SMED30025284

Overview
NameSMED30025284
Smed IDSMED30025284
Length (bp)3666
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 SMED30025284 (SMED30025284) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30025284 (SMED30025284) 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



SMED30025284

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 cellSMED30025284 SmedASXL_072979SmedAsxl_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 SMED30025284 vs. Planmine SMEST
Match: SMESG000013157.1 (SMESG000013157.1)

HSP 1 Score: 250.366 bits (638), Expect = 4.012e-75
Identity = 118/147 (80.27%), Postives = 131/147 (89.12%), Query Frame = -1 
Query:    1 DSWIDASRVIARFPAHSVARCRQAMLDAGFSISPVHETRSGTQRDSDEIDLPYVTIKREPGRNPAREIRGQAEYLLVRLETHQAETNRQVEQAKQYLQRVSADIAAGRIPSTDGYAPRYNVSYELDDPKLQERMVDMNVVIPRRILP 441
            DSWIDASRVIARFPAHS ARCRQAM DAGFSI PV ETR GTQ DS+E+DL YV IKREPGR+PARE+RGQAEYLL RLE HQAETNRQVEQA+QYL+RV+ DIAAGRIPSTDGYAP+YNVS+ELDDP+LQ +M +M V +PR ILP
Sbjct:   90 DSWIDASRVIARFPAHSAARCRQAMWDAGFSIFPVRETRGGTQGDSNEVDLSYVAIKREPGRSPAREMRGQAEYLLARLERHQAETNRQVEQARQYLRRVNEDIAAGRIPSTDGYAPQYNVSFELDDPRLQRQMSEMRVAVPRHILP 236
[Close]
BLAST of SMED30025284 vs. Planmine SMEST
Match: SMESG000063851.1 (SMESG000063851.1)

HSP 1 Score: 232.646 bits (592), Expect = 5.290e-70
Identity = 113/142 (79.58%), Postives = 123/142 (86.62%), Query Frame = -1 
Query:    1 ASRVIARFPAHSVARCRQAMLDAGFSISPVHETRSGTQRDSDEIDLPYVTIKREPGRNPAREIRGQAEYLLVRLETHQAETNRQVEQAKQYLQRVSADIAAGRIPSTDGYAPRYNVSYELDDPKLQERMVDMNVVIPRRILP 426
            ASRVIARFP HS ARCRQAM DAGFSISPV E R GTQ DSDE+ LPYV IKRE GR+PAREIRGQAE+LL RLE HQAETNRQVEQA+QYLQRV+ DIAAG IPSTDGYAP+YNVSYEL+DP+LQ RM +M V +PR ILP
Sbjct:   18 ASRVIARFPTHSAARCRQAMWDAGFSISPVREARGGTQGDSDEVYLPYVAIKRESGRSPAREIRGQAEHLLARLEHHQAETNRQVEQARQYLQRVNEDIAAGWIPSTDGYAPQYNVSYELNDPRLQRRMPEMRVAVPRHILP 159
[Close]
BLAST of SMED30025284 vs. Planmine SMEST
Match: SMESG000065931.1 (SMESG000065931.1)

HSP 1 Score: 222.246 bits (565), Expect = 3.768e-66
Identity = 106/153 (69.28%), Postives = 125/153 (81.70%), Query Frame = -1 
Query:    1 IYHFLGDSWIDASRVIARFPAHSVARCRQAMLDAGFSISPVHETRSGTQRDSDEIDLPYVTIKREPGRNPAREIRGQAEYLLVRLETHQAETNRQVEQAKQYLQRVSADIAAGRIPSTDGYAPRYNVSYELDDPKLQERMVDMNVVIPRRILP 459
            I++ L DSWIDA RVIARFPAH+ ARCRQAM DAGFSIS V ETR G Q  S++++LPYV IKREPG N AREIRGQAE+LL RLE HQ ET RQ+ +A++YL +V+ DIA GRIPSTDGYAP YNVS+ELDDP L  R+  MNV++PRR+LP
Sbjct:    7 IHYNLEDSWIDAPRVIARFPAHAAARCRQAMWDAGFSISTVRETRFGNQGSSEDVELPYVAIKREPGGNLAREIRGQAEFLLGRLEEHQKETERQIIKARRYLAQVNKDIAEGRIPSTDGYAPSYNVSFELDDPSLCNRLETMNVILPRRVLP 159
[Close]
BLAST of SMED30025284 vs. Planmine SMEST
Match: SMESG000028747.1 (SMESG000028747.1)

HSP 1 Score: 215.698 bits (548), Expect = 7.878e-64
Identity = 100/131 (76.34%), Postives = 114/131 (87.02%), Query Frame = -1 
Query:   67 IYHFLGDSWIDASRVIARFPAHSVARCRQAMLDAGFSISPVHETRSGTQRDSDEIDLPYVTIKREPGRNPAREIRGQAEYLLVRLETHQAETNRQVEQAKQYLQRVSADIAAGRIPSTDGYAPRYNVSYEL 459
            +   L +SWIDASRVIARFPAHS ARCRQAM DA FSISPV E RS  QR+SDE+DLPYV IKREPGRNPARE+RGQAEYLL RLE HQ ETN+QVE+ +QYL++++ADIAAG+IPSTDGYAP YN+SYEL
Sbjct:   11 VSFLLENSWIDASRVIARFPAHSAARCRQAMWDARFSISPVREARSDKQRNSDEVDLPYVVIKREPGRNPAREMRGQAEYLLARLEKHQKETNKQVEKPRQYLRQINADIAAGKIPSTDGYAPPYNISYEL 141
[Close]
BLAST of SMED30025284 vs. Planmine SMEST
Match: SMESG000032540.1 (SMESG000032540.1)

HSP 1 Score: 206.068 bits (523), Expect = 1.540e-60
Identity = 95/152 (62.50%), Postives = 120/152 (78.95%), Query Frame = -1 
Query:    4 IYHFLGDSWIDASRVIARFPAHSVARCRQAMLDAGFSISPVHETRSGTQRDSDEIDLPYVTIKREPGRNPAREIRGQAEYLLVRLETHQAETNRQVEQAKQYLQRVSADIAAGRIPSTDGYAPRYNVSYELDDPKLQERMVDMNVVIPRRIL 459
            + HFL +SWI ASRV  RFPAHS  RCRQAM DAGFSISPV E+R G++ ++D++DLP+V IKREPGRNPAREIRGQAEYLL RLE H+ +T+ +V++A+++L+ ++ DIAAG IPSTDGYAP YN  + LDDP+L      M VV+PR  L
Sbjct:    1 MSHFLENSWIYASRVTLRFPAHSAVRCRQAMWDAGFSISPVRESRMGSRSNTDDVDLPFVAIKREPGRNPAREIRGQAEYLLARLEEHKRQTDHEVDKARRHLEEINWDIAAGIIPSTDGYAPPYNTPFNLDDPRLNRSSSAMKVVVPRETL 152
The following BLAST results are available for this feature:
BLAST of SMED30025284 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 SMED30025284 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 SMED30025284 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 SMED30025284 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 SMED30025284 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 SMED30025284 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 SMED30025284 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 SMED30025284 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 SMED30025284 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 SMED30025284 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 SMED30025284 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 SMED30025284 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 SMED30025284 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 SMED30025284 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000013157.14.012e-7580.27SMESG000013157.1[more]
