FYVE-type domain-containing protein

Overview
NameFYVE-type domain-containing protein
Smed IDSMED30015532
Length (bp)1047
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-type domain-containing protein (SMED30015532) t-SNE clustered cells

Violin plots show distribution of expression levels for FYVE-type domain-containing protein (SMED30015532) 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-type domain-containing protein (SMED30015532) in the t-SNE clustered sub-lethally irradiated X1 and X2 cells.

Violin plots show distribution of expression levels for FYVE-type domain-containing protein (SMED30015532) 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



SMED30015532

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



PAGE Curations: 5

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
protonephridiaSMED30015532SMESG000008512.1 dd_Smed_v4_5283_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30015532SMESG000008512.1 dd_Smed_v4_5283_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30015532SMESG000008512.1 dd_Smed_v4_5283_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30015532SMESG000008512.1 dd_Smed_v6_5283_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
glial cellSMED30015532SMESG000008512.1 dd_Smed_v6_5283_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
Note: Hover over icons to view figure legend
Homology
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BLAST of FYVE-type domain-containing protein vs. Ensembl Celegans
Match: eea-1 (EEA1 (Early Endosome Antigen, Rab effector) homolog [Source:UniProtKB/TrEMBL;Acc:Q5FC45])

HSP 1 Score: 51.9878 bits (123), Expect = 4.286e-7
Identity = 17/40 (42.50%), Postives = 26/40 (65.00%), Query Frame = 1 
Query:  133 QDNQEMEGFICPMCMAKFSSPDMVQKHFDDTHNDMDVKEN 252
            +++QE+EGF+CPMCM +   PD +  HF+  H+D     N
Sbjct:   40 ENDQEIEGFLCPMCMVELGGPDELTVHFEKEHSDTSANRN 79
[Close]
BLAST of FYVE-type domain-containing protein vs. Ensembl Celegans
Match: eea-1 (EEA1 (Early Endosome Antigen, Rab effector) homolog [Source:UniProtKB/TrEMBL;Acc:Q5FC45])

HSP 1 Score: 51.9878 bits (123), Expect = 4.600e-7
Identity = 17/40 (42.50%), Postives = 26/40 (65.00%), Query Frame = 1 
Query:  133 QDNQEMEGFICPMCMAKFSSPDMVQKHFDDTHNDMDVKEN 252
            +++QE+EGF+CPMCM +   PD +  HF+  H+D     N
Sbjct:   40 ENDQEIEGFLCPMCMVELGGPDELTVHFEKEHSDFQTSAN 79
[Close]
BLAST of FYVE-type domain-containing protein vs. Ensembl Zebrafish
Match: eea1 (early endosome antigen 1 [Source:ZFIN;Acc:ZDB-GENE-041111-270])

HSP 1 Score: 48.9062 bits (115), Expect = 6.243e-6
Identity = 25/79 (31.65%), Postives = 40/79 (50.63%), Query Frame = 1 
Query:  136 DNQEMEGFICPMCMAKFSSPDMVQKHFDDTHNDMDVKENDKSTKLNILSPATERKESIQNIQENFNDLKQSLDEEIWFN 372
            +N+  EGFICP CM   +S + + KH++  H   D             SP +  +E +  +++   DL+ SL EE WF+
Sbjct:   28 NNESSEGFICPQCMKSHNSAEELFKHYEVFHEPGDQP-----------SPFSPGREDLTLLRQEIQDLQASLKEERWFS 95
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BLAST of FYVE-type domain-containing protein vs. Ensembl Zebrafish
Match: eea1 (early endosome antigen 1 [Source:ZFIN;Acc:ZDB-GENE-041111-270])

HSP 1 Score: 48.9062 bits (115), Expect = 7.488e-6
Identity = 25/79 (31.65%), Postives = 40/79 (50.63%), Query Frame = 1 
Query:  136 DNQEMEGFICPMCMAKFSSPDMVQKHFDDTHNDMDVKENDKSTKLNILSPATERKESIQNIQENFNDLKQSLDEEIWFN 372
            +N+  EGFICP CM   +S + + KH++  H   D             SP +  +E +  +++   DL+ SL EE WF+
Sbjct:   28 NNESSEGFICPQCMKSHNSAEELFKHYEVFHEPGDQP-----------SPFSPGREDLTLLRQEIQDLQASLKEERWFS 95
[Close]
BLAST of FYVE-type domain-containing protein vs. Ensembl Sea Lamprey
Match: eea1 (early endosome antigen 1 [Source:ZFIN;Acc:ZDB-GENE-041111-270])

