SMED30027751

Overview
NameSMED30027751
Smed IDSMED30027751
Length (bp)830
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 SMED30027751 (SMED30027751) t-SNE clustered cells

Violin plots show distribution of expression levels for SMED30027751 (SMED30027751) 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 SMED30027751 (SMED30027751) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for SMED30027751 (SMED30027751) 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



SMED30027751

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



PAGE Curations: 4

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30027751SMESG000014111.1 Contig4084newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30027751SMESG000014111.1 Contig4084newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
eyeSMED30027751SMESG000054763.1 SMESG000054762.1 SMESG000037691.1 SMESG000037688.1 Contig28920newmark_estsPMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
eyeSMED30027751SMESG000054763.1 SMESG000054762.1 SMESG000037691.1 SMESG000037688.1 Contig28920uc_Smed_v2PMID:27612384
Roberts-Galbraith et al., 2016		whole organism asexual adult colorimetric in situ hybridization evidence
Note: Hover over icons to view figure legend
Alignments
SMED30027751 aligns in the following genomic locations:
Alignment LocationAlignment Score
v31.028990:2145..2967 -3620
v31.004326:60675..61500 +3594
v31.016466:3058..3896 +2973
Homology
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BLAST of SMED30027751 vs. UniProt/SwissProt
Match: sp|P29129|ICP0_SUHVF (E3 ubiquitin-protein ligase ICP0 OS=Suid herpesvirus 1 (strain Indiana-Funkhauser / Becker) OX=31523 GN=EP0 PE=2 SV=1)

HSP 1 Score: 56.225 bits (134), Expect = 8.478e-8
Identity = 25/61 (40.98%), Postives = 37/61 (60.66%), Query Frame = 3 
Query:  180 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVE 362
            M+C ICL    ++ A+ + C H+FC DCI +W L +  CP C +R+  +  H  SD +FVE
Sbjct:   44 MDCPICLDVAATE-AQTLPCMHKFCLDCIQRWTLTSTACPLCNARVTSILHHVDSDASFVE 103
[Close]
BLAST of SMED30027751 vs. Planmine SMEST
Match: SMESG000037691.1 (SMESG000037691.1)

HSP 1 Score: 258.07 bits (658), Expect = 7.712e-88
Identity = 127/128 (99.22%), Postives = 127/128 (99.22%), Query Frame = 3 
Query:  180 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLVRAIDSDEGDSEEYYSDMDCVEDLFFNHSLSDSNNYVITNYIDESGYLS 563
            MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLVRAIDSDEGDSEEYYSDMDCVEDLF NHSLSDSNNYVITNYIDESGYLS
Sbjct:    1 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLVRAIDSDEGDSEEYYSDMDCVEDLFCNHSLSDSNNYVITNYIDESGYLS 128
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BLAST of SMED30027751 vs. Planmine SMEST
Match: SMESG000037688.1 (SMESG000037688.1)

HSP 1 Score: 256.914 bits (655), Expect = 2.539e-87
Identity = 126/128 (98.44%), Postives = 127/128 (99.22%), Query Frame = 3 
Query:  180 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLVRAIDSDEGDSEEYYSDMDCVEDLFFNHSLSDSNNYVITNYIDESGYLS 563
            MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLVRAIDSDEGDSEEYYSDMDCV+DLF NHSLSDSNNYVITNYIDESGYLS
Sbjct:    1 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLVRAIDSDEGDSEEYYSDMDCVDDLFCNHSLSDSNNYVITNYIDESGYLS 128
[Close]
BLAST of SMED30027751 vs. Planmine SMEST
Match: SMESG000054762.1 (SMESG000054762.1)

HSP 1 Score: 254.603 bits (649), Expect = 2.335e-86
Identity = 125/128 (97.66%), Postives = 126/128 (98.44%), Query Frame = 3 
Query:  180 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLVRAIDSDEGDSEEYYSDMDCVEDLFFNHSLSDSNNYVITNYIDESGYLS 563
            MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNL+RAIDSDEGDSEEYYSDMDCVEDLF NHSLSDSNNYVITNYIDESG LS
Sbjct:    1 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLIRAIDSDEGDSEEYYSDMDCVEDLFCNHSLSDSNNYVITNYIDESGNLS 128
[Close]
BLAST of SMED30027751 vs. Planmine SMEST
Match: SMESG000054763.1 (SMESG000054763.1)

HSP 1 Score: 252.677 bits (644), Expect = 1.067e-85
Identity = 124/128 (96.88%), Postives = 126/128 (98.44%), Query Frame = 3 
Query:  180 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLVRAIDSDEGDSEEYYSDMDCVEDLFFNHSLSDSNNYVITNYIDESGYLS 563
            MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNL++AIDSDEGDSEEYYSDMDCVEDLF NHSLSDSNNYVITNYIDESG LS
Sbjct:    1 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLIQAIDSDEGDSEEYYSDMDCVEDLFCNHSLSDSNNYVITNYIDESGNLS 128
[Close]
BLAST of SMED30027751 vs. Planmine SMEST
Match: SMESG000054764.1 (SMESG000054764.1)

