Phosphodiesterase

Overview
NamePhosphodiesterase
Smed IDSMED30017021
Length (bp)133
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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Homology
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BLAST of Phosphodiesterase vs. TrEMBL
Match: C3Y1E6 (Uncharacterized protein OS=Branchiostoma floridae OX=7739 GN=BRAFLDRAFT_83680 PE=4 SV=1)

HSP 1 Score: 58.5362 bits (140), Expect = 9.777e-9
Identity = 22/42 (52.38%), Postives = 33/42 (78.57%), Query Frame = 3 
Query:    6 FWPWTVPNDSQPVYVLYMFKDLFGLE*FDAEILMRFVLTVKK 131
            + PW++P+D +P+YV+ MFKDLF +  FD E L+RF +TV+K
Sbjct:  551 YSPWSIPDDVKPLYVILMFKDLFCMSKFDMEQLIRFTMTVRK 592
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BLAST of Phosphodiesterase vs. TrEMBL
Match: R7UJM9 (Phosphodiesterase OS=Capitella teleta OX=283909 GN=CAPTEDRAFT_155235 PE=3 SV=1)

HSP 1 Score: 58.151 bits (139), Expect = 1.300e-8
Identity = 24/42 (57.14%), Postives = 31/42 (73.81%), Query Frame = 3 
Query:    6 FWPWTVPNDSQPVYVLYMFKDLFGLE*FDAEILMRFVLTVKK 131
            F PW+V ND +P+YV+YMF+DLF    FD   L+RF LTV+K
Sbjct:  281 FSPWSVTNDEKPLYVIYMFRDLFSTARFDMGSLIRFTLTVRK 322
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BLAST of Phosphodiesterase vs. TrEMBL
Match: A0A1W0WNA2 (Phosphodiesterase OS=Hypsibius dujardini OX=232323 GN=BV898_09205 PE=3 SV=1)

HSP 1 Score: 52.7582 bits (125), Expect = 1.102e-6
Identity = 22/42 (52.38%), Postives = 30/42 (71.43%), Query Frame = 3 
Query:    6 FWPWTVPNDSQPVYVLYMFKDLFGLE*FDAEILMRFVLTVKK 131
            F PW +    +P+ V+YMF+DLFGL  FD + L+RF LTV+K
Sbjct:  497 FSPWKLTEFQKPLSVIYMFRDLFGLTRFDLDTLIRFSLTVRK 538
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BLAST of Phosphodiesterase vs. TrEMBL
Match: A0A2T7NR97 (Phosphodiesterase OS=Pomacea canaliculata OX=400727 GN=C0Q70_16967 PE=3 SV=1)

HSP 1 Score: 51.9878 bits (123), Expect = 2.003e-6
Identity = 22/43 (51.16%), Postives = 30/43 (69.77%), Query Frame = 3 
Query:    3 SFWPWTVPNDSQPVYVLYMFKDLFGLE*FDAEILMRFVLTVKK 131
            +F PW+V ++ +P+ VLYM +DLF    FD   LMRF LTV+K
Sbjct:  629 TFSPWSVEDNKKPLQVLYMLRDLFSPMRFDTTDLMRFTLTVRK 671
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BLAST of Phosphodiesterase vs. TrEMBL
Match: V4BHX7 (PDEase domain-containing protein OS=Lottia gigantea OX=225164 GN=LOTGIDRAFT_228057 PE=3 SV=1)

HSP 1 Score: 51.6026 bits (122), Expect = 2.637e-6
Identity = 22/42 (52.38%), Postives = 29/42 (69.05%), Query Frame = 3 
Query:    6 FWPWTVPNDSQPVYVLYMFKDLFGLE*FDAEILMRFVLTVKK 131
            + PW++ +  +P+YVL MFKDLF    FD   LMRF LTV+K
Sbjct:  140 YSPWSINDTEKPMYVLDMFKDLFSYTRFDINDLMRFTLTVRK 181
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BLAST of Phosphodiesterase vs. Planmine SMEST
Match: SMESG000044149.1 (SMESG000044149.1)