HSP 1 Score: 52.373 bits (124), Expect = 1.036e-7
Identity = 20/73 (27.40%), Postives = 38/73 (52.05%), Query Frame = 1 
Query:  154 GFICPMCMAKFSSPDMVQKHFDDTHNDMDVKENDKSTKLNILSPATERKESIQNIQENFNDLKQSLDEEIWFN 372
            GFICP+CM    S D + +H+   HN+    +     +L I      ++  +  +++  N+++ SL EE W++
Sbjct:    1 GFICPVCMKSLGSADELSRHYQSCHNEGSSADGVSQMQLQI------KEGEVTILRQELNEVQTSLKEERWYS 67
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BLAST of FYVE-type domain-containing protein vs. Ensembl Nematostella
Match: EDO39044 (Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7SB89])

HSP 1 Score: 48.9062 bits (115), Expect = 1.366e-6
Identity = 18/32 (56.25%), Postives = 27/32 (84.38%), Query Frame = 1 
Query:  136 DNQEM-EGFICPMCMAKFSSPDMVQKHFDDTH 228
            DN+ + EGFICPMCM +F++PD++ KHF++ H
Sbjct:    2 DNETIKEGFICPMCMKEFNAPDLLVKHFEEFH 33
[Close]
BLAST of FYVE-type domain-containing protein vs. Planmine SMEST
Match: SMESG000008512.1 (SMESG000008512.1)

HSP 1 Score: 564.688 bits (1454), Expect = 0.000e+0
Identity = 322/323 (99.69%), Postives = 323/323 (100.00%), Query Frame = 1 
Query:   79 MFNSISKRFKGDQPQPKPQDNQEMEGFICPMCMAKFSSPDMVQKHFDDTHNDMDVKENDKSTKLNILSPATERKESIQNIQENFNDLKQSLDEEIWFNXXXXXXXXXXXXXXXXXXXXXXXVFKNNQISFEELERTRDALIEKLERVQMSRDSLADENNTLKSDFDICETKLSDQIKYKDELEKLIDKQKQDLDLMTEQLNSAKLSVNSHNIEAAELSAEIQHKYDASLDSVKELSNELERIKNESKLENSELIEKCSILSKSLSENETEKSNMIDEHSQLVTKXXXXXXXXXXXXXXIHDSFQSSEDKILQMKRSWNTDQIT 1047
            MFNSISKRFKGDQPQPKPQDNQEMEGFICPMCMAKFSSPDMVQKHFDDTHNDMDVKENDKSTKLNILSPATERKESIQNIQENFNDLKQSLDEEIWFNKELQKECERLKKLLEEKEEEKNLVFKNNQISFEELERTRDALIEKLERVQMSRDSLADENNTLKSDFDICETKLSDQIKYKDELEKLIDKQKQDLDLMTEQLNSAKLSVNSHNIEAAELSAEIQHKYDASLDSVKELSNELERIKNESKLENSELIEKCSILSKSLSENETEKSNMIDEHSQLVTKLNNQLESLQQENQ+IHDSFQSSEDKILQMKRSWNTDQIT
Sbjct:    1 MFNSISKRFKGDQPQPKPQDNQEMEGFICPMCMAKFSSPDMVQKHFDDTHNDMDVKENDKSTKLNILSPATERKESIQNIQENFNDLKQSLDEEIWFNKELQKECERLKKLLEEKEEEKNLVFKNNQISFEELERTRDALIEKLERVQMSRDSLADENNTLKSDFDICETKLSDQIKYKDELEKLIDKQKQDLDLMTEQLNSAKLSVNSHNIEAAELSAEIQHKYDASLDSVKELSNELERIKNESKLENSELIEKCSILSKSLSENETEKSNMIDEHSQLVTKLNNQLESLQQENQRIHDSFQSSEDKILQMKRSWNTDQIT 323
The following BLAST results are available for this feature:
BLAST of FYVE-type 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-type domain-containing protein vs. Ensembl Celegans
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX Celegan e!99)
Total hits: 2
Match NameE-valueIdentityDescription
eea-14.286e-742.50EEA1 (Early Endosome Antigen, Rab effector) homolo... [more]
eea-14.600e-742.50EEA1 (Early Endosome Antigen, Rab effector) homolo... [more]
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BLAST of FYVE-type 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-type domain-containing protein vs. Ensembl Zebrafish
Analysis Date: 2016-08-08 (Schmidtea mediterranea smed_20140614 BLASTX Zebrafish e!99)
Total hits: 2
Match NameE-valueIdentityDescription
eea16.243e-631.65early endosome antigen 1 [Source:ZFIN;Acc:ZDB-GENE... [more]
eea17.488e-631.65early endosome antigen 1 [Source:ZFIN;Acc:ZDB-GENE... [more]
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BLAST of FYVE-type 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-type 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-type 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-type domain-containing protein 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 FYVE-type 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-type domain-containing protein vs. Ensembl Sea Lamprey
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Sea Lamprey e!99)
Total hits: 1
Match NameE-valueIdentityDescription
eea11.036e-727.40early endosome antigen 1 [Source:ZFIN;Acc:ZDB-GENE... [more]
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BLAST of FYVE-type 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-type domain-containing protein vs. Ensembl Nematostella
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Nematostella e!Metazoa46)
Total hits: 1
Match NameE-valueIdentityDescription
EDO390441.366e-656.25Predicted protein [Source:UniProtKB/TrEMBL;Acc:A7... [more]
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BLAST of FYVE-type 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-type domain-containing protein vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 1
Match NameE-valueIdentityDescription
SMESG000008512.10.000e+099.69SMESG000008512.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30015532 ID=SMED30015532|Name=FYVE-type domain-containing protein|organism=Schmidtea mediterranea sexual|type=transcript|length=1047bp
AAATTATTTTAAAATTAATTAAAGATTAAAGAAATACTAATTTAATTGAG
AAAATTATGGTTTCTTAAAACTTTTTAGATGTTTAACTCTATCAGCAAAA
GATTTAAAGGTGATCAACCTCAACCTAAACCTCAAGATAATCAAGAAATG
GAAGGATTTATTTGTCCTATGTGCATGGCCAAATTTTCTTCACCAGATAT
GGTTCAAAAACATTTTGATGATACTCATAATGACATGGATGTTAAAGAGA
ATGATAAATCTACCAAACTTAATATTTTATCTCCTGCAACTGAACGGAAA
GAAAGTATACAAAATATACAAGAGAATTTTAATGACCTTAAACAATCACT
GGATGAAGAAATATGGTTTAATAAAGAATTACAGAAAGAATGTGAAAGAT
TGAAAAAATTATTAGAGGAAAAGGAAGAAGAAAAGAATTTGGTTTTCAAA
AATAATCAAATTTCTTTTGAAGAGTTAGAAAGAACACGAGATGCGTTAAT
TGAAAAATTAGAAAGGGTTCAAATGTCCAGAGATTCACTGGCTGATGAAA
ACAATACTCTGAAATCAGATTTTGATATATGTGAGACTAAATTATCCGAC
CAAATCAAATACAAAGATGAATTAGAAAAATTAATCGATAAGCAGAAGCA
AGATTTGGATTTGATGACAGAGCAATTGAACTCCGCGAAATTGTCTGTTA
ATTCTCACAATATAGAGGCTGCAGAATTATCTGCAGAAATTCAACACAAA
TATGATGCCAGTCTGGATTCGGTTAAAGAGCTGTCAAATGAATTAGAAAG
AATCAAGAATGAAAGTAAATTAGAGAATTCTGAATTGATTGAAAAGTGCT
CAATACTAAGCAAATCTCTGAGCGAAAATGAAACAGAAAAATCCAACATG
ATTGATGAACATTCACAACTCGTTACGAAATTGAATAACCAATTGGAATC
TCTTCAACAAGAAAATCAACAAATACATGATAGTTTTCAATCCAGTGAAG
ATAAAATTCTTCAGATGAAAAGAAGTTGGAACACTGATCAAATTACA
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protein sequence of SMED30015532-orf-1