HSP 1 Score: 216.853 bits (551), Expect = 1.574e-71
Identity = 109/128 (85.16%), Postives = 115/128 (89.84%), Query Frame = 3 
Query:  180 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTIPPLINKSLEENWNLVRAIDSDEGDSEEYYSDMDCVEDLFFNHSLSDSNNYVITNYIDESGYLS 563
            MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILT PPL+NKSLEENWNL+RAIDSDE DSE+    + C+EDLF +H LSDS  YVITNYIDES  LS
Sbjct:    1 MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMYIHNKSDDNFVEILTNPPLMNKSLEENWNLIRAIDSDEEDSEK---GIGCIEDLFRDHFLSDSKKYVITNYIDESECLS 125
The following BLAST results are available for this feature:
BLAST of SMED30027751 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 SMED30027751 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 SMED30027751 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 SMED30027751 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 SMED30027751 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 SMED30027751 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 SMED30027751 vs. UniProt/SwissProt
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI UniProt)
Total hits: 1
Match NameE-valueIdentityDescription
sp|P29129|ICP0_SUHVF8.478e-840.98E3 ubiquitin-protein ligase ICP0 OS=Suid herpesvir... [more]
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BLAST of SMED30027751 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 SMED30027751 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 SMED30027751 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 SMED30027751 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 SMED30027751 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 SMED30027751 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 SMED30027751 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000037691.17.712e-8899.22SMESG000037691.1[more]
SMESG000037688.12.539e-8798.44SMESG000037688.1[more]
SMESG000054762.12.335e-8697.66SMESG000054762.1[more]
SMESG000054763.11.067e-8596.88SMESG000054763.1[more]
SMESG000054764.11.574e-7185.16SMESG000054764.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30027751 ID=SMED30027751|Name=SMED30027751|organism=Schmidtea mediterranea sexual|type=transcript|length=830bp
AGATGATTAAATTTCTGTTTGTAAACATAACAGTCAAATTTATCATTTTA
CATTGAACAGTCTGTCAACATTTTCCAATTAAAAACTTTATGAAACTATA
AATTTTTACGGAAATTATTATGACGTCATTGCATTAATTTTGTTTTAATT
AAAAATATGTTCTGATATTTTCTGATAATATGGAGTGCTGTATTTGCTTA
TCAAATAATTGTTCCCAAACCGCGAAGGCAGTTGGATGTGAACATCAATT
CTGTGAAGATTGCATATGGAAATGGATCCTAATTACGAACAAGTGCCCAT
CGTGTGGATCAAGAATCGAAGAAATGTATATTCACAATAAAAGTGATGAT
AACTTTGTGGAAATTTTAACAATTCCTCCACTGATAAACAAATCTCTCGA
GGAAAATTGGAACTTGGTTCGAGCCATAGATTCAGATGAAGGAGATAGTG
AGGAATACTATTCAGACATGGACTGTGTTGAGGATCTATTTTTCAATCAT
TCTCTCTCTGATAGTAATAATTATGTTATAACAAATTACATAGATGAATC
TGGATATCTTTCCAATATTATAAGGAATATTGAAGTTAATAATAACAACG
AATTGTAAATGAATTAGGAGTGCAAAATTGTTTGTGATTTATTCCCGTCC
CTGTTTATAACGCTGTGTTGATTATGAATAAATATGTTGAAAAAAATAAA
TTATTTTATTTTTAATTATTTTCATTTAAAATTCAATTAAGTTACTATTA
AACTTGAAATGGATTATTTTTCTGTTAAAATAATAATTTGTATTAAAAAT
ATTTTATTAAAAAAATATTAATTAACTTTT
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protein sequence of SMED30027751-orf-1

>SMED30027751-orf-1 ID=SMED30027751-orf-1|Name=SMED30027751-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=143bp
MECCICLSNNCSQTAKAVGCEHQFCEDCIWKWILITNKCPSCGSRIEEMY
IHNKSDDNFVEILTIPPLINKSLEENWNLVRAIDSDEGDSEEYYSDMDCV
EDLFFNHSLSDSNNYVITNYIDESGYLSNIIRNIEVNNNNEL*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000036eye
PLANA:0000070intestinal phagocyte
Vocabulary: INTERPRO
TermDefinition
IPR001841Znf_RING
IPR013083Znf_RING/FYVE/PHD
IPR017907Znf_RING_CS
Vocabulary: molecular function
TermDefinition
GO:0008270zinc ion binding
GO:0005515protein binding
GO:0016740transferase activity
GO:0003677DNA binding
GO:0046872metal ion binding
Vocabulary: biological process
TermDefinition
GO:0006355regulation of transcription, DNA-templated
GO:0016032viral process
GO:0006351transcription, DNA-templated
GO:0030683evasion or tolerance by virus of host immune response
GO:0039503suppression by virus of host innate immune response
GO:0039548suppression by virus of host IRF3 activity
GO:0039593suppression by virus of host exit from mitosis
GO:0039648modulation by virus of host protein ubiquitination
GO:0060153modulation by virus of host cell cycle
GO:0075342disruption by symbiont of host cell PML body
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
IPR001841Zinc finger, RING-typeSMARTSM00184ring_2coord: 3..42
e-value: 6.6E-4
score: 29.0
IPR001841Zinc finger, RING-typePFAMPF13639zf-RING_2coord: 2..42
e-value: 6.5E-7
score: 29.6
IPR001841Zinc finger, RING-typePROSITEPS50089ZF_RING_2coord: 3..42
score: 10.837
IPR013083Zinc finger, RING/FYVE/PHD-typeGENE3DG3DSA:3.30.40.10coord: 1..63
e-value: 4.6E-10
score: 40.6
IPR017907Zinc finger, RING-type, conserved sitePROSITEPS00518ZF_RING_1coord: 20..29
NoneNo IPR availableSUPERFAMILYSSF57850RING/U-boxcoord: 2..49