FYVE_2 domain-containing protein

Overview
NameFYVE_2 domain-containing protein
Smed IDSMED30003595
Length (bp)235
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 FYVE_2 domain-containing protein (SMED30003595) t-SNE clustered cells

Violin plots show distribution of expression levels for FYVE_2 domain-containing protein (SMED30003595) 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 FYVE_2 domain-containing protein (SMED30003595) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for FYVE_2 domain-containing protein (SMED30003595) 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



SMED30003595

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
head regionSMED30003595h1SMcG0005152 SmedASXL_017660SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30003595h1SMcG0005152 SmedASXL_012646SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
nervous systemSMED30003595h1SMcG0005152 dd_Smed_v4_21937_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30003595h1SMcG0005152 dd_Smed_v4_21937_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30003595h1SMcG0005152 dd_Smed_v4_21937_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
nervous systemSMED30003595h1SMcG0005152 dd_Smed_v4_9615_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
cephalic gangliaSMED30003595h1SMcG0005152 dd_Smed_v4_9615_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neuronSMED30003595h1SMcG0005152 dd_Smed_v4_9615_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		whole organism asexual adult colorimetric in situ hybridization evidence
neoblastSMED30003595h1SMcG0005152 dd_Smed_v4_9615_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
non-ciliated neuronSMED30003595h1SMcG0005152 dd_Smed_v4_9615_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30003595h1SMcG0005152 Contig40700newmark_estsPMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
Smed sexual biotypeSMED30003595h1SMcG0005152 Contig40700uc_Smed_v2PMID:29674431
Fincher et al., 2018		FACS sorted cell population adult hermaphrodite single-cell RNA-sequencing evidence
head regionSMED30003595h1SMcG0005152 dd_Smed_v6_9615_0_1dd_Smed_v6PMID:28171748
Stückemann et al., 2017		whole organism asexual adult RNA-sequencing evidence
oocyteSMED30003595h1SMcG0005152 Contig29245newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
oocyteSMED30003595h1SMcG0005152 Contig29245uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30003595h1SMcG0005152 Contig29245newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
vitelline glandSMED30003595h1SMcG0005152 Contig29245uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30003595h1SMcG0005152 Contig29245newmark_estsPMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
reproductive organSMED30003595h1SMcG0005152 Contig29245uc_Smed_v2PMID:28434803
Rouhana et al., 2017		whole organism adult hermaphrodite RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
[Close]
BLAST of FYVE_2 domain-containing protein vs. TrEMBL
Match: A0A267DWZ0 (Uncharacterized protein OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig009117g1 PE=4 SV=1)

HSP 1 Score: 54.6842 bits (130), Expect = 4.985e-8
Identity = 23/43 (53.49%), Postives = 31/43 (72.09%), Query Frame = 2 
Query:  104 SRIDDLLCSICQKKRHIILSSGMWFHGLCHDPFPKTLSIQDLL 232
            S+  + +CSICQKKRH+ +SSG W+HGL H P    +S+Q LL
Sbjct:  269 SKFAEWMCSICQKKRHLAMSSGAWYHGLRHQP----ISLQTLL 307

HSP 2 Score: 30.0314 bits (66), Expect = 4.985e-8
Identity = 10/21 (47.62%), Postives = 14/21 (66.67%), Query Frame = 3 
Query:   51 CVNCGRKVCNECGMYNSDPGS 113
            C +C R VC +CG + +D GS
Sbjct:  249 CTDCNRLVCYDCGNFCNDSGS 269
[Close]
BLAST of FYVE_2 domain-containing protein vs. TrEMBL
Match: A0A267DFR7 (Uncharacterized protein (Fragment) OS=Macrostomum lignano OX=282301 GN=BOX15_Mlig014632g1 PE=4 SV=1)

HSP 1 Score: 54.6842 bits (130), Expect = 4.986e-8
Identity = 23/43 (53.49%), Postives = 31/43 (72.09%), Query Frame = 2 
Query:  104 SRIDDLLCSICQKKRHIILSSGMWFHGLCHDPFPKTLSIQDLL 232
            S+  + +CSICQKKRH+ +SSG W+HGL H P    +S+Q LL
Sbjct:  269 SKFAEWMCSICQKKRHLAMSSGAWYHGLRHQP----ISLQTLL 307

