MACPF domain-containing protein 3

Overview
NameMACPF domain-containing protein 3
Smed IDSMED30004193
Length (bp)249
Neoblast Clusters

Zeng et. al., 2018



▻ Overview

▻ 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



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 MACPF domain-containing protein 3 (SMED30004193) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for MACPF domain-containing protein 3 (SMED30004193) 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.
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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



SMED30004193

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



PAGE Curations: 19

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
gutSMED30004193SMESG000044682.1 Contig721newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30004193SMESG000044682.1 Contig721uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30004193SMESG000044682.1 Contig721newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004193SMESG000044682.1 Contig721uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
gutSMED30004193SMESG000058940.1 Contig721newmark_estsPMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
gutSMED30004193SMESG000058940.1 Contig721uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		whole organism asexual adult colorimetric in situ hybridization evidence
intestinal phagocyteSMED30004193SMESG000058940.1 Contig721newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30004193SMESG000058940.1 Contig721uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
Smed sexual biotypeSMED30004193SMESG000044682.1 Contig721newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004193SMESG000044682.1 Contig721uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004193SMESG000044682.1 Contig50098newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004193SMESG000044682.1 SMESG000044677.1 Contig3899newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004193SMESG000044682.1 SMESG000044677.1 Contig3899uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004193SMESG000058940.1 Contig721newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004193SMESG000058940.1 Contig721uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004193SMESG000052764.1 SMESG000052762.1 SMESG000052759.1 SMESG000052750.1 SMESG000052741.1 SMESG000052739.1 Contig3899newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30004193SMESG000052764.1 SMESG000052762.1 SMESG000052759.1 SMESG000052750.1 SMESG000052741.1 SMESG000052739.1 Contig3899uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
neoblastSMED30004193SMESG000044682.1 SMESG000044677.1 SMED_02677_V2_1rGPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
neoblastSMED30004193SMESG000044682.1 SMED_02677_V2_1rGPL14150_gene_modelsPMID:22385657
Wagner et al., 2012		whole organism asexual adult cDNA to DNA expression microarray evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of MACPF domain-containing protein 3 vs. TrEMBL
Match: A5A508 (Macrophage expressed protein OS=Haliotis diversicolor supertexta OX=283615 PE=2 SV=1)

HSP 1 Score: 56.225 bits (134), Expect = 3.401e-7
Identity = 31/80 (38.75%), Postives = 44/80 (55.00%), Query Frame = 1 
Query:   16 LCFNDLERTSKKFYLQGRG---CSAGNPLA---KEYVNKKPKLPS-NSKMEGLLYWPKTCAKGYVAHIVSIEQGCQISYC 234
            +C +D      K+ +   G   C++GNPLA   K   NK   LPS +S  +    WPK C KGY  H+  ++QGC+I+YC
Sbjct:  515 ICISDDYELGMKYSMPFGGFISCTSGNPLAMSPKPEGNKNSALPSLHSFFQSSKSWPKHCPKGYSQHLAYVDQGCEINYC 594
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BLAST of MACPF domain-containing protein 3 vs. TrEMBL
Match: Q6RYF9 (Macrophage expressed protein OS=Haliotis corrugata OX=6453 GN=mpeg1 PE=2 SV=1)

HSP 1 Score: 54.299 bits (129), Expect = 1.623e-6
Identity = 33/85 (38.82%), Postives = 46/85 (54.12%), Query Frame = 1 
Query:   16 LCFNDLERTSKKFYLQGRG---CSAGNPLAKEYVNKKPK--------LPS-NSKMEGLLYWPKTCAKGYVAHIVSIEQGCQISYC 234
            +C +D      K+ +   G   C+ GNPLA   +N KPK        LPS +S  +G   WPK C KGY  H+  ++QGC+I+YC
Sbjct:  515 ICISDDYELGMKYSMPFGGFISCTTGNPLA---MNPKPKSKGDMNSALPSLHSFFQGSKTWPKHCPKGYSQHLAYVDQGCEINYC 596
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BLAST of MACPF domain-containing protein 3 vs. TrEMBL
Match: A0A1R7T0A1 (Macrophage expressed protein OS=Haliotis madaka OX=81897 PE=2 SV=1)

