SMED30028817

Overview
NameSMED30028817
Smed IDSMED30028817
Length (bp)3021
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 SMED30028817 (SMED30028817) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30028817 (SMED30028817) 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 SMED30028817 (SMED30028817) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30028817 (SMED30028817) 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



SMED30028817

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
body wall musculatureSMED30028817h1SMcG0002375 dd_Smed_v4_17389_0_1dd_Smed_v4PMID:30471994
Scimone et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30028817 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006446:34630..38047 +13243
Homology
[Close]
BLAST of SMED30028817 vs. Planmine SMEST
Match: SMESG000075714.1 (SMESG000075714.1)

HSP 1 Score: 80.8777 bits (198), Expect = 1.127e-15
Identity = 90/337 (26.71%), Postives = 157/337 (46.59%), Query Frame = 3 
Query: 1500 MEVIKECLICYSPMSEESRVIFEDCGHDFCMSCAKEWIFENTNCPIDRIETNTLRVVKGTKSYLMRRGDFDDFVCLSKVLIEIN---FISTILSNMSEIRTVIPVNIEKTDELKETLNNFGNSYEKIWKSLQFPELMVSCNYCDIFFRVSQRVNWVNLLDEFEILFYNINLLIERKSIFLKDISSNTDICVNLLNKKQ------TVVYSEKLQE-HLEYSTNLFQLFLKRTFIFFKSLMTKEMDYFFPILTTQQDQLDFISPGIPVKNIQVQNRXXXXXXXXXXNLYAGRSEYYQK--FQIAVTSLEYLLESINSVSKAAGLKNISAFEKEILRNEL 2474
            ME  +ECLICYSP+  E  + F  CGH FC  C  E +     CP+DR E + L++  GT    M     D F+ LS  +  IN   F    +S    + +   VN +  +  K+T N    S   I+  ++F    VS      + + + ++    L  ++  LF +     E +++FL + +   ++  N ++K+Q       ++ S  L E  +E    LF+  + + FIFF   + +++   FP L T+ +  DF    IP +NI  +N +  L+  +  N+     E+  +    + +  L+ L+ESI SV K      +S  E++++  E+
Sbjct:    1 MENDQECLICYSPLINEISITFISCGHFFCRDCVIESLQIKHICPLDRGEVSLLKINDGTTEQTMM---VDTFMKLSNAIHNINSKFFDFPQISQNKFLFSRFKVN-DVFEYYKDTYNRV--SIISIFYDIKFISNFVSQESSGTWNKKTHQMLVYELQKQYSKLFDHCQS--EIQTLFLAE-NCYKNLQRNKISKEQFQDSITRIINSLNLSENQIETYAKLFEFLMNKIFIFFNKFLKEKLKDLFPNLPTKYNSKDFCEFRIPYRNIDTENEMKFLKDRLLGNIDQSFEEFISEDYLDVVIQHLKDLMESIESVLKIHFKVGLSFIEQKLIPIEI 328
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BLAST of SMED30028817 vs. Planmine SMEST
Match: SMESG000014717.1 (SMESG000014717.1)

HSP 1 Score: 80.1073 bits (196), Expect = 2.276e-15
Identity = 40/116 (34.48%), Postives = 65/116 (56.03%), Query Frame = 3 
Query: 1500 MEVIKECLICYSPMSEESRVIFEDCGHDFCMSCAKEWIFENTNCPIDRIETNTLRVVKGTKSYLMRRGDFDDFVCLSKVLIEINFISTILSNMSEIRTVIPVNIEKTDELKETLNN 1847
            ME+ +ECL+CYS MS E ++ FE C H FC+ CAK W+  NT CP+DRI+  +L+ +  + + L+   D  D + L +   +  +I  +LS + ++          +D+L   L N
Sbjct:    1 MEIYQECLMCYSQMSNEMQIKFEICKHSFCIECAKHWLAINTTCPLDRIQITSLKCITKSGNILINTEDIVDMLILGR---DNEYIEILLSLVDDLTKYCEYLRNNSDDLSNILAN 113
[Close]
BLAST of SMED30028817 vs. Planmine SMEST
Match: SMESG000067246.1 (SMESG000067246.1)

HSP 1 Score: 79.7221 bits (195), Expect = 3.024e-15
Identity = 75/267 (28.09%), Postives = 121/267 (45.32%), Query Frame = 3 
Query: 1512 KECLICYSPMSEESRVIFEDCGHDFCMSCAKEWIF-ENTNCPIDRIETNTLRVVKGTKSYLMRRG-----DFDDFVCLSKVLIEINFISTILSNMSEIRTVIPVNIEKTD-ELKETLNN-FGNSYEKIWKSLQFPELMVSCNYCDIFFRVSQRVNWVNLLDEFEILFY---NINLLIERKSIFLKDISSNTDICVN-----LLNKKQTVVY----SEKLQEHLE---YSTNLFQLFLKRTFIFFKSLMTKEMDYFFPILTTQQDQLD 2243
            +ECLICYSPMS E+  IFE+CGH +C  C +EW+  ++  CP+D I   +L V   T + +         +F DF            I T L           V++E TD E KE + + F NS   I++S     ++     C++F+              ++IL Y   +I L IE  +    DI  N+  C N     L+++ Q + Y    S+ L +H +   Y  NL++L   +        ++ +M  FFP  +T   +++
Sbjct:    3 QECLICYSPMSNETSFIFEECGHSYCSDCVEEWMSRKHKRCPLDSIVIESLNVPNRTNTAIATNTYKAVLEFLDF----------EVIHTRLQQKLSFPHFHAVDLETTDEEFKEMVADFFTNSKFLIYRSHSNDPILSMIIQCNLFYE-----------SIYQILTYELQSICLKIEFITKINADIIDNSKDCFNQYREQLIDRAQFIEYLRIVSDMLNKHYQQYCYHVNLYKLIFTKLLEQLNRFISDKMKAFFPNFSTDSRKIN 248
[Close]
BLAST of SMED30028817 vs. Planmine SMEST
Match: SMESG000067028.1 (SMESG000067028.1)

HSP 1 Score: 77.0258 bits (188), Expect = 2.350e-14
Identity = 34/84 (40.48%), Postives = 49/84 (58.33%), Query Frame = 3 
Query: 1500 MEVIKECLICYSPMSEESRVIFEDCGHDFCMSCAKEWIFENTNCPIDRIETNTLRVVKGTKSYLMRRGDFDDFVCLSKVLIEIN 1751
            ME   EC ICYSP+  E+R+   DCGH FC  C KE++  +  CP+DRI   T+++    K +++   DF   + LS  +I IN
Sbjct:    1 MEDNLECFICYSPLDSETRIFLWDCGHSFCKDCPKEFMKTSFTCPLDRIPITTVKIFHDEKVFVINSKDFIGCIKLSDAIININ 84
[Close]
BLAST of SMED30028817 vs. Planmine SMEST
Match: SMESG000046851.1 (SMESG000046851.1)