>SMED30015532-orf-1 ID=SMED30015532-orf-1|Name=SMED30015532-orf-1|organism=Schmidtea mediterranea sexual|type=polypeptide|length=323bp
MFNSISKRFKGDQPQPKPQDNQEMEGFICPMCMAKFSSPDMVQKHFDDTH
NDMDVKENDKSTKLNILSPATERKESIQNIQENFNDLKQSLDEEIWFNKE
LQKECERLKKLLEEKEEEKNLVFKNNQISFEELERTRDALIEKLERVQMS
RDSLADENNTLKSDFDICETKLSDQIKYKDELEKLIDKQKQDLDLMTEQL
NSAKLSVNSHNIEAAELSAEIQHKYDASLDSVKELSNELERIKNESKLEN
SELIEKCSILSKSLSENETEKSNMIDEHSQLVTKLNNQLESLQQENQQIH
DSFQSSEDKILQMKRSWNTDQIT
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0003116parenchymal cell
PLANA:0007528glial cell
Vocabulary: INTERPRO
TermDefinition
IPR013087Znf_C2H2_type
IPR007087Znf_C2H2
Vocabulary: molecular function
TermDefinition
GO:0003676nucleic acid binding
GO:0046872metal ion binding
GO:0032266phosphatidylinositol-3-phosphate binding
Vocabulary: cellular component
TermDefinition
GO:0005769early endosome
GO:0030139endocytic vesicle
Vocabulary: biological process
TermDefinition
GO:0006897endocytosis
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableCOILSCoilCoilcoord: 179..206
NoneNo IPR availableCOILSCoilCoilcoord: 130..157
NoneNo IPR availableCOILSCoilCoilcoord: 225..256
NoneNo IPR availableCOILSCoilCoilcoord: 98..125
NoneNo IPR availableCOILSCoilCoilcoord: 275..309
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..25
NoneNo IPR availableMOBIDB_LITEmobidb-litedisorder_predictioncoord: 1..20
IPR013087Zinc finger C2H2-typePROSITEPS00028ZINC_FINGER_C2H2_1coord: 29..50