SMED30023889

Overview
NameSMED30023889
Smed IDSMED30023889
Length (bp)397
Neoblast Clusters

Zeng et. al., 2018




 



 

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




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




SMED30023889

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



PAGE Curations: 17

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
pharynxSMED30023889SMESG000055805.1 dd_Smed_v4_857_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
protonephridiaSMED30023889SMESG000055805.1 dd_Smed_v4_857_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30023889SMESG000055805.1 dd_Smed_v4_857_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gutSMED30023889SMESG000055805.1 dd_Smed_v4_857_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30023889SMESG000055805.1 dd_Smed_v4_857_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30023889SMESG000055805.1 dd_Smed_v4_857_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
muscle cellSMED30023889SMESG000055805.1 dd_Smed_v4_857_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30023889SMESG000055805.1 dd_Smed_v4_857_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymaSMED30023889SMESG000055805.1 dd_Smed_v4_857_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30023889SMESG000055805.1 dd_Smed_v4_857_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30023889SMESG000055805.1 dd_Smed_v4_857_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30023889SMESG000055805.1 dd_Smed_v4_857_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
prepharyngeal regionSMED30023889SMESG000055805.1 dd_Smed_v6_857_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017
whole organism asexual adult RNA-sequencing evidence
head regionSMED30023889SMESG000055805.1 OX_Smed_1.0.20014ox_Smed_v2PMID:24238224
Kao et al., 2013
whole organism asexual adult RNA-sequencing evidence
neoblastSMED30023889SMESG000055805.1 dd_Smed_v6_857_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
gamma neoblastSMED30023889SMESG000055805.1 dd_Smed_v6_857_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
pharynx progenitor cellSMED30023889SMESG000055805.1 dd_Smed_v6_857_0dd_Smed_v6PMID:29674432
Plass et al., 2018
FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30023889 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006565:11075..11542 +1742
Homology
BLAST of SMED30023889 vs. TrEMBL
Match: V9XTG6 (X1.D.A5.1 OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 60.8474 bits (146), Expect = 1.932e-9
Identity = 33/93 (35.48%), Postives = 53/93 (56.99%), Query Frame = 2
Query:   44 IALCAIFCTTFVHSSVSFGNGYF-KDGKPFVKISETEYPADESLEVEVGEGDNCNLCSISPPTSTDTNPTFECQGPSPAEIDGETIYLPVCKE 319
            +A+C +   ++ +S + +G G+  KDG+  V+I + ++ A +  EVEV     C  C I P  S +  P FEC+GPS   +D + IYL  C+E
Sbjct:   10 LAMCLM---SYTNSELVYGRGFVDKDGRQIVEIFDQQFDASKQKEVEVNFVKKCYKCLIEPAVSGE-QPLFECEGPSLVRVDEKDIYLDPCQE 98          
BLAST of SMED30023889 vs. Planmine SMEST
Match: SMESG000055805.1 (SMESG000055805.1)

HSP 1 Score: 195.667 bits (496), Expect = 4.639e-66
Identity = 96/97 (98.97%), Postives = 96/97 (98.97%), Query Frame = 2
Query:   32 MKVIIALCAIFCTTFVHSSVSFGNGYFKDGKPFVKISETEYPADESLEVEVGEGDNCNLCSISPPTSTDTNPTFECQGPSPAEIDGETIYLPVCKEK 322
            MKVIIALCAIFCT FVHSSVSFGNGYFKDGKPFVKISETEYPADESLEVEVGEGDNCNLCSISPPTSTDTNPTFECQGPSPAEIDGETIYLPVCKEK
Sbjct:    1 MKVIIALCAIFCTKFVHSSVSFGNGYFKDGKPFVKISETEYPADESLEVEVGEGDNCNLCSISPPTSTDTNPTFECQGPSPAEIDGETIYLPVCKEK 97          
BLAST of SMED30023889 vs. Planmine SMEST
Match: SMESG000020860.1 (SMESG000020860.1)

HSP 1 Score: 90.5077 bits (223), Expect = 1.294e-24
Identity = 44/96 (45.83%), Postives = 60/96 (62.50%), Query Frame = 2
Query:   32 MKVIIALCAIFCTTFVHSSVSFGNGYFKDGKPFVKISETEYPADESLEVEVGEGDNCNLCSISPPTSTDTNPTFECQGPSPAEIDGETIYLPVCKE 319
            MKVI+ + ++   T  ++SVSFG GYF+DGK +VKI+  EY A+E  E++ GEGD C +C+          PT+ C GPSP  IDG+  Y   CKE
Sbjct:    1 MKVILLVLSVL--TVAYASVSFGRGYFRDGKGYVKINGVEYLAEEDGEIQYGEGDRCVVCNYFASKDKVKPPTYSCYGPSPMMIDGKLTYRSQCKE 94          
BLAST of SMED30023889 vs. Planmine SMEST
Match: SMESG000062897.1 (SMESG000062897.1)