SMESG000063851.15.290e-7079.58SMESG000063851.1[more]
SMESG000065931.13.768e-6669.28SMESG000065931.1[more]
SMESG000028747.17.878e-6476.34SMESG000028747.1[more]
SMESG000032540.11.540e-6062.50SMESG000032540.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30025284 ID=SMED30025284|Name=SMED30025284|organism=Schmidtea mediterranea sexual|type=transcript|length=3666bp
TGGCAAGATACGTCGTGGAATCACCACATTCATGTCCACCATCCGCTCTT
GTAGTTTCGGATCGTCTAGTTCGTAAGAAACGTTGTAGCGTGGGGCATAC
CCGTCAGTGCTGGGTATCCTGCCCGCCGCGATGTCCGCACTGACCCTCTG
TAGATATTGCTTGGCTTGTTCTACTTGTCGGTTGGTCTCTGCTTGATGTG
TCTCGAGGCGCACTAGTAAGTATTCGGCCTGACCTCTTATCTCCCTAGCC
GGGTTGCGTCCTGGCTCTCTCTTGATTGTCACATACGGAAGATCTATCTC
GTCAGAATCTCTTTGCGTGCCGGATCGGGTTTCATGCACCGGGGAGATAG
AAAATCCCGCGTCCAACATCGCCTGCCTACATCTGGCAACCGAGTGAGCG
GGGAATCGGGCTATTACTCGGGATGCGTCAATCCACGAGTCTCCTAGAAA
ATGATAAATATATTAGTCACTAATTGATGTCTGGCATTTTATTCATTTTG
GTTGTCTAGTTTCGGGCCTGGGTATGTCGACGTTACTCATTTGGTTGCGG
TACTTCTACATCATAGGTCGAAAACTCTTGACTATGGGTCCTATTCAAGT
AATGGTTTTCCAAAAGTTTCGCAGTTCGTTGGTAGTGGCCCGGAGTGCGC
ATACGGTGTCATTCCATGAAGCCCTCACCAAGGTTAACTCCTCAATCGAT
CTTGTTTCATCTTGGGTTAACGAATTATTATTGATCACCCTTTTATTTAA
TGAACTGAATAAATCATGCTCTATCAAAAATTCACTCTAGGTGATAGTAT
TTAATTTCTCATTTTTTCTTTTTATCTTTATAAATATTTCTAATTATACT
CATTTAGTTTGATAATTTTGTTTTAATAATCAAGGCCTCTCTTCCATGAC
TCCCAAAAGTCTATGCTAAGTAATTATTATTTAAATATTTCGTACTAATA
CTCATTAAAGGACCAAATTGACTAATTTTACCCTTATAATTACTATTAGC
TTATGGTTATAAGATCTTATCACTTGTTCCTTCTAGTTTGAATACGATCT
GTCCCTCTTATGTCTATTAGCGTACGTATTCATATATTATCGGCCGTGGT
GAAAAACGCTCACCGACATAGGATGCATTTATAAATATCACTTTAACCCG
TAATATTGGAAATCCTTAACCAAGGTTTGATTTAGTTATTATGGCTCTCC
ATACTAGACGGTAATTTGATTGAAATATGGTTTGGCTTTGATGGTAATTT
ACTCCACTTTCATTCTGAGTTCGATAAATCTCTAATTTACTTATGATAAT
AATCTGCTTCACCCTCATCTAATAGATGTCAGGTTTAATTCCAATAGTAG
TTTATTAAATACCTAAGTTAAACCTAATACAATAAACATTTAATTTAATC
ACAATAGCAGTTTAATGAAGGCTTAATTCAATCATAATAATAATTTTAAT
AAAGGTCTACCTTTATCGCAATAATAATTCTAATAAGTCTCATTTAATCA
TAATATTACTTTAACAAAGGTCTGATTTAATCATAATAATAACAATCTAG
CGAATATTTAAGTTAATCATGATAACAATTTAATAAGTCTAGTTCAAGCA
CGATAGTAATTTACTTTATTTTTCATTACAGTTGCGAATCGGAAGGTAAA
TCTCAATCTCAAAAAGCGTATTCGATATCACCGTGGGTCTGCGTCAATCG
ACTCCTGGCCTCCACCAACGACTTGCAATAGTAGTTCGGGGTTTCAACAT
TCACAGGGATTAATTAAAACTATTGCACGTCATTCGGCACTTGCTCGGTA