HSP 1 Score: 54.299 bits (129), Expect = 1.721e-6
Identity = 33/85 (38.82%), Postives = 46/85 (54.12%), Query Frame = 1 
Query:   16 LCFNDLERTSKKFYLQGRG---CSAGNPLAKEYVNKKPK--------LPS-NSKMEGLLYWPKTCAKGYVAHIVSIEQGCQISYC 234
            +C +D      K+ +   G   C+ GNPLA   +N KPK        LPS +S  +G   WPK C KGY  H+  ++QGC+I+YC
Sbjct:  515 ICISDDYELGMKYSMPFGGFISCTTGNPLA---MNPKPKSKGGMNSALPSLHSFFQGSKTWPKHCPKGYSQHLAYVDQGCEINYC 596
[Close]
BLAST of MACPF domain-containing protein 3 vs. TrEMBL
Match: A0A076U635 (Macrophage expressed protein OS=Haliotis discus discus OX=91233 GN=MPEG1 PE=4 SV=1)

HSP 1 Score: 54.299 bits (129), Expect = 1.755e-6
Identity = 33/85 (38.82%), Postives = 46/85 (54.12%), Query Frame = 1 
Query:   16 LCFNDLERTSKKFYLQGRG---CSAGNPLAKEYVNKKPK--------LPS-NSKMEGLLYWPKTCAKGYVAHIVSIEQGCQISYC 234
            +C +D      K+ +   G   C+ GNPLA   +N KPK        LPS +S  +G   WPK C KGY  H+  ++QGC+I+YC
Sbjct:  515 ICISDDYELGMKYSMPFGGFISCTTGNPLA---MNPKPKSKGGMNSALPSLHSFFQGSKTWPKHCPKGYSQHLAYVDQGCEINYC 596
[Close]
BLAST of MACPF domain-containing protein 3 vs. TrEMBL
Match: Q6RYF8 (Macrophage expressed protein OS=Haliotis rufescens OX=6454 PE=2 SV=1)

HSP 1 Score: 53.9138 bits (128), Expect = 1.954e-6
Identity = 33/85 (38.82%), Postives = 46/85 (54.12%), Query Frame = 1 
Query:   16 LCFNDLERTSKKFYLQGRG---CSAGNPLAKEYVNKKPK--------LPS-NSKMEGLLYWPKTCAKGYVAHIVSIEQGCQISYC 234
            +C +D      K+ +   G   C+ GNPLA   +N KPK        LPS +S  +G   WPK C KGY  H+  ++QGC+I+YC
Sbjct:  515 ICISDDYELGMKYSMPFGGFISCTTGNPLA---MNPKPKSKGDMNSALPSLHSFFQGSKTWPKHCPKGYSQHLAYVDQGCEINYC 596
[Close]
BLAST of MACPF domain-containing protein 3 vs. Planmine SMEST
Match: SMESG000044682.1 (SMESG000044682.1)

HSP 1 Score: 126.716 bits (317), Expect = 1.530e-35
Identity = 59/59 (100.00%), Postives = 59/59 (100.00%), Query Frame = 1 
Query:   73 CSAGNPLAKEYVNKKPKLPSNSKMEGLLYWPKTCAKGYVAHIVSIEQGCQISYCTETNK 249
            CSAGNPLAKEYVNKKPKLPSNSKMEGLLYWPKTCAKGYVAHIVSIEQGCQISYCTETNK
Sbjct:  510 CSAGNPLAKEYVNKKPKLPSNSKMEGLLYWPKTCAKGYVAHIVSIEQGCQISYCTETNK 568
[Close]
BLAST of MACPF domain-containing protein 3 vs. Planmine SMEST
Match: SMESG000044681.1 (SMESG000044681.1)

HSP 1 Score: 105.145 bits (261), Expect = 5.480e-28
Identity = 50/59 (84.75%), Postives = 52/59 (88.14%), Query Frame = 1 
Query:   73 CSAGNPLAKEYVNKKPKLPSNSKMEGLLYWPKTCAKGYVAHIVSIEQGCQISYCTETNK 249
            CSAGNPLA+EYV  KPKL S+SKM  L YWPKTCAKGYVAHI SIEQGCQISYCTETNK
Sbjct:  492 CSAGNPLAQEYVKNKPKLYSSSKMADLKYWPKTCAKGYVAHISSIEQGCQISYCTETNK 550
[Close]
BLAST of MACPF domain-containing protein 3 vs. Planmine SMEST
Match: SMESG000044678.1 (SMESG000044678.1)

HSP 1 Score: 98.2117 bits (243), Expect = 1.281e-25
Identity = 49/69 (71.01%), Postives = 53/69 (76.81%), Query Frame = 1 
Query:   52 FYLQGRG---CSAGNPLAKEYVNKKPKLPSNSKMEGLLYWPKTCAKGYVAHIVSIEQGCQISYCTETNK 249
            F +Q  G   CSAGNPLAKEYVN K K   N KM  + YWPKTCAKG+VAHI +IEQGCQISYCTETNK
Sbjct:  321 FVIQFGGLFSCSAGNPLAKEYVNGKAKSFQNLKMNDIKYWPKTCAKGFVAHIATIEQGCQISYCTETNK 389
[Close]
BLAST of MACPF domain-containing protein 3 vs. Planmine SMEST
Match: SMESG000044678.1 (SMESG000044678.1)

HSP 1 Score: 98.2117 bits (243), Expect = 1.470e-25
Identity = 49/69 (71.01%), Postives = 53/69 (76.81%), Query Frame = 1 
Query:   52 FYLQGRG---CSAGNPLAKEYVNKKPKLPSNSKMEGLLYWPKTCAKGYVAHIVSIEQGCQISYCTETNK 249
            F +Q  G   CSAGNPLAKEYVN K K   N KM  + YWPKTCAKG+VAHI +IEQGCQISYCTETNK
Sbjct:  337 FVIQFGGLFSCSAGNPLAKEYVNGKAKSFQNLKMNDIKYWPKTCAKGFVAHIATIEQGCQISYCTETNK 405
[Close]
BLAST of MACPF domain-containing protein 3 vs. Planmine SMEST
Match: SMESG000044672.1 (SMESG000044672.1)

HSP 1 Score: 69.3218 bits (168), Expect = 1.465e-16
Identity = 31/36 (86.11%), Postives = 32/36 (88.89%), Query Frame = 1 
Query:  142 MEGLLYWPKTCAKGYVAHIVSIEQGCQISYCTETNK 249
            M  L YWPKTCAKGYVAHI SIEQGCQISYC+ETNK
Sbjct:    1 MAELKYWPKTCAKGYVAHISSIEQGCQISYCSETNK 36
The following BLAST results are available for this feature:
BLAST of MACPF domain-containing protein 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 MACPF domain-containing protein 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 MACPF domain-containing protein 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 MACPF domain-containing protein 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 MACPF domain-containing protein 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 MACPF domain-containing protein 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 MACPF domain-containing protein 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 MACPF domain-containing protein 3 vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A5A5083.401e-738.75Macrophage expressed protein OS=Haliotis diversico... [more]
Q6RYF91.623e-638.82Macrophage expressed protein OS=Haliotis corrugata... [more]
A0A1R7T0A11.721e-638.82Macrophage expressed protein OS=Haliotis madaka OX... [more]
A0A076U6351.755e-638.82Macrophage expressed protein OS=Haliotis discus di... [more]
Q6RYF81.954e-638.82Macrophage expressed protein OS=Haliotis rufescens... [more]
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BLAST of MACPF domain-containing protein 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 MACPF domain-containing protein 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 MACPF domain-containing protein 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 MACPF domain-containing protein 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 MACPF domain-containing protein 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 MACPF domain-containing protein 3 vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000044682.11.530e-35100.00SMESG000044682.1[more]
SMESG000044681.15.480e-2884.75SMESG000044681.1[more]
SMESG000044678.11.281e-2571.01SMESG000044678.1[more]
SMESG000044678.11.470e-2571.01SMESG000044678.1[more]
SMESG000044672.11.465e-1686.11SMESG000044672.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30004193 ID=SMED30004193|Name=MACPF domain-containing protein 3|organism=Schmidtea mediterranea sexual|type=transcript|length=249bp
ATGGTGACTCATTGTCTTTGTTTCAATGACCTTGAACGAACTTCGAAAAA
ATTTTATCTCCAGGGGAGGGGCTGCAGTGCCGGAAATCCATTAGCTAAAG
AATATGTAAACAAAAAACCAAAGTTACCGTCTAATTCCAAGATGGAAGGT
TTATTATATTGGCCTAAAACCTGTGCCAAAGGGTATGTGGCTCATATTGT
GTCAATAGAACAAGGCTGTCAGATTTCATACTGTACAGAGACAAATAAA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000026gut
PLANA:0000070intestinal phagocyte
PLANA:0000429neoblast
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane