Otopetrin

Overview
NameOtopetrin
Smed IDSMED30011465
Length (bp)204
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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Anatomical Expression

PAGE et. al., 2020



SMED30011465

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



PAGE Curations: 13

  
Expressed InReference TranscriptGene ModelsPublished TranscriptTranscriptomePublicationSpecimenLifecycleEvidence
intestinal phagocyteSMED30011465h1SMcG0003404 Contig3509uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30011465h1SMcG0003404 Contig3509newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30011465h1SMcG0021430 Contig3509uc_Smed_v2PMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
intestinal phagocyteSMED30011465h1SMcG0021430 Contig3509newmark_estsPMID:23079596
Forsthoefel et al., 2012		FACS sorted cell population asexual adult cDNA to DNA expression microarray evidence
head regionSMED30011465h1SMcG0003404 SmedASXL_013120SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
head regionSMED30011465h1SMcG0003406 SmedASXL_013120SmedAsxl_ww_GCZZ01PMID:27034770
Currie et al., 2016		whole organism asexual adult RNA-sequencing evidence
protonephridiaSMED30011465h1SMcG0003404 dd_Smed_v4_13612_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
neoblastSMED30011465h1SMcG0003404 dd_Smed_v4_13612_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
parenchymal cellSMED30011465h1SMcG0003404 dd_Smed_v4_13612_0_1dd_Smed_v4PMID:29674431
Fincher et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
glial cellSMED30011465h1SMcG0003406 dd_Smed_v6_13612_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
glial cellSMED30011465h1SMcG0003404 dd_Smed_v6_13612_0dd_Smed_v6PMID:29674432
Plass et al., 2018		FACS sorted cell population asexual adult single-cell RNA-sequencing evidence
epidermisSMED30011465h1SMcG0003404 dd_Smed_v4_13612_0_1dd_Smed_v4PMID:28292427
Wurtzel et al., 2017		whole organism asexual adult single-cell RNA-sequencing evidence
ciliated epithelial cellSMED30011465h1SMcG0003404 dd_Smed_v4_13612_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 Otopetrin vs. TrEMBL
Match: A0A4S2LI03 (Uncharacterized protein OS=Opisthorchis felineus OX=147828 GN=CRM22_008757 PE=4 SV=1)

HSP 1 Score: 75.8702 bits (185), Expect = 1.987e-14
Identity = 33/59 (55.93%), Postives = 40/59 (67.80%), Query Frame = 3 
Query:   36 FIFHDNDGINVYLRLGAVGFGFGVMVHDGFKIADQVRAQ---NSSCHNHLWTPKQCLHL 203
            +   D +G+N+YLRLGAVGFGFGVM+ DGFKIA+   A+     SCHNH W P   LH 
Sbjct:  388 YFSRDTEGVNLYLRLGAVGFGFGVMIFDGFKIAEPWEARLNDQESCHNHFWIPIHILHF 446
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BLAST of Otopetrin vs. TrEMBL
Match: A0A3R7G764 (Uncharacterized protein OS=Clonorchis sinensis OX=79923 GN=CSKR_3215s PE=4 SV=1)

HSP 1 Score: 75.8702 bits (185), Expect = 1.987e-14
Identity = 33/59 (55.93%), Postives = 40/59 (67.80%), Query Frame = 3 
Query:   36 FIFHDNDGINVYLRLGAVGFGFGVMVHDGFKIADQVRAQ---NSSCHNHLWTPKQCLHL 203
            +   D +G+N+YLRLGAVGFGFGVM+ DGFKIA+   A+     SCHNH W P   LH 
Sbjct:  388 YFSRDTEGVNLYLRLGAVGFGFGVMIFDGFKIAEPWEARLNDQESCHNHFWIPIHILHF 446
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BLAST of Otopetrin vs. TrEMBL
Match: A0A5K3EP08 (Uncharacterized protein OS=Mesocestoides corti OX=53468 PE=4 SV=1)

HSP 1 Score: 75.485 bits (184), Expect = 2.545e-14
Identity = 35/67 (52.24%), Postives = 47/67 (70.15%), Query Frame = 3 
Query:    6 INSFSMTMNKFIFHDNDGINVYLRLGAVGFGFGVMVHDGFKIADQVRAQNS--SCHNHLWTPKQCLH 200
            + +FS +   F   DN+GIN+YLRLGAV FGFGVM+ DGF++ADQ RA+    +CH+ LW P   +H
Sbjct:  289 LGTFSKSNPPFT-QDNEGINLYLRLGAVVFGFGVMIMDGFRVADQFRAEKIIFACHSVLWIPVNLIH 354
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BLAST of Otopetrin vs. TrEMBL
Match: A0A158RFB0 (Uncharacterized protein OS=Hydatigena taeniaeformis OX=6205 GN=TTAC_LOCUS9377 PE=4 SV=1)

