SMED30034380

Overview
NameSMED30034380
Smed IDSMED30034380
Length (bp)621
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 SMED30034380 (SMED30034380) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30034380 (SMED30034380) 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 SMED30034380 (SMED30034380) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30034380 (SMED30034380) 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



SMED30034380

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
parapharyngeal regionSMED30034380SMESG000020144.1 SmedASXL_004248SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30034380SMESG000020144.1 dd_Smed_v4_677_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30034380SMESG000020144.1 dd_Smed_v4_677_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30034380SMESG000020144.1 dd_Smed_v4_677_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30034380SMESG000020144.1 dd_Smed_v4_677_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30034380SMESG000020144.1 dd_Smed_v4_677_0_1dd_Smed_v4PMID:30962434
Cote et al., 2019		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Alignments
SMED30034380 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.006341:16563..17223 -2970
Homology
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BLAST of SMED30034380 vs. Planmine SMEST
Match: SMESG000020144.1 (SMESG000020144.1)

HSP 1 Score: 216.083 bits (549), Expect = 1.470e-72
Identity = 104/105 (99.05%), Postives = 105/105 (100.00%), Query Frame = 2 
Query:  257 AFWCPPCDMSSCTPVSSSCPESRIVPSICNCCKVCGLQEGEKCTSNSGTRCANGLRCETSFGCRYQYYLPWQTPVSGTCVQEKPDEDETPSYCYDMGWIMKQSGR 571
            AFWCPPCDMSSCTPVSSSCPESRIVPSIC+CCKVCGLQEGEKCTSNSGTRCANGLRCETSFGCRYQYYLPWQTPVSGTCVQEKPDEDETPSYCYDMGWIMKQSGR
Sbjct:   18 AFWCPPCDMSSCTPVSSSCPESRIVPSICSCCKVCGLQEGEKCTSNSGTRCANGLRCETSFGCRYQYYLPWQTPVSGTCVQEKPDEDETPSYCYDMGWIMKQSGR 122
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BLAST of SMED30034380 vs. Planmine SMEST
Match: SMESG000020144.1 (SMESG000020144.1)

HSP 1 Score: 195.282 bits (495), Expect = 1.053e-64
Identity = 96/97 (98.97%), Postives = 97/97 (100.00%), Query Frame = 2 
Query:  281 MSSCTPVSSSCPESRIVPSICNCCKVCGLQEGEKCTSNSGTRCANGLRCETSFGCRYQYYLPWQTPVSGTCVQEKPDEDETPSYCYDMGWIMKQSGR 571
            MSSCTPVSSSCPESRIVPSIC+CCKVCGLQEGEKCTSNSGTRCANGLRCETSFGCRYQYYLPWQTPVSGTCVQEKPDEDETPSYCYDMGWIMKQSGR
Sbjct:    1 MSSCTPVSSSCPESRIVPSICSCCKVCGLQEGEKCTSNSGTRCANGLRCETSFGCRYQYYLPWQTPVSGTCVQEKPDEDETPSYCYDMGWIMKQSGR 97
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BLAST of SMED30034380 vs. Planmine SMEST
Match: SMESG000020133.1 (SMESG000020133.1)

HSP 1 Score: 117.087 bits (292), Expect = 1.302e-33
Identity = 57/102 (55.88%), Postives = 66/102 (64.71%), Query Frame = 2 
Query:  257 AFWCPPCDMSSCTPVSSSCPESRIVPSICNCCKVCGLQEGEKCTSNSGTRCANGLRCETSFGCRYQYYLPWQTPVSGTCVQEKPDEDETPSYCYDMGWIMKQ 562
             FWCPPC    C     +C     V   CNCC VCG+ EGE CTS S +RCANGLRC T+FGCRYQYYLP +  V G C +EKP E  TP +CY + +IMKQ
Sbjct:   18 GFWCPPCFQQECPKNDLNCRLENTVSDRCNCCNVCGITEGEICTSISSSRCANGLRCVTNFGCRYQYYLPTEIMVRGRCEKEKPKEPNTPDHCYKIEFIMKQ 119
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BLAST of SMED30034380 vs. Planmine SMEST
Match: SMESG000020136.1 (SMESG000020136.1)

HSP 1 Score: 92.0485 bits (227), Expect = 6.098e-24
Identity = 45/102 (44.12%), Postives = 62/102 (60.78%), Query Frame = 2 
Query:  257 AFWCPPCDMSSCTPVSSSCPESRIVPSICNCCKVCGLQEGEKCTSNSGTRCANGLRCETSFGCRYQYYLPWQTPVSGTCVQEKPDEDETPSYCYDMGWIMKQ 562
            +  C PC+   C   + +CP+S+ V  IC CC VCGLQEG+ CTS S   C  G  CET+FGCRY+  LP+  P  G CV+EK +E+     CY+  +++ Q
Sbjct:   16 SLSCIPCNEVKCNDANLNCPKSQFVKGICGCCNVCGLQEGKICTSFS--ICMKGTLCETAFGCRYRNTLPFYIPFKGVCVKEKENEEPIEPNCYNYKYVVSQ 115
[Close]
BLAST of SMED30034380 vs. Planmine SMEST
Match: SMESG000039126.1 (SMESG000039126.1)