HSP 1 Score: 77.0258 bits (188), Expect = 3.259e-19
Identity = 34/83 (40.96%), Postives = 50/83 (60.24%), Query Frame = 2
Query:   65 CTTFVHSSVSFGNGYFKDGKPFVKISETEYPADESLEVEVGEGDNCNLCSISPPTSTDTNPTFECQGPSPAEIDGETIYLPVC 313
            C      S+S G GY+++GKP VKI+   +PAD++   ++G GD C  C I+ P + D  P F+C GPSP  +DG+  Y+  C
Sbjct:   23 CILNSKGSLSRGIGYYENGKPVVKINNQVFPADKNSVQQIGSGDRCLKCFINAPANNDEKPKFQCHGPSPVYMDGKMAYISEC 105          
BLAST of SMED30023889 vs. Planmine SMEST
Match: SMESG000062896.1 (SMESG000062896.1)

HSP 1 Score: 75.8702 bits (185), Expect = 7.493e-19
Identity = 36/97 (37.11%), Postives = 55/97 (56.70%), Query Frame = 2
Query:   32 MKVIIALCAI-FCTTFVHSSVSFGNGYFKDGKPFVKISETEYPADESLEVEVGEGDNCNLCSISPPTSTDTNPTFECQGPSPAEIDGETIYLPVCKE 319
            MK +IAL  +  C  +VH  +   +GY++DG+P VKI +  YPAD +   ++G G  C  C I+ P+    NP FEC   SPA  + + +Y+  C +
Sbjct:    1 MKYLIALFLVSVCILYVHGGMFGASGYYEDGRPVVKIEDQVYPADTNNVQQIGTGQGCKKCYINAPSEKGQNPDFECHTASPAIENNKVVYVSPCDQ 97          
BLAST of SMED30023889 vs. Planmine SMEST
Match: SMESG000054105.1 (SMESG000054105.1)

HSP 1 Score: 70.0922 bits (170), Expect = 1.314e-16
Identity = 37/96 (38.54%), Postives = 50/96 (52.08%), Query Frame = 2
Query:   32 MKVIIALCAIFCTTFVHSSVSFGNGYFKDGKPFVKISETEYPADESLEVEVGEGDNCNLCSISPPTSTDTNPTFECQGPSPAE-IDGETIYLPVCK 316
            M  I+ L  I  +    SS + G G+++ GK +V ++ TEY AD    V +G GD C  CSI+P  S + N TF CQ P   + I G   Y   CK
Sbjct:    1 MNSILLLTVILFSILSCSSDTNGRGFWRKGKQYVVLNGTEYSADLKASVNIGTGDKCIYCSITPSKSANQNSTFYCQDPMTTKTITGYVTYYSFCK 96          
The following BLAST results are available for this feature:
BLAST of SMED30023889 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 SMED30023889 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 SMED30023889 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 SMED30023889 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 SMED30023889 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 SMED30023889 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 SMED30023889 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 SMED30023889 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
V9XTG61.932e-935.48X1.D.A5.1 OS=Schmidtea mediterranea OX=79327 PE=2 ... [more]
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BLAST of SMED30023889 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 SMED30023889 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 SMED30023889 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 SMED30023889 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 SMED30023889 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 SMED30023889 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000055805.14.639e-6698.97SMESG000055805.1[more]
SMESG000020860.11.294e-2445.83SMESG000020860.1[more]
SMESG000062897.13.259e-1940.96SMESG000062897.1[more]
SMESG000062896.17.493e-1937.11SMESG000062896.1[more]
SMESG000054105.11.314e-1638.54SMESG000054105.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023889 ID=SMED30023889|Name=SMED30023889|organism=Schmidtea mediterranea sexual|type=transcript|length=397bp
TCGCATTTTTTTTTTTTTTTTTTCATAAATAATGAAGGTAATTATTGCTC
TATGTGCAATTTTTTGCACTACATTTGTTCACTCTTCGGTTTCTTTTGGG
AATGGTTACTTCAAAGATGGTAAACCATTCGTAAAAATATCTGAAACAGA
ATATCCTGCTGATGAATCTTTAGAAGTAGAGGTAGGAGAGGGAGATAATT
GCAATCTTTGCAGTATTTCTCCACCCACCAGCACAGACACGAATCCGACC
TTTGAATGCCAAGGACCATCTCCTGCTGAAATAGATGGGGAGACTATTTA
CTTACCAGTTTGTAAAGAAAAATGAACTTAATATTGCTTGTTAAAATATA
ATAAATGTGACCTATCTTGAAAAAAAAAAAAAAAAAAAAAAAAAAAC
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000026gut
PLANA:0000039gamma neoblast
PLANA:0000101muscle cell
PLANA:0000110pharynx progenitor cell
PLANA:0000418head
PLANA:0000419prepharyngeal region
PLANA:0000429neoblast
PLANA:0002032epidermal cell
PLANA:0003116parenchymal cell
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..18
score: 0.632