1.B9.3

Overview
Name1.B9.3 (AHD24736.1)
Smed IDSMED30023233
Length (bp)474
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 1.B9.3 (SMED30023233) t-SNE clustered cells

Violin plots show distribution of expression levels for 1.B9.3 (SMED30023233) 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 1.B9.3 (SMED30023233) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for 1.B9.3 (SMED30023233) 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



SMED30023233

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



PAGE Curations: 6

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
head regionSMED30023233SMESG000000901.1 SmedASXL_004233SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30023233SMESG000000901.1 dd_Smed_v4_13104_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30023233SMESG000000901.1 dd_Smed_v4_13104_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cilated neuronSMED30023233SMESG000000901.1 dd_Smed_v4_13104_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
head regionSMED30023233SMESG000000901.1 dd_Smed_v6_13104_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
head regionSMED30023233SMESG000000901.1 OX_Smed_1.0.12925ox_Smed_v2PMID:24238224
Kao et al., 2013		whole organism asexual adult RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of 1.B9.3 vs. TrEMBL
Match: V9XTE7 (1.B9.3 (Fragment) OS=Schmidtea mediterranea OX=79327 PE=2 SV=1)

HSP 1 Score: 202.601 bits (514), Expect = 8.000e-65
Identity = 100/100 (100.00%), Postives = 100/100 (100.00%), Query Frame = 1 
Query:   73 MKISFLIILMLFIVNYSKAQCPPGYYLNTYPHNSQNCFPCPKDPAGQMCGDGDTVCQTCMGQNYKCIFLQQGNFCKPCIPRLGICGVINICCSGLVCKPT 372
            MKISFLIILMLFIVNYSKAQCPPGYYLNTYPHNSQNCFPCPKDPAGQMCGDGDTVCQTCMGQNYKCIFLQQGNFCKPCIPRLGICGVINICCSGLVCKPT
Sbjct:    1 MKISFLIILMLFIVNYSKAQCPPGYYLNTYPHNSQNCFPCPKDPAGQMCGDGDTVCQTCMGQNYKCIFLQQGNFCKPCIPRLGICGVINICCSGLVCKPT 100
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BLAST of 1.B9.3 vs. Planmine SMEST
Match: SMESG000000901.1 (SMESG000000901.1)

HSP 1 Score: 249.98 bits (637), Expect = 7.424e-87
Identity = 123/123 (100.00%), Postives = 123/123 (100.00%), Query Frame = 1 
Query:   73 MKISFLIILMLFIVNYSKAQCPPGYYLNTYPHNSQNCFPCPKDPAGQMCGDGDTVCQTCMGQNYKCIFLQQGNFCKPCIPRLGICGVINICCSGLVCKPTTTATDLPSRNRCIEPTYIFTVTK 441
            MKISFLIILMLFIVNYSKAQCPPGYYLNTYPHNSQNCFPCPKDPAGQMCGDGDTVCQTCMGQNYKCIFLQQGNFCKPCIPRLGICGVINICCSGLVCKPTTTATDLPSRNRCIEPTYIFTVTK
Sbjct:    1 MKISFLIILMLFIVNYSKAQCPPGYYLNTYPHNSQNCFPCPKDPAGQMCGDGDTVCQTCMGQNYKCIFLQQGNFCKPCIPRLGICGVINICCSGLVCKPTTTATDLPSRNRCIEPTYIFTVTK 123
[Close]
BLAST of 1.B9.3 vs. Planmine SMEST
Match: SMESG000000901.1 (SMESG000000901.1)

HSP 1 Score: 232.261 bits (591), Expect = 5.876e-80
Identity = 114/114 (100.00%), Postives = 114/114 (100.00%), Query Frame = 1 
Query:  100 MLFIVNYSKAQCPPGYYLNTYPHNSQNCFPCPKDPAGQMCGDGDTVCQTCMGQNYKCIFLQQGNFCKPCIPRLGICGVINICCSGLVCKPTTTATDLPSRNRCIEPTYIFTVTK 441
            MLFIVNYSKAQCPPGYYLNTYPHNSQNCFPCPKDPAGQMCGDGDTVCQTCMGQNYKCIFLQQGNFCKPCIPRLGICGVINICCSGLVCKPTTTATDLPSRNRCIEPTYIFTVTK
Sbjct:    1 MLFIVNYSKAQCPPGYYLNTYPHNSQNCFPCPKDPAGQMCGDGDTVCQTCMGQNYKCIFLQQGNFCKPCIPRLGICGVINICCSGLVCKPTTTATDLPSRNRCIEPTYIFTVTK 114
[Close]
BLAST of 1.B9.3 vs. Planmine SMEST
Match: SMESG000022784.1 (SMESG000022784.1)