HSP 2 Score: 30.0314 bits (66), Expect = 4.986e-8
Identity = 10/21 (47.62%), Postives = 14/21 (66.67%), Query Frame = 3 
Query:   51 CVNCGRKVCNECGMYNSDPGS 113
            C +C R VC +CG + +D GS
Sbjct:  249 CTDCNRLVCYDCGNFCNDSGS 269
[Close]
BLAST of FYVE_2 domain-containing protein vs. TrEMBL
Match: A0A1I8JL15 (FYVE_2 domain-containing protein OS=Macrostomum lignano OX=282301 PE=4 SV=1)

HSP 1 Score: 54.6842 bits (130), Expect = 5.057e-8
Identity = 23/43 (53.49%), Postives = 31/43 (72.09%), Query Frame = 2 
Query:  104 SRIDDLLCSICQKKRHIILSSGMWFHGLCHDPFPKTLSIQDLL 232
            S+  + +CSICQKKRH+ +SSG W+HGL H P    +S+Q LL
Sbjct:   66 SKFAEWMCSICQKKRHLAMSSGAWYHGLRHQP----ISLQTLL 104

HSP 2 Score: 30.0314 bits (66), Expect = 5.057e-8
Identity = 10/21 (47.62%), Postives = 14/21 (66.67%), Query Frame = 3 
Query:   51 CVNCGRKVCNECGMYNSDPGS 113
            C +C R VC +CG + +D GS
Sbjct:   46 CTDCNRLVCYDCGNFCNDSGS 66
[Close]
BLAST of FYVE_2 domain-containing protein vs. Planmine SMEST
Match: SMESG000050479.1 (SMESG000050479.1)

HSP 1 Score: 97.0561 bits (240), Expect = 3.506e-25
Identity = 43/51 (84.31%), Postives = 44/51 (86.27%), Query Frame = 2 
Query:   83 MWNVQ**SRIDDLLCSICQKKRHIILSSGMWFHGLCHDPFPKTLSIQDLLL 235
            M+N    S   DLLCSICQKKRHIILSSGMWFHGLCHDPFPKTLSIQDLLL
Sbjct:  182 MYNSDPGSTFADLLCSICQKKRHIILSSGMWFHGLCHDPFPKTLSIQDLLL 232

HSP 2 Score: 86.2705 bits (212), Expect = 1.887e-21
Identity = 38/38 (100.00%), Postives = 38/38 (100.00%), Query Frame = 3 
Query:    3 ICSKSVIQTDSTVNLACVNCGRKVCNECGMYNSDPGST 116
            ICSKSVIQTDSTVNLACVNCGRKVCNECGMYNSDPGST
Sbjct:  153 ICSKSVIQTDSTVNLACVNCGRKVCNECGMYNSDPGST 190
[Close]
BLAST of FYVE_2 domain-containing protein vs. Planmine SMEST
Match: SMESG000050479.1 (SMESG000050479.1)

HSP 1 Score: 97.0561 bits (240), Expect = 3.575e-25
Identity = 43/51 (84.31%), Postives = 44/51 (86.27%), Query Frame = 2 
Query:   83 MWNVQ**SRIDDLLCSICQKKRHIILSSGMWFHGLCHDPFPKTLSIQDLLL 235
            M+N    S   DLLCSICQKKRHIILSSGMWFHGLCHDPFPKTLSIQDLLL
Sbjct:  182 MYNSDPGSTFADLLCSICQKKRHIILSSGMWFHGLCHDPFPKTLSIQDLLL 232

HSP 2 Score: 89.3521 bits (220), Expect = 1.639e-22
Identity = 38/38 (100.00%), Postives = 38/38 (100.00%), Query Frame = 3 
Query:    3 ICSKSVIQTDSTVNLACVNCGRKVCNECGMYNSDPGST 116
            ICSKSVIQTDSTVNLACVNCGRKVCNECGMYNSDPGST
Sbjct:  153 ICSKSVIQTDSTVNLACVNCGRKVCNECGMYNSDPGST 190
[Close]
BLAST of FYVE_2 domain-containing protein vs. Planmine SMEST
Match: SMESG000050479.1 (SMESG000050479.1)

