTTGCTCCATTTTCTTGATAATAAGGTGATAATA
ACAATAAAAATTTACCGATTTTAAATATTTATTAAAAATTGAAAAAT
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protein sequence of SMED30007436-orf-1

>SMED30007436-orf-1 ID=SMED30007436-orf-1|Name=SMED30007436-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=104bp
MDEEYYLHIIKETLEIRNANNQVWWELKTFTPWKVQKEAVSKIIRAANEE
AVIVLEIRTKIEVNEVSKAHPIGMRFNIVANFGRHVEEENVFDRKGNGSL
RNP*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002109X1 cell
PLANA:0002111X2 cell