SMED30011063

Overview
NameSMED30011063
Smed IDSMED30011063
Length (bp)962
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 SMED30011063 (SMED30011063) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30011063 (SMED30011063) 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



SMED30011063

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 cellSMED30011063 SmedASXL_016391SmedAsxl_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 SMED30011063 vs. Planmine SMEST
Match: SMESG000013825.1 (SMESG000013825.1)

HSP 1 Score: 175.637 bits (444), Expect = 8.557e-75
Identity = 88/110 (80.00%), Postives = 93/110 (84.55%), Query Frame = -3 
Query:  631 FQIGININIHLSGMTNLDFNSEDLLINIIINSLPAEITAEVRPQGSTSIYAIGDIVSILNLVQRHQSDFAVETKNVQCFICNENHLARNCVNNKKIQCSRHEMLGH*SRY 960
            FQIG NINIHLS M NL FNS DLL+NIIINSLP EI AEVR +GSTSI AIGDIVS LNLVQRHQS FAV+TKNVQCFICNE+H AR C+N KKIQCSR EMLGH  RY
Sbjct:   92 FQIGDNINIHLSEMKNLAFNSGDLLVNIIINSLPTEIAAEVRREGSTSIDAIGDIVSRLNLVQRHQSVFAVKTKNVQCFICNESHFARKCMNKKKIQCSRCEMLGHQYRY 201

HSP 2 Score: 124.02 bits (310), Expect = 8.557e-75
Identity = 67/86 (77.91%), Postives = 69/86 (80.23%), Query Frame = -1 
Query:  276 FGCSTTIIVG*SNTSLNAQVFLADGSILLVSQSKAEI*LEGKYFFIDCFISRKMIAENDFILGMNAIIALGGVIISKYARLRCELK 533
            FGCSTTII G SNTS NAQVFLADGSIL VSQSKAEI LEGKYF ID FISRKMIA  D ILGMN I+ALG V IS+  R  CELK
Sbjct:  203 FGCSTTIIRGESNTSHNAQVFLADGSILPVSQSKAEIELEGKYFLIDSFISRKMIAGYDVILGMNTIMALGCVTISEDVRFGCELK 288
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BLAST of SMED30011063 vs. Planmine SMEST
Match: SMESG000020160.1 (SMESG000020160.1)

HSP 1 Score: 176.407 bits (446), Expect = 6.714e-51
Identity = 88/111 (79.28%), Postives = 95/111 (85.59%), Query Frame = -3 
Query:  628 FQIGININIHLSGMTNLDFNSEDLLINIIINSLPAEITAEVRPQGSTSIYAIGDIVSILNLVQRHQSDFAVETKNVQCFICNENHLARNCVNNKKIQCSRHEMLGH*SRYC 960
            F+IG NINIHLS M NL FNS DLL+NIIINSLP +I AEVR  GSTSI +IGDIVS LNLVQRHQS FAV+TKNVQCFICNE+H ARNC+N KKIQCSR EMLGH SRYC
Sbjct:   57 FKIGDNINIHLSEMKNLAFNSGDLLVNIIINSLPTKIAAEVRRLGSTSIDSIGDIVSRLNLVQRHQSVFAVKTKNVQCFICNESHFARNCMNKKKIQCSRCEMLGHQSRYC 167
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BLAST of SMED30011063 vs. Planmine SMEST
Match: SMESG000019634.1 (SMESG000019634.1)

HSP 1 Score: 165.236 bits (417), Expect = 1.018e-50
Identity = 85/117 (72.65%), Postives = 91/117 (77.78%), Query Frame = -1 
Query:  180 GCSTTIIVG*SNTSLNAQVFLADGSILLVSQSKAEI*LEGKYFFIDCFISRKMIAENDFILGMNAIIALGGVIISKYARLRCELKCLKATNRNKVQSLTIQR*NLEAKFNNKWTVSW 530
            G STT I G  NTS NAQVFLADGSIL VSQSKAEI LEG YFFIDCF+SRKMIA  D ILGMNAI+ LGGV IS+YAR  CELKCL   N ++V SLTIQR N EAKFN +W  SW
Sbjct:    8 GYSTTNIGGEFNTSSNAQVFLADGSILPVSQSKAEIELEGIYFFIDCFVSRKMIAGYDVILGMNAIMTLGGVTISEYARFGCELKCLTVANSDEVHSLTIQRKNFEAKFNKEWMTSW 124
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BLAST of SMED30011063 vs. Planmine SMEST
Match: SMESG000067566.1 (SMESG000067566.1)

HSP 1 Score: 139.428 bits (350), Expect = 2.370e-47
Identity = 71/93 (76.34%), Postives = 75/93 (80.65%), Query Frame = -3 
Query:  643 MTNLDFNSEDLLINIIINSLPAEITAEVRPQGSTSIYAIGDIVSILNLVQRHQSDFAVETKNVQCFICNENHLARNCVNNKKIQCSRHEMLGH 921
            M NL FNS DLLINIIINSL  EI A+VR QGST I AIGDIVS LNL QRHQ  FAV+TKNVQCFICNE+H  RNC+N KKIQC R EMLGH
Sbjct:    1 MKNLAFNSGDLLINIIINSLRTEIAADVRRQGSTPIDAIGDIVSRLNLGQRHQFVFAVKTKNVQCFICNESHFVRNCMNKKKIQCFRCEMLGH 93

HSP 2 Score: 68.5514 bits (166), Expect = 2.370e-47
Identity = 48/90 (53.33%), Postives = 53/90 (58.89%), Query Frame = -1 
Query:  387 VNHGKAKGSRTFRSLYRSPKCVK*K-------KNALPHRFGCSTTIIVG*SNTSLNAQVFLADGSILLVSQSKAEI*LEGKYF--FIDCF 629
            VN  K K SR F SL R  +  K +       K  L    GCSTTII G SN S NAQVFLADG IL VSQSKAEI LEGK    ++D +
Sbjct:   96 VNREKTKESRLFWSLSRPQEDAKKRFLSINGLKMVLFIDSGCSTTIIRGESNMSPNAQVFLADGLILPVSQSKAEIELEGKALNHYLDVY 185
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BLAST of SMED30011063 vs. Planmine SMEST
Match: SMESG000055549.1 (SMESG000055549.1)

HSP 1 Score: 140.584 bits (353), Expect = 4.577e-39
Identity = 74/96 (77.08%), Postives = 77/96 (80.21%), Query Frame = -1 
Query:  204 SLNAQVFLADGSILLVSQSKAEI*LEGKYFFIDCFISRKMIAENDFILGMNAIIALGGVIISKYARLRCELKCLKATNRNKVQSLTIQR*NLEAKF 491
            S NAQVFLADGSIL VSQSKAEI LEGKYF IDCFISRKMIA  D IL MNAIIALGGV IS+  R  CELKCL A N N+V SLTIQR NLEA +
Sbjct:    2 SPNAQVFLADGSILPVSQSKAEIELEGKYFLIDCFISRKMIAGYDVILDMNAIIALGGVKISEDVRFGCELKCLTAANSNEVHSLTIQRKNLEANW 97
The following BLAST results are available for this feature:
BLAST of SMED30011063 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 SMED30011063 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 SMED30011063 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 SMED30011063 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 SMED30011063 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 SMED30011063 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 SMED30011063 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 SMED30011063 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 SMED30011063 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 SMED30011063 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 SMED30011063 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 SMED30011063 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 SMED30011063 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 SMED30011063 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000013825.18.557e-7580.00SMESG000013825.1[more]
SMESG000020160.16.714e-5179.28SMESG000020160.1[more]
SMESG000019634.11.018e-5072.65SMESG000019634.1[more]
SMESG000067566.12.370e-4776.34SMESG000067566.1[more]
SMESG000055549.14.577e-3977.08SMESG000055549.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011063 ID=SMED30011063|Name=SMED30011063|organism=Schmidtea mediterranea sexual|type=transcript|length=962bp
CACAAAAAATAATTTCAAAATAAATATGCACACACAAAATTAATTATCTT
GATTGCATAATTATGTAATCAAGACACATCGTGATCAATTGCGCAATTAC
GCAATTTAATCATTGATAACCCCCCCCTTATTCACTATGCAATGGCATGT
GGACACACAAAGCTAATAACTACCTACTTCCATGATACCGTCCATTTGTT
GTTGAACTTTGCTTCTAAGTTTTATCTTTGAATTGTCAAACTCTGAACTT
TATTTCTGTTTGTAGCCTTCAAACATTTCAATTCGCATCTTAATCTGGCA
TATTTACTAATTATCACACCTCCTAGAGCTATAATAGCGTTCATGCCTAA
TATGAAATCATTTTCCGCTATCATTTTCCTAGAAATAAAACAGTCAATAA
AAAAGTACTTTCCTTCTAATTAGATTTCTGCTTTGCTTTGACTCACCAAC
AGTATAGACCCATCTGCTAGGAACACTTGAGCGTTGAGCGACGTGTTAGA
TTATCCGACTATGATTGTTGTCGAGCAGCCGAATCTATGAGGCAAAGCAT
TTTTCTTTCATTTAACACATTTTGGTGATCGATAGAGACTCCTAAATGTT
CTAGATCCCTTTGCCTTTCCATGATTTACAATATCGGGATTAATGTCCAA
GCATTTCATGCCGGGAGCATTGAATTTTCTTATTGTTCACACAGTTACGG
GCTAAATGGTTTTCGTTGCAAATGAAGCATTGCACATTCTTGGTTTCCAC
TGCAAAATCAGACTGATGTCTTTGTACTAAATTCAATATTGAAACGATGT
CACCAATTGCGTAGATTGACGTTGATCCTTGTGGTCTCACCTCAGCTGTA
ATTTCTGCTGGCAAGGAGTTGATTATAATGTTTATCAGTAAATCTTCAGA
ATTAAAATCCAGATTCGTCATTCCTGATAAATGAATGTTAATATTGATCC
CGATCTGGAATT
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protein sequence of SMED30011063-orf-1

>SMED30011063-orf-1 ID=SMED30011063-orf-1|Name=SMED30011063-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=107bp
FQIGININIHLSGMTNLDFNSEDLLINIIINSLPAEITAEVRPQGSTSIY
AIGDIVSILNLVQRHQSDFAVETKNVQCFICNENHLARNCVNNKKIQCSR
HEMLGH*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0002111X2 cell
Vocabulary: INTERPRO
TermDefinition
IPR001878Znf_CCHC
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
GO:0008270zinc ion binding