HSP 1 Score: 97.0561 bits (240), Expect = 3.577e-25
Identity = 43/51 (84.31%), Postives = 44/51 (86.27%), Query Frame = 2 
Query:   83 MWNVQ**SRIDDLLCSICQKKRHIILSSGMWFHGLCHDPFPKTLSIQDLLL 235
            M+N    S   DLLCSICQKKRHIILSSGMWFHGLCHDPFPKTLSIQDLLL
Sbjct:  182 MYNSDPGSTFADLLCSICQKKRHIILSSGMWFHGLCHDPFPKTLSIQDLLL 232

HSP 2 Score: 89.3521 bits (220), Expect = 1.640e-22
Identity = 38/38 (100.00%), Postives = 38/38 (100.00%), Query Frame = 3 
Query:    3 ICSKSVIQTDSTVNLACVNCGRKVCNECGMYNSDPGST 116
            ICSKSVIQTDSTVNLACVNCGRKVCNECGMYNSDPGST
Sbjct:  153 ICSKSVIQTDSTVNLACVNCGRKVCNECGMYNSDPGST 190
[Close]
BLAST of FYVE_2 domain-containing protein vs. Planmine SMEST
Match: SMESG000050479.1 (SMESG000050479.1)

HSP 1 Score: 97.0561 bits (240), Expect = 3.583e-25
Identity = 43/51 (84.31%), Postives = 44/51 (86.27%), Query Frame = 2 
Query:   83 MWNVQ**SRIDDLLCSICQKKRHIILSSGMWFHGLCHDPFPKTLSIQDLLL 235
            M+N    S   DLLCSICQKKRHIILSSGMWFHGLCHDPFPKTLSIQDLLL
Sbjct:  182 MYNSDPGSTFADLLCSICQKKRHIILSSGMWFHGLCHDPFPKTLSIQDLLL 232

HSP 2 Score: 88.9669 bits (219), Expect = 2.055e-22
Identity = 38/38 (100.00%), Postives = 38/38 (100.00%), Query Frame = 3 
Query:    3 ICSKSVIQTDSTVNLACVNCGRKVCNECGMYNSDPGST 116
            ICSKSVIQTDSTVNLACVNCGRKVCNECGMYNSDPGST
Sbjct:  153 ICSKSVIQTDSTVNLACVNCGRKVCNECGMYNSDPGST 190
The following BLAST results are available for this feature:
BLAST of FYVE_2 domain-containing protein 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 FYVE_2 domain-containing protein 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 FYVE_2 domain-containing protein 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 FYVE_2 domain-containing protein 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 FYVE_2 domain-containing protein 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 FYVE_2 domain-containing protein 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 FYVE_2 domain-containing protein 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 FYVE_2 domain-containing protein vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 3
Match NameE-valueIdentityDescription
A0A267DWZ04.985e-853.49Uncharacterized protein OS=Macrostomum lignano OX=... [more]
A0A267DFR74.986e-853.49Uncharacterized protein (Fragment) OS=Macrostomum ... [more]
A0A1I8JL155.057e-853.49FYVE_2 domain-containing protein OS=Macrostomum li... [more]
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BLAST of FYVE_2 domain-containing protein 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 FYVE_2 domain-containing protein 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 FYVE_2 domain-containing protein 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 FYVE_2 domain-containing protein 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 FYVE_2 domain-containing protein 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 FYVE_2 domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 4
Match NameE-valueIdentityDescription
SMESG000050479.13.506e-2584.31SMESG000050479.1[more]
SMESG000050479.13.575e-2584.31SMESG000050479.1[more]
SMESG000050479.13.577e-2584.31SMESG000050479.1[more]
SMESG000050479.13.583e-2584.31SMESG000050479.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30003595 ID=SMED30003595|Name=FYVE_2 domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=235bp
CAATATGTTCCAAATCAGTGATCCAAACAGATTCTACAGTAAATTTAGCA
TGTGTAAATTGTGGAAGAAAAGTTTGCAATGAATGTGGAATGTACAATAG
TGATCCAGGATCGACGACTTGCTTTGTTCAATTTGTCAGAAGAAGCGTCA
CATAATCCTCAGTTCCGGTATGTGGTTCCACGGTCTGTGTCACGATCCAT
TTCCAAAGACGCTTTCAATACAAGACCTGCTTCTA
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: molecular function
TermDefinition
GO:0046872metal ion binding
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000099neuron
PLANA:0000418head
Vocabulary: INTERPRO
TermDefinition
IPR013083Znf_RING/FYVE/PHD