HSP 1 Score: 81.6481 bits (200), Expect = 7.308e-20
Identity = 42/99 (42.42%), Postives = 55/99 (55.56%), Query Frame = 2 
Query:  275 CDMSSCTPVSSSCPESRIVPSICNCCKVCGLQEGEKCTSNSGTRCANGLRCETSFGCRYQYYLPWQTPVSGTCVQEKPDEDETPSYCYDMGWIMKQSGR 571
            C  SSC  V  +CP S+ +   CNCC VC   EG+ C SN    CA GLRC T +GCRY  +LPW  P+ G C +E P+E      CY   ++ +Q  +
Sbjct:   21 CFASSCNSVKLNCPRSQQIRDSCNCCYVCANLEGQICESNIKA-CAPGLRCVTEYGCRYSNHLPWFLPIQGVCEKELPNEPPADINCYRYSYLQQQKLK 118
The following BLAST results are available for this feature:
BLAST of SMED30034380 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 SMED30034380 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 SMED30034380 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 SMED30034380 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 SMED30034380 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 SMED30034380 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 SMED30034380 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 SMED30034380 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 SMED30034380 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 SMED30034380 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 SMED30034380 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 SMED30034380 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 SMED30034380 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 SMED30034380 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000020144.11.470e-7299.05SMESG000020144.1[more]
SMESG000020144.11.053e-6498.97SMESG000020144.1[more]
SMESG000020133.11.302e-3355.88SMESG000020133.1[more]
SMESG000020136.16.098e-2444.12SMESG000020136.1[more]
SMESG000039126.17.308e-2042.42SMESG000039126.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30034380 ID=SMED30034380|Name=SMED30034380|organism=Schmidtea mediterranea sexual|type=transcript|length=621bp
GAAAATTTTCCCATAAATAAATACTTCAAGAAAATAACAATTTTCAGTTT
CTGTTAATAACCAAAGAAACTTTCAATAAACCGCAATTAGCAAGATAATT
TGATGCGTTTAAAATTTCCACCAAATTACAGATAAACAAGAATAATTGGT
CTCATTTAACTATAAATTGTGCAAATTTTTCCTGTCAATCATTCAATTTT
GGAAAATGACACTTCAATTAATTTTGTTATTATCAGTCAGTGTACTTTCT
ATTCAGGCATTTTGGTGTCCTCCATGCGACATGTCTAGCTGTACTCCAGT
AAGTTCCAGTTGCCCTGAATCAAGAATCGTACCAAGCATTTGCAATTGCT
GTAAAGTTTGTGGGCTTCAAGAAGGAGAGAAATGCACCTCAAATTCCGGA
ACTAGATGTGCTAATGGTTTGCGATGTGAAACAAGCTTTGGTTGTCGATA
TCAATATTATCTTCCATGGCAGACACCTGTATCCGGAACCTGTGTTCAGG
AGAAACCGGACGAAGATGAGACGCCAAGCTATTGTTATGATATGGGATGG
ATAATGAAACAATCAGGACGATAAATAAATGTTCATGTTTTTCAATAAAT
ATAAAATTTTCCAGATCGGAA
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protein sequence of SMED30034380-orf-1

>SMED30034380-orf-1 ID=SMED30034380-orf-1|Name=SMED30034380-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=123bp
MTLQLILLLSVSVLSIQAFWCPPCDMSSCTPVSSSCPESRIVPSICNCCK
VCGLQEGEKCTSNSGTRCANGLRCETSFGCRYQYYLPWQTPVSGTCVQEK
PDEDETPSYCYDMGWIMKQSGR*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000025nervous system
PLANA:0000099neuron
PLANA:0000420parapharyngeal region
PLANA:0003116parenchymal cell
Vocabulary: INTERPRO
TermDefinition
IPR011390IGFBP_rP_mac25
IPR000867IGFBP-like
IPR009030Growth_fac_rcpt_cys_sf
Vocabulary: cellular component
TermDefinition
GO:0005576extracellular region
Vocabulary: biological process
TermDefinition
GO:0001558regulation of cell growth
GO:0006508proteolysis
Vocabulary: molecular function
TermDefinition
GO:0005520insulin-like growth factor binding
GO:0004252serine-type endopeptidase activity
GO:0008233peptidase activity
GO:0008236serine-type peptidase activity
GO:0016787hydrolase activity
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR000867Insulin-like growth factor-binding protein, IGFBPSMARTSM00121IB_2coord: 27..106
e-value: 3.3E-8
score: 43.3
IPR000867Insulin-like growth factor-binding protein, IGFBPPFAMPF00219IGFBPcoord: 29..82
e-value: 4.2E-9
score: 36.9
IPR000867Insulin-like growth factor-binding protein, IGFBPPROSITEPS51323IGFBP_N_2coord: 25..91
score: 14.547
NoneNo IPR availableGENE3DG3DSA:3.30.60.30coord: 28..119
e-value: 1.9E-6
score: 30.4
NoneNo IPR availableSIGNALP_EUKSignalP-noTMSignalP-noTMcoord: 1..26
score: 0.877
IPR011390Insulin-like growth factor binding protein-related protein (IGFBP-rP), MAC25PANTHERPTHR14186INSULIN-LIKE GROWTH FACTOR BINDING PROTEIN-RELATEDcoord: 11..107
IPR009030Growth factor receptor cysteine-rich domain superfamilySUPERFAMILYSSF57184Growth factor receptor domaincoord: 26..107