AATCAATCTGTATCGCATTCCCTATTAAATTCCTTGTAGGATACTCCAAG
ATTTTTTAAATAACACGAATTGATCAACTCAATAATTATATTTATACTGT
TAATGAGAGGCTATCATAATTCCTTGCTTATTCTTGTTAGTGGGTCTTCA
CTGGTGATGGTCCGTTAGTTGGGTCACGTCTGTGCTGCTGCTCGCAATGA
GTTAATATTATGATGAAGAAAATTTTAATAATTACTCGAATATGGTGGTT
TGCCAGCGCTTGCCGTGTTAGGCTCTTTATATCCTTGCTGTTCTCTCGAA
GCTGGTGCGTATTTTTTAGACATCACAGTGAGTTTTTTTTTAATGAATAA
TTTTCGCTCGATCTAACTTTTATAACTAGCAGGTGTGTCCAGTGGTGAGA
AAAATTTTGTGACCCACGCACACTTCCTCGACCGCGAGTTGGTGTGTGTA
TCCGAGGTCGATTCGTTTGATCTACTCGTCATTTTCTCTAGGCGTTGGTG
TGTTTCCATTACCAAAAAGGTCGTGGCCCGCTCTAATTTGCTTTCCCACT
ATTATCTTGCTATTCTAGTTGTCTAAATTCATTTATTAAGAATTATTTTG
GGCGTTCACAGTGGATACATTTTCTGGTGGTCTATTAGCTCTGCTTTCCT
TAGTAAGTTTTAGTTTTAATCTTATTTCATTTGCGCTCTGGTTTACTAGA
AATTGCTTTATGAGAGTGGCGACTAGACTGGATACGATCTCACTTTATTC
ATCTCTATTTCGGGTGAGGAAATTAATTATCGGCGATATAGTTAATCGGA
TGACTCGAATATTATCCGGATAATCTCGAAACTTATTAACTGCGCTCTGC
GGGGATTTTGACGTCGATGGCAAATTCTCTTTTCGGTTGGCTCAATTTCT
GTATCAAGAGGAACTATACCTGCGATTTTTGCGAGTCAGTTAGAGACGAC
GACGGTGATCAATTTTCCGTAGGGCTTAAGACTATGTCTCGCAAGGTATG
AACGAGGATTGGTTAGCGTGTTCGCAATATTTAGATGACCGTAACCACGG
AAGAGTGGATGAATATGAAAAATTTTTTGAGATCACATTTCTAATTTCCT
TTTAATACACGGAAAGAATTTATCAATTTTCTGTGAATAAATAATTCCGA
AACTTGTTTCCTTCGTTAATGTTGTGTATCTTATAATAAACCCACCTCTA
AATGATGTTCCGCTCATCAGATGACATATGTTAAAGGACATTTTATTGAT
GTTAATCCTGTAGAGGTAATTGTAAGTTTATATTATATGGATAGCCGAAT
TCATAAAGCGATCAGGCCTCGAGTGGATCCTGCTATTTTATTTGAAGTGC
CGTAACTTATAGTTCGAATTTATTTTCAAATTTAATACCGATTTGTGACG
ATTGCGAATTAATTAATTCTCCATGTGATTGTGAGTATTTTTTGTGCCTA
ATTACTCATTATTATGTTGAGGAATTGCTTTCCCCTCCTCCCACAAAAAA
CCTTACTGCTATATTCCTTTGCACATTTTTTCTTTAAATTCATTTACTGT
GATCCGTGGCTATTTATCCAATATTTATTACTGATTATAATTTCATTACG
CGGGATCTCATTGTAGCTCGTTTTGGTTTGATTTTATTTATCTAATATTT
ATTATTGATGATAACTTTATTACGCGGCGTTTCATAGTAGCTCGTGCTTT
TCTATATTTTTGATTCGATTTGGTTCATTTAGAACGTGATATTAGGGTCC
TACATAGTTTATATTTATTCTGCGGTTGATTTCGTTATGACGTACTATTA
GAGTTTATTTTATAGATATTTTAGAAAGTCAGCAATAATTTCGCATCTTT
AGTTTTCCGTCACCAT
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protein sequence of SMED30025284-orf-1

>SMED30025284-orf-1 ID=SMED30025284-orf-1|Name=SMED30025284-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=123bp
MLDAGFSISPVHETRSGTQRDSDEIDLPYVTIKREPGRNPAREIRGQAEY
LLVRLETHQAETNRQVEQAKQYLQRVSADIAAGRIPSTDGYAPRYNVSYE
LDDPKLQERMVDMNVVIPRRILP
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002111X2 cell