HSP 1 Score: 75.485 bits (184), Expect = 8.011e-14
Identity = 40/105 (38.10%), Postives = 59/105 (56.19%), Query Frame = 3 
Query: 1500 MEVIKECLICYSPMSEESRVIFEDCGHDFCMSCAKEWIFENTNCPIDRIETNTLRVVKGTKSYLMRRGDFDDFVCLSKVLIEINFISTILSNMSEIRTVIPVNIE 1814
            ME  +ECLICY+PM++   V FEDCGH  C  CAK  +  N +CP DRI  N+LR ++G+   ++R  DF     L      I+  + IL ++ +   V+  N+ 
Sbjct:    1 MENDQECLICYNPMTD-FIVKFEDCGHSVCRDCAKTCMLCNPSCPFDRISINSLRYIRGSLEDVLRAEDFIALSTLETYECIIDKFNDILDDLLKYHCVLTSNLH 104
The following BLAST results are available for this feature:
BLAST of SMED30028817 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 SMED30028817 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 SMED30028817 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 SMED30028817 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 SMED30028817 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 SMED30028817 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 SMED30028817 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 SMED30028817 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 SMED30028817 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 SMED30028817 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 SMED30028817 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 SMED30028817 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 SMED30028817 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 SMED30028817 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000075714.11.127e-1526.71SMESG000075714.1[more]
SMESG000014717.12.276e-1534.48SMESG000014717.1[more]
SMESG000067246.13.024e-1528.09SMESG000067246.1[more]
SMESG000067028.12.350e-1440.48SMESG000067028.1[more]
SMESG000046851.18.011e-1438.10SMESG000046851.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30028817 ID=SMED30028817|Name=SMED30028817|organism=Schmidtea mediterranea sexual|type=transcript|length=3021bp
ATTGAAGGATTGGTAGCAATTCTAGTAATTTTTGATTGATTAATAGCTAA
CGAACTTTATAATTAGATTTTATTGTAACAAATACAATTATTATATTATT
TGAGAAATAATATTATGTATTAGCTCTATATATATAAATCCTTTTAATAA
AAAATTTTAATTAATTGCTAATAGAAATAAAAAAAGTTATTGTTAAATTA
ATGAAACAATTTTTAGGCTTCAAAAAATATTTTTTAACTTCAAGAGATAT
GCAAACGTTTTAAAAAGTCCCCATCGAAACAGATATTTAAAGAAAATTAT
AAGTTAATAAATGTAATGTCATTTAATATTGATCAGAACAAATGAAATTT
GATGAGTGTAATGAAATGTAAAAAATAAAGATCATGTATCGTCACATTTC
TAAAACATTACTCCCTATTTAACTCCTCCCACCGTGAGCGTGACGTAATT
TATGGATGATACCAAGGATATTCTATTTCCGTGAGTGTCAAAAATACATG
CTGGCAAAGGTAAAAGCTTCAAAGTAGTAACCACGATTCTATAGCTCTAT
TGAGTAAATTCCGCGCTTAAATATAGAGAAAATTTTTCTGTAGACTAGGT
TATTTCTTTAATGAATAAAATTATTTGTTTTATCCTCTTCAAGAAATTGC
CATGTATTTTTGTGACCAATGTTGAGCTAACATTTAATCGGTTACGTACA
AGGATTATTGTACTCGTACTCTAGTGTAAAATTATATGCACATATATCTT
TTTGATAAACAAGGGTTGAATAAGTTTCATCTAATCCTATAGAATATCAT
TTCCTAGAGTTATAAATTCCTCATTTTCATTCAAGTCGACAATAATTTCA
AAGCACTTGGTTCAAACTAGAGCAATTAGCATTGTTTTTCTGGATTTTTG
AAATATAGTAAGTGTTGGATTTGACTTACTGGCTCCCTGAGGACAGAAAT
ATTATTGCACCCCATCTCAAAAAAATTTAACATTTTTTTAATTTAAAAGT
TACGATTTAGGTATCATTTTCTTTTAAGCAAAATCGTTTATGATGTCGGT
ATATTCTTTTTTTGACAGGTTGAATAGGAAATAACTTTATTCTTAAAAAA
ATATGTTTAAAATAAGATTTTTTTTCTAAAATTTTTTCCTGTACAAAAAC
CAGTATCTTATTTCTTATTTAGTAAATTGAATCACCTATCTGGCTTAGAC
TTGACCTAACAGTAGATCCAGCCCTGGATATACAAAATAAATGAGCTAAT
TTGTTCTGAATTTTATTTATATTTCCTTTTATAAAGCATTTATAAAAATA
CTTTGTTAATTTTATCTAATATAGAATAGAACATAAAAAGCTAAAATAAA
ATAAATTATTATAATGAATTTATTTAATTCTATTGACGTTTTATTAATTA
GAATTATACATTTTAAATATCAATTTAAAAATTTTGTTCATTTTAATAAA
TTAATAAAATCTATGGTTGTTTAAATATTCGCGAAAGAATCTGTTTTAAA
TGGAGGTAATTAAAGAATGCCTAATATGTTATTCTCCAATGAGTGAGGAA
TCGCGTGTAATATTTGAAGATTGTGGGCATGACTTTTGTATGAGCTGTGC
TAAAGAATGGATTTTCGAAAATACAAATTGTCCAATTGATAGAATAGAAA
CTAATACACTGAGGGTTGTTAAAGGAACTAAATCATATTTGATGAGGCGT
GGAGATTTCGATGATTTTGTTTGCTTATCAAAAGTTCTAATTGAGATTAA
TTTTATTTCCACTATTTTATCTAATATGTCAGAAATCAGAACTGTAATTC
CCGTAAATATCGAAAAGACAGATGAACTCAAAGAAACTTTAAATAACTTT
GGGAATTCGTATGAAAAGATTTGGAAATCATTGCAATTTCCAGAGTTAAT
GGTTTCATGTAATTATTGTGATATCTTTTTTAGAGTTAGTCAAAGAGTAA
ATTGGGTCAATCTACTTGATGAATTTGAAATACTTTTCTACAATATCAAT
TTGTTAATAGAAAGAAAATCAATATTTCTTAAAGACATTTCATCCAATAC
TGATATTTGTGTTAATTTATTGAATAAAAAACAAACAGTTGTATACTCCG
AGAAACTTCAAGAACATTTGGAATATTCAACAAATCTATTTCAATTATTT
CTAAAAAGAACTTTCATTTTTTTTAAAAGTCTGATGACAAAAGAAATGGA
CTATTTTTTCCCAATATTGACAACACAACAAGACCAGTTAGATTTCATTT
CACCAGGTATTCCTGTTAAAAATATTCAAGTACAAAACAGGTTAATAGAA
CTAGAATTTCTGATATTCGAAAACCTCTATGCAGGTCGTAGTGAATACTA
TCAAAAATTTCAAATCGCCGTCACTTCTTTAGAGTATTTATTGGAATCAA
TCAATTCGGTTTCGAAAGCAGCAGGCTTAAAAAATATTTCAGCTTTCGAA
AAAGAAATTCTTAGAAATGAACTGGCTTATTATGACGCTAAACTTCACCT
TGAAGATAAAGAACCCTTTGAACCTGATCACAACCTTAATGAATTAATTA
AAGTTGTATCAGATCTAATAGGAAATATTTCATATCTGATTACGGAATGT
TATACAATGGAAAGCGTCGAATGCATTAAAAGCGAGTGTAAAGCAAATCT
AAAAGCCATCAAATTTCGATGTATCAAAATAAAAATTGGCGAAGAAAGTT
GGCACTTTTTGTATTTACTAAAACAACTTTATTCAATTTTGGGAGAATTT
TAGTAACCATTCCTTGTTATTGATTATGTTTTTAAAATATAAGTTGTAAA
GGAAACATTTTTCAATTTAATTTTTTATGTTGACTCTTATTCATTGTCTG
TTAGAATGATCTTAAAGGTGAGATTAGCTCAATTTAAAATGAATAAAAAT
TGTCAACAGAAGTTCCTAGAGAGAATTAATTAAATATTAATCGATAAGGC
TCTACATTTGCTTGAAATTACGGGAATATTTAAAAATCCTTAGTAAATAA
TACATGTTTATTGATCTTACA
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protein sequence of SMED30028817-orf-1

