Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM

Overview
NameRetrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM
Smed IDSMED30006359
Length (bp)524
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 Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM (SMED30006359) t-SNE clustered cells

Violin plots show distribution of expression levels for Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM (SMED30006359) 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.
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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



SMED30006359

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



PAGE Curations: 3

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
cephalic gangliaSMED30006359 dd_Smed_v4_32082_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30006359 dd_Smed_v4_32082_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
zeta neoblastSMED30006359 dd_Smed_v4_32082_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM vs. Planmine SMEST
Match: SMESG000019752.1 (SMESG000019752.1)

HSP 1 Score: 109.768 bits (273), Expect = 3.156e-28
Identity = 59/94 (62.77%), Postives = 69/94 (73.40%), Query Frame = 3 
Query:    3 GVGLDLNASKCATMMVLKNGKEKET*LSMKSISINGNEIPAMKATETYKYLGLQMGFKSKE-NMMGVCFICKHCPIAEMPLCNQSHVKVINNFI 281
            G GLDLNASKCATMMVLKNGKEK T LS  +ISING+ IPAMKATETYKYLGLQMGFK+KE N   +      C I + PL  Q  + ++ +F+
Sbjct:  144 GAGLDLNASKCATMMVLKNGKEKATYLSTTTISINGSNIPAMKATETYKYLGLQMGFKAKEKNTNEIIEKGLEC-ITKAPLKPQQRMHILRDFL 236
[Close]
BLAST of Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM vs. Planmine SMEST
Match: SMESG000030694.1 (SMESG000030694.1)

HSP 1 Score: 100.523 bits (249), Expect = 6.637e-25
Identity = 50/93 (53.76%), Postives = 62/93 (66.67%), Query Frame = 3 
Query:    3 GVGLDLNASKCATMMVLKNGKEKET*LSMKSISINGNEIPAMKATETYKYLGLQMGFKSKENMMGVCFICKHCPIAEMPLCNQSHVKVINNFI 281
            G GL+LNASKCAT+MV+KNGKEK T +S K I I  N+IP MKATETYKYLGLQMGFK++E             I   PL  Q  + ++ +F+
Sbjct:  550 GAGLELNASKCATLMVMKNGKEKSTYISTKVIKIKENDIPTMKATETYKYLGLQMGFKAREQNANEVITEGLENITRAPLKPQQRIHILRDFL 642
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BLAST of Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM vs. Planmine SMEST
Match: SMESG000032557.1 (SMESG000032557.1)

HSP 1 Score: 78.1814 bits (191), Expect = 4.256e-18
Identity = 38/55 (69.09%), Postives = 43/55 (78.18%), Query Frame = 3 
Query:  297 RSTPCQKYYRLHCHCKHYTSHDFTASISTPNVSQIAPDHFFEDDVKDHFEHGVEE 461
            +  P QK  +LHC+CKHYTSHDFTASI TPNVS I PD+FFE    DHFEHG+EE
Sbjct:  150 QGDPLQKE-QLHCYCKHYTSHDFTASIPTPNVSPIVPDNFFE----DHFEHGIEE 199
[Close]
BLAST of Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM vs. Planmine SMEST
Match: SMESG000032557.1 (SMESG000032557.1)

HSP 1 Score: 77.7962 bits (190), Expect = 4.408e-18
Identity = 38/55 (69.09%), Postives = 43/55 (78.18%), Query Frame = 3 
Query:  297 RSTPCQKYYRLHCHCKHYTSHDFTASISTPNVSQIAPDHFFEDDVKDHFEHGVEE 461
            +  P QK  +LHC+CKHYTSHDFTASI TPNVS I PD+FFE    DHFEHG+EE
Sbjct:  148 QGDPLQKE-QLHCYCKHYTSHDFTASIPTPNVSPIVPDNFFE----DHFEHGIEE 197
The following BLAST results are available for this feature:
BLAST of Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM 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 Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM 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 Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM 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 Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM 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 Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM 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 Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM 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 Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM 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 Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM 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 Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM 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 Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM 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 Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM 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 Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM 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 Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM 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 Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000019752.13.156e-2862.77SMESG000019752.1[more]
SMESG000030694.16.637e-2553.76SMESG000030694.1[more]
SMESG000032557.14.256e-1869.09SMESG000032557.1[more]
SMESG000032557.14.408e-1869.09SMESG000032557.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30006359 ID=SMED30006359|Name=Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM|organism=Schmidtea mediterranea sexual|type=transcript|length=524bp
ATGGTGTGGGACTTGATTTGAATGCCTCGAAATGCGCAACAATGATGGTG
CTAAAGAATGGTAAAGAAAAAGAAACTTAACTATCAATGAAATCAATATC
AATAAACGGAAATGAAATACCTGCAATGAAAGCGACAGAAACATACAAAT
ATCTGGGATTACAAATGGGGTTCAAATCAAAAGAAAATATGATGGGCGTT
TGCTTTATCTGCAAACATTGCCCAATTGCAGAGATGCCTTTATGCAACCA
GAGCCACGTCAAGGTGATTAATAATTTTATAAAAAATTATTGTATTCGAT
CTACCCCATGTCAGAAATATTATAGGCTGCATTGTCACTGCAAACATTAT
ACAAGTCATGATTTTACGGCATCAATTTCAACTCCAAATGTGTCTCAAAT
TGCACCAGATCATTTTTTTGAAGATGATGTTAAAGATCATTTTGAACATG
GTGTTGAAGAATTCACAAAACGATGGACAAAATGAAGCACAAAATAATGC
ACAAAAATGGTGCACAAAACAAAT
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protein sequence of SMED30006359-orf-1

>SMED30006359-orf-1 ID=SMED30006359-orf-1|Name=SMED30006359-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=133bp
MKSISINGNEIPAMKATETYKYLGLQMGFKSKENMMGVCFICKHCPIAEM
PLCNQSHVKVINNFIKNYCIRSTPCQKYYRLHCHCKHYTSHDFTASISTP
NVSQIAPDHFFEDDVKDHFEHGVEEFTKRWTK*
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000014zeta neoblast
PLANA:0000429neoblast
Vocabulary: molecular function
TermDefinition
GO:0003964RNA-directed DNA polymerase activity
GO:0004190aspartic-type endopeptidase activity
GO:0004518nuclease activity
GO:0004519endonuclease activity
GO:0008233peptidase activity
GO:0016740transferase activity
GO:0016779nucleotidyltransferase activity
GO:0016787hydrolase activity
GO:0046872metal ion binding
Vocabulary: biological process
TermDefinition
GO:0006278RNA-dependent DNA biosynthetic process
GO:0006508proteolysis
GO:0090305nucleic acid phosphodiester bond hydrolysis