HSP 1 Score: 75.485 bits (184), Expect = 2.944e-14
Identity = 33/54 (61.11%), Postives = 42/54 (77.78%), Query Frame = 3 
Query:   45 HDNDGINVYLRLGAVGFGFGVMVHDGFKIADQVRAQNS--SCHNHLWTPKQCLH 200
             D++GIN+YLRLG V FGFGV++ DGF++ADQ RA NS  SCH+ LWTP   +H
Sbjct:  337 QDSEGINLYLRLGTVVFGFGVIIMDGFRVADQFRAVNSERSCHSILWTPLNAVH 390
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BLAST of Otopetrin vs. TrEMBL
Match: G7YVK5 (Otopetrin OS=Clonorchis sinensis OX=79923 GN=CLF_111941 PE=4 SV=1)

HSP 1 Score: 75.0998 bits (183), Expect = 4.001e-14
Identity = 33/59 (55.93%), Postives = 40/59 (67.80%), Query Frame = 3 
Query:   36 FIFHDNDGINVYLRLGAVGFGFGVMVHDGFKIADQVRAQ---NSSCHNHLWTPKQCLHL 203
            +   D +G+N+YLRLGAVGFGFGVM+ DGFKIA+   A+     SCHNH W P   LH 
Sbjct:  309 YFSRDTEGVNLYLRLGAVGFGFGVMIFDGFKIAEPWEARLNDQESCHNHFWIPIHILHF 367
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BLAST of Otopetrin vs. Planmine SMEST
Match: SMESG000018670.1 (SMESG000018670.1)

HSP 1 Score: 130.183 bits (326), Expect = 2.913e-37
Identity = 58/58 (100.00%), Postives = 58/58 (100.00%), Query Frame = 3 
Query:   30 NKFIFHDNDGINVYLRLGAVGFGFGVMVHDGFKIADQVRAQNSSCHNHLWTPKQCLHL 203
            NKFIFHDNDGINVYLRLGAVGFGFGVMVHDGFKIADQVRAQNSSCHNHLWTPKQCLHL
Sbjct:  192 NKFIFHDNDGINVYLRLGAVGFGFGVMVHDGFKIADQVRAQNSSCHNHLWTPKQCLHL 249
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BLAST of Otopetrin vs. Planmine SMEST
Match: SMESG000018670.1 (SMESG000018670.1)

HSP 1 Score: 130.183 bits (326), Expect = 2.940e-37
Identity = 58/58 (100.00%), Postives = 58/58 (100.00%), Query Frame = 3 
Query:   30 NKFIFHDNDGINVYLRLGAVGFGFGVMVHDGFKIADQVRAQNSSCHNHLWTPKQCLHL 203
            NKFIFHDNDGINVYLRLGAVGFGFGVMVHDGFKIADQVRAQNSSCHNHLWTPKQCLHL
Sbjct:  190 NKFIFHDNDGINVYLRLGAVGFGFGVMVHDGFKIADQVRAQNSSCHNHLWTPKQCLHL 247
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BLAST of Otopetrin vs. Planmine SMEST
Match: SMESG000018672.1 (SMESG000018672.1)

HSP 1 Score: 105.145 bits (261), Expect = 3.439e-28
Identity = 45/58 (77.59%), Postives = 51/58 (87.93%), Query Frame = 3 
Query:   30 NKFIFHDNDGINVYLRLGAVGFGFGVMVHDGFKIADQVRAQNSSCHNHLWTPKQCLHL 203
            N ++  + +GIN+YLRLGAVGFGFGVMVHDGFK+ADQVR QNS CHN LWTPKQCLHL
Sbjct:  188 NYYVIKETNGINLYLRLGAVGFGFGVMVHDGFKVADQVRLQNSFCHNQLWTPKQCLHL 245
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BLAST of Otopetrin vs. Planmine SMEST
Match: SMESG000018671.1 (SMESG000018671.1)