>SMED30028817-orf-1 ID=SMED30028817-orf-1|Name=SMED30028817-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=418bp
MEVIKECLICYSPMSEESRVIFEDCGHDFCMSCAKEWIFENTNCPIDRIE
TNTLRVVKGTKSYLMRRGDFDDFVCLSKVLIEINFISTILSNMSEIRTVI
PVNIEKTDELKETLNNFGNSYEKIWKSLQFPELMVSCNYCDIFFRVSQRV
NWVNLLDEFEILFYNINLLIERKSIFLKDISSNTDICVNLLNKKQTVVYS
EKLQEHLEYSTNLFQLFLKRTFIFFKSLMTKEMDYFFPILTTQQDQLDFI
SPGIPVKNIQVQNRLIELEFLIFENLYAGRSEYYQKFQIAVTSLEYLLES
INSVSKAAGLKNISAFEKEILRNELAYYDAKLHLEDKEPFEPDHNLNELI
KVVSDLIGNISYLITECYTMESVECIKSECKANLKAIKFRCIKIKIGEES
WHFLYLLKQLYSILGEF*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000240body wall musculature
Vocabulary: INTERPRO
TermDefinition
IPR001841Znf_RING
IPR013083Znf_RING/FYVE/PHD
IPR017907Znf_RING_CS
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
GO:0008270zinc ion binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR001841Zinc finger, RING-typeSMARTSM00184ring_2coord: 7..47
e-value: 6.7E-5
score: 32.3
IPR001841Zinc finger, RING-typePFAMPF13639zf-RING_2coord: 5..48
e-value: 1.2E-9
score: 38.3
IPR001841Zinc finger, RING-typePROSITEPS50089ZF_RING_2coord: 7..48
score: 12.607
IPR013083Zinc finger, RING/FYVE/PHD-typeGENE3DG3DSA:3.30.40.10coord: 3..63
e-value: 2.2E-10
score: 41.7
IPR017907Zinc finger, RING-type, conserved sitePROSITEPS00518ZF_RING_1coord: 25..34
NoneNo IPR availableSUPERFAMILYSSF57850RING/U-boxcoord: 6..54