HSP 1 Score: 95.5153 bits (236), Expect = 2.495e-25
Identity = 42/43 (97.67%), Postives = 42/43 (97.67%), Query Frame = 3 
Query:    3 SFWPWTVPNDSQPVYVLYMFKDLFGLE*FDAEILMRFVLTVKK 131
            SFWPWTVPNDSQPVYVLYMFKDLFGLE FDAEILMRFVLTVKK
Sbjct:  590 SFWPWTVPNDSQPVYVLYMFKDLFGLELFDAEILMRFVLTVKK 632
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BLAST of Phosphodiesterase vs. Planmine SMEST
Match: SMESG000044149.1 (SMESG000044149.1)

HSP 1 Score: 84.3445 bits (207), Expect = 1.974e-21
Identity = 42/61 (68.85%), Postives = 42/61 (68.85%), Query Frame = 3 
Query:    3 SFWPWTVPNDSQPVYVLYMFKDLFGLE------------------*FDAEILMRFVLTVKK 131
            SFWPWTVPNDSQPVYVLYMFKDLFGLE                   FDAEILMRFVLTVKK
Sbjct:  590 SFWPWTVPNDSQPVYVLYMFKDLFGLELINVERRTGSESYIEFDDRFDAEILMRFVLTVKK 650
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BLAST of Phosphodiesterase vs. Planmine SMEST
Match: SMESG000044149.1 (SMESG000044149.1)

HSP 1 Score: 84.3445 bits (207), Expect = 2.352e-21
Identity = 42/61 (68.85%), Postives = 42/61 (68.85%), Query Frame = 3 
Query:    3 SFWPWTVPNDSQPVYVLYMFKDLFGLE------------------*FDAEILMRFVLTVKK 131
            SFWPWTVPNDSQPVYVLYMFKDLFGLE                   FDAEILMRFVLTVKK
Sbjct:  572 SFWPWTVPNDSQPVYVLYMFKDLFGLELINVERRTGSESYIEFDDRFDAEILMRFVLTVKK 632
The following BLAST results are available for this feature:
BLAST of Phosphodiesterase 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 Phosphodiesterase 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 Phosphodiesterase 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 Phosphodiesterase 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 Phosphodiesterase 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 Phosphodiesterase 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 Phosphodiesterase 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 Phosphodiesterase vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
C3Y1E69.777e-952.38Uncharacterized protein OS=Branchiostoma floridae ... [more]
R7UJM91.300e-857.14Phosphodiesterase OS=Capitella teleta OX=283909 GN... [more]
A0A1W0WNA21.102e-652.38Phosphodiesterase OS=Hypsibius dujardini OX=232323... [more]
A0A2T7NR972.003e-651.16Phosphodiesterase OS=Pomacea canaliculata OX=40072... [more]
V4BHX72.637e-652.38PDEase domain-containing protein OS=Lottia gigante... [more]
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BLAST of Phosphodiesterase 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 Phosphodiesterase 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 Phosphodiesterase 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 Phosphodiesterase 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 Phosphodiesterase 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 Phosphodiesterase vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 3
Match NameE-valueIdentityDescription
SMESG000044149.12.495e-2597.67SMESG000044149.1[more]
SMESG000044149.11.974e-2168.85SMESG000044149.1[more]
SMESG000044149.12.352e-2168.85SMESG000044149.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30017021 ID=SMED30017021|Name=Phosphodiesterase|organism=Schmidtea mediterranea sexual|type=transcript|length=133bp
TGTCTTTTTGGCCATGGACAGTTCCCAATGACAGTCAACCTGTCTACGTG
CTATACATGTTTAAGGATCTCTTTGGTTTGGAATGATTTGACGCTGAAAT
TCTCATGAGATTCGTATTGACTGTGAAAAAGAA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000016pharynx
PLANA:0000420parapharyngeal region
Vocabulary: molecular function
TermDefinition
GO:00041143',5'-cyclic-nucleotide phosphodiesterase activity
GO:0008081phosphoric diester hydrolase activity
GO:0016787hydrolase activity
GO:0046872metal ion binding
Vocabulary: biological process
TermDefinition
GO:0007165signal transduction