HSP 1 Score: 97.0561 bits (240), Expect = 2.196e-25
Identity = 41/55 (74.55%), Postives = 47/55 (85.45%), Query Frame = 3 
Query:   39 IFHDNDGINVYLRLGAVGFGFGVMVHDGFKIADQVRAQNSSCHNHLWTPKQCLHL 203
            I  D++GIN+YLRLGAVGFGFGVMVHDGFKIAD+ R +  +CHN LWTPK CLHL
Sbjct:  171 IMRDHEGINLYLRLGAVGFGFGVMVHDGFKIADKFRLEGENCHNELWTPKHCLHL 225
[Close]
BLAST of Otopetrin vs. Planmine SMEST
Match: SMESG000018671.1 (SMESG000018671.1)

HSP 1 Score: 97.0561 bits (240), Expect = 2.389e-25
Identity = 41/55 (74.55%), Postives = 47/55 (85.45%), Query Frame = 3 
Query:   39 IFHDNDGINVYLRLGAVGFGFGVMVHDGFKIADQVRAQNSSCHNHLWTPKQCLHL 203
            I  D++GIN+YLRLGAVGFGFGVMVHDGFKIAD+ R +  +CHN LWTPK CLHL
Sbjct:  198 IMRDHEGINLYLRLGAVGFGFGVMVHDGFKIADKFRLEGENCHNELWTPKHCLHL 252
The following BLAST results are available for this feature:
BLAST of Otopetrin 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 Otopetrin 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 Otopetrin 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 Otopetrin 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 Otopetrin 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 Otopetrin 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 Otopetrin 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 Otopetrin vs. TrEMBL
Analysis Date: 2020-05-01 (Schmidtea mediterranea smed_20140614 BLASTX EMBL-EBI TrEMBL)
Total hits: 5
Match NameE-valueIdentityDescription
A0A4S2LI031.987e-1455.93Uncharacterized protein OS=Opisthorchis felineus O... [more]
A0A3R7G7641.987e-1455.93Uncharacterized protein OS=Clonorchis sinensis OX=... [more]
A0A5K3EP082.545e-1452.24Uncharacterized protein OS=Mesocestoides corti OX=... [more]
A0A158RFB02.944e-1461.11Uncharacterized protein OS=Hydatigena taeniaeformi... [more]
G7YVK54.001e-1455.93Otopetrin OS=Clonorchis sinensis OX=79923 GN=CLF_1... [more]
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BLAST of Otopetrin 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 Otopetrin 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 Otopetrin 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 Otopetrin 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 Otopetrin 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 Otopetrin vs. Planmine SMEST
Analysis Date: 2020-05-08 (Schmidtea mediterranea smed_20140614 BLASTX Planmine SMEST)
Total hits: 5
Match NameE-valueIdentityDescription
SMESG000018670.12.913e-37100.00SMESG000018670.1[more]
SMESG000018670.12.940e-37100.00SMESG000018670.1[more]
SMESG000018672.13.439e-2877.59SMESG000018672.1[more]
SMESG000018671.12.196e-2574.55SMESG000018671.1[more]
SMESG000018671.12.389e-2574.55SMESG000018671.1[more]
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Sequences
The following sequences are available for this feature:

transcript sequence

>SMED30011465 ID=SMED30011465|Name=Otopetrin|organism=Schmidtea mediterranea sexual|type=transcript|length=204bp
TGATAATAAATTCATTTTCCATGACAATGAATAAATTCATTTTCCATGAC
AATGATGGGATTAATGTTTATTTGCGCCTGGGAGCTGTCGGTTTTGGGTT
TGGTGTCATGGTACATGATGGTTTTAAGATTGCTGATCAAGTTAGAGCAC
AAAACAGCAGTTGTCATAATCATTTATGGACTCCAAAGCAATGTCTTCAT
TTAG
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Annotated Terms
The following terms have been associated with this transcript:
Vocabulary: Planarian Anatomy
TermDefinition
PLANA:0000020protonephridia
PLANA:0000034epidermis
PLANA:0000106ciliated epithelial cell
PLANA:0000418head
PLANA:0003116parenchymal cell
PLANA:0007528glial cell
Vocabulary: INTERPRO
TermDefinition
IPR004878Otopetrin
Vocabulary: cellular component
TermDefinition
GO:0016020membrane
GO:0016021integral component of membrane
InterPro
Analysis Name: Schmidtea mediteranean smed_20140614 Interproscan
Date Performed: 2020-05-01
IPR TermIPR DescriptionSourceSource TermSource DescriptionAlignment
NoneNo IPR availableTMHMMTMhelixcoord: 10..32