HSP 1 Score: 51.9878 bits (123), Expect = 3.756e-9
Identity = 33/98 (33.67%), Postives = 47/98 (47.96%), Query Frame = 1 
Query:   73 MKISFLIILMLFIVNYSKAQCPPGYYLNTYPHNSQNCFPCPKDPAGQMCGDGDTVCQTCMGQNYKCIFLQQGNFCKPCIPRLGICGVINICCSGLVCK 366
            MKI+ L++  L         C   ++    PH+++ C  C   P       G + C TC G N+ C+ LQ GN CK C+     CG  ++CC GL CK
Sbjct:    1 MKINLLLLGFLLNHFLFNHGCEIDFFEVKCPHSTEICLNCNDFPQYSCFIGGTSQCTTCYGDNFICLALQSGNKCKECLSEGTRCGQSDLCCDGLKCK 98
[Close]
BLAST of 1.B9.3 vs. Planmine SMEST
Match: SMESG000022786.1 (SMESG000022786.1)

HSP 1 Score: 50.0618 bits (118), Expect = 1.966e-8
Identity = 29/105 (27.62%), Postives = 47/105 (44.76%), Query Frame = 1 
Query:   97 LMLFIVNYSKAQCPPGYYLNTYPHNSQNCFPCPKDPAGQMCGDGDTVCQTCMGQNYKCIFLQQGNFCKPCIPRLGICGVINICCSGLVCKPTTTATDLPSRNRCI 411
            + +F+ +    +C    ++    H+++ C  C   P       G   C +C G N+ CI  +  N C  CIP+   C V +ICC  L CKP +  +   + N  I
Sbjct:    1 MSVFLYSVFSDKCSSRQFVYNPTHSNEICLNCNDFPRFSCIIGGTKQCNSCFGSNFICISRKSSNVCIQCIPQGSRCTVKDICCPNLSCKPGSFVSKNATNNLSI 105
[Close]
BLAST of 1.B9.3 vs. Planmine SMEST
Match: SMESG000062402.1 (SMESG000062402.1)

HSP 1 Score: 49.6766 bits (117), Expect = 2.405e-7
Identity = 25/66 (37.88%), Postives = 33/66 (50.00%), Query Frame = 1 
Query:  175 QNCFP-CPKDPAGQMCG-DGDTVCQTCMGQNYKCIFLQQGNFCKPCIPRLGICGVINICCSGLVCK 366
            QN FP C K    + C  +G+  CQ C+G  + C    QGNFC+ C      C   ++CC   VCK
Sbjct: 2848 QNSFPICNKCNQNKTCMVNGNKECQECLGDGHICSIEPQGNFCRSCKLENTPCFPFDLCCENSVCK 2913
The following BLAST results are available for this feature:
BLAST of 1.B9.3 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 1.B9.3 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 1.B9.3 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 1.B9.3 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 1.B9.3 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 1.B9.3 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 1.B9.3 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 1.B9.3 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 1
Match NameE-valueIdentityDescription
V9XTE78.000e-65100.001.B9.3 (Fragment) OS=Schmidtea mediterranea OX=793... [more]
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BLAST of 1.B9.3 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 1.B9.3 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 1.B9.3 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 1.B9.3 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 1.B9.3 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 1.B9.3 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000000901.17.424e-87100.00SMESG000000901.1[more]
SMESG000000901.15.876e-80100.00SMESG000000901.1[more]
SMESG000022784.13.756e-933.67SMESG000022784.1[more]
SMESG000022786.11.966e-827.62SMESG000022786.1[more]
SMESG000062402.12.405e-737.88SMESG000062402.1[more]
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Cross References
External references for this transcript
DatabaseAccession
SmedGD GBrowseSMED30023233
GenBankAHD24736.1
Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30023233 ID=SMED30023233|Name=1.B9.3|organism=Schmidtea mediterranea sexual|type=transcript|length=474bp
TATTAAGTTATATTTTTACCTATGCAAACAGAATAATAAATATTTCTTTG
CAGTCGATTTTATTTATAAGAAATGAAAATTTCCTTTTTAATAATTTTGA
TGTTATTTATTGTGAATTATTCCAAAGCTCAGTGCCCCCCTGGATATTAT
CTGAATACATATCCGCACAACTCACAAAATTGCTTTCCTTGTCCAAAAGA
TCCTGCTGGACAAATGTGTGGTGATGGAGACACGGTTTGTCAGACTTGCA
TGGGCCAAAATTACAAATGTATATTTCTCCAGCAAGGCAACTTTTGCAAA
CCATGTATACCACGTTTGGGCATTTGTGGGGTAATAAATATATGTTGTTC
TGGCTTAGTTTGCAAACCAACCACGACTGCTACGGACTTGCCGTCTCGGA
ATAGATGCATTGAACCAACCTATATTTTTACTGTTACAAAATAGAAAAAA
AATTATGTATGATTTTGTTATTCA
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protein sequence of SMED30023233-orf-1

>SMED30023233-orf-1 ID=SMED30023233-orf-1|Name=SMED30023233-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=124bp
MKISFLIILMLFIVNYSKAQCPPGYYLNTYPHNSQNCFPCPKDPAGQMCG
DGDTVCQTCMGQNYKCIFLQQGNFCKPCIPRLGICGVINICCSGLVCKPT
TTATDLPSRNRCIEPTYIFTVTK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR001368TNFR/NGFR_Cys_rich_reg
Vocabulary: molecular function
TermDefinition
GO:0005515protein binding
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR001368TNFR/NGFR cysteine-rich regionPROSITEPS50050TNFR_NGFR_2coord: 20..66
score: 8.953
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..